title: Transcriptomic Analysis Identifies B-Lymphocyte Kinase as a Therapeutic Target for Desmoplastic Small Round Cell Tumor Cancer Stem Cell-Like Cells [ATAC-seq]

first: Sean

middle: Bong

last: Lee

state: LA

address: 1700 Tulane Ave

department: Pathology

summary: Desmoplastic Small Round Cell Tumor (DSRCT) is an aggressive pediatric cancer caused by the EWSR1-WT1 fusion oncoprotein. The tumor is refractory to treatment with a 5-year survival rate of only 15-25%, necessitating the development of novel therapeutics, especially those able to target chemoresistant subpopulations. Novel in vitro cancer stem cell-like (CSC-like) culture conditions increase the expression of stemness markers (SOX2, NANOG) and reduce DSRCT cell line susceptibility to chemotherapy, while maintaining the ability of DSRCT cells to form xenografts. To gain insights into this chemoresistant model, RNA-seq was performed to elucidate transcriptional alterations between DSRCT cells grown in CSC-like spheres and normal 2-dimensional adherent state. Commonly upregulated and downregulated genes were identified and utilized in pathway analysis revealing upregulation of pathways related to chromatin assembly and disassembly and downregulation of pathways including cell junction assembly and extracellular matrix organization. Alterations in chromatin assembly suggest a role for epigenetics in the DSRCT CSC-like state which was further investigated with ATAC-seq, identifying over 10,000 differentially accessible peaks including 4,444 sphere accessible peaks and 6,120 adherent accessible peaks. Accessible regions were associated with higher gene expression including increased accessibility of the CSC marker SOX2 in CSC-like culture conditions. These analyses were further utilized to identify potential CSC therapeutic targets, leading to the identification of B-lymphocyte kinase (BLK) as a CSC-enriched, EWSR1-WT1 regulated, druggable target. BLK inhibition and knockdown reduced CSC-like properties including abrogation of tumorsphere formation and stemness marker expression. Importantly, BLK knockdown reduced DSRCT CSC-like cell chemoresistance making its inhibition a promising target for future combination therapy.

overall_design: DSRCT cell lines were cultured in sphere or adherent culture conditions for 4-days and then harvested for analysis by RNA-seq (JN-DSRCT-1, BER-DSRCT, BOD-DSRCT), ATAC-seq (BER-DSRCT), or scRNA-seq (JN-DSRCT-1, BER-DSRCT).

first: Justin

middle: W

last: Magrath


title: EWSR1::ATF1 Orchestrates the Clear Cell Sarcoma Transcriptome in Human Tumors and A Mouse Genetic Model [RNA-Seq 2]

status: Public on Dec 01 2023

city: Salt Lake City

first: Li

last: Li

state: Utah

address: 201 PRESIDENTS CIRCLE

country: USA

institute: University of Utah

type: Expression profiling by high throughput sequencing

summary: a particular fusion protein that drives the rare, but deadly pediatric cancer, clear cell sarcoma. The fusion protein was expressed in mice, leading to the formation of similar tumors as those it causes in humans. This permitted the study of fusion protein function in these tumors.

overall_design: To investigate the fusion protein EA1' role in CCS formation, we KD EA1 and perform RNASeq for the total RNA.

first: Benjamin

middle: B

last: Ozenberger

first: Kevin

last: Jones


title: EWSR1::ATF1 Orchestrates the Clear Cell Sarcoma Transcriptome in Human Tumors and A Mouse Genetic Model

type: Genome binding/occupancy profiling by high throughput sequencing

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: EWSR1::ATF1 Orchestrates the Clear Cell Sarcoma Transcriptome in Human Tumors and A Mouse Genetic Model [ChIP-Seq 2]

summary: A particular fusion protein that drives the rare, but deadly pediatric cancer, clear cell sarcoma. The fusion protein was expressed in mice, leading to the formation of similar tumors as those it causes in humans. This permitted the study of fusion protein function in these tumors.

overall_design: Chromatin immunoprecipitation sequencing (chip-seq) for H3K27ac with Abcam ab4279 anti-H3K27ac in SU-CCS-1


title: EWSR1::ATF1 Orchestrates the Clear Cell Sarcoma Transcriptome in Human Tumors and A Mouse Genetic Model [ChIP-Seq 1]

overall_design: Chromatin immunoprecipitation sequencing (chip-seq) for V5 (fusion-tag), H3K27ac and pol2 in EWSR1::ATF1 mouse CCS model


title: Transcriptomic Analysis Identifies B-Lymphocyte Kinase as a Therapeutic Target for Desmoplastic Small Round Cell Tumor Cancer Stem Cell-Like Cells

city: New Orleans

institute: Tulane University School of Medicine


title: Characterization of in vitro cultured alveolar macrophages (AM) transcriptomes

status: Public on Dec 02 2023

city: Charlottesville

first: Xiaoqin

last: Wei

state: Virginia

address: 2512 Fontaine Ave

institute: University of Virginia

summary: To identify molecular characteristics of mouse AMs stimulated with or without Poly(I:C) in the presence of vehicle or MSDC overnight in vitro, we isolated RNA from AMs with various treatments and examined by bulk RNA-seq. We found a large number of cytokine gene profiles were reduced following MSDC treatment in WT AMs, suggesting that MSDC treatment recuced inflammatory response in AMs.

overall_design:
Examined with bulk RNA-seq of mouse AMs stimulated with or without Poly(I:C) in the presence of vehicle or MSDC overnight in vitro for overnight
-------------------------
The authors state that they have lost the raw data.

first: Jie

last: Sun


title: EWSR1::ATF1 Orchestrates the Clear Cell Sarcoma Transcriptome in Human Tumors and A Mouse Genetic Model [RNA-Seq 1]

overall_design: To investigate the transcriptome Clear Cell Sarcoma, We performed RNA-seq on 5 frozen human CCS tumor, and used 3 human muscle samples from study GSE163434 (GSM4618168, GSM4618167 and GSM4618170) as control.


title: Personalized neoantigen-based T cell therapy triggers cytotoxic lymphocytes expressing polyclonal TCR against metastatic ovarian cancer

city: Taaoyuan

first: HUNG

last: SHUENIU

address: 6F, Research building, Wenhua 1st Rd,

country: Taiwan

institute: Chang Gung Memorial Hospital

summary: Neoantigen-reactive cytotoxic T lymphocytes play a vital role in precise cancer cell elimination. In this study, we demonstrate the effectiveness of personalized neoantigen-based T cell therapy in inducing tumor regression in two patients suffering from heavily-burdened metastatic ovarian cancer. Our approach involved the development of a robust pipeline for ex vivo expansion of neoantigen-reactive T lymphocytes. Neoantigen peptides were designed and synthesized based on the somatic mutations of the tumors and their predicted HLA binding affinities. These peptides were then presented to T lymphocytes through co-culture with neoantigen-loaded dendritic cells for ex vivo expansion. Subsequent to cell therapy, both patients exhibited significant reductions in tumor marker levels and experienced substantial tumor regression. One patient achieved repeated cancer regression through infusions of T cell products generated from newly identified neoantigens. Transcriptomic analyses revealed a remarkable increase in neoantigen-reactive cytotoxic lymphocytes in the peripheral blood of the patients following cell therapy. These cytotoxic T lymphocytes expressed polyclonal T cell receptors (TCR) against neoantigens, along with abundant cytotoxic proteins and pro-inflammatory cytokines. The efficacy of neoantigen targeting was significantly associated with the immunogenicity and TCR polyclonality. Notably, the neoantigen-specific TCR clonotypes persisted in the peripheral blood after cell therapy. Our findings indicate that personalized neoantigen-based T cell therapy triggers cytotoxic lymphocytes expressing polyclonal TCR against ovarian cancer, suggesting its promising potential in cancer immunotherapy.

overall_design: PBMC samples were obtained from two patients and subjected for scRNA and TCR sequencing.

first: Hung

last: Shuen-Iu

first: Chu

last: Mu-Tzu

first: Lee

last: Yun-Shien

first: Lai

last: Chyong-Huey


title: In vitro throughput screening of anticancer drugs by patient-derived cell lines cultured　on vascularized three-dimensional stromal tissues

city: Sugito-machi

first: Rii

last: Morimura

state: Saitama

address: 4-2-3 Takanodaiminami

country: Japan

institute: TOPPAN Holdings Inc.

summary: The development of high-throughput anticancer drug screening using patient-derived cancer cell lines (PDCs) that maintain their original characteristics in an in vitro three-dimensional (3D) culture system poses a significant challenge for achieving personalized cancer medicine. Because stromal tissue plays a critical role in the composition and maintenance of the cancer microenvironment, in vitro 3D-culture using reconstructed stromal tissues has attracted much attention. Here, a simple and unique in vitro 3D-culture method using heparin and collagen together with fibroblast and endothelial cells to fabricate vascularized 3D-stromal tissues for in vitro culture of PDCs is reported. While co-treatment with bevacizumab, a monoclonal antibody against the vascular endothelial growth factor, and 5-fluorouracil (5-FU) significantly reduced the survival rate of the 3D-cultured PDCs to 30%, separate addition of each drug did not induce such strong cytotoxicity, suggesting the possibility of evaluating the combined effect of anticancer drug and an angiogenesis inhibitor. Surprisingly, drug evaluation using eight PDCs with the 3D-culture method resulted in a drug efficacy concordance rate of 75% with clinical history. The model is expected to be applied to in vitro throughput drug screening for the development of personalized cancer medicine.

overall_design: The gene expression of fibroblast cells in 3D tissue and 2D was measured at 4days after constructing 3D tissue and seeding fibroblast on 10cm dish.

first: Yuki

last: Takahashi

first: Kei

last: Tsukamoto

first: Sayaka

last: Gomi

first: Asuka

last: Kato

first: Miki

last: Mizukami

first: Yasuyuki

last: Naito

first: Shinji

last: Irie

first: Satoshi

last: Nagayama

first: Eiji

last: Shinozaki

first: Kensei

last: Yamaguchi

first: Naoya

last: Fujita


title: Transcriptomic Analysis Identifies B-Lymphocyte Kinase as a Therapeutic Target for Desmoplastic Small Round Cell Tumor Cancer Stem Cell-Like Cells [RNA-seq]

first: Sean

last: Lee

first: Justin

last: Magrath


title: mRNA profiles of bone marrow and splenic hematopoietic stem cells after 5-FU challenge

city: Kumamoto

first: Terumasa

last: Umemoto

state: Kumamoto

address: 2-2-1 Honjo, Chuo-ku

institute: Kumamoto University

summary: Under stress hematopoiesis, previous studies have suggested the migration of hematopoietic stem cells (HSCs) from bone marrow (BM) to extramedullary sites such as spleen. However, there is little direct evidence of HSC migration from BM to spleen. Here, we induced myeloablation via 5-fluorouracil (5-FU) and showed the direct evidence of HSC migration from BM to spleen during hematopoietic regeneration via a photoconvertible fluorophore. We found that during hematopoietic regeneration, there were mechanistic differences for HSC migration during early (day 3 to 8) and late phase (day 11 to 14). During steady-state, HSCs preferentially migrated to BM rather than spleen, but during the early phase HSC migration to spleen predominated. Indeed, in the early phase, HSC mobilization from BM was induced in G-CSF-dependent manners, while HSCs in the late phase gained significantly enhanced cell-autonomous motility, which was independent of chemotaxis. Collectively, HSC migration was dynamically changed during hematopoietic regeneration.

overall_design: To investigate the transcriptional differences in bone marrow versus splenic hematopoietic stem cells after administration of the chemotherapeutic agent 5-fluorouracil (5-FU), we performed gene expression profiling. Mice were 8-12 weeks at the time of cell isolation

first: Alban

last: Johansson


title: Gene expression profile of bone marrow derived M-CSF-dependent macrophage from Ogfrl1 KO mouse

city: Indianapolis

first: Yasuyoshi

last: Ueki

state: IN

address: 635 N. Barnhill Dr.

institute: Indiana University

summary: To investigate the role of Ogfrl1 in macrophages, we isolated bone marrow derived M-CSF-dependent macrophages (BMMs) from femur and tibia of Ogfrl1 deficient mouse and wildtype littermate mouse.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for BMMs from Ogfrl1 deficient and wildtype control mouse

first: Mizuho

last: Kittaka


title: The identification of Ogfrl1 expressing cells in jawbone tissue

summary: Human data demonstrates loss of function mutations of OGFRL1 are a cause of autosomal recessive forms of cherubism. However, the gene function of OGFRL1 is unknown. We performed scRNAseq to investigate the cell types expressing Ogfrl1 in jawbone tissue.

overall_design: Jawbone cells isolated from mouse maxilar and madibular with collagenase/EDTA digestion and analyzed using scRNAseq


title: Gene expression profile of bone marrow cells from Ogfrl1 deficient mouse at single cell level

summary: Human data demonstrates loss of function mutations of OGFRL1 are a cause of autosomal recessive forms of cherubism. However, the gene function of OGFRL1 is unknown. We performed scRNAseq to investigate the gene function in bone marrow cells.

overall_design: Bone marrow cells were isolated from Ogfrl1 deficient and lettermate control mice.


title: Gene expression profiling of shCtrl and shGABRD AGS cells from Clariom S array

city: Chengdu

first: Weibing

last: Leng

state: Sichuan

address: West China Hospital of Sichuan University, 37 Guoxue Xiang, Chenngdu, Sichuan Pr

department: West China Hospital

country: China

institute: Sichuan University

summary: GABRD is identified as a tumor promotor in the development of gastric cancer. Herein, to further explore the downstream regulated genes involved in GABRD mediated tumor progression, an Affymetrix Clariom S human Assay was performed to profile the expression of GABRD regulated genes in AGS cells. Gene expression profiling of shCtrl and shGABRD AGS cells was acquired and analyzed. Differentially expressed genes were identified based on fold change of mean of expression (fold change ≥ 1.5) and FDR (< 0.05) from P value calculated based on linear model of empirical Bayesian distribution. GABRD expression regulated the expression of 2644 genes in AGS cells, of which 1199 were upregulated and 1445 were downregulated upon GABRD silencing.

overall_design: Gene expression in shGABRD (GABRD knockdown) AGS cells and shCtrl (negative control) AGS cells was detected using Human gene expression array. Gene chip was performed with Clariom S array according to the instructions.


title: Transcriptomic Analysis Identifies B-Lymphocyte Kinase as a Therapeutic Target for Desmoplastic Small Round Cell Tumor Cancer Stem Cell-Like Cells [scRNA-seq]


title: Determinng global implications of the ADAR3 R-domain on mediating ADAR3-RNA interactions

city: Bloomington

first: Heather

middle: Ann

last: Hundley

address: 1001 E. 3rd Street

department: Biology

summary: Although R-domain has been implicated in RNA binding in vitro, whether ADAR3 uses the arginine-rich R-domain to mediate ADAR3-RNA interactions in vivo remain to be explored. Here, an unbiased, high-throughput approach was undertaken to understand if mutating the R-domain would affect the ability of ADAR3 to either bind and/or recognize target transcripts. Although R-domain doesn’t confer target specificity to ADAR3, the R-domain mutant is associated with decreased protein stability and might reduce the ability of ADAR3 to bind target RNAs.

overall_design: RNA Immunoprecipitation-Sequencing (RIP-Seq) for FLAG-tagged ADAR3 Wild type and R-domain mutant protein exogenously expressed in U373 glioblastoma cells. To achieve exogenous expression of wild type or mutant protein, U373 cells were retrovirally transduced with either empty vector encoding for antiobiotic resistance (Control), or ADAR3 wild type (ADAR3 WT) or R-domain (ADAR3 R-Mutant) mutant protein.

first: Priyanka

last: Mukherjee

middle: A


title: Effect of Sirt7 depletion on gene expression of primary murine vascular smooth muscle cells isolated from c57bl/6

city: Guangzhou

first: Dongxing

last: Zhu

state: Guangdong

address: Xinzao, Panyu District

department: School of Basic Medical Sciences

institute: Guangzhou Medical University

summary: To investigate the functional role of Sirt7 in VSMCs calcification, we knockdowned Sirt7 expression in VSMCs using siRNAs, and performed RNA-seq to identify the downstream genes regulated by Sirt7

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of 3 different cells transefected with siScrambled and 3 different cells transfected with siSirt7.Comparative gene expression profiling analysis of RNA-seq data for control VSMCs and VSMCs with Sirt7 depletion


title: RNAseq of Wild Type and  pikfyveΔ8 zebrafish.

city: Shenzhen

first: sejie

last: yu

address: 1017 East Gate North Road

institute: The Second Clinical Medical College, Jinan University

summary: Purpose: Phosphoinositide kinase, FYVE-type zinc finger containing (PIKFYVE) is a newly identified pathogenic gene involved in cataract. This study aimed to investigate the nature and mechanism of vacuoles related to PIKFYVE. Methods: We generated Pikfyve phosphatidylinositol phosphate kinase domain-deficient ( pikfyveΔ8) zebrafish using CRISPR/Cas9-directed gene editing. The pikfyveΔ8 homozygous and wild-type zebrafish were subjected to transcriptomic analyses. Results: Transcriptomic analyses revealed 8694 differentially expressed genes (DEGs). Conclusion: Our study represents the first detalis transcriptomic analysis of pikfyve disruption zebrafish.

overall_design: We generated Pikfyve phosphatidylinositol phosphate kinase domain-deficient (pikfyveΔ8) zebrafish using CRISPR/Cas9-directed gene editing. We then performed gene expression profiling analysis using data obtained from RNAseq of three samples respectively in pikfyveΔ8 homozygous and wild-type zebrafish.


title: Identifying molecular targets of endogenous ADAR3 in gliolastoma cells

summary: Through immunoprecipitation of epitope-tagged ADAR3 protein, several ADAR3-bound RNAs have been reported till date. However, exogenous expression of proteins are usually associated with altered gene expression profiles and thus, can influence binding profiles of RNA-binding proteins (RBPs) being studied.  Here, we used affinity-purified antibody to pull down ADAR3 endogenously expressed in U373 glioblastoma cells and identified transcripts significantly enriched in the ADAR3 immunoprecipitants over control. To serve as control, antisera isolated from rabbit prior to immunization with ADAR3 antigen was used to perform the IP.

overall_design: RNA Immunoprecipitation-Sequencing (RIP-Seq) for endogenously-expressed ADAR3 protein in U373 glioblastoma cells.


title: Tumor Explants Elucidate a Cascade of Paracrine SHH, WNT, and VEGF Signals Driving Pancreatic Cancer Angiosuppression

city: New York City

first: Lukas

last: Vlahos

state: New York

address: 1130 St Nicholas Ave

department: Systems Biology

institute: Columbia University

summary: The sparse vascularity of Pancreatic Ductal Adenocarcinoma (PDAC) presents a mystery: what prevents this aggressive malignancy from undergoing neoangiogenesis to counteract hypoxia and better support growth? An incidental finding from prior work on paracrine communication between malignant PDAC cells and fibroblasts revealed that inhibition of the Hedgehog (HH) pathway partially relieved angiosuppression, increasing tumor vascularity through unknown mechanisms. Initial efforts to study this phenotype were hindered by difficulties replicating the complex interactions of multiple cell types in vitro. Here we identify a cascade of paracrine signals between multiple cell types that act sequentially to suppress angiogenesis in PDAC. Malignant epithelial cells promote HH signaling in fibroblasts, leading to inhibition of non-canonical WNT signaling in fibroblasts and epithelial cells, thereby limiting VEGFR2-dependent activation of endothelial hypersprouting. This cascade was elucidated using human and murine PDAC explant models, which effectively retain the complex cellular interactions of native tumor tissues.

overall_design:
To investigate cell specific changes upon in vivo Smoothened inhibition, tumor bearing KPC mice were treated with either IPI-926 or vehicle for two days and collected tumor tissue for single cell RNA sequencing.
We then performed single cell regulatory network analysis, with a focus on the activity of Hedgehog, WNT, and VEGF signaling pathways.

first: Marie

middle: C

last: Hasselluhn

first: Amanda

middle: R

last: Decker-Farrell

first: Dafydd

middle: H

last: Thomas

first: Alvaro

last: Curiel-Garcia

first: Carlo

last: Maurer

first: Urszula

middle: N

last: Wasko

first: Lorenzo

last: Tomassoni

first: Stephen

last: Sastra

first: Carmine

middle: F

last: Palermo

first: Tanner

last: Dalton

first: Alice

last: Ma

first: Fangda

last: Li

first: Ezequiel

middle: J

last: Tolosa

first: Hanina

last: Hibshoosh

first: Martin

middle: E

last: Fernandez-Zapico

first: Alexander

last: Muir

first: Andrea

last: Califano

first: Kenneth

middle: P

last: Olive


title: Multi-omic screening of invasive GBM cells in engineered biomaterials and patient biopsies reveals targetable transsulfuration pathway alterations

city: San Francisco

first: Saket

last: Jain

state: CA

address: 1450 3rd Street, HD 415

institute: University of California San Francisco

summary: Metabolic gene expression analysis of Glioblastoma cells from patient tumors edge vs core and the GBM cells from the edge and core of the 3d invasion model was carried out using Nanostring N counter platform

overall_design:
Gene expression analysis using nanostring ecounter platform
The experiment contained a total of 12 samples from four sample types in triplicate. The differential gene expression between paired edge vs core samples from 3d devices and patient biopsies was compared

first: Manish

last: Aghi

first: Joseph

last: Garcia


title: Gene expression profie at single cell level of lung cells in healthy rats and rats with pulmonary hypertension treated with sham-stimulation or ultrasound

city: Glen Cove

first: Stefanos

last: Zafeiropoulos

address: 21 Walnut Road

institute: Feinstein Institutes for Medical Research

summary: Focused ultrasound of the spleen is an emerging therapeutic modality and recent reports have shown efficacy in reducing inflammation. We used scRNA seq to identify the gene expression changes in lungs of healthy animals,  animals with pulmonary hypertension treated with focused ultrasound of the spleen or sham stimulation.

overall_design: We collected the lungs of animals with pulmonary hypertnension (SuHx model) after delivering focused ultrasound stimulation of the spleen or sham-stimulation for 2 weeks. We also used aged-matched controls. We then performed scRNA seq on these tissues. Focused ultrasound stimulation downregulates several inflammatory genes and pathways in nonclassical and classical monocytes, and macrophages in the lung; differentially expressed genes in those cell types are significantly enriched for genes associated with human PAH.

first: Stavros

last: Zanos


title: Nitric Oxide controls shoot meristem activity controlling DNA methylation in Arabidopsis thaliana [ChIP-seq]

city: Heidelberg

first: Jian

last: Zeng

address: Im Neuenheimer Feld 230

department: Department of Stem Cell Biology

country: Germany

institute: Heidelberg University

summary: Despite the importance of Nitric oxide (NO) in both plant and animal development, the regulatory and mechanism of NO function remain elusive. Here, we show that NO promotes Arabidopsis shoot stem cell differentiation via the RNA directed DNA Methylation (RdDM) pathway. Knocking out of the components of the RdDM pathway causes meristematic defects, and at least in part could block the stem cell and niche-specific genes responding to the NO signaling. Moreover, the homeobox WUSCHEL protein, known to control stem cell pool, has been found to interact with the ARGONAUTE protein, thus mediating NO signaling in the shoot apical meristem (SAM) is crucial for the stem cell fate. Our results reveal an important mechanism that NO is key to stem cell maintenance and differentiation.

overall_design: pUBI10::mCherry-GR-linker-WUS (WUS-GR); seedling; 4hours Dex; ChIP-Seq profile of WUS-GR binding (chromotek, rtma-20, 203012-03)

first: Jan

middle: U

last: Lohmann

first: Inés

last: Hidalgo

first: Michael

last: Gebert


title: Transcriptome profiling of the Nitric Oxide reponsive genes in the Col-0 and ap1/cal mutant

summary: Despite the importance of Nitric oxide (NO) in both plant and animal development, the regulatory and mechanism of NO function remain elusive. To test if response to NO in the ap1/cal mutant is comparable to the Col-o wild type, we then analysed the genome wide transcriptome profiling of NO responsive genes both in the wild type and ap1/cal seedling using RNA-seq. We observed that about 88% of differential expressed genes in wild type were overlapped with ap1/cal mutant.

overall_design: To test if the response to Nitric Oxide (NO) in ap1/cal mutant is comparable to Col-0 wild type, we performed mRNA seq both on the Col-0 and ap1/cal mutant seedling with and without NO donor SNP treatments. We then analysed gene expression profiling using the mRNA seq data.

first: Xin’Ai

last: Zhao

first: Zhe

last: Liang


title: The transcriptomic landscape of PBMC in SARS-CoV-2 variants-infected Rhesus monkeys via digital RNA-seq analysis

city: 昆明市

first: Lin

last: dongdong

state: 云南

address: 云南省昆明市五华区茭菱路

institute: Peking Union Medical College

summary: The ensuing COVID-19 epidemic and the highly frequent mutations of SARS-CoV-2 have brought an immense social burden to all fields of society worldwide, including public health, socioeconomic development, and school education since 2020. Increasing genome evolution and mutation resulted in the birth of variants of concern (VOC), with the latter presenting differential structural features and gene functions associated with specific clinical symptoms or manifestations. Moreover, SARS-CoV-2-induced inflammation, immune response, and other biological processes involve a mountain of gene molecules and signaling pathways, still requiring further and more effort spent on them. Consequently, in this study, we comprehensively illustrate the transcriptomic landscape of different SARS-CoV-2 strains (Prototype, Beta, Delta, and Omicron) at functional clustering results level (GO and KEGG). Through our deep function analysis, we discovered AGE-RAGE signaling pathway in diabetes complications and its related downstream signaling pathways and gene molecules. Moreover, all Alzheimer disease-related gene identified in our study, such as EPHA4, FYN, CASP4 are almost validated in some authoritative journals. In all, our findings in this study provided quite a few candidate hub genes or potentially therapeutic targets, which could be a significant clue for modern precision medicine in the future.

overall_design: Conducting a joint transcriptomic comparison of four SARS-CoV-2 variant infections (Prototype, Beta, Delta, Omicron) is in an effort to  depict the total transcriptomic landscape of different SARS-CoV-2 variants at gene function and signalling pathway level.

first: Dongdong

last: Lin

first: Cong

last: Tang


title: A high-throughput screen identifies RNA Binding Proteins that affect fertility in C. elegans and reveals a functional relationship between ADR-2 and SQD-1

city: BLOOMINGTON

first: Emily

last: Erdmann

address: 1001 E Third Street

summary: A high-throughput screen was performed to identify RNA binding proteins that impact fertility in Caenorhabditis elegans hermaphrodites. This screen makes use of animals expressing a vitellogenin (yolk protein) fusion with GFP, in a background (adr-2(-)) that corrects for a previously identified fertility defect in this strain. In addition to identifying several RNA binding proteins that regulate fertility, the screen also uncovered an interaction between the RNA binding proteins adr-2 and sqd-1, which were found to coregulate many transcripts important for fertility.

overall_design: N2 (wildtype) and adr-2(-) animals were hatched and grown for 60 hours on ctrl (empty vector) RNAi or sqd-1 RNAi. Young adult worms were collected and total RNA was isolated from these samples. RNA was poly-A selected before proceeding with library preparation.

first: Heather

last: Hundley


title: Leukotriene B4 receptor 2 governs macrophage migration during tissue inflammation

city: Chicago

first: Sarah

last: Tersey

state: IL

department: Medicine

institute: University of Chicago

summary: Chronic inflammation is the underlying cause of many diseases, including type 1 diabetes, obesity, and non-alcoholic fatty liver disease. Macrophages are continuously recruited to tissues during chronic inflammation where they exacerbate or resolve the pro-inflammatory environment. Although leukotriene B4 receptor 2 (BLT2) has been characterized as a low affinity receptor to several key eicosanoids and chemoattractants, its precise roles in the setting of inflammation and macrophage function remain incompletely understood. Here we used zebrafish and mouse models to probe the role of BLT2 in macrophage function during inflammation. We detected BLT2 expression in bone marrow derived and peritoneal macrophages of mouse models. Transcriptomic analysis of Ltb4r2-/- and WT macrophages suggested a role for BLT2 in macrophage migration, and studies in vitro confirmed that whereas BLT2 does not mediate macrophage polarization, it is required for chemotactic function, possibly mediated by downstream genes Ccl5 and Lgals3. Using a zebrafish model of tailfin injury, we demonstrated that antisense morpholino-mediated knockdown of blt2a or chemical inhibition of BLT2 signaling impairs macrophage migration. We further replicated these findings in zebrafish models of islet injury and liver inflammation. Moreover, we established the applicability of our zebrafish findings to mammals by showing that macrophages of Ltb4r2-/- mice have defective migration during lipopolysaccharide stimulation in vivo. Collectively, our results demonstrate that BLT2 mediates macrophage migration during inflammation, which implicates it as a potential therapeutic target for inflammatory pathologies.

overall_design: Bone marrow-derived macrophages (BMDM) were isolated as described previously and cultured for 7 days in complete medium (RPMI containing 10% FBS, 10 mM HEPES, and 100 U/ml penicillin/ streptomycin) supplemented with 10 ng/ml M-CSF.  On day 7, BMDM were stimulated with 10 ng/ml LPS and 25 ng/mL IFN-γ for M1-like polarization and 10 ng/mL IL-4 for M2-like macrophage polarization for 16 h. RNA was isolated using RNAeasy Mini kit (Qiagen) and did RNA sequencing experiments.

first: Raghavendra

middle: G

last: Mirmira

first: Ebru

last: Ermis

first: Titli

last: Nargis


title: Targeted down-regulation of SRSF1 exerts anti-cancer activity in OSCC through impairing lysosomal function and autophagy

city: Beijing

first: Yi

last: Qu

address: NO.4 Tian Tan Xi Li

institute: Beijing Stomatological Hospital, Capital Medical University

summary: OSCC is a common cancer of the head and neck. Despite ongoing efforts, there remains a dearth of targeted drugs capable of effectively inhibiting OSCC growth. As the earliest discovered proto-oncogene in the SRSF family, targeted inhibition of SRSF1 plays an important role in tumor suppression. However, a comprehensive report on the expression, function, and mechanism of SRSF1 in OSCC has yet to be presented. This study retrospectively analyzed clinical samples from OSCC patients and discovered a significant correlation between the SRSF1 expression level and poor prognosis. In vitro experimentation demonstrated that SRSF1 knockdown inhibited OSCC growth, survival, lysosomal biogenesis and autophagy. To confirm the significance of lysosomal function and autophagy in the regulation of OSCC growth by SRSF1, cell rescue models were constructed. The aforementioned findings were subsequently validated in xenograft models. Ultimately, targeted knockdown of SRSF1 was found to significantly suppress OSCC growth by impeding lysosomal biogenesis and autophagy.

overall_design: RNA-sequencing of the stable si-NC and si-SRSF1 groups of SCC-4 and CAL-27 cells was carried out by GeneChem. The mRNA samples were collected, processed, and prepared for library creation following the producer's guidelines. In summary, total mRNA was obtained, and the Qubit® RNA Assay Kit in a Qubit® 2.0 fluorometer was utilized to determine the RNA concentration. Subsequently, NEBNext® UltraTM RNA Library Prep Kit for Illumina® was employed to produce sequence libraries following the manufacturer's recommendations. DESeq2 R package (1.16.1) was used to analyze the expression differences between si-NC and si-SRSF1 cells. The threshold levels were log2 (fold change) >1.5 and q<0.05.


title: Rare intercellular material transfer as a confound to interpreting inner retinal neuronal transplantation

city: Baltimore

first: Weifeng

last: Li

state: Maryland

address: 400 N Broadway

institute: Johns hopkins university

summary: Intercellular cytoplasmic material transfer (MT) occurs between transplanted and developing photoreceptors and ambiguates cell origin identification in developmental, transdifferentiation, and transplantation experiments. Whether MT is a photoreceptor-specific phenomenon is unclear. Retinal ganglion cell (RGC) replacement, through transdifferentiation or transplantation, holds potential for restoring vision in optic neuropathies. During careful assessment for MT following human stem cell-derived RGC transplantation into mice, we identified RGC xenografts occasionally giving rise to labeling of donor-derived cytoplasmic, nuclear, and mitochondrial proteins within recipient Müller glia. Critically, nuclear organization is distinct between human and murine retinal neurons, which enables unequivocal discrimination of donor from host cells. MT was dependent on internal limiting membrane disruption, which is also required for retinal engraftment following transplantation. Our findings demonstrate that retinal MT is not unique to photoreceptors and challenge the isolated use of species-specific immunofluorescent markers for xenotransplant identification. Assessment for MT is critical when analyzing neuronal replacement interventions.

overall_design: human ESC derived retinal ganglion cells were differentiated according to the small molecule-based method and purified on day 42 of differentiation. Purified RGCs then underwent single-cell RNA-seq according to the Drop-seq protocol.


title: snRNA-seq of aldosterone producing adenoma

city: Kashiwa

first: BIN

last: WU

state: Chiba

address: #304, 6-6-2, Kashiwanoha

department: Research

institute: ImmunoGeneTeqs

summary: Recent advances in omics techniques have allowed detailed genetic characterization of aldosterone-producing adenoma (APA). The pathogenesis of APA is characterized by tumorigenesis-associated aldosterone synthesis. The pathophysiological intricacies of APAs have not yet been elucidated at the level of individual cells . Therefore, a single-cell level analysis is speculated to be valuable in studying the differentiation process of APA. We conducted single-nuclei RNA sequencing (snRNA-seq) of APAs and non-functional adenomas (NFA) obtained from three and two patients, respectively.The snRNA-seq revealed the intratumoral heterogeneity of APA and identified cell populations consisting of a shared cluster of NFA and APA. In addition, we extracted two cell differentiation pathways in APA and obtained a cell population specialized in aldosterone synthesis. Genes related to ribosomes and neurodegenerative diseases were upregulated in one of these pathways, whereas those related to the regulation of actin cytoskeleton were upregulated in the other pathway. Furthermore, the total RNA reads in the nucleus were higher in highly differentiated clusters, indicating a marked activation of transcription per cell. The snRNA-seq provides novel differentiation pathways within APA tumors, which will further support our understanding of its pathophysiology including endocrine function and tumorigenesis.

overall_design: single-nuclei RNA sequencing (snRNA-seq) of 3 APAs and 2 non-functional adenomas (NFA)

first: Masanori

last: Murakami

first: Kazunari

last: Hara

first: Kenji

last: Ikeda

first: Tetsuya

last: Yamada


title: The early effects of radiotherapy on gene expression in RM9 and MC38 tumor tissues.

city: Dallas

first: Sangeetha

last: Reddy

state: Texas

address: 2280 Inwood Road

institute: UT Southwestern Medical Center

summary:
To investigate irradiation-induced gene expression profile changes in the tumor microenvironment with a focus on DNA sensing pathways and CXCL/CXCR2 axis at early time points (3h, 12h, 24h) after irradiation.
We then performed gene expression profiling analysis using data obtained from 4 tumor tissue from different mice at each time points and the unirradiated control group in both RM9 and MC38 tumor models.

overall_design: Comparative gene expression profiling analysis of mRNA-seq data for unirradiated group and irradiated groups at 3h, 12h, 24h after irradiation.

first: Faya

last: Zhang

first: Raquibul

last: Hannan

first: Chaoying

last: Liang

first: Carlos

last: Arana

first: Prithvi

last: Raj

first: James

last: Zhu


title: Mouse embryonic stem cells (mESCs) and neurons overexpressing DNMT1 and DNMT1 Y495C mutant form

city: Hyderabad

first: Sumana

last: Choudhury

address: Dept of Biological Sciences

country: India

institute: Birla Institute of Technology and Sciences

type: Methylation profiling by genome tiling array

summary: Genome wide DNA methylation profiling of mESCs and neurons overexpressing DNMT1 and DNMT1 Y495C mutant form. The Infinium Mouse methylation Beadchip  was used to obtain DNA methylation profiles across approximately > 285k methylation sites in DNA samples of mESCs and neurons. Samples included wild-type cell line (R1) and transgenic cell lines (R1wtDnmt1 and R1Dnmt1Y495C).

overall_design: Bisulphite converted DNA from mESCs and neuron samples were hybridized to the Illumina Infinium Mouse methylation Beadchip

first: Kommu

last: Naga Mohan


title: The epigenetic landscape of oligodendrocyte progenitors changes with time

city: New York

first: Patrizia

last: Casaccia

state: NY

address: 85 St Nicholas Terrace

department: Neuroscience

institute: ASRC-CUNY

summary: Adult oligodendrocyte progenitors (aOPCs) share with their neonatal counterpart (nOPCs) the ability to give rise to myelinating oligodendrocytes, but they also display unique functional features. This study addresses the molecular mechanisms underlying the intrinsic differences between these two populations. Using RNA-sequencing and unbiased histone proteomics analysis, we define the unique transcriptome and histone marks of aOPCs. We describe the lower proliferative capacity and higher levels of expression of oligodendrocyte specific genes in aOPC compared to nOPC. We also identify greater levels of activating H4K8ac histone marks in aOPCs compared to nOPCs, and increased occupancy of this mark at chromatin locations corresponding to oligodendrocyte-specific transcription factors and lipid metabolism genes. Pharmacological inhibition of H4K8ac deposition reduces the levels of these transcripts in aOPCs, rendering their transcriptome more similar to nOPCs. The repressive H4K20me3 mark is also higher in aOPCs compared to nOPCs and pharmacological  inhibition of its deposition results in increased levels of genes related to the mature oligodendrocyte state. Overall, this study identifies two histone marks which are important for the unique transcriptional identity of aOPCs.

overall_design: Chromatin immunoprecipitaion with H4K8ac antibody followed by sequencing (ChIP-seq) on sorted neonatal oligodendrocyte progenitors (nOPCs) and adult OPCs (aOPCs) from PdgfrαH2BEGFP mice.

first: David

middle: K

last: Dansu

first: Dennis

last: Huang

first: Meng

first: Sami

last: Sauma

first: Sarah

last: Moyon


title: Next Generation Sequencing Facilitates Quantitative Analysis of B73 and zmuvr8-1 mutant in low white with or without UVB treat Transcriptomes

first: Zhao

last: Zhiwei

address: 1066, Xueyuan Rd

department: College of Life Sciences and Oceanography

institute: Shenzhen univerisity

summary: Analysis of differential gene expression regulated by UVB. The hypothesis tested in the present study was that ZmUVR8 mediates mostly UVB regulated genes' expression

overall_design: mRNA profiles of 7 days of B73 and zmuvr8-1 seedlings  grown in low white with or without UVB treatment 1 hour were generated by deep sequencing, in triplicate, using Illumina Hiseq6000

first: Zhiwei

last: Zhao

first: Hongtao

last: Liu


title: Gene expression profile at single cell level on cells from the lungs of mice infected with Mycobacterium tuberculosis

city: Berkeley

first: Marietta

middle: Milou

last: Ravesloot-Chavez

state: Alameda

address: 500E Li Ka Shing, 1951 Oxford St

department: Plant and Microbial Biology

institute: University of California Berkeley

summary: We used single-cell RNA sequencing (scRNAseq) to compare cells from the lungs of Mycobacterium tuberculosis infected mice between C57BL/6J mice and a cohort of wild-derived mouse lines MANA, MANB and MANC (Jackson Laboratories: ManA/NachJ #035354; ManB/NachJ #035355).

overall_design: Lung lobes were pooled from five infected mice per genotype and cells were isolated for analysis by scRNAseq.

last: Stanley

middle: M


title: Overexpression of ZmSUS1 increased drought resistance of maize (Zea mays L.) by regulating sucrose metabolism and soluble sugar content

city: jinan

first: xiao

last: ning

address: changqing

department: School of Bioengineering

institute: Qilu University of Technology (Shandong Academy of Sciences)

summary: Sucrose synthase (SUS), a key enzyme of sugar metabolism, plays an important role in the regulation of carbon partitioning in plant, and affects important agronomic traits and abiotic responses to adversity. However, the function of ZmSUS1 in plant drought tolerance is still unknown. In this study, the expression patterns of ZmSUS1 in different tissues and under drought stress were analyzed in maize (Zea mays L.). It was found that ZmSUS1 was highly expressed during kernel development but also in leaves and roots of maize, and ZmSUS1 was induced by drought stress. Homozygous transgenic maize lines of ZmSUS1 overexpressing increased the content and activity of SUS under drought stress and exhibited higher relative water content, proline and abscisic acid content in leaves. Specifically, the net photosynthetic rate and the soluble sugar contents including sucrose、glucose、fructose、UDP-glucose and ADP-glucose in transgenic plants was significantly improved after drought stress. RNA-seq analysis showed that overexpressing of ZmSUS1 mainly affected the expression level of carbon metabolism-related genes, especially the expression level of  sucrose metabolism-related genes including ZmSUS、ZmSPS and ZmINV were significantly up-regulated in transgenic maize. Overall, these results suggested that ZmSUS1 improved drought tolerance by regulating sucrose metabolism and increasing soluble sugar content, and endowing transgenic maize with higher relative water content and photosynthesis levels, which can be served as a new gene candidate for cultivating drought resistant maize varieties.

overall_design: A transgenic strain (T) was selected with its non-transgenic negative control (CK) for RNA-seq analysis, with three biological replicates selected each. RNA is extracted from leaf after 5 days of drought. RNA sequencing

first: Ning

last: Xiao

first: Haizhen

last: Ma

first: Wanxia

last: Wang

first: zengkun

last: Sun

first: Panpan

last: Li

first: Tao

last: Xia


title: Bone Marrow Interstitial Light-chain Amyloid and its Microenvironment

city: Boston

first: Raymond

last: Comenzo

state: MA

address: 800 Washington Street

institute: Tufts Medical Center

summary: Amyloid deposition and neighboring tissue responses remain poorly understood. Twenty percent of patients with systemic light-chain amyloidosis (AL) have interstitial marrow amyloid  containing clonal Ig light-chain fibrils and apolipoprotein chaperone proteins. We compared CD138-depleted aspirate mononuclear cells (MNC) from marrows of AL patients with (+MA) and without (-MA) interstitial amyloid by gene expression profiling (GEP) and single-cell RNA-sequencing (scRNA seq). GEP showed no differential expression of genes for proteolytic enzymes or apolipoproteins between the groups but +MA cases had significantly up-regulated erythroid genes involved in oxygen transport, including transmembrane and coiled-coil domain family 2 (TMCC2). In +MA marrows at the single-cell level, CD14+ monocytes were increased by 22%, granulocyte-monocyte progenitors decreased by 66%, and erythroid-megakaryocyte progenitors and early and late erythroid progenitors increased up to five-fold. Gene enrichment studies showed that in +MA marrows pathways for TNFα signaling, immune activation, monocyte hypoxia and erythropoiesis were significantly enriched. We also compared peripheral blood and marrow plasma by immunoprecipitation and immunoblot with respect to apolipoproteins and light chains in complex with the erythroid protein TMCC2, and by ELISA for marrow apolipoprotein E and J levels. Apolipoprotein J is strongly associated with light chains in blood and E is not, while in +MA marrow plasma J and E are strongly present in association with light chains. There is also significantly more apolipoprotein E and J in +MA marrow plasma. In summary, marrows with interstitial amyloid provide opportunities to study amyloid’s impact on cellular and regenerative activity and chaperone involvement in amyloid formation.

overall_design: RNA was obtained from CD138-depleted marrow mononuclear cells (MNC) and used to prepare libraries with the Illumina TruSeq Stranded Total RNA kit for sequencing on the Illumina HiSeq 2500.  Following preparation, the libraries were denatured, introduced into the flow cell, and subjected to bridge amplification in order to create clonal clusters of single stranded cDNA molecules. Sequencing and analysis were performed in our core facility as previously described. Bioinformatic analyses were performed on the Tufts University High Performance Cluster (Medford, MA). Tuxedo Tools were used to analyze the RNASeq results. Briefly, reads were mapped to the UCSC hg19 human genome with Tophat 2/Bowtie 2. Normalization and differential expression analyses were performed with Cuffdiff.

first: Ping

last: Zhou

first: Tanya

last: Karagiannis

first: Albert

last: Tai

first: Xun

first: Denis

last: Toskic

first: Teresa

last: Fogaren

first: Nancy

last: Coady Lyons

first: Xia

last: Wu

first: Monika

last: Pilichowksa

first: Stephanie

last: Scalia

first: Paola

last: Sebastiani


title: Primary Cilia-Mediated Regulation of Microglial Secretion in Alzheimer's Disease

city: Daegu

first: Jaemyung

last: Jang

address: 61, Cheomdan-ro, Dong-gu

country: South Korea

institute: Korea Brain Research Institute

summary: Alzheimer's disease (AD) is a brain disorder manifested by a gradual decline in cognitive function due to the accumulation of extracellular amyloid plaques, disruptions in neuronal substance transport, and the degeneration of neurons. In affected neurons, incomplete clearance of toxic proteins by neighboring microglia leads to irreversible brain inflammation, for which cellular signaling is poorly understood. Through single-cell transcriptomic analysis, we discovered distinct regional differences in the ability of microglia to clear damaged neurites. Specifically, microglia in the septal region of wild type mice exhibited a transcriptomic signature resembling disease-associated microglia (DAM). These Lateral septum (LS)-enriched microglia (SEM) were associated with dense axonal bundles originating from the hippocampus. Further transcriptomic and proteomic approaches revealed that primary cilia, small hair-like structures found on cells, played a role in the regulation of microglial secretory function. Notably, primary cilia were transiently observed in less than 10% of microglia, and their presence was significantly reduced in microglia from AD mice. We observed significant changes in the expression and distribution of the secretome after inhibiting the primary cilia gene intraflagellar transport particle 88 (Ift88) in microglia. Intriguingly, inhibiting primary cilia in the SEM of AD mice resulted in the expansion of extracellular amyloid plaques and damage to adjacent neurites. These results indicate that DAM-like microglia are present in the LS, a critical target region for hippocampal nerve bundles, and that the primary ciliary signaling system regulates microglial secretion, affecting extracellular proteostasis. Age-related primary ciliopathy probably contributes to the selective sensitivity of microglia, thereby exacerbating AD. Targeting the primary ciliary signaling system could therefore be a viable strategy for modulating neuroimmune responses in AD treatments.

overall_design: We performed single-cell transcriptome profiling isolated from the hippocampus, the septum, and the habenula of WT and 5xFAD mice using an inDropTM platform

first: Seungun

last: Yeo

first: Hyun

last: Jung

first: Youngshik

last: Choe


title: ZNF714 – a novel oncogene in lung cancer cells [RNA-seq]

city: Poznan

first: Marta

last: Machnik

state: Wielkopolska

address: Rokietnicka 8

department: Chair of Medical Biotechnology

country: Poland

institute: Poznan University of Medical Sciences

summary: Despite the ongoing progress in diagnosis and treatments, cancer remains a threat to more than one-third of the human population. It is a complex disorder characterized by multi-omic aberrations affecting cell proliferation, death, migration, plasticity, interaction with the immune system, and other features. The emerging data indicate that many KRAB-ZNF factors belonging to a large gene family may be involved in carcinogenesis. Our previous study identified ZNF714, a KRAB-ZNF gene of unknown function, as commonly overexpressed in many tumors, pointing to its hypothetical oncogenic role. Here, we harnessed the TCGA-centered online databases, performed functional studies and transcriptomic and methylomic profiling to test this hypothesis, and explore ZNF714 function in cancer. Our pan-cancer analyses confirmed that ZNF714 is frequently upregulated in multiple tumors, possibly as a result of regional amplification, promoter hypomethylation, and NFYB signaling. We also showed that ZNF714 expression correlates with tumor immunosuppressive features. The in vitro studies indicated that ZNF714 expression positively associates with proliferation, migration, and invasion. In line with these observations, the transcriptomic analysis of ZNF714 knocked-down cells demonstrated deregulation of cell adhesion, migration, proliferation, apoptosis, and differentiation. Importantly, we provided evidence that ZNF714 negatively regulates the expression of a number of known TSGs via promoter methylation. However, as ZNF714 did not show nuclear localization in our research model, the regulatory mechanisms exerted by ZNF714 require further investigation. In conclusion, our results reveal, for the first time, that ZNF714 may have oncogenic functions.

overall_design: We analyzed 6 samples from two different lung cancer cell lines in biological triplicates (total 18 samples). For each cell line (H2073 and SKMES) we analyzed unmodified cells (WT), cells with knocked-down expression of ZNF714 (shZNF714) and cells carrying control shRNA sequence (shLUC).Pair-end RNA sequencing was performed for all samples on a NovaSeq 6000 Sequencing System (Illumina). DEG (Differentially Expressed Genes) analysis was performed on two different comparison pairs (sh714 vs. two control samples WT and shLUC separately) using edgeR.

first: Machnik

last: Marta

first: Urszula

last: Oleksiewicz


title: Mouse spleen LCM-ATACseq (B and T cell zones)

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

summary: In situ transposition followed by laser capture microdissection was applied to spleen mouse tissue sections to demonstrate feasibility of LCM-based spatial chromatin accessibility analysis of regions of interest. B220 and CD3e immunostained B and T cell zones were analyzed.

overall_design: Fresh frozen spleen tissue sections from C57BL/6J WT mice were tagmented in situ to assess chromatin accessibility. LCM was employed to collect a mini bulk of immunostained B and T cells. Two mini-bulk sizes were investigated: 100 single-captured nuclei or 10 larger captured-areas (patches) composed each of roughly 100 nuclei, for a total of ~1000 nuclei. Four technical replicates were collected at least per condition.

first: Caterina

last: Carraro

first: Adem

last: Saglam

middle: L

first: Marc

last: Beyer


title: BET bromodomain Inhibition Potentiates Radiosensitivity by Reprograming DNA Damage Repair in H3K27M-Mutant Glioma

city: Birmingham

first: Rintaro

last: Hashizume

state: Alabama

address: 1670 University Blvd

department: Pediatrics

institute: UAB

summary: Diffuse intrinsic pontine glioma (DIPG) is one of the devastating childhood cancers. Radiation therapy remains the only effective treatment yet provides a 5-year survival rate of only1%. Several clinical trials have attempted to enhance radiation anti-tumor activity using radiosensitizing agents, though none have been successful in doing so. Given this, there is a critical need for identifying effective therapeutics to enhance radiation sensitivity for the treatment of DIPG. Using high-throughput radiosensitivity screening, we identified bromo- and extra-terminal domain (BET) protein inhibitors as potent radiosensitizers in DIPG. Genetic and pharmacologic inhibition of BET bromodomain activity reduced DIPG cell proliferation and enhanced radiation-induced DNA damage by inhibiting DNA repair pathways. RNA- and CUT-RUN-sequencing showed that BET bromodomain inhibitors regulate the expression of DNA repair genes mediated by H3K27acetylation at enhancers. BET bromodomain inhibitors enhanced DIPG radiation-response in patient-derived xenografts as well as genetically engineered mouse models. Together, our results highlight BET bromodomain inhibitor as a novel radiosensitizer and provide a rationale for developing combination therapy with radiation for the treatment DIPG.

overall_design: Differential gene expression and H3K27Ac differential peak analyses were performed in SF8628 cells treated with AZD5153 or DMSO

first: Jun

last: Watanabe

first: Samantha

last: Gadd


title: Mouse lung, brain and spleen LCM-ATACseq

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

overall_design: Refer to individual Series


title: Hypoxia-sensing by Colitogenic CD4+ T cells Is Regulated by the Histone Demethylase UTX.

city: los angeles

first: Mandy

last: Cheng

address: 615 Charles E Young Dr S

department: MIMG

institute: UCLA


title: Effect of supplementation of a minimal culture medium with inulin, corn fiber and pectin, compared with a glucose condition, on the gene expression of a set of bacteria of the intestinal microbiota

city: JOUY EN JOSAS

first: paul

last: Biscarrat

state: ile de france

address: 4 AVENUE JEAN JAURES-DOMAINE VILVERT

country: France

institute: INRAE

summary: The aim of this RNA-sequencing study is to measure differential gene expression in 4 intestinal bacteria (Bacteroides xylanisolvens, Bacteroides thetaiotaomicron, Subdoligranulum variabile and Roseburia intestinalis). The data highlight the coordinated action of genes within the same locus involved in the degradation of complex carbohydrates. These loci are well characterized in Bacteroidetes species and referred to as polysaccharide utilization loci. In Firmicutes species, these loci are not so clear-cut, athough the GP-PUL concept has already been proposed. Here we compare the differential gene expression in minimal culture medium supplemented with a complex carbohydrate with a minimal culture medium supplemented with glucose. This differential analysis reveals a source-specific genetic response and a coordinated expression of genes involved in carbohydrate transport, carbohydrate degradation and transcriptional activation of these complex enzymatic machineries.

sample_organism:
Bacteroides thetaiotaomicron
Roseburia intestinalis
Subdoligranulum variabile
Bacteroides xylanisolvens

overall_design: To investigate this differential expression, bacterial RNA was extracted after 12h of culture in minimum medium supplemented with one complex carbohydrate or glucose. RNA was extracted using RNAeasy Qiagen kit.

first: Cassandre

last: Bedu-Ferrari

first: Paul


title: Hypoxia-sensing by Colitogenic CD4+ T cells Is Regulated by the Histone Demethylase UTX [H3K27me3 CUT&Tag]

summary: Hypoxia exacerbates tissue damage in inflammatory bowel disease (IBD). To counteract the deleterious effects of oxygen deprivation, cells within hypoxic tissues activate multiple adaptive mechanisms. Much attention has focused on adaptive pathways regulated by HIF (hypoxia inducible factor) transcription factors, and pharmacologic HIF stabilization is a promising therapeutic approach for IBD. However, recent evidence suggests that hypoxia-induction of cellular transcriptional programs can be mediated not only by HIF transcription factors, but also by oxygen-sensing epigenetic regulator, UTX. Here, we identify a key role for an UTX in modulating colitis severity. Unlike HIF-mediated pathways that act on gut epithelial cells, UTX-mediated pathways function in a T cell-intrinsic manner to protect against colitis. Hypoxia impairs the histone demethylase activity of UTX, which leads to accumulation of repressive H3K27me3 marks at IL12/STAT4 pathway genes (Il12rb2, Tbx21, and Ifng), decreased CD4+ T cell IFN-γ production, and increased CD4+ regulatory T cells (Tregs). Moreover, T cell specific UTX deletion protects mice from autoimmune colitis, which demonstrates that deactivation of UTX restores immune regulation in hypoxia-associated inflammation.  Together these findings suggest that modulating UTX’s histone demethylase activity in T cells may be a new pharmacologic target for harnessing hypoxia-induced adaptive pathways in colitis.

overall_design: To identify changes in H3K27me3 levels at gene loci  in response to loss of UTX in CD4+ T cells, we performed H3K27me3 CUT&Tag on CD4+ T cells isolated from B6.WT and B6.UTX TCD (Mice lacking UTX specifically in T cells) mice that were activated for 48 hours using plate-bound anti-CD3 and soluble anti-CD28.  Three mice per genotype were used in this experiment.

middle: I

first: Lee

last: Hong

first: Bryan

last: Chen

first: Scott

last: Chin

first: Shezhad

last: Sheikh

first: Christopher

last: Luthers

first: Maureen

last: Su


title: CircTLCD4-RWDD3 promotes lymphatic metastasis in non-small cell lung cancer

first: Shanqing

last: Li

address: No.1 Shuaifuyuan, Wangfujing Street

department: Department of Thoracic Surgery

institute: Peking Union Medical College Hospital

type: Non-coding RNA profiling by high throughput sequencing

summary: Lung cancer is the leading cause of cancer-related death worldwide, and non-small cell lung cancer (NSCLC) accounts for approximately 85% of lung cancers. Lymphatic metastasis serves as a predominant NSCLC metastatic route and an essential predictor of patient prognosis. Recently, circular RNA (circRNA) has emerged as critical mediator in various tumor initiation and progression. To identify essential circRNA that involves in the lymphatic metastasis of NSCLC, Next generation sequencing (NSG) was performed in 6 paired NSCLC tissues and normal adjacent tissues (NAT).

overall_design: To identify essential circRNA that is involved in the lymphatic metastasis of NSCLC, next generation sequencing (NSG) was performed in 6 paired NSCLC tissues and normal adjacent tissues (NAT).

first: Xiayao

last: Diao


title: Hypoxia-sensing by Colitogenic CD4+ T cells Is Regulated by the Histone Demethylase UTX [RNA-seq]

overall_design: To identify gene expression changes in response to loss of UTX in CD4+ T cells, we performed bulk RNA-sequencing on CD4+ T cells isolated from B6.WT and B6.UTX TCD (Mice lacking UTX specifically in T cells) mice that were activated for 48 hours using plate-bound anti-CD3 and soluble anti-CD28.  Three mice per genotype were used in this experiment.


title: Sperm chromatin accessibility's involvement in the intergenerational effects of stress hormone receptor activation

city: Basel

first: Faiza

last: Noreen

address: Mattenstrasse 28

department: Department of Biomedicine

country: Switzerland

institute: University of Basel

summary: Dexamethasone is a stress hormone receptor agonist used widely in clinics. We and others previously showed that paternal administration of dexamethasone in mice affects the phenotype of their offspring. The substrate of intergenerational transmission of environmentally induced effects often involves changes in sperm RNA, yet other epigenetic modifications in the germline can be affected and are also plausible candidates. First, we tested the involvement of altered sperm RNAs in the transmission of dexamethasone induced phenotypes across generations. We did this by injecting sperm RNA into naïve fertilized oocytes, before performing metabolic and behavioral phenotyping of the offspring. We observed phenotypic changes in discordance with those found in offspring generated by in vitro fertilization using sperm from dexamethasone exposed males. Second, we investigated the effect of dexamethasone on chromatin accessibility using ATAC sequencing and found significant changes at specific genomic features and gene regulatory loci. Employing q-RT-PCR, we show altered expression of a gene in the tissue of offspring affected by accessibility changes in sperm. Third, we establish a correlation between specific DNA modifications and stress hormone receptor activity as a likely contributing factor influencing sperm accessibility. Finally, we independently investigated this dependency by genetically reducing thymine-DNA glycosylase levels and observing concomitant changes at the level of chromatin accessibility and stress hormone receptor activity.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for mESC dpending on genotype.

first: David

last: Schürmann

first: Primo

last: Schär

first: Vincent

last: Fischer

first: Katharina

last: Gapp


title: Analysis of UV-induced DNA damage in human cells using CPD-seq 2.0

city: Albuquerque

first: Peng

last: Mao

state: NM

address: 2325 Camino de Salud

institute: University of New Mexico

summary: Noncoding mutation hotspots have been identified in melanoma and many of them occur at the binding sites of E26 transformation-specific (ETS) proteins; however, their formation mechanism and functional impacts are not fully understood. Here, we used UV damage sequencing data and analyzed cyclobutane pyrimidine dimer (CPD) formation, DNA repair, and CPD deamination in human cells at single-nucleotide resolution. Our data shows prominent CPD hotspots immediately after UV irradiation at ETS binding sites, particularly at sites with a conserved TTCCGG motif, which correlate with mutation hotspots identified in cutaneous melanoma. Additionally, CPDs are repaired slower at ETS binding sites than in flanking DNA. Cytosine deamination in CPDs to uracil is suggested as an important step for UV mutagenesis. However, we found that CPD deamination is significantly suppressed at ETS binding sites, particularly for the CPD hotspot on the 5’ side of the ETS motif, arguing against a role for CPD deamination in promoting ETS-associated UV mutations.  Finally, we analyzed a subset of frequently mutated promoters, including the ribosomal protein genes RPL13A and RPS20, and found that mutations in the ETS motif can significantly reduce the promoter activity. Thus, our data identifies high UV damage and low repair, but not CPD deamination, as the main mechanism for ETS-associated mutations in melanoma and uncover new roles of often-overlooked mutation hotspots in perturbing gene transcription.

overall_design: Human skin fibroblast cells were grown in DMEM/F-12 medium with 10% FBS. Media was removed and cells were exposed to UV-C at 6 and 8 J/m2 to induce UV damage. A portion of the cells were harvested immediately after UV treatment as time 0 (i.e., no repair). The rest of cells were incubated in fresh DMEM for repair. Repair time points were taken at 6 and 24 h post UV irradiation. Genomic DNA was isolated from cells and used for the preparation of CPD-seq 2.0 libraries. After Illumina sequencing, locations of UV-induced photolesions were identified using our published protocol. Formation and repair of UV damage was analyzed in gene promoters, particularly those containing ETS binding sites.

first: Mingrui

last: Duan


title: Single cell and spatial transcriptomics analysis of kidney double negative T lymphocytes in normal and ischemic mouse kidneys

first: Emily

last: Lo

state: MD

address: 733 N Broadway

institute: Johns Hopkins


title: Single cell and spatial transcriptomics analysis of kidney double negative T lymphocytes in normal and ischemic mouse kidneys [scRNA-Seq]

summary: T cells are important in the pathogenesis of acute kidney injury (AKI), and TCR+CD4-CD8- (double negative-DN) are T cells that have a regulatory role. However, little is understood about these cells in comparison to traditional CD4+ and CD8+ cells. To elucidate the molecular and spatial dynamics of DN T cells during AKI, we performed single-cell RNA sequencing (scRNA-seq) on sorted murine DN, CD4+, and CD8+ cells, combined with spatial transcriptomic profiling of normal and post-AKI mouse kidneys. scRNA-seq revealed distinct transcriptional profiles for DN, CD4+, and CD8+ T cells of mouse kidneys, with enrichment of Kcnq5, Klrb1c, Fcer1g, and Klre1 expression in DN T cells compared to CD4+ and CD8+ T cells in normal kidney tissue. We validated the expression of these genes in mouse and human kidney DN, CD4+ and CD8+ T cells using RT-PCR and in the NIH kidney precision medicine project (KPMP). Spatial transcriptomics in normal and ischemic mouse kidney tissue showed a localized cluster of T cells in the outer medulla expressing DN T cell genes including Fcer1g. These results provide a template for future studies in DN T as well as CD4+ and CD8+ cells in the normal and diseased kidney.

overall_design: CD4+, CD8+, and double negative T cells from normal kidney and kidney treated with ischemic reperfusion injury were analyzed using single-cell RNA-Seq.

first: Sepideh

last: Gharaie

first: Kyungho

last: Lee

first: Kathleen

last: Noller

first: Brendan

last: Miller

first: Hyun

last: Jung

first: Andrea

last: Newman-Rivera

first: Johanna

middle: T

last: Kurzhagen

first: Nirmish

last: Singla

first: Paul

last: Welling

first: Jean

last: Fan

first: Patrick

last: Cahan

first: Sanjeev

last: Noel

first: Hamid

last: Rabb


title: Single cell and spatial transcriptomics analysis of kidney double negative T lymphocytes in normal and ischemic mouse kidneys [spatial transcriptomics]

overall_design: Normal kidneys and kidneys treated with ischemic reperfusion injury were analyzed using spatial transcriptomics.


title: Single-cell transcriptomics reveal the dynamic of cancer stem-like cells during cholangiocarcinoma progression

city: Bethesda

first: Margaret

last: Cam

address: 9000 Rockville Pike

institute: NCI

summary: We investigated YAP/AKT hydrodynamic tail vein injected murine models and we analyzed the correlative change of immune cell profile and stemness during cholangiocarcinoma progression using single-cell RNA sequencing

overall_design: Mouse liver/tumor samples were prepared with three replicate per sample. Empty vector injected sample was used as a control

first: Jihye

last: Golino

first: Jing

last: Bian

first: Xin

last: Wang

first: Jinyang

last: Fu

first: Michael

last: Kelly

first: Freddy

last: Escorcia

first: Maggie

first: Changqing

last: Xie


title: Eosinophils exert direct and indirect anti-tumorigenic effects in the development of esophageal squamous cell carcinoma [eos]

city: Nashville

first: Justin

last: Jacobse

state: Tennessee

address: 2215 Garland Avenue

institute: Vanderbilt University Medical Center

summary: Eosinophils are present in several solid tumors and have context-dependent function. The role of eosinophils in the development of esophageal squamous cell cancer (ESCC), 85% of esophageal cancers worldwide, is unknown. Mice were treated with 4-nitroquinolone-1-oxide (4-NQO) for 8 weeks followed by vehicle for 8 weeks to induce esophageal squamous pre-cancer. Eosinophil depletion using three mouse models resulted in exacerbated 4-NQO tumorigenesis.  In order to study the transcriptional profiles of eosinophils specifically, we isolated eosinophils from esophageal tissue of WT mice which had been treated with 4-NQO in the pre-cancer model. Because eosinophils are not present in the esophagus normally, we isolated eosinophils from the colons of a random subset of the same mice. Additionally, we derived eosinophils from the bone marrow of a random subset of the same mice.

overall_design: C57/BL6 WT mice received 4-NQO for 8 weeks and propylene glycol for 8 weeks resulting in pre-cancer. Eosinophils were acquired from esophageal lamina propria and colonic lamina propria using immunomagnetic positive selection. Bone marrow-derived eosinophils were acquired.

first: Yash

middle: A

last: Choksi


title: Mesenchymal WNT2B is required for the maintenance of the human small intestinal epithelium

city: Cincinnati

first: Konrad

last: Thorner

state: OH

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

summary: In this study, we utilize a scaffolding tray for organoid development. Conventional organoids are compared to those generated using the scaffolding tray.

overall_design: Single nucleus RNA sequencing was preformed on transplanted organoids.

first: Holly

last: Poling

first: Akaljot

last: Singh


title: JAK2 as a surface marker for enrichment of human pluripotent stem cells-derived ventricular cardiomyocytes

city: Singapore

first: Boon Seng

last: SOH

address: 61 Biopolis Drive, Proteos

department: Institute of Molecular and Cell Biology (IMCB)

country: Singapore

institute: A*STAR

summary: The generation and purification of cardiomyocyte sub-population are critical for precise modelling of cardiac diseases, drug screening, and regenerative medicine due to their distinct phenotypic and functional characteristics. Therefore, identifying surface markers for cardiomyocyte subtypes that facilitate live cell sorting of homogenous population of cardiomyocytes is of utmost importance for successful translation of cardiovascular research and therapeutic applications. Using MARIS method coupled with RNA sequencing analysis on MLC2A- and MLC2V-expressing cardiomyocytes, we identified JAK2 as a potential cell surface marker for purifying ventricular cardiomyocytes. We demonstrated that that SIRPA+/JAK2+ population sorted expressed high levels of ventricular-specific marker and had electrophysiological properties that corresponded to ventricular-like cardiomyocytes. Functionally, SIRPA+/JAK2+ cardiomyocytes do not response to vernakalant, an atrial-selective anti-arrhythmic agent, confirming their identity as ventricular-like cells.

overall_design: We used MARIS to isolate SIRPA+ CMs based on intracellular MLC2A or MLC2V expression and identified potential surface markers for ventricular specification through RNA sequencing analysis. To validate the effectiveness of these surface markers, we performed immunostaining and western blot analysis to measure MLC2A and MLC2V protein expressions in SIRPA+ cardiomyocytes that were either positive or negative for the putative surface markers. We then characterized the electrophysiological properties of surface marker-sorted cardiomyocytes by measuring cellular calcium transient using fluo-4 AM. For functional validation, we investigated the response of the surface marker-sorted cardiomyocytes to vernakalant, an atrial-selective anti-arrhythmic agent.

first: Lee

middle: C

last: Liew

first: Boon

last: Poh

first: Omer

last: An

first: Beatrice

middle: X

last: Ho

first: Christina

middle: Y

last: Lim

first: Henry

last: He

first: Boon-Seng

last: Soh


title: Transcriptional response to gut pathobiont Streptococcus gallolyticus subsp. gallolyticus infection of huham colon cells

city: Paris

first: Hugo

last: Varet

address: 28 rue du Docteur Roux

institute: Institut Pasteur

summary: Streptococcus gallolyticus sp. gallolyticus (SGG) is a gut pathobiont involved in the development of colorectal cancer (CRC). To  decipher SGG contribution in tumor initiation and/or acceleration respectively, a global transcriptome was performed in normal colonic cells (FHC) and in tumoral colonic cells (HT29).  To identify SGG-specific alterations, we chose the phylogenetically closest relative, Streptococcus gallolyticus subsp. macedonicus  (SGM) as control bacterium. We show that SGM, a bacterium generally considered as safe, did not induce any transcriptional changes on the two human colonic cells FHC and HT29. The transcriptional reprogramming induced by SGG in FHC and HT29 cells was significantly different, however most of the genes up- and down-regulated were associated with cancer disease. Top up-regulated genes related to cancer were: (i) IL-20, CLK1, SORBS2, ERG1, PIM1, SNORD3A for normal FHC cells and (ii) TSLP, BHLHA15, LAMP3, ZNF27B, KRT17, ATF3 for cancerous HT29 cells. SGG induces much stronger transcriptional changes in cancerous than in normal colonic cells (2090 vs genes 128). Gene set enrichment analysis reveals that SGG-induced strong ER- (endoplasmic reticulum) stress and UPR- (unfolded protein response) activation in colonic epithelial cells. Our results suggest that SGG induces a pro-tumoral shift in human colonic cells particularly in transformed cells potentially accelerating tumor development in the colon.

overall_design: FHC cells were seeded into 6-well plates at a density of 2 x 105 cells per well and HT29 cells at 4 x 105 cells per well and incubated for 16-20 hours. Stationary phase bacteria were scratched from fresh THY plates (overnight culture) and washed with sterile phosphate buffered saline, pH 7.4 (PBS) to get an OD600 of 1 (corresponding to 6.5 x 108 CFU). The bacteria were diluted in DMEM (Gibco, Ref. 12320032, low glucose, pyruvate, HEPES) to obtain the desired concentration as follows (i) SGM of 6.5 x 105 CFU/ml and (ii) SGG UCN34 of 6.5 x 104 CFU/ml. Cells are washed once with DMEM and then infected with the medium containing the bacteria by adding 25 ml of bacterial suspension per well in the 6-well plate. For the non-treated (NT) condition, only 2 ml of fresh media was added. For each condition, a complete 6-well plate was used and then pooled together to obtain enough cellular material for further RNA extraction. Trimethoprim (Sigma, Ref. T7883), a bacteriostatic antibiotic was added at 50 μg.ml-1 final concentration after 6 h of co-culture to prevent media acidification due to bacterial growth. The total co-culture incubation time was 24 h. Total RNA was extracted from cell monolayers with the RNeasy Plus Mini kit (Qiagen, USA), according to the manufacturer's instructions. Three independent replicates for each condition were performed and analyzed. RNAs were conserved at -80°C and used in transcriptome Illumina assay and quantitative RT-PCR.

first: Ewa

last: Pasquereau-Kotula

first: Laurence

last: du Merle

first: Odile

last: Sismeiro

first: Natalia

last: Pietrosemoli

first: Rachel

last: Legendre

first: Patrick

last: Trieu-Cuot

first: Shaynoor

last: Dramsi


title: Effect of PRMT5 knockout on gene expression in epididymal white adipose tissues

city: West Lafayette

first: Shihuan

last: Kuang

state: IN

address: 901 W State St

institute: Purdue University

summary: In this study, we applied RNA sequencing  of WT (Prmt5flox/flox) and Adiponectin-Cre driven Prmt5 knockout (Prmt5AKO) adipose tissue to uncover the molecular mechanisms underlying PRMT5 function.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for epididymal white adipose tissue of WT (Prmt5flox/flox) and Prmt5 knockout (Prmt5AKO)  mice

first: Xiyue

last: Chen

first: Zhihao

last: Jia


title: CD146 accelerates malignant progression of phyllodes tumor cells

city: Guangzhou

first: Nie

last: Yan

state: Guangdong

address: 107 Yangxi Road, Yuexiu District,

department: Sun Yat-sen Memorial Hospital,

institute: Sun Yat-sen University

summary: Breast malignant phyllodes tumors (PTs) are rapid-progressing tumors, known to lack effective treatment and suitable prognostic markers as well as elaborate studies. Herein,we found that level of CD146 is progressively elevated with malignant progression of PTs and is an independent predictor for prognosis of PT patients.Mechanistically, CD146 activates the PI3K/AKT signaling pathway, thereby enhancing malignant behaviors of PT cells.This study unveils a CD146-PI3K/AKT axis in modulating the malignant progression of PTs, and open avenues to develop a novel target for precise prognosis and treatment for breast malignant PTs.

overall_design: Total RNA in the cells from different treatment group (benign PT cell B1 or CD146 overexpression cell B2; malignant PT cell M1 or CD146 silencing cell M2 ) was obtained by Trizol. Transcriptome sequencing was applied to analyze the expression profiling of human transcripts in the samples and performed by BGI Technology lnc (Shenzhen, China). The raw data were extracted by Feature Extraction software and further quantile normalized.

first: Jiewen

first: Qingji

last: Xu


title: Murine lung: Control vs Diesel Exhaust Exposed

city: Delhi

first: Naveen

last: Arora

address: Mallroad

institute: IGIB

summary: MicroRNA microarray profiling of Murine lung exposed to diesel exhaust

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: Two Control replicates, two stimuli-1 replicates and two stimuli-2 replicates

first: Naresh

last: Singh

first: Anshu

last: Gautam

first: Ekta

last: Nagar


title: Transcriptome profiling of the liver and pectoralis major muscle in slow-growing chickens under an organic raising system

city: Mueang Nakhon Ratchasima

first: Panpradub

last: Sinpru

state: Nakhon Ratchasima

address: Maha Witthayalai Rd

department: School of Animal Technology and Innovation

country: Thailand

institute: Suranaree University of Technology

summary: The strategy to improve the competitiveness of smallholder farmers and to serve highly nutritious meat for consumers is the major goal of Korat chicken (KRC) production in Thailand. Organic KRC meat contains high n-3 polyunsaturated fatty acids (PUFA) and docosahexaenoic acid (DHA), which have a wide range of health-related benefits. However, limited scientific investigations have been conducted on the modulations of PUFA and DHA in KRC. In this study, we compared two rearing systems, conventional (CO) and organic raising (OR) systems, and their effects on global gene expression related to the accumulation of n-3 PUFA and DHA in the liver and pectoralis major muscle were investigated by using RNA-sequencing (RNA-seq). Total RNA was isolated from the liver and pectoralis major muscle of male KRC in each treatment group (n = 5). RNA-seq revealed a total of 561 and 361 differentially expressed genes between CO and OR groups identified in the liver and pectoralis major muscle, respectively. ELOVL fatty acid elongase 2 (ELOVL2) may activate n-3 PUFAs synthesis via the fatty acid elongation pathway. The KRC seems suitable to raise under the organic raising system, since it improved lipid metabolism and immune response in the liver. However, thermal environmental management and growth performance need to be considered. ELOVL2 can use as a gene marker for n-3 PUFAs synthesis in the liver. This study provides a genetic basis for future breeding strategies to improve the genetics of slow-growing chickens to fit with an organic raising system.

overall_design: Liver and pectoralis major muscle tissues were collected from chicken in conventional (n=5) and organic (n=5) raising systems and differentially expressed genes were identified using RNA-sequencing.

first: Kasarat

last: Promkhun

first: Saknarin

last: Pengsanthia

first: Tom

last: Porter

first: Nathawat

last: Tanpol

first: Wittawat

last: Molee

first: Amonrat


title: Eosinophils exert direct and indirect anti-tumorigenic effects in the development of esophageal squamous cell carcinoma

first: Justin

last: Jacobse

overall_design: Refer to individual Series


title: ROBO1 deficiency impairs hematopoietic stem progenitor cell self-renewal and erythropoiesis via CDC42 and predicts poor prognosis in MDS

city: Shanghai

first: Jiaying

last: Zhang

state: Shanghai

address: 320 Yue Yang Road

department: CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health

institute: Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences

summary: We previously identified inactivating mutations in roundabout guidance receptor 1 (ROBO1) in patients with myelodysplastic syndrome (MDS), which was associated with poor prognosis and susceptibility to acute myeloid leukemia (AML) transformation. Nonetheless, the exact role of ROBO1 in hematopoiesis remains poorly delineated. Here we report that the ablation of Robo1 in mice is sufficient to confer MDS-like disease with anemia and multilineage dysplasia. More specifically, Robo1 deficiency impairs the self-renewal and differentiation capacity of hematopoietic stem progenitor cells (HSPCs) and disrupts HSPC pool, especially the reduction of megakaryocyte erythroid progenitors (MEPs), which causes a blockage in the early stages of erythropoiesis in mice. Similarly, Robo1-deficienct HSPCs recapitulated MDS-like disease with anemia and multilineage dysplasia in transplanted mice. Correspondingly, clinical data also reveal that low expression of ROBO1 is associated with shortened survival, severe anemia and a high risk of AML transformation in patients with MDS. Mechanistically, transcriptional profiling indicates that Cdc42, a member of the Rho-GTPase family, serves as a downstream target gene for Robo1 in HSPCs. Overexpression of Cdc42 partially restores the proliferation of erythroid colonies in Robo1 deficient mice. In contrast, Cdc42 inhibitor (CASIN) effectively attenuates the erythroid colony formation of HSPCs. Collectively, our results suggest that Robo1 deficiency may provide a promising therapeutic target against MDS by impairing HSPC self-renewal and erythropoiesis via CDC42, predicting a poor prognosis for severe anemia and a high risk of AML transformation in MDS.

overall_design: Knockout of Robo1 by Mx1-cre in mice after three doses of poly (I:C),

first: Jia-Cheng

last: Jin

first: Bing-yi

first: Lan

last: Wang

first: Ling-yun

last: Wu


title: High-throughput reporter assay for human genetic variants overlapping ATF4 binding sites

city: Tartu

first: Tiit

last: Örd

address: Riia 23b/2

department: Institute of Genomics

country: Estonia

institute: University of Tartu

summary: Activating Transcription Factor 4 (ATF4) is a transcription factor that regulates cellular responses to nutrient deficiency, endoplasmic reticulum stress and oxidative stress. At the organism level, it is implicated in processes such as hematopoiesis, skeletogenesis, eye development, memory, muscle atrophy, and carbohydrate and lipid metabolism. Here, we carried out a massively parallel reporter assay (MPRA) to identify allelic regulatory effects of human genetic variants that reside in ATF4 binding sites identified in ChIP-Seq experiments.

overall_design: Massively parallel reporter assay (MPRA) in HepG2 cells to analyze allelic regulatory effects.

first: Daima

first: Tõnis


title: The synergestic effect of adaptive laboratory evolution on H2O2 and galactose on the gene expression profiles of genetically modified, taxadiene-producing Saccharomyces cerevisiae before and during the oxidative stress re-exposure

city: Edinburgh

first: Behnaz

last: Nowrouzi

address: Mary Bruck Building, Colin Maclaurin Road

department: School of Engineering

country: United Kingdom

institute: The University of Edinburgh

summary: We attempted to improve the resistance of taxadiene-producing yeast strain to oxidative stress to develop a more robust yeast cell factory for improved Taxol® drug oxyenated taxanes precursors production from taxadiene. To this end, we evolved a yeast strain on H2O2-containing defined growth medium, supplemented with galactose as carbon source to induce the heterologous taxadiene biosynthesis pathway genes in that strain. The oxidative stress re-induction effect on the expression profiles of the superior evolved yeast strain (E_LRS5) was then studied before (steady state I) and during its continous use (steady state II) in galactose-limited chemostats, in parallel with the parent strain (LRS5).

overall_design: Comparative gene expression profiling analysis of RNA-seq data for parent (LRS5) and H2O2 and galactose-evolved taxadiene-producing S. cerevisiae (E_LRS5) strains before (steady state I) and during the exposure to H2O2 (steady state II) in galactose-limited chemostats

first: Pablo

last: Torres-Montero

first: Eduard

last: Kerkhoven

first: José

last: Martínez

first: Leonardo

last: Rios-Solis


title: Spinal tuberculosis infection induces osteopenia by reducing the migration and osteogenesis of bone marrow mesenchymal stem cells

city: Changsha

first: Qile

last: Gao

state: Hunan

address: 932, Lushan Nan Lu, Yuelu District

institute: Department of Spine Surgery and Orthopaedics, Xiangya Hospital, Central South University, Changsha 410008, China.

summary:
Objectives: Bone marrow mesenchymal stem cells (BMSC) play an important role in osteogenesis. However, the role of BMSC in osteopenia in spinal tuberculosis (STB) patients is unclear.
Methods: Bone mineral density (BMD) of 53 STB patients and 55 controls was measured. The migration and osteogenesis of BMSC were assessed by wound healing assays and alizarin red staining, and osteoclast marker expression was measured. RNA-seq was performed on BMSC and the enriched signaling pathways were verified.
Results:BMD of STB patients was significantly decreased and BMSC migration and osteogenesis were significantly reduced. After verification, we found that the B-cell receptor signaling pathway, tuberculosis, osteoclast differentiation, Th17-cell differentiation, Ras signaling pathway and PI3K-Akt signaling pathway were affected.And of these pathways, the B-cell receptor signaling, Th17-cell differentiation, Ras signaling pathway and PI3K-Akt signaling pathway were not previously known to be involved in osteopenia. The MAPK signaling pathway and ECM-receptor interactions were correlated with STB prognosis.
Conclusion: STB infection can significantly reduce BMSC migration and osteogenesis, decreasing BMD. This process is regulated by multiple pathways and is associated with STB prognosis. Our study suggests that reduced BMSC migration and osteogenesis play important roles in osteopenia in STB patients, and BMSC may be a therapeutic target.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for BMSCs in STB patients and controls

first: Chaofeng

last: Guo

first: Tao

last: Li

first: Hongqi


title: Cis and Trans Gene Transcription Regulatory Mechanisms Underpin Variation of a Maize Agronomic Trait

city: East Lasing

first: Erich

last: Grotewold

state: MI

address: 603 Wilson Rd.

department: Biochemistry and Molecular Biology

institute: Michigan State University

summary: P1 is the major QTL for maysin and chlorogenic acid accumulation in silk.  Both compounds were important for plant defenses. Silk is an important reproductive organ that is critical for good seed setting in corn ear and needs to be protected against various stresses, therefore, metabolics compounds (ex: phenolics) were highly enriched in silk. Here we characterize transcriptome changes in maize protoplast, and natural variants of P1 silks, and pericards to characterize the regulatory landscape. Also we evaluated profiles of silk in B73 x A632 hybrids in order to cis and trans specific effect driven by P1 in maize. Our study identifies new P1 targets in the silk and protoplast. Together with the RNA-seq data (P1-rr vs P1-ww in silk and pericarp and protoplast 35S:P1 vs empty vector control), we observed new P1 functions in silk that were not observed in pericarp. Also, Protoplast and silk ChIP-seq in F1 silk, as well as DAP-seq analysis of P1 -  shows specific P1 targets with highlight cis and trans effect on the F1 hybrids.

overall_design: DAP-seq: We generated Maize genomic DNA library through collecting leaves of Maize 2-week-old young seedlings of B73xA632 F1 hybrid. gDNA is fragmented to 200-300 bp.  and sent for either Illumina Hiseq 4000 SE50 sequencing (MSU genomic core facility). Halo-TF was compared to the Halo negative control. The TFs have  2 replicates. Ideally, each TF will have 2 replicates for both demethylated and methylated gDNA libraries (when required). ChIP-seq protoplast: For protoplast 35S:P1 ChIP-seq, 3 biological reps of pooled 35S:P1 transformed cells as well as the input  were used to make ChIP-seq libraries. ChIP-seq Silks: For silk ChIP-seq, 3 biological reps of P1-ww, F1 (B73xA632) as well as their inputs were used to make ChIP-seq libraries. All ChIP were processed using P1 specific Antibody (serum), ID:344-3 (Erich Grotewold lab, Michigan State University). All ChIP-seq libraries were made using NEBNext Ultra II DNA library Prep kit for Illumina (NEB#7645 S/L, $E7103 S/L). Hiseq4000 were used for all SE50 sequencing. RNA-seq protoplast: RNAseq of  12-day-old maize hybrid (B73xA632) transformed with 35S:P1-rr vector (DP2019) as well as empty vector control(DP611), in triplicate, using Illumina Hiseq4000 SE50. Protoplast was collected ~18 hrs after transformation. RNA-seq silks and pericarp: 2 individual plants in the field were collected per replicate, and a total of 3 replicates were collected. For pericarp, 14 DAP ears were used to collect pericarps. More than 10 kernels were collected per individual and 2 individual plants were used per replicate. A total of 3 replicates were collected for the pericarp experiment.  Sequencing was completed using  Illumina Hiseq4000 SE50.

first: Yi-Hsuan

last: Chu

first: Fabio

last: Gomez-Cano


title: Eosinophils exert direct and indirect anti-tumorigenic effects in the development of esophageal squamous cell carcinoma [4NQOinDBLgata]

first: Justin

last: Jacobse

summary: Eosinophils are present in several solid tumors and have context-dependent function. The role of eosinophils in the development of esophageal squamous cell cancer (ESCC), 85% of esophageal cancers worldwide, is unknown. Mice were treated with 4-nitroquinolone-1-oxide (4-NQO) for 8 weeks followed by vehicle for 8 weeks to induce esophageal squamous pre-cancer. Eosinophil depletion using three mouse models resulted in exacerbated 4-NQO tumorigenesis.  RNA-sequencing on the whole esophagus of WT and ?dblGATA mice was done in the pre-cancer model to understand how the presence of eosinophils affects the pre-cancer esophageal environment.

overall_design: We performed RNA-sequencing on the whole esophagus of C57/BL6 WT and DdblGATA mice after treatment with 4-NQO for 8 weeks followed by propylene glycol vehicle for 8 weeks resulting in pre-cancer.

first: Yash

last: Choksi


title: Mitochondrial-Targeted Antioxidant Attenuates Preeclampsia-Like Phenotypes Induced by Syncytiotrophoblast-Specific Gαq Signaling

city: Milwaukee

last: Grobe

state: WI

address: 8701 W Watertown Plank Road

department: Physiology

institute: Medical College of Wisconsin

summary: This experiment explored the placental transcriptomic effects of syncytiotrophoblast-specific Gαq signaling at gestational day 14.5 in mice and assessed whether these responses were altered upon administration of a mitochondrial-targeted antioxidant.

overall_design: Activation of the Gαq cascade in syncytiotrophoblast cells was achieved by crossing dams harboring a Cre-dependent Gαq-coupled DREADD (hM3Dq) with Gcm1-Cre+/- sires to elicit syncytiotrophoblast-restricted hM3Dq expression in ~50% of placentas within a dam. The synthetic DREADD ligand clozapine N-oxide (CNO; 2 mg/kg/d, ip) or saline (2 mL/kg/d, ip) was administered mid-gestation (gestational days 12.5-14.5) before the profiling of placenta gene expression at gestational day 14.5. In a separate cohort of double transgenic (hM3Dq+, Gcm1-Cre+) pregnancies, the mitochondrial-targeted antioxidant, Mitoquinone (MitoQ; 5 mg/kg/d, ip), was co-administered with CNO.

first: Megan

last: Opichka

first: Anne

last: Kwitek

first: Curt

middle: D

last: Sigmund

first: Jennifer

last: McIntosh


title: RNA-seq HepG2 cell line treated with TRPV2 inhinitor or agonist

city: Shenzhen

first: Jing

address: 1098 Xueyuan Street

institute: Shenzhen University

summary: HepG2 cell line was co-cultured with 1ml/L Fat emulsion, after 24h treatment with agonist (2-APB) or inhibitor (SKF-96365). RNA-seq was performed.

overall_design: Control vs agonist (2-APB) vs inhibitor (SKF-96365)


title: Gene expression profile at single cell level of CD45+ cells from AB1 mesothelioma treated with either vaccinia virus Tiantan strain or mock-treated

city: Hong Kong

first: Zhiwu

last: Tan

address: 21 Sassoon Road, Pokfulam

department: Microbiology

country: Hong Kong

institute: University of Hong Kong

summary: To understand the immune infiltrates in the tumor microenvironment in response to vaccinia virotherapy, we used single cell RNA sequencing (scRNAseq) to analyze the diversity of total CD45+ isolated from AB1 mesothelioma

overall_design: Balb/c mice bearing 7-day-old subcutaneous AB1 tumors were intratumorally treated with either modified vaccinia virus Tiantan strain (MVTT) or mock-treated, total tumor-infiltrating CD45+ cells were sorted by flow cytometry 2 days post treatment and processed in the BD Rhapsody system for scRNA-seq

first: Zhiwei

last: Chen


title: Total RNAseq of HepG2 cells treated with Sorafenib

city: Sevilla

first: Patricia

last: de la Cruz-Ojeda

address: Avda. Manuel Siurot s/n

country: Spain

institute: Institute of Biomedicine of Seville

summary: Hepatocellular carcinoma (HCC) is one of the most common causes of death worldwide and the fourth most prevalent type of cancer. Whereas curative treatments such as liver transplantation, ablation or surgery are optimal for early stages, only paliative treatments are given to intermediate and advanced stages of the disease. Sorafenib is still a suitable therapeutic option for patients in whom immunotherapy is not feasible. To gain information about therapy response, we sequenced HepG2 cells treated with Sorafenib 10 µM (24 hours)

overall_design: Transcriptomic analysis of  hepatocellular carcinoma cell lines HepG2 treated with Sorafenib 10 µM. Four biological replicates are provided for control and treated cells

first: Jordi

last: Muntané


title: Multi-Omic investigation of the Skin Microbiome of Cutaneous T Cell Lymphoma

city: Mainz

first: Philipp

last: Licht

address: Langenbeckstrasse 1

department: Dept. of Dermatology

institute: University Medical Center Mainz

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


title: Integrating into dairy goats chromatin accessible sites during lactation promotes transgene expression efficiency

city: Yangling

first: Zhenliang

last: Zhu

address: 3 Taicheng Road

institute: Northwest A&F University

summary: Combining RNA-seq with ATAC-seq, we screened the open chromatin of dairy goat mammary epithelial cells during lactation and then integrated human lysozyme into various open regions using the CRISPR/Cas9 system. A comparison of lysozyme gene expression and integration efficiency showed that chromatin accessibility at target sites was significantly positively correlated with gene insertion efficiency, and the insertion of foreign genes into highly accessible chromatin regions could enhance its expression.

overall_design: 3 dry period and 3 lactation period samples for Capra hircus species were sequenced using  ATAC-Seq and RNA-seq by the Beijing Genomics institution (Nanjing, China).

first: Yuanpeng

last: Gao

last: Han


title: Analysis of the function and mechanisms of TFEB in podocyte

first: Cuili

last: Li

address: No.106 Zhongshan Road 2

department: Nephrology

institute: South China University of Technology

summary: To investigate the function of TFEB in podocyte, we established TFEB-knockdown podocyte by siRNA.

overall_design:
We performed gene expression profiling analysis using data obtained from RNA-seq of TFEB siRNA group and its scrambled siRNA group
Comparative gene expression profiling analysis of RNA-seq data for TFEB siRNA and its scrambled siRNA in podocyte


title: RNAseq of the skin of patients with Mycosis fungoides

summary: We performed transcriptome analysis and multimodal data integration of the transcriptome and the microbiome of the skin of Mycosis fungoides Patients.

overall_design:
We profiled the skin microbiome and the  TCR reperoire of Mycosis fungoides patients. Here, we performed RNAseq in a subset of the same patients with Mycosis fungoides. Samples were were taken at the same tame point as the other samples were taken  (Microbiome and TCR). 10 Patients were included (5 Plaque stage, 5 Patch stage). Nonlesional skin of the same patient served as control.
RNAseq libraries were generated from the same RNA extraction as the TCRseq libraries. Samples were taken at the same visit and from the same body site sampled for WMS.