title: BTG1 mutation yields super-competitive B cells primed for malignant transformation

city: New York

first: Matt

last: Teater

state: NY

address: 445 E 69th St

institute: Weill Cornell Medical College

summary: Mutations in the BTG1 tumor suppressor gene are exclusive to germinal center (GC)-derived B cell lymphomas and associate with low clinical outcome. To elucidate the effect of BTG1 mutations in mature B cells, we generated a mouse model for the conditional expression of mutant Btg1 Unlike conventional lymphoma oncogenes, mutated Btg1 expression in B cells did not induce GC hyperplasia. However, placing mutant and wild-type GC B cells in direct competition revealed that mutant Btg1 provides a massive advantage during the GC reaction. Furthermore, mutant Btg1 accelerates and dramatically increases the aggressiveness of BCL2-driven lymphomas in vivo.  NGS, cellular and molecular profiling showed activation of Myc and mTORC1 anabolic programs in Btg1 mutant GC B cells, murine lymphomas and patient DLBCLs. These programs characterize T cell-selected GC B cells that enter a growth phase prior to clonal burst. We find that mutant Btg1 sensitizes GC B cells to T cell signals, resulting in a lower threshold to Myc activation, through mRNA translational biochemical mechanisms. Together, we link recurrent mutations of BTG1 to a massive fitness gain of GC B cells that confers an agressive and invasive phenotype to B cell lymphomas in vivo and associate with low clinical outcome in patients with agressive DLBCL.  This work reveals a fine-tuned metabolic regulatory network that controls normal GC development and can be hijacked by lymphoma cells during disease progression. These findings have implications for fitness processes and natural selection at a broad level by providing fundamental insight into the power of subtle biochemical shifts to enhance biological fitness of cells.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
RNAseq, RIPseq
scRNAseq:  BD Rhapsody Single Cell RNA sequencing in competing Btg1 Q36H and CREneg Germinal Center B cells

first: Coraline

last: Mlynarczyk

first: Christopher

last: Chin

first: Ari

last: Melnick


title: PLK1 Inhibitors and Abiraterone Synergistically Disrupt Mitosis and Kill Cancer Cells of Disparate Origin Independently of Androgen Receptor Signaling

status: Public on Jan 24 2023

city: San Diego

first: Peter

last: Croucher

state: CA

address: 11055 Flintkote Avenue

country: USA

institute: Cardiff Oncology Inc

type: Expression profiling by high throughput sequencing

summary:
We found that synergy between the antiandrogen abiraterone and Plk1 inhibitors was completely independent of abiraterone's effects on AR signaling. To identify AR-independent effects of abiraterone we designed a comprehensive RNA seq experiment. This identified an AR-independent synergy-specific gene set signature that was induced by abiraterone treatment and was dominated by gene sets related to mitosis and the mitotic spindle.
AR-independent effects of abiraterone were isolated by including an enzalutamide treatment arm and by utilizing cancer cell lines that do not express the AR.
Synergy-specific gene expression changes were identified by using cell lines that responded synergistically or non-synergistically to combined abiraterone and onvansertib.

overall_design: Prostate cancer cells that either did or did not respond synergistically to combined abiraterone and Plk1 inhibition treatment were treated with DMSO, abiraterone, enzalutamide, onvansertib, the abiraterone-onvansertib combination or the enzalutamide-onvansertib combination. Non-prostate cancer cells were treated with DMSO, abiraterone, onvansertib or the abiraterone-onvansertib combination. Gene expression was analyzed by RNA sequencing and data was transformed to gene set scores using Gene set variation analysis (GSVA).

first: Jesse

last: Patterson


title: Oxycodone withdrawal induces HDAC1/2-dependent transcriptional maladaptations in the reward pathway in a murine model of peripheral nerve injury

status: Public on Jan 23 2023

first: Aarthi

last: Ramakrishnan

state: New York

address: 1425 Madison Avenue

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

summary: The development of physical dependence and addiction disorders due to misuse of opioid analgesics is a major concern with pain therapeutics. In this study, we developed a mouse model of oxycodone exposure to gain insight into genes and molecular pathways in reward-related brain regions that are affected by prolonged exposure to oxycodone and subsequent withdrawal in the presence or absence of chronic neuropathic pain. RNA-Sequencing (RNA-Seq) and bioinformatic analyses revealed that oxycodone withdrawal alone triggers robust gene expression adaptations in the nucleus accumbens (NAc), medial prefrontal cortex (mPFC), and ventral tegmental area (VTA), with numerous genes and pathways selectively affected by oxycodone withdrawal under peripheral nerve injury states. Our pathway analysis predicted that histone deacetylase 1 (HDAC1), an epigenetic modifier with a prominent role in striatal plasticity, is a top upstream regulator in opioid withdrawal in both the NAc and mPFC. Indeed, treatment with the novel HDAC1/2 inhibitor RBC1HI (Regenacy Brain Class 1 HDAC Inhibitor) attenuated behavioral manifestations of oxycodone withdrawal, with the drug being more efficacious under states of neuropathic pain. Since RBC1HI displays antiallodynic actions in models of neuropathic pain, inhibition of HDAC1/2 may provide an avenue for chronic pain patients dependent on opioids to transition to non-opioid analgesics. Overall, our study highlights transcriptomic events in components of the reward circuitry associated with oxycodone withdrawal under pain-free and prolonged neuropathic pain states, thereby providing information on possible new targets for the treatment of physical dependence to opioids and transitioning individuals to non-opioid medications for chronic pain management.

overall_design: Male C57BL6/J animals underwent sham or tibial spared nerve injury 2.5 months prior to oxycodone administration. Animals were then given daily subcutaneous injections of either saline or oxycodone (30 mg/kg) for 14 days. Animals then underwent spontaneous withdrawal for 21 days prior to sacrifice.

first: Kerri

middle: D

last: Pryce

first: Randal

last: Serafini

first: Eric

middle: J

last: Nestler

first: Venetia

last: Zachariou


title: Genetic analysis, ultrasound phenotype, and pregnancy outcome of fetuses  with Xp22.33 or Yp11.32 microdeletion

city: Fuzhou

first: Hailong

last: Huang

state: Fujian

address: No.18 Daoshan Road, Gulou District

country: China

institute: Fujian Maternity and Child Health Hospital

summary:
The phenotypes of Xp22.33 or Yp11.32 microdeletions containing short-stature homeobox (SHOX) gene have been extensively described in adults and children, however, few have been reported in prenatal fetuses.
We analyzed the prenatal ultrasound phenotype and pregnancy outcomes of fetuses with Xp22.33 or Yp11.32 microdeletion containing SHOX gene to improve the understanding, diagnosis, and monitoring of the disease in the fetal period.

overall_design: Chromosomal analysis and chromosomal microarray analysis (CMA) were performed

first: Meiying

last: Cai


title: MHCC97H, HEP3B AND Huh7 UT, AZD8055 or AZD8055 + Compound #57

city: Amsterdam

first: Antonio

last: Mulero-Sánchez

state: Nord-Holland

address: Plesmanlaan 121

department: Molecular Carcinogenesis

country: Netherlands

institute: Netherlands Cancer Institute

summary: HCC tumors have poor prognosis and few therapeutic options. Here, Mulero-Sánchez et al. show that the combination of SHP2 inhibitors and mTOR inhibitor)  effectively impairs tumor growth in vitro and in vivo.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for 3 different HCC human cell lines untreated or treated with AZD8055 or AZD8055 + Compound #57 (24-48h)

first: Sara

last: Mainardi

first: Cor

last: Lieftink

first: Cun

last: Wang


title: The enhanced immune response of healthy individuals after vaccination with SARS CoV-2 inactivated vaccine, BBIBP-CorV

city: Guangzhou

first: Jinbao

last: Gu

address: No.1023, South Shatai Road

institute: Southern Medical University

summary: BBIBP-CorV, an inactivated vaccine, has demonstrated safety, efficacy, and immunogenicity against COVID-19 in in-vitro studies and clinical trials. This study sought to comprehensively understand the development and duration of virus-specific antibodies and  characterize the TCR-β repertoire changes in patients with BBIBP-CorV

overall_design: We comprehensively analyzed antibody response, anti- and  proinflammatory cytokines concentration, and TCR-β repertoire induced by BBIBP-CorV vaccination in peripheral blood samples from 54 uninfected-vaccinated recipients who were enrolled in the phase 3 trial and 16 healthy donors as well as 54 COVID-19 patients with different disease courses

first: Zhihui

last: Quan

first: Aihong

last: Qi

first: Shuwen

last: Ma

first: Yanling

last: Li

first: Hui

last: Chen

first: Xue

last: Yu

first: Tingyan

last: Dong

first: Kui

first: Yurong

last: Qiu


title: Expression data from Arabidopsis seedling dark and dark with Rifampicin

city: Hannover

first: Thomas

last: Pflannschmidt

address: Herrenhäuser Straße 2

country: Germany

institute: Leibniz-Universität Hannover

summary:
For establishing the photosynthetic apparatus plant cells must orchestrate the expression of genes encoded in both nucleus and chloroplast. Therefore a crosstalk between the two compartments is necessary.
We employed a gene expression profiling approach in order to elucidate the changes in gene expression that occur at different stages of plastid development.

overall_design: The two conditions compared were: Arabidopsis thaliana wildtype Col-0 grown in dark for 4 days after germination. Arabidopsis thaliana wildtype  Col-0 for 4 days in dark with Rifampicin. Plants were grown separately on MS medium in Petri dish per condition. around 50 seedlings per petridish.

first: Björn

last: Grübler

first: Livia

last: Merendino

last: Pfannschmidt


title: Identification of midbody-enriched RNAs

city: Aurora

first: Matthew

last: Taliaferro

state: CO

department: Biochemistry and Molecular Genetics

institute: University of Colorado Anschutz Medical Campus

summary: Midbodies function during telophase as a recruiting hub for proteins that regulate cell abscission. However, the contents of midbodies remain unclear. In this study, we profiled the RNA contents of purified midbodies using RNAseq.

overall_design: RNA profiling using RNAseq of the transcripts contained within purified midbodies and, as a comparison, intact HeLa cells.

first: Rytis

last: Prekeris


title: Filamin C is Essential for Mammalian Myocardial Integrity

city: La Jolla

first: Ju

state: California

address: 9500 Gilman Drive 0613

institute: University of California San Diego

summary: Gene expression profiling in whole heart of control and Flnc global knockout (FlncgKO) mouse at embryonic day 9.5 (E9.5).

overall_design: Three pairs of whole hearts isolated  from FlncgKO and littermate control mice were subject to RNA-seq analysis to identify differentially expressed genes (DEGs).

first: Tongbin

last: Wu

first: Zhengyu

last: Liang


title: Time-resolved RNA signatures of CD4+ T cells in Parkinson's disease [microRNAarray]

city: Homburg

first: Caroline

last: Diener

address: Kirrberger Str., Building 60

department: Institute of Human Genetics

institute: Saarland University

summary: We employed time-resolved microRNA expression analyses upon the activation of peripheral CD4+ T cells to track and functionally relate changes on cellular signaling in patients at different stages of PD

overall_design: A cohort of elderly male (age 53-85 yrs.; non-smokers), representative for different stages of Parkinson´s disease were tested (P1-5). Corresponding healthy controls (C1-5) (n=4) were matched for age (age 53-63 yrs.; non-smokers) and gender. One control was carried out twice (C1 and C1_2), representing independent replicates from the same healthy donor but from two different days of blood collection. CD4+ T cells were isolated from peripheral blood samples and were in vitro activated by αCD2/αCD3/αCD28 beads. Cellular samples were collected at 0, 2, 4, 8, 12 and 24 h after activation for subsequent RNA expression analyses.

first: Martin

last: Hart

first: Tim

last: Kehl

first: Anouck

last: Becker-Dorison

first: Tanja

last: Tänzer

first: David

last: Schub

first: Lena

last: Krammes

first: Martina

last: Sester

first: Andreas

last: Keller

first: Marcus

last: Unger

first: Barbara

last: Walch-Rückheim

first: Hans-Peter

last: Lenhof

first: Eckart

last: Meese


title: The high-throughput cleavage assays on 137 C.elegans pri-miRNAs

city: Hong Kong

first: Duc

middle: Trung

last: Nguyen

address: Clear Water Bay

department: Life Science

country: Hong Kong

institute: The Hong Kong University of Science and Technology

type: Non-coding RNA profiling by high throughput sequencing

summary: Microprocessor (MP), cleaving primary microRNAs (pri-miRNAs) to initiate the biogenesis of thousands of miRNAs, was discovered in animals in 2004. Understanding the molecular mechanism of MP is critical for interpreting the gene-silencing roles of miRNAs in various cellular processes and human diseases. Though the molecular mechanism of human MP (hMP) has been comprehensively investigated for nearly two decades and is well understood, that of Caenorhabditis elegans MP (cMP, cDrosha-Pasha complex) is still unknown. In this study, we revealed a comprehensive molecular mechanism of cMP, distinctively from that of hMP. In the proposed mechanism, cDrosha and Pasha (DGCR8 in humans) measure ~16 bp and ~25 bp of the pri-miRNA stem, respectively, and they are coordinated in determining cleavage sites of cMP in pri-miRNAs. In addition, we also demonstrated the molecular basis for their substrate measurement. Our findings illustrate an unknown molecular mechanism of cMP, clarify differences between the mechanism of hMP and cMP,  and provide a foundation for understanding multiple mechanisms regulating miRNA expression acting on cMP.

overall_design: The high-throughput cleavage assays for cDrosha, cMP WT and cMP mutants with 137 C.elegans pri-miRNAs

first: Tuan

middle: A

first: Trung

first: Thuy

middle: L


title: Time-resolved RNA signatures of CD4+ T cells in Parkinson's disease [mRNAarray]

first: Caroline

summary: We employed time-resolved RNA expression analyses upon the activation of peripheral CD4+ T cells to track and functionally relate changes on cellular signaling in patients at different stages of PD


title: Single cell multiomic readouts reveal that cellular heterogeneity impacts lipid nanoparticle-mediated mRNA delivery

city: Atlanta

first: James

last: Dahlman

state: ga

address: 311 Ferst dr

institute: Georgia Institute of Technology

summary: We report the development of a new multiomic nanoparticle delivery system called Single cEll Nanoparticle Transcriptome-sequencing (SENT-seq), which quantifies how dozens of lipid nanoparticles (LNPs) deliver DNA barcodes and mRNA into cells, subsequent protein production, and the transcriptome, with single cell resolution. We show from the sequencing data that cell heterogeneity influences the efficiency with which LNPs deliver mRNA therapies, and identify cell subtypes that exhibit particularly high or low LNP uptake as well as genes associated with those subtypes. These data suggest that cell subsets have distinct responses to LNPs, and that these differential interactions can affect mRNA therapies.

overall_design: Examination of FACS isolated liver cells the day after systemically injecting mice with PBS, or 19 pooled chemically distinct barcoded LNPs

first: Curtis

middle: N

last: Dobrowolski

first: Kalina

last: Paunovska

first: Elisa

middle: S

last: Echeverri

last: Loughrey

first: Huanzhen

last: Ni

first: Marine

middle: Z

last: Hatit

first: Melissa

middle: P

last: Lokugamage

first: Yanina

last: Kuzminich

first: Hannah

middle: E

last: Peck

first: Philip

last: Santangelo


title: RNA seq analysis of LuCaP Prostate Cancer Patient-Derived Xenografts

first: Michael

middle: M

last: Shen

address: 1130 St. Nicholas Avenue

institute: Columbia University Irving Medical Center

summary: We assembled a prostate xenograft interactome from a large data set with 128 RNA sequencing expression profiles generated through administration of 13 small molecule perturbagens in vivo to 5 distinct and genetically diverse LuCaP xenograft lines (LuCaP 73, LuCaP77, LuCaP 78, LuCaP 81, LuCaP 147), with half of the xenograft samples collected from hosts castrated for 1 week.

overall_design: Gene expression profiles were obtained from LuCaP series human prostate cancer xenograft lines treated with one of 13 perturbagens in non-castrated and and castrated hosts.

first: Maho

last: Shibata

first: Chee

middle: W

last: Chua

first: Antonina

last: Mitrofanova


title: Time-resolved RNA signatures of CD4+ T cells in Parkinson's disease

last: Diener

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

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

overall_design: Refer to individual Series


title: Pharmacological depletion of RNA splicing factor RBM39 by indisulam synergizes with PARP inhibitors in high-grade serous ovarian carcinoma

status: Public on Jan 22 2023

city: London

first: Anke

last: Nijhuis

state: London

address: Du Cane road, IRDB building 2nd floor

country: United Kingdom

institute: Imperial College London

summary: Ovarian high-grade serous carcinoma (HGSC) is the most common and lethal subtype of ovarian cancer with limited therapeutic options. In recent years, PARP inhibitors have demonstrated significant clinical benefits, especially in patients with BRCA1/2 mutations. However, acquired drug resistance and relapse is a major challenge. Therapies disrupting the spliceosome alter cancer transcriptomes and have shown potential to improve PARP inhibitor response. Indisulam (E7070) has been identified as a molecular glue that brings splicing factor RBM39 and DCAF15 E3 ubiquitin ligase in close proximity. Exposure to indisulam induces RBM39 proteasomal degradation through DCAF15-mediated polyubiquitination and subsequent RNA splicing defects. In this study, we demonstrate that loss of RBM39 induces splicing errors in DNA damage repair genes in ovarian cancer, leading to increased sensitivity to PARP inhibitors such as olaparib. Indisulam synergized with olaparib in multiple in vitro models of ovarian cancer regardless of PARP inhibitor sensitivity and improved olaparib response in mice bearing PARP inhibitor-resistant tumors. DCAF15 expression, but not BRCA1/2 mutational status, was essential for the synergy between indisulam and olaparib, suggesting that the combination therapy may benefit patients irrespective of their BRCA1/2 status. These findings demonstrate that combining RBM39 degraders and PARP inhibitors is a promising therapeutic approach to improving PARP inhibitor response in ovarian HGSC

overall_design: HGSOC KURAMOCHI cells were exposed to 0.1% DMSO (Vehicle control) or 10uM indisulam for 24h before RNA extraction and RNAseq

first: Yuewei

last: Xu

first: Sarah

last: Spear

first: Yurui

last: Ma

first: Marc

last: Lorentzen

last: Gruet

first: Flora

last: McKinney

first: Yitao

first: Chiharu

last: Wickremesinghe

first: Madelen

middle: R

last: Shepherd

first: Iain

last: McNeish

first: Hector

middle: C

last: Keun


title: Ablation of Adar1 in myeloid cells imprints a global antiviral state in the lung and heightens early immunity against SARS-CoV-2 [scRNA-Seq]

city: Palo Alto

first: Dmitri

last: Kazmin

address: 240 Pasteur Dr

department: Institute for Immunity, Transplantation and Infection

institute: Stanford University

summary: Under normal homeostatic conditions, self double-stranded RNA (self-dsRNA) is modified by adenosine deaminase acting on RNA 1 (ADAR1) to prevent the induction of a type I interferon (IFN) mediated inflammatory cascade. Antigen presenting cells (APCs) sense pathogen associated molecular patterns (PAMPs), such as dsRNA, to activate the immune response. The impact of ADAR1 on the function of APCs and the consequences on immunity is poorly understood. Here, we show that ADAR1 deletion in CD11c+ APCs leads to: (i) a skewed myeloid cell compartment enriched in inflammatory cDC2s (inf-cDC2) like cells; (ii) enhanced numbers of activated tissue resident memory T cells (TRMs) in the lung; and (iii) the imprinting of a broad antiviral transcriptional signature across both immune and non-immune cells. Further the resulting changes can be partially reversed by blocking IFNAR1 signaling and promote early resistance against SARS-CoV-2 infection. Our study provides insight into the consequences of self-dsRNA sensing in APCs on the immune system in the context of viral challenge.

overall_design: Given the impact of ADAR1 ablation in APCs on APC and T cell homeostasis, we sought to characterize the broader consequences of ADAR1 deficient APCs on the immune system. To this end, we combined the 10x Chromium Single Cell RNA sequencing (scRNAseq) platform with a FACS based enrichment strategy to uncover minor cell populations such as AMs and DCs . Single cell suspensions were stained with a panel of cell surface marker antibodies. Sorted T cells, alveolar macrophages (AMs), and CD11c+SiglecF- cells, and other immune cells were pooled at a ratio 15:15:5:65, respectively, and subjected to 10x single cell RNAseq.

first: Julia

last: Adamska

first: Bali

last: Pulendran


title: High Throughput Sequencing of a Mouse Model for Benign Prostatic Hyperplasia (BPH)

city: Madison

first: Paul

last: Marker

state: WI

address: 777 Highland Ave

department: School of Pharmacy

institute: University of Wisconsin-Madison

summary: The goal of this study is to identify genes of interest through high throughput sequencing of a mouse model for BPH and compare with control, WT mice. Additionally, to use the generated RNA expression profile to compare with a previously established human microarray for BPH. Through these comparisons we hope to identify novel genes contributing to the disease in humans. Specific results of these analyses are in progress and publication content is yet to be determined.

overall_design: An RNA expression profile of the anterior prostate (AP), dorsal lateral prostate (DLP), and urethra, from control and T+E2 treated mice and from the urogogenital sinus (UGS) of E16.5 mice cultured in testosterone and without hormone. Four samples were used for each tissue in each group (control and T+E2 treated or cultured in testosterone ), making 8 samples per tissue type. All samples labelled "control" recieved no treatment.

first: Paige

last: Arneson


title: Ablation of Adar1 in myeloid cells imprints a global antiviral state in the lung and heightens early immunity against SARS-CoV-2 [RNA-Seq]

overall_design: We challenged Adar1ΔCd11c mice and controls with the B.1.351 strain of SARS-CoV-2 virus. At 3 days post infection (dpi), mice were sacrificed, lungs were collected, processed into a single cell suspension and stained with a panel of fluorophore conjugated antibodies. Immune cells (CD45+), epithelial cells (CD45-EpCAM+CD31-), and endothelial cells (CD45-EpCAM-CD31+),  were purified and bulk RNA was extracted.


title: Ablation of Adar1 in myeloid cells imprints a global antiviral state in the lung and heightens early immunity against SARS-CoV-2


title: Hypoxia-induced cysteine metabolism reprogramming are crucial for the tumorigenesis of colorectal cancer [tissue pair]

status: Public on Jan 21 2023

city: 上海市

first: Shiyi

last: Yang

state: 上海

address: 中国上海市徐汇区华山路1954号

institute: Shanghai Jiao Tong University

summary: Metabolic reprogramming is a hallmark of human cancer and cancer-specific metabolism provide opportunities for cancer diagnosis, prognosis, and treatment. However, how metabolic pathways affect the initiation and progression of colorectal cancer remain largely unknown. Here, we showed cysteine is highly enriched in colorectal tumors compared with adjacent non-tumor tissues to promote tumorigenesis of CRC. Both cystine and cysteine imports are essential to maintain intracellular cysteine level and promote tumor growth and survival. Transporter genes of cystine and cysteine are all upregulated in colorectal cancer by tumor microenvironment induced ROS through transcription factor ATF4. Glutathione synthetase GSS is upregulated and increases cysteine to reduced glutathione flux to support tumor growth and survival in colorectal cancer. Depletion of cystine and cysteine by a recombinant cyst(e)inase effectively reduced the growth of colorectal tumors. Moreover, scavenging cystine and cysteine induces autophagy of colorectal cancer cells through mTOR-ULK signaling axis. With this study, we demonstrate that cysteine metabolism is a key signature of CRC metabolic reprogramming and targeting cysteine metabolism might be an effective approach to treat colon cancer.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for tumor samples and adjacent non-tumor samples from CRC patients at Shanghai Renji Hospital since 2019 to 2021.

first: Zhang

last: Lin

first: Qianqian

last: Qiu

first: Gaoping

last: Cui

first: Meilian

last: Yao

first: Jun

last: Gu

first: Ting

last: Wang

first: Qing

first: Longci

last: Sun

first: Yujun

last: Hao


title: Hypoxia-induced cysteine metabolism reprogramming are crucial for the tumorigenesis of colorectal cancer [HCT116]

address: 中国上海市徐汇区华山路1954号

overall_design: Comparative gene expression profiling analysis of RNA-seq data for HCT116 cells after cystine/cysteine abundance or deprivation culture for either 24 hours or 48 hours.

last: Xu


title: Hypoxia-induced cysteine metabolism reprogramming are crucial for the tumorigenesis of colorectal cancer.

address: 中国上海市徐汇区华山路1954号


title: Single-cell transcriptional analysis of mouse bronchoalveolar lavage (BAL) cells

city: Chicago

first: Gye Young

last: Park

state: IL

address: 909 S. Wolcott Avenue CMRB 3080

department: Medicine

institute: University of Illinois at Chicago

summary: We performed high-throughput single-cell RNA sequence using mouse BAL cells to identify subpopulations of airway cells.

overall_design: scRNA-sequencing of BAL cells in WT mice.

first: Hyung

middle: G

last: Moon

first: Seung

last: Kim

first: Gye

middle: Y


title: Modulation of Notch signaling at early stages of differentiation of human induced pluripotent stem cells to dopaminergic neurons.

city: Saint-Petersburg

first: Nataliia

middle: Victorovna

last: Katolikova

address: Universitetskaya emb. 7-9-11

department: Institute of Translational Biomedicine

country: Russia

institute: Saint-Petersburg State University

summary: Elaboration of protocols for differentiation of human pluripotent stem cells to dopaminergic neurons is an important issue for development of cell replacement therapy for Parkinson’s disease. А number of protocols have been already developed, however, their efficiency and specificity still can be improved. Investigating the role of signaling cascades, important for neurogenesis, can help to solve this problem and to provide a deeper understanding of their role in neuronal development.  Notch signaling plays an essential role in development and maintenance of the central nervous system after birth. In our study, we analyzed the effect of Notch activation and inactivation at the early stages of differentiation of human induced pluripotent stem cells to dopaminergic neurons. We found, that during first 7 days of differentiation the cells were not sensitive to the Notch inhibition. In contrary, activation of Notch signaling during the same time period led to significant changes and was associated with an increase in expression of genes, specific for caudal parts of the brain, a decrease of expression of genes, specific for forebrain, as well as a decrease of expression of genes, important for the formation of axons and dendrites and microtubule stabilizing proteins.

overall_design: RNA sequencing from cells during differentiation of human induced pluripotent stem cells (IPSC) to dopaminergic neurons from three IPSC lines (AD3, WTSIi004-A, WTSIi046-A). Cells were collected at two stages 1) pluripotent stage (IPSC) and 2) at day 7 of differentiation. At day 7 cell were collected in 4 conditions: non-treated cells (CONTR); cells with RBPJ knockdown (SH); cells with NICD overexpression (NICD); cells treated with DAPT (DAPT)

middle: V

first: Aleksandr

last: Khudiakov

first: Daria

last: Shafranskaya

first: Andrey

last: Prjibelski

first: Mikael

last: Mor

first: Alexey

last: Golovkin

first: Anastasia

middle: K

last: Zaytseva

first: Irina

last: Neganova

first: Evgeniya

last: Efimova

first: Raul

last: Gainetdinov

first: Anna

middle: B

last: Malashicheva


title: Transcriptome of Xanthoceras sorbifolia Bunge leaves under low nitrogen condition

city: Dalian

first: Li

middle: Xin

last: Lin

address: Dalian

institute: Dalian Minzu University

summary: Transcriptome sequencing (RNA-seq) was used to sequence the leaves of Xanthoceras sorbifolia Bunge under low nitrogen, so as to analyze the resistance of Xanthoceras sorbifolia Bunge to low nitrogen.

overall_design:
In this study, Xanthoceras sorbifolia was divided into control, low-nitrogen, and nitrogen-free groups for treatment. Samples were treated for 15 days before assessing physiological characteristics and transcriptome analysis.
This work was financially supported by Science Technology Yuanjiang Project of Xinjiang Uygur Autonomous Region (2016E02045).


title: Genomic resources enable study of the blastoclad fungus, Coelomomyces lativittatus, an obligate parasite of mosquitoes and microcrustaceans, during infection and sporulation

city: Riverside

first: Jason

last: Stajich

address: 900 University Ave

department: Microbiology and Plant Pathology

institute: University of California-Riverside

summary: Blastocladiomycota, early diverging zoosporic (flagellated) lineages of fungi, are vastly understudied. This phylum includes the genus Coelomomyces which consists of more than eighty fungal species that are obligate parasites of arthropods. Coelomomyces lack a complete asexual life cycle, instead surviving through an obligate heteroecious alternation of generations life cycle. Despite their global distribution and interesting life cycle, little is known about Coelomomyces species. To begin to address this, we analyzed transcriptomes from across host-associated life stages including infection of larva and excised mature sporangia from the mosquito, Anopheles quadrimaculatus. We identified differentially expressed genes and over-enriched GO terms both across and within life stages and used these to make hypotheses about C. lativittatus biology. Generally, we found the C. lativittatus transcriptome to be a complex and dynamic expression landscape; GO terms related to metabolism and transport processes were over-enriched during infection and terms related to dispersal were over-enriched during sporulation.  The C. lativittatus transcriptomes reported here are a valuable resource and may be leveraged toward furthering understanding of the biology of these and other early diverging fungal lineages.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Coelomomyces lativittatus developmental stages

first: Cassandra

last: Ettinger

first: Talieh

last: Ostovar

first: Mark

last: Yacoub

first: Steven

last: Ahrendt

first: Robert

last: Hice

first: Brian

last: Federici


title: The profile of circular RNA in hypoxic exosomes from lung adenocarcinoma cell line

city: shanghai

last: Xu

address: 1239，Siping Road

institute: Tongji University

summary: Hypoxia is a common feature of solid tumors and is associated with aggressiveness and poor prognosis of patients. Exosomes are involved in mediating cellular environment interactions. circRNAs are a class of non-coding RNAs (ncRNAs) broadly expressed in cells and exosomes. However, in lung adenocarcinoma tumor development, functions and regulatory mechanisms of exosomal circ-RNAs induced by hypoxia remain poorly understood.To further explore the differences in recombinant RNA expression in hypoxic and normoxic exosomes derived from lung adenocarcinoma cell line

overall_design: Circular RNA expression in A549 cell supernatant was measured at 12 and 24 hours after exposure to hypoxic and normoxic situation. 2 independent experiments were performed at each time (12 or 24 hours).


title: Modelling of Red Blood Cell Trait GWAS Variants in HUDEP-2 Cells (RNA-seq)

city: Headington

first: Damien

last: Downes

state: Oxfordshire

address: John Radcliffe Hospital

department: MRC Weatherall Institute of Medicine

institute: The University of Oxford

summary: Genome Wides Association Studies (GWAS) have identified tens of thousands of associations between human genetic variation and common disease. Despite the abundance of GWAS associations, functional identification and characterization of causative variants and effector genes remains a challenging prospect. Human erythropoiesis provides a highly tractable model system for the development of tools for GWAS analysis. Using the Human Umbilical Derived Erythroid Progenitor 2 (HUDEP-2) cell line we have modelled the effects of two variants associated with red blood cell traits using CRISPR/Cas9 facilitated HDR editing.

overall_design: CRISPR/Cas9 editing was carried out to generate homozygous clones at two trait associated variants (rs10758656 and rs9349205) as well as a non-disease associated SNP (rs4508712) as an editing control. Following editing clonal populations were isolated by single cell sorting and expansion. Effects of edited variants were determined by ATAC-seq (carried out in technical duplicates), ChIP-seq, and RNA-seq on multiple days for at least 3 independent clones. Experiments were carried out during growth in both expansion, and erythroid differentiation media.

middle: J

first: Lea

last: Nussbaum

first: Stephanie

last: Hill

first: Jim

last: Hughes


title: Modelling of Red Blood Cell Trait GWAS Variants in HUDEP-2 Cells (ATAC-seq)

type: Genome binding/occupancy profiling by high throughput sequencing

first: Matthew

last: Gosden

first: Priscila

last: Hirschfeld

first: Jelena

last: Telenius


title: Modelling of Red Blood Cell Trait GWAS Variants in HUDEP-2 Cells (ChIP-seq)


title: Effect of Bcl11b deletion in resting and activated mouse CD4+ T cells.

status: Public on Jan 20 2023

city: Nashville

first: Andrew

middle: R.

last: Patterson

state: TN

address: 1161 21st Avenue South

department: Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center

institute: Vanderbilt University Medical Center

summary:
To investigate the function of Bcl11b in activated C57Bl/6 mouse CD4+ T cells, we deleted Bcl11b in vivo using a Bcl11b-fl/fl;Cd4cre-ert2 tamoxifen-inducible strategy.
We then cultured CD4 T cells isolated from these mice 3 days in resting or activating condtions.
Finally, we performed gene expression profiling analysis using data obtained from RNA-seq of 3-5 samples per genotype per condition.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for mouse CD4+ T cells resting or stimulated in vitro 3 days. Bcl11b was deleted in vivo using a CD4-cre-ert2 system via tamoxifen injection.

first: Patterson

last: Andrew

first: Needle

last: Gabriel

first: Rathmell

last: Jeff


title: Cholinergic stress signals promote microRNA-mediated stereotypic behavior via glutamatergic neuromodulation

city: Jerusalem

first: Hermona

last: Soreq

state: Israel

address: The Edmond J. Safra Campus, Givat Ram

department: Biological Chemistry

country: Israel

institute: The Hebrew University of Jerusalem

summary: Stereotypic behavior (SB) is common in emotional stress-involved psychiatric disorders and is often attributed to glutamatergic impairments, but the underlying mechanisms are unknown. To challenge the causal involvement of cholinergic neuromodulation in SB, we studied TgR mice with impaired cholinergic transmission due to over-expression of the stress-inducible soluble ‘readthrough’ acetylcholinesterase-R (AChE-R) variant. RNA-sequencing revealed 37 differentially expressed microRNAs in TgR mice hippocampi, 8 of which targeting over 5 human cholinergic-related transcripts each. Further, microarray tests of TgR prefrontal cortices displayed up to 428 long RNA transcripts differentially expressed from those of FVB/N mice, primarily glutamatergic-related mRNA transcripts (P<1x10-3). Suggesting behavioral relevance, TgR brains presented c-fos over-expression at motor behavior-regulating brain regions and immune-labeled AChE-R excess in SB-regulating basal ganglia, limbic brain nuclei and the brain stem. Compatible with this, TgR mice showed impaired organization of behavior, performance errors in a serial maze test, escape-like locomotion and less rearing under changed environmental familiarity/novelty conditions. Our findings attribute stress-induced SB to previously unknown microRNA-mediated perturbation of cholinergic/glutamatergic networks, support malfunctioning hierarchical control of cholinergic signaling as impairing the behavioral inhibitory regulation via glutamatergic neuromodulation and underscore new therapeutic strategies for correcting stereotypic behaviors.

overall_design: Examination of small-ncRNA changes in control and transgenic mice overexpressing the human AChE-R gene

first: Gilli

last: Moshitzky


title: Modelling of Red Blood Cell Trait GWAS Variants in HUDEP-2 Cells


title: UV irradiation remodels the specificity landscape of transcription factors [85438_Proteins]

city: Durham

first: Raluca

last: Gordan

state: NC

address: 101 Science Dr, CIEMAS 2179

department: Center for Genomic and Computational Biology

institute: Duke University

summary: Somatic mutations are highly enriched at transcription factor (TF) binding sites, with the strongest trend being observed for ultraviolet light (UV)-induced mutations in melanomas. One of the main mechanisms proposed for this hyper-mutation pattern is the inefficient repair of UV lesions within TF-binding sites, caused by competition between TFs bound to these lesions and the DNA repair proteins that must recognize the lesions to initiate repair. However, TF binding to UV-irradiated DNA is poorly characterized, and it is unclear whether TFs maintain specificity for their DNA sites after UV exposure. We developed UV-Bind, a high-throughput approach to investigate the impact of UV irradiation on protein-DNA binding specificity. We applied UV-Bind to ten TFs from eight structural families, and found that UV lesions significantly altered the DNA-binding preferences of all TFs tested. The main effect was a decrease in binding specificity, but the precise effects and their magnitude differ across factors. Importantly, we found that despite the overall reduction in DNA-binding specificity in the presence of UV lesions, TFs can still compete with repair proteins for lesion recognition, in a manner consistent with their specificity for UV-irradiated DNA. In addition, for a subset of TFs we identified a surprising but reproducible effect at certain non-consensus DNA sequences, where UV irradiation leads to a high increase in the level of TF binding. These changes in DNA-binding specificity after UV irradiation, at both consensus and non-consensus sites, have important implications for the regulatory and mutagenic roles of TFs in the cell.

sample_organism:
Arabidopsis thaliana
Homo sapiens

overall_design: The UV-Bind assay was performed for 10 transcription factors and 1 repair protein (UV-DDB) for UV-irradiated arrays. This array uses a universal design that allows for the measurement of k-mers along with a PDB variations library. It was used to measure CREB1, EGR1, ELK1, ETS1, STAT3, TBP, UV-DDB, and UV-DDB with ETS1 competitive binding. A detailed description is provided in the manuscript.

first: Zachery

last: Mielko


title: UV irradiation remodels the specificity landscape of transcription factors [86684_Proteins]

overall_design: The UV-Bind assay was performed for 10 transcription factors and 1 repair protein (UV-DDB) for UV-irradiated arrays. This array contains the following designs: MITF flanking sequence, dinucleotide variants, UV-preferred concatenated k-mer sequences, 5U01 full and half-sites. It was measured for CREB1, EGR1, and MITF. A detailed description is provided in the manuscript.


title: UV irradiation remodels the specificity landscape of transcription factors [85400_Proteins]

overall_design: The UV-Bind assay was performed for 10 transcription factors and 1 repair protein (UV-DDB) for UV-irradiated arrays. This array uses a universal design that allows for the measurement of k-mers, and it was used to measure GATA1 and P53 binding. A detailed description is provided in the manuscript.


title: UV irradiation remodels the specificity landscape of transcription factors [86688_PhotoProduct_Antibody]

overall_design: The UV-Bind assay was performed for CPD and 6-4PP antibodies for UV-irradiated arrays. This array includes the increasing pyrimidine dinucleotides library. A detailed description is provided in the manuscript.


title: UV irradiation remodels the specificity landscape of transcription factors [86688_Proteins]

overall_design: The UV-Bind assay was performed for UV-DDB for UV-irradiated arrays. This array includes the increasing pyrimidine dinucleotides library. A detailed description is provided in the manuscript.


title: UV irradiation remodels the specificity landscape of transcription factors [84702_Proteins]

overall_design: The UV-Bind assay was performed for 10 transcription factors and 1 repair protein (UV-DDB) for UV-irradiated arrays. This array uses a universal design that allows for the measurement of k-mers, and it was used to measure ETS1 and c-MYC binding. A detailed description is provided in the manuscript.


title: Effect of sarsasapogenin (SAR) on non-alcoholic fatty liver disease in mice fed with methionine choline deficiency (MCD) diet

city: Nanning

first: xing

last: lin

address: Shuangyong Road

institute: Guangxi medical university

summary: This study aimed to investigate the effects and underlying mechanisms of sarsasapogenin (SAR) on dietary methionine choline deficiency induced non-alcoholic fatty liver disease in mice, The differentially expressed genes in liver tissue in “Normal VS model ”and “Model VS SAR” were identified by RNA-seq.

overall_design: Mouse were randomly devided into three groups, including normal group, model group (MCD diets ) and SAR group

first: Xing

last: Lin

first: Cuiyu

last: Li

first: Bin

last: Fang

first: Yuhua

last: Xiong


title: UV irradiation remodels the specificity landscape of transcription factors

sample_organism:
Arabidopsis thaliana
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Elucidating the corneal endothelial cell proliferation capacity through an interspecies transcriptome comparison

city: Maastricht

first: Vanessa

last: LaPointe

address: Universiteitssingel 40

institute: MERLN Institute

summary: The regenerative capacity of corneal endothelial cells (CECs) differs between species; in bigger mammals such as humans and sheep, CECs are arrested in a non-proliferative state. Damage to these cells can compromise its function leading to corneal opacity and impaired vision. Corneal transplantation is the current treatment for the recovery of a clear eyesight, but the donor tissue demand is higher than the offer and there is the need to develop novel treatment modalities. In contrast, rabbit CECs retain a high proliferative profile and have the capacity to repopulate the endothelium upon injury. There is currently a lack of fundamental knowledge to explain the difference in the proliferation capacity of these cells across species. Gaining information on the transcriptomic differences across species could allow the identification of crucial proliferation drivers of CEC proliferation to develop novel regenerative medicine therapies. In this study we have analyzed at the transcriptomic level corneal endothelial samples originating from human, sheep, and rabbit. To understand the differences across the CECs proliferation capacity in each species, we have generated an automated pipeline for the analysis of pathways with different activity. Our results revealed that 52 pathways had commonly different activity when comparing species with non-proliferative endothelium (human and sheep) to species with proliferative endothelium (rabbit).

sample_organism:
Homo sapiens
Ovis aries
Oryctolagus cuniculus

overall_design: This study presents an interspecies transcriptome comparison of CECs originating from species with proliferative (rabbit) and quiescent endothelium (sheep and human). This study was performed in compliance with the tenets of the Declaration of Helsinki. All human research-grade corneal tissue (n=5) was obtained from the ETB-BISLIFE Multi-Tissue Center (Beverwijk, the Netherlands), with informed consent from the next of kin. All human corneas were stored up to 22 days in organ culture media at 31 °C and had a minimum endothelial cell density of 2300 cells/mm2. Organ culture media comprised the following: minimum essential medium (MEM) supplemented with 20 mM HEPES, 26 mM sodium bicarbonate, 2% (v/v) newborn calf serum (Thermo Fisher Scientific), 10 IU/mL penicillin, 0.1 mg/mL streptomycin and 0.25 μg/mL amphotericin. All eyes from rabbits (n=5) and sheep (n=5) were enucleated from the animals used for other experimental procedures approved by the regulatory authorities of Maastricht University, Utrecht University, and MSD and performed in accordance with Dutch national and European guidelines. All animal ocular tissue was used within 4 h after sacrifice. All donor and animal tissue information is specified in Table 1.

first: Martina

last: Kutmon

first: Pere

last: Catala


title: Effect of IFNa2 treatment in affecting gene expression in monocytes and the differential gene expression between the monocytes from healthy donors and SLE patients

city: Taipei

first: Szu-Ting

last: Chen

address: No. 155, 2nd Sec. Li Nong Street

department: Clincal medicine

country: Taiwan

institute: National Yang Ming Chiao Tung University

summary: To investigate the effect of IFNa2 treatment in CD14+ monocytes, monocytes isolated from healthy donors were treated with or without IFNa2, and SLE monocytes were also harvested for the comparison of the differential expression genes.

overall_design: We performed gene expression profiling analysis using data obtained from RNA-seq of three groups including healthy monocyte, IFNA2-treated monocytes (for 6 hours) and SLE monocytes. Comparative gene expression profiling analysis of RNA-seq data for human CD14+ monocyte and the IFN-a2 treated monocyte and CD14+ monocyte from SLE patients.

first: Szu

middle: T


title: DNMT3B supports meso-endoderm differentiation from mouse embryonic stem cells

city: Turin

first: Andrea

last: Lauria

address: Via Accademia Albertina, 13

department: Life Sciences and Systems Biology

country: Italy

institute: University of Turin

type: Methylation profiling by high throughput sequencing

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


title: Targeting class A GPCRs for hard tissue regeneration [RNA-seq]

city: Seoul

first: SoYoung

last: Park

state: Korea,Seoul

address: Seoul, Republic of Korea,, 1 Gwanak-ro, Gwanak-gu, Seoul, 86-509

country: South Korea

institute: Seoul National University

summary:
To investigate class A G protein-coupled receptors (GPCR)-targeted drugs in the regulation of osteogenic differentiation, we investigated the effects of drugs using mesenchymal stromal cells.
We conducted whole-transcriptome analysis using bulk RNA sequencing (RNA-seq) of six drugs.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for six drugs.

first: So

first: Jin

last: Kim


title: Targeting class A GPCRs for hard tissue regeneration [microarray]

summary:
To investigate class A G protein-coupled receptors (GPCR)-targeted drugs in the regulation of osteogenic differentiation, we investigated the effects of drugs using mesenchymal stromal cells.
By applying microarray dataset, we idntified the mRNA expressions profiles in hDPSCs.

overall_design: Comparative gene expression profiling analysis of human dental pulp stromal cells.


title: Targeting class A GPCRs for hard tissue regeneration


title: Targeting class A GPCRs for hard tissue regeneration [ATAC-seq]

summary: To investigate class A G protein-coupled receptors (GPCR)-targeted drugs in the regulation of osteogenic differentiation, we investigated the effects of drugs using mesenchymal stromal cells.

overall_design: We treated human dental pulp-derived mesenchymal stromal cells (hDPSCs) with nutlin-3; MDM2 inhibitors, and conducted transposase-accessible chromatin using sequencing (ATAC-Seq) to compare the biomineralization potency.


title: ETV2 upregulation marks the specification of early cardiomyocytes and endothelial cells during co-differentiation

city: Leiden

first: Valeria

last: Orlova

address: Einthovenweg 20

institute: Leiden University Medical Center

summary: The ability to differentiate human induced pluripotent stem cells (hiPSCs) efficiently into defined cardiac lineages, such as cardiomyocytes and cardiac endothelial cells, is crucial to study human heart development and model cardiovascular diseases in vitro. The mechanisms underlying the specification of these cell types during human development are not well-understood which limits fine-tuning and broader application of cardiac model systems. Here, we used the expression of ETV2, a master regulator of hematoendothelial specification in mice, to identify functionally distinct subpopulations during the co-differentiation of endothelial cells and cardiomyocytes from hiPSCs. Targeted analysis of single-cell RNA sequencing data revealed differential ETV2 dynamics in the two lineages. A newly created fluorescent reporter line allowed us to identify early lineage-predisposed states and show that a transient ETV2-high state initiates the specification of endothelial cells. We further demonstrated, unexpectedly, that functional cardiomyocytes can originate from progenitors expressing ETV2 at a low level. Our study thus sheds light on the in vitro differentiation dynamics of two important cardiac lineages.

overall_design: scRNA-seq data: Two batches of  day 6 cardiac mesoderm derived endothelial cells (CMEC) differentiated from hiPSCs.

first: Xu

last: Cao

first: Stefan

last: Semrau


title: Expression data from mesenchymal stem cells isolated from the bone marrow of tumor-bearing NeuT mice and relative BALB/c controls

city: Milano

first: Milena

last: Perrone

address: Via Amadeo 42

institute: IRCCS Istituto Nazionale dei Tumori

summary: We performed gene expression profiling of bone marrow-mesenchymal cells (BM-MSCs) isolated from BALB/c and NeuT mice at 12 and 24 weeks of age, representative of early and late stages of breast cancer tumorigenesis, respectively.

overall_design: BM-MSCs were purified from the femurs and tibias of mice by immunomagnetic beads (CD45-, Ter119-, CD11b-, CD11c-, CD3-, Gr1-, B220-) and phenotypically characterized by flow citometry prior the transcriptome analysis (CD45-; CD29+; CD44+).

first: Matteo

last: Milani

first: Sabina

last: Sangaletti

first: Mario

last: Colombo


title: Isolation of extracellular fluids reveals novel secreted bioactive proteins from muscle and fat tissues

city: Boston

first: Melanie

last: Mittenbühler

address: 360 Longwood Ave

institute: Dana-Farber Cancer Institute

summary: Proteins are secreted from cells to send information to neighboring cells or distant tissues. Because of the highly integrated nature of energy balance systems, there has been particular interest in myokines and adipokines. These are challenging to study through proteomics because serum or plasma contain highly abundant proteins that limit the detection of proteins with lower abundance. We show here that extracellular fluid (EF) from muscle and fat tissues of mice show a different protein composition than either serum or tissues. Mass spectrometry analyses of EFs from mice with physiological perturbations, like exercise or cold exposure, allowed quantification of many potentially novel myokines and adipokines. Using this approach, we identify prosaposin as a secreted product of muscle and fat. Prosaposin expression stimulates thermogenic gene expression and induces mitochondrial respiration in primary fat cells. These studies together illustrate the utility of EF isolation as a discovery tool for adipokines and myokines.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for primary iWAT cells transduced with either GFP adenovirus (pAd) or PSAP pAd

first: Bruce

last: Spiegelman


city: Beijing

first: Quancan

last: Hou

address: Xueyuan road No. 30

institute: University of Science and Technology Beijing

summary: Maize LOB30 (Zm00001d036435) is a transcription factor and is specifically expressed in anthers. Our previous RNA-seq data showed that expression of some genes were upregualted in maize lob30 mutant maize anthers. To confirm these genes are the downstrem target genes, we generated proLOB30: GFP-LOB30 transgenic maize lines, collected stage 9 to stage10 anther materials and performed ChIP-seq using the GFP antibody.

overall_design: ChIP-seq of maize transcription factor LOB30, transgenic maize anthers expressing the fused protein GFP-LOB30 driven by its native promoter were collected and crosslinked. The GFP antibody was used for chromatin immunoprecipitation.

first: Xiangyuan

last: Wan


title: Effect of Lemd2 p.L13R mutation on gene expression in mouse hearts at 9 months old

city: Würzburg

first: Ruping

state: Bavaria

address: Am Schwarzenberg 15

department: Comprehensive Heart Failure Center

institute: University hospital Würzburg

summary:
To determine transcriptional changes caused by the Lemd2 mutation and to gain insights into the mechanisms responsible for the phenotype of arrhythmic cardiomyopathy
we performed RNA-sequencing in 9 months old mouse hearts

overall_design: Comparative gene expression profiling analysis of RNA-seq data for 9 months old wild-type (WT) and Lemd2 p.L13R knock-in (KI) mouse hearts

first: Brenda

last: Gerull


title: Pan-cancer tumor-specific antigens and membrane targets from transposable elements

city: SAINT LOUIS

first: Daofeng

last: Li

state: MO

address: 4515 McKinley Avenue

department: Genetics

institute: Washington University in St. Louis

summary: We charted the transcription start sites (TSSs) landscape globally to determine the expressed isoform of each gene and validate the precence of transposable element-derived transcript. Cryptic promoters within transposable elements (TEs) are transcriptionally reactivated in tumors to create novel TE-gene chimeric transcripts, which can produce immunogenic antigens. We performed the most comprehensive screen to date for these TE exaptation events in 33 TCGA tumortypes,675 cancer cell lines, and 11,686 GTEx adult tissue transcriptomes and identified 201,068 TE-exapted candidates with the potential to generate shared tumor-specific TE-chimeric antigens (TS-TEAs). Resultant whole lysate and HLA-pull down mass spectrometry data confirmed that TS-TEAs are presented on cancer cell surfaces. In addition, we highlight the tumor-specific membrane proteins transcribed from TE promoters that can expose novel epitopes on the extracellular surface of cancer cells. Here, we showcase the high pan-cancer prevalence of TS-TEAs and atypical membrane proteins that can be therapeutically exploited through immunotherapy approaches.

overall_design: nanoCAGE libraries was generated for variuos cancer cell lines across different cancer types.

first: Nakul

last: Shah

first: Hyo

middle: S

last: Jang

first: Yonghao

last: Liang

first: Ting

last: Wang


title: ETV2 Upregulation Marks the Specification of Early Cardiomyocytes and Endothelial Cells During Co-differentiation

first: Valeria

last: Orlova

overall_design: 4-5 batches of ETV2 positive endothelial cells and non-endothelial cells on differentiation day 4, 5, 6 and 8 from ETV2 reporter hiPSC line.

first: Xu


title: RNA-Seq analysis of gene expression changes by wildtype and Nlrx1 deficient BEAS-2B airway epithelial cells in response to A. fumigatus viable conidia

city: Blacksburg

first: Shiv

middle: D.

last: Kale

state: VA

address: 1015 Steger Hall, Life Science Circle

department: Biocomplexity Institute

institute: Virginia Tech

summary: Aspergillus fumigatus is an opportunistic fungal pathogen of the respiratory system that may cause invasive infection or an allergic response. Bronchial airway epithelial cells compromise the most abundant cell type of the pulmonary-air interface. Our recent findings suggest loss of Nlrx1 by BEAS-2B airway epithelial cells result in a hyper inflammatory response as well as decreased conidial processing. We challenged wildtype Nlrx1 deficient BEAS-2B cells with viable A. fumigatus AF293 conidia to identify early response differentially expressed genes and pathways between the two cell populations.

overall_design: Wildtype and Nlrx1 deficient BEAS-2B cells were challenged with viable Aspergillus fumigatus conidia for 0 and 3 hours. Total RNA was extracted prior to challenge (0 hrs) and 3 hours post challenge.

middle: D

first: Bridget

last: Kastelberg


title: Liver-restricted deletion of the biliary atresia candidate gene Pkd1l1 causes bile duct dysmorphogenesis and ciliopathy

city: Atlanta

first: Saul

middle: Joseph

last: Karpen

state: GA

address: 1760 Haygood Dr NE

department: Pediatrics

institute: Emory School of Medicine

summary:
A recent multicenter genetic exploration of the biliary atresia splenic malformation (BASM) syndrome identified mutations in the ciliary gene PKD1L1 as candidate etiologic contributors.  We hypothesized that deletion of Pkd1l1 in hepatoblasts would provide a mouse model of the developmental cholangiopathy of BA.
We then performed gene expression profiling analysis using data obtained from total RNA-seq, isolated from the livers of Pkd1l1Fl/Fl (Fl/Fl) and  Pkd1l1Fl/Fl x AFP-CRE mice (Pkd1l1ΔExon8/ΔExon8 Liver knockout ; LKO) at 7 weeks.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for total RNA extracted from Fl/Fl and LKO livers.

first: Dominick

last: Hellen

first: Ashley

last: Bennett

first: Sudarshan

last: Malla

first: Caroline

last: Klindt

first: Anuradha

last: Rao

first: Paul

middle: A

last: Dawson


title: Effect of culture/microexpansion in various conditions on virus-specific CD8+ T cells

status: Public on Jan 19 2023

city: Pittsburgh

first: Daniella

last: Schwartz

state: PA

address: 200 Lothrop St

institute: University of Pittsburgh

summary:
To investigate the conditions for the optimal expansion ot T cell therapeutic products, we used a microexpansion platform to screen various cytokine cocktails (no cytokines, IL-4 + IL-7, IL-15, IL-15 + IL-4, IL-15 + IL-6, and IL-15 + IL-7).
We then performed gene expression profiling analysis using data obtained from RNA-seq of 4 different donors under 6 different culture/microexpansion conditions

overall_design: Gene expression profiling analysis (fpkm) of RNA-seq data for CD8+ T cells expanded under six culture conditions: (1) no cytokines, (2) IL-4 + IL-7, (3) IL-15, (4) IL-15 + IL-4, (5) IL-15 + IL-6, and (6) IL-15 + IL-7. BMCs from 4 donors were thawed and incubated with media containing overlapping peptide libraries containing SARS-CoV-2 structural proteins for spike, membrane, envelope, and nucleocapsid (A&A Peptide, San Diego, CA, USA). Pulsed PBMCs were plated in 96-well plates at 200,000 cells/well in media with one of six cytokine conditions, specifically IL-4 (400 IU/mL) + IL-7 (10 ng/mL), IL-7 (10 ng/mL) + IL-15 (5 ng/mL), IL-4 (400 IU/mL) + IL-15 (5 ng/mL), IL-6 (100 ng/mL) + IL-15 (5 ng/mL), IL-15 alone (5 ng/mL), or no cytokines (R&D Systems, Minneapolis, MN, USA).  Cells were split on day 7 of culture and supplemented with additional media and cytokines. On day 10, expanded VSTs from 4 donors were re-stimulated with SARS-CoV-2 pepmixes encompassing spike, nucleocapsid, membrane, and envelope with CD28/CD89d (BD Biosciences) and incubated for 4 h. Cell viability was assessed using Live-Dead-near-infrared (IR). Cells were surface stained with fluorophore-conjugated antibodies against CD8-BV605, CD8-BV421, CD19-FITC, CD16-FITC, and CD14-FITC (Biolegend) and then sorted for CD8+ and CD8+ cells. Cells were not stained with CD3+ antibodies to prevent non-specific cell activation. Cells were then frozen and preserved in Trizol (Invitrogen, Waltham, MA, USA). Total RNA was extracted from 10,000–50,000 cells, and mRNA sequencing libraries were generated (NEBNext), Novaseq6000 was used for 50-cycle single-end read sequencings, which were processed with bcl2fastq 2.17.1 to generate FastQ files. Reads were mapped to the human transcriptome hg19 using STAR 2.7.0; gene expression values (fragments per kilobase exon per million mapped reads [fpkm]) were calculated and normalized with RSEM 1.3.0.


title: Effect of culture/microexpansion in various conditions on virus-specific CD4+ T cells

overall_design: Gene expression profiling analysis (fpkm) of RNA-seq data for CD4+ T cells expanded under six culture conditions: (1) no cytokines, (2) IL-4 + IL-7, (3) IL-15, (4) IL-15 + IL-4, (5) IL-15 + IL-6, and (6) IL-15 + IL-7. BMCs from 4 donors were thawed and incubated with media containing overlapping peptide libraries containing SARS-CoV-2 structural proteins for spike, membrane, envelope, and nucleocapsid (A&A Peptide, San Diego, CA, USA). Pulsed PBMCs were plated in 96-well plates at 200,000 cells/well in media with one of six cytokine conditions, specifically IL-4 (400 IU/mL) + IL-7 (10 ng/mL), IL-7 (10 ng/mL) + IL-15 (5 ng/mL), IL-4 (400 IU/mL) + IL-15 (5 ng/mL), IL-6 (100 ng/mL) + IL-15 (5 ng/mL), IL-15 alone (5 ng/mL), or no cytokines (R&D Systems, Minneapolis, MN, USA).  Cells were split on day 7 of culture and supplemented with additional media and cytokines. On day 10, expanded VSTs from 4 donors were re-stimulated with SARS-CoV-2 pepmixes encompassing spike, nucleocapsid, membrane, and envelope with CD28/CD49d (BD Biosciences) and incubated for 4 h. Cell viability was assessed using Live-Dead-near-infrared (IR). Cells were surface stained with fluorophore-conjugated antibodies against CD4-BV605, CD8-BV421, CD19-FITC, CD16-FITC, and CD14-FITC (Biolegend) and then sorted for CD4+ and CD8+ cells. Cells were not stained with CD3+ antibodies to prevent non-specific cell activation. Cells were then frozen and preserved in Trizol (Invitrogen, Waltham, MA, USA). Total RNA was extracted from 10,000–50,000 cells, and mRNA sequencing libraries were generated (NEBNext), Novaseq6000 was used for 50-cycle single-end read sequencings, which were processed with bcl2fastq 2.17.1 to generate FastQ files. Reads were mapped to the human transcriptome hg19 using STAR 2.7.0; gene expression values (fragments per kilobase exon per million mapped reads [fpkm]) were calculated and normalized with RSEM 1.3.0.


title: Transcriptomic analysis reveals optimal cytokine combinations for SARS-CoV-2-specific T cell therapy products

overall_design: Refer to individual Series


title: LncRNA CCRR Attenuates Inflammatory Response after Myocardial Infarction by Inhibiting TLR Signaling Pathway

city: Harbin

first: Lihua

last: Sun

state: Heilongjiang

address: 157 Baojian Road

institute: Harbin Medical University

summary:
Inflammatory response plays a bidirectional regulatory role in myocardial infarction (MI). TLR signaling pathway plays an important role in the development of inflammation. Additionally, we discovered that CCRR is an anti-arrhythmic lncRNA in a prior work. Here we show, it is decreased in mice with 3-day MI followed by a sharp increase of pro-inflammatory cytokines and activation of the TLR pathway. Overexpression of CCRR could effectively inhibit the inflammatory response, reduce the infarct area, and improve cardiac function. And also reduced hypoxia-induced inflammation in cardiomyocytes and macrophages induced by IFN and LPS. It produced a similar protective effect in cardiomyocytes co-cultured with macrophages. Through microarray analysis, RNA-binding protein immunoprecipitation analysis, and other related experiments verification, TLR2 and TLR4 may be as potential targets of CCRR after MI. Our findings provide the evidence that lncRNA CCRR plays a key cardioprotective role against MI injury by targeting the TLR signaling pathway.
nflammatory response plays a bidirectional regulatory role in myocardial infarction (MI). TLR signaling pathway plays an important role in the development of inflammation. Additionally, we discovered that CCRR is an anti-arrhythmic lncRNA in a prior work. Here we show, it is decreased in mice with 3-day MI followed by a sharp increase of pro-inflammatory cytokines and activation of the TLR pathway. Overexpression of CCRR could effectively inhibit the inflammatory response, reduce the infarct area, and improve cardiac function. And also reduced hypoxia-induced inflammation in cardiomyocytes and macrophages induced by IFN and LPS. It produced a similar protective effect in cardiomyocytes co-cultured with macrophages. Through microarray analysis, RNA-binding protein immunoprecipitation analysis, and other related experiments verification, TLR2 and TLR4 may be as potential targets of CCRR after MI. Our findings provide the evidence that lncRNA CCRR plays a key cardioprotective role against MI injury by targeting the TLR signaling pathway.

overall_design: The expression of heart mRNA was detected in 12 samples in 4 subgroups of WT, TG-CCRR,WT+MI,TG-CCRR+MI, with 3 samples in each group.

first: Shengjie


title: Time course RNA-Seq analysis of wildtype and Nlrx1 deficient bone marrow derived monocytoid dendritic cells indicate decision tree in response to A. fumigatus viable conidia

summary: Aspergillus fumigatus is an opportunistic fungal pathogen of the respiratory system that may cause invasive infection or an allergic response. Monocytoid dendritic cells (moDCs) are a known recruited cell population during fungal colonization and are believed to be a critical player in balancing innate versus adaptive immune responses. We conducted an RNA-Seq time course analysis of moDCs challenged against A. fumigatus, to gain an appreciation of gene expression changes.  We concurrently utilized Nlrx1 deficient  moDCs as we have recently shown the importance of Nlrx1 during invasive pulmonary aspergillosis and shown the absence of Nlrx1 results in a robust shift towards a detrimental Th2 response.  Our findings suggest a decision tree by moDCs in response to A. fumigatus viable conidia that is absent in Nlrx1-/- moDCs.

overall_design: Wildtype and Nlrx1 deficient bone marrow derived dendritic cells were challenged with viable Aspergillus fumigatus conidia for 12 hours. RNA was extracted every three hours post challenge and prior to challenge.


title: RNA sequence analysis to compare MCF7 Tamoxifen resistant cells with and without DLL1

city: Philadelphia

first: Rumela

last: Chakrabarti

address: 380 S University Ave

institute: University of Pennsylvania School of Veterinary Medicine

summary: Several signatures including Tgb pathway, cytokines, Notch signaling is altered whe DLL1 is reduced

overall_design: Examination of MCF7 TamR plko.1(n=2),  MCF7 shRNA64 (n=2) and  MCF7 TamR shRNa65(n=2)

first: John

middle: W

last: Tobias


title: Impact of gas plasma-induced chronic oxidative stress on head and neck cancer

city: Greifswald

first: Julia

last: Berner

address: Felix-Hausdorff-Straße 2

institute: Leibniz Institute for Plasma Science and Technology

summary:
We have employed whole genome microarray expression profiling to identify genes that are differentially expressed after a single gas plasma exposure in two different head and neck cancer cell lines.
Additionally, we aimed to identify genes correlating with cellular adaptation upon repetitive oxidative stress wherefore two different head and neck cancer celllines were exposed to gas plasma weekly in eight treatment cycles.

overall_design: Plasma induced gene expression in human head and neck cancer cells was measured 7 days following a single gas plasma exposure or 7 days following the eighth gas plasma exposure. Due to the high complexity and elaborateness of this study only one independet experiment was performed, but 48 technical replicates were pooled for sample collection.


title: MYTHO: a novel regulator of skeletal muscle autophagy and integrity [3 weeks]

city: Montreal

first: Gilles

last: Gouspillou

state: Québec

address: 141 Avenue du Président Kennedy

department: Département des sciences de l'activité physique

country: Canada

institute: UQAM

summary:
Short-term MYTHO knockdown (KD)
mRNA expression data for the mouse muscle (n=4 per group) were obtained using Affymetrix Mouse Clariom S Assay (Affymetrix, Santa Carla, CA) according to the manufacturer’s recommendations.

overall_design: Mouse (~10-wk-old) Gastroc muscles were transfected with an AAV containing a U6 promoter, a sequence coding for a sh-RNA targeted the product of the 230025D16Rik gene (the gene coding for Mytho). A control AAV containing a scramble sh-RNA sequence under the control of the U6 promoter was injected into the contralateral leg. Mice were sacrificed 3 weeks later and total RNA was extracted. 4 muscles were used for each condition.

first: J

middle: P

last: Leduc-Gaudet

first: A

last: Franco-Romero

first: M

last: Sandri

first: S

last: Hussain

first: G


title: Insect-Specific Chimeric Viruses Potentiated Antiviral Responses and Inhibited Pathogenic Alphavirus Growth in Mosquito Cells

city: Hong Kong

first: Xudong

last: Liu

address: Tat Chee Avenue Kowloon Tong

institute: City University of Hong Kong

summary: Most alphaviruses are transmitted by mosquito vectors and infect a wide range of vertebrate hosts, with a few exceptions. Eilat virus (EILV) in this genus is characterized by a host range restricted to mosquitoes. Its chimeric viruses have been developed as safe and effective vaccine candidates and diagnostic tools. Here, we investigated the interactions between these insect-specific viruses (ISVs) and mosquito cells, unveiling their potential roles in determining vector competence and arbovirus transmission. By RNA sequencing, we found that these ISVs profoundly modified host cell gene expression profiles. Two EILV-based chimeras, consisting of EILV’s nonstructural genes and the structural genes of Chikungunya virus (CHIKV) or Venezuelan equine encephalitis virus (VEEV), namely EILV/CHIKV (E/C) and EILV/VEEV (E/V), induced more intensive transcriptome regulation than parental EILV and activated different antiviral mechanisms in host cells. We demonstrated that E/C robustly promoted antimicrobial peptide production and E/V strongly upregulated the RNA interference pathway components. This also highlighted the intrinsic divergences between CHIKV and VEEV, representatives of the Old World and New World alphaviruses. In contrast, EILV triggered a limited antiviral response. We further showed that initial chimera infections efficiently inhibited subsequent pathogenic alphavirus replication, especially in the case of E/V infection, which almost prevented VEEV and Sindbis virus (SINV) superinfections. Altogether our study provided valuable information on developing ISVs as biological control agents.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Aedes albopictus C636 cells infected with EILV or EILV-based chimeric viruses.

first: Lu

last: Tan

first: Yiwen

last: Zhang

first: Dal

last: Kim

first: Runsheng

last: Li


title: SGLT2 inhibitors mitigate kidney tubular metabolic and mTORC1 perturbations in youth onset type 2 diabetes

city: Aurora

first: Petter

last: Bjornstad

state: Colorado

institute: University of Colorado School of Medicine

summary: Single cell RNA-sequencing analysis allows for a more complete cell-by-cell analysis of the effects of SGLT2 inhibitors on the kidneys of patients with youth onset type 2 diabetes.

overall_design:
Cryostor-preserved kidney biopsies were subjected to single cellular RNA-sequencing.
*** Raw data not provided due to patient privacy concerns. ***

first: Phillip

last: McCown

first: Jennifer

last: Schaub

first: Fadhl

middle: M

last: Alakwaa

first: Abhijit

last: Naik

first: Viji

last: Nair

first: Sean

last: Eddy

first: Rajasree

last: Menon

first: Edgar

last: Otto

first: Matthias

last: Kretzler


title: DNMT3A-coordinated splicing governs the stem state switch toward differentiation in embryonic and hematopoietic stem cells [RNA-seq]

city: Houston

first: Margaret

last: Goodell

state: TX

address: One Baylor Plaza, N1030

institute: Baylor College of Medicine

summary: Upon stimulation by extrinsic stimuli, stem cells initiate a program that enables differentiation or self-renewal. Disruption of the stem-state exit has catastrophic consequences for embryogenesis and can lead to cancer. While some elements of this stem-state switch are known, major regulatory mechanisms remain unclear. Here, we show this switch involves a global increase in splicing efficiency coordinated by DNMT3A, an enzyme typically involved in DNA methylation. Proper activation of murine and human embryonic and hematopoietic stem cells depends on mRNA processing influenced by DNMT3A in response to stimuli. DNMT3A coordinates splicing through recruitment of the core spliceosome protein SF3B1 to RNA polymerase and mRNA. Importantly, the DNA methylation function of DNMT3A is not required and loss of DNMT3A leads to impaired splicing during stem cell turnover. Finally, we identify the spliceosome as a potential therapeutic target in DNMT3A-mutated leukemias. Together, our results reveal a modality through which DNMT3A and the spliceosome govern exit from the stem-state towards differentiation.

overall_design:
mRNA sequencing (RNA-seq) of DNMT3A WT and KO cells in mouse and human HSCs and ESCs
Total RNA was isolated from mouse HSCs and human HSPCs using PicoPure RNA isolation kit (KIT0204). RNA from mESC and hESC was isolated using the Qiagen mini kit. Quality of isolated RNA was verified with Nanodrop and tapestation prior to library preparation. 500-750ng of total RNA was used was used as input for the Illumina TruSeq Stranded mRNA LT Prep Kit (20020594). Libraries were made following Illumina’s recommended protocol. Amplified libraries were purified and quantified using the KAPA quantification kit. RNA sequencing libraries were sequenced on an Illumina NextSeq 500 instrument (paired-end).

first: Raghav

last: Ramabadran

first: Jaime

last: Reyes

first: Jarey

last: Wang


title: Transcriptional response to collateral RNA cleavage by LbuCas13a

first: Niels

last: Geijsen

department: Anatomy and Embryology

institute: LUMC

summary: LbuCas13a exhibits widespread collateral RNA cleavage in human cells after activation by a specific target RNA. We wanted to explore the cells response to this collateral RNA cleavage. Therefore we performed RNA-seq at 16 hours after RNP transduction. From prior experiments we know that at this timepoint RNA integrity has largely recovered and cells are entering apoptosis.

overall_design: dEGFP expressing HAP1 cells were transduced with either an empty transduction, LbuCas13a protein, LbuCas13a protein and a non-targeting crRNA or LbuCas13a protein an a dEGFP targeting crRNA. RNA was harvested 16 hours after transduction and gene expression profiles compared using RNA-seq.

first: Jorik

middle: F

last: Bot

first: Zhihan

last: Zhao

first: Darnell

last: Kammeron

first: Peng

last: Shang


title: Genome-wide assessment of DNA methylation alterations induced by superovulation, sexual immaturity and in vitro follicle growth in mouse blastocysts

city: Cambridge

first: Simon

middle: Richard

last: Andrews

state: Cambs

address: Babraham Research Campus

department: Science Services

institute: The Babraham Institute

summary: In their attempt to fulfill the wish of having children, women who suffer from fertility issues often undergo assisted reproductive technologies (ART) such as ovarian stimulation, which has been associated with adverse health outcomes and imprinting disorders in children. However, given the crucial role of exogenous hormone stimulation in improving human infertility treatments, a more comprehensive analysis of the potential impacts on DNA methylation in embryos following ovarian stimulation is needed. Here, we provide genome-wide DNA methylation profiles of blastocysts generated after superovulation of prepubertal or adult mice, compared with blastocysts derived from non-stimulated adult mice. Additionally, we assessed the impact of the in vitro growth and maturation of oocytes on methylation in blastocysts.

overall_design: Mouse blastocysts (F1xF1; C57BL/6JxCBACa) derived from oocytes obtained after superovulation of adult (SOa; 8-10 week) and prepubertal (SOp; 23 days) mice compared with blastocysts produced with naturally ovulated oocytes (NO) from adult mice.  All zygotes were subject to the same in vitro culture conditions.  Hatched blastocysts were collected on day 5 of in vitro culture. Additionally, in a separete group of blastocysts the oocytes were collected at primordial or early pre-antral stages  and subjected to in vitro follicule culture maturation process. All samples were processed for  library generation to assess whole-genome DNA methylation profile.

first: Laura

last: Saucedo-Cuevas

first: Elena

last: Ivanova

first: Anamaria-Cristina

last: Herta

first: Katy

last: Billooye

first: Felix

last: Krueger

first: Johan

last: Smitz

first: Gavin

last: Kelsey

first: Ellen

last: Anckaert


title: MYTHO: a novel regulator of skeletal muscle autophagy and integrity [3 months]

first: Gilles

last: Gouspillou

summary:
MYTHO: a novel regulator of skeletal muscle autophagy and integrity
mRNA expression data for the mouse muscle (n=4 per group) were obtained using Affymetrix Mouse Clariom S Assay (Affymetrix, Santa Carla, CA) according to the manufacturer’s recommendations.

overall_design: Mouse (~10-wk-old) Gastroc muscles were transfected with an AAV containing a U6 promoter, a sequence coding for a sh-RNA targeted the product of the 230025D16Rik gene (the gene coding for Mytho). A control AAV containing a scramble sh-RNA sequence under the control of the U6 promoter was injected into the contralateral leg.  Mice were sacrificed 3 months later and total RNA was extracted. 4 muscles were used for each condition.

first: J

last: Leduc-Gaudet

first: A

last: Franco-Romero

first: M

last: Sandri

first: S

last: Hussain

first: G


title: Cut&Run sequencing of WT  HSCs with 1-mon M.avium infection

first: Duy

middle: Tri

last: Le

state: Texas

address: 1102 Bates Ave

summary:
Purpose: to identify the binding sites for BATF2 in HSCs during M. avium infection, we conducted CUT&RUN sequencing of the HSCs from infected WT mice using an anti-BATF2 antibody. We used an anti-IgG antibody as a control to exclude noise and nonspecific binding and an anti-H3K27ac to assess open chromatin
Methods: 10,000-50,000 HSCs (CD45.1/CD45.2 KL CD150+ CD48-) into HBSS from1-month infected WT mice (n=10-12 per group). CUT&RUN sequencing was performed with modified methods as previously described (Henikoff et al., 2020; Skene et al., 2018). 50,000 HSCs (LK CD150+, CD48-) were sorted pools of naïve or 1-month (M. avium) infected WT mice for CUT&RUN sequencing (N=7-8). Cells were washed with Wash Buffer (50mL total with 20 mM HEPES pH 7.5, 150mM NaCl, 0.5 mM Spermidine, and one Roche Complete protein inhibitor tablet) and bound to Concanavalin A-coated magnetic beads (Bang Laboratories L200731C) for 15 minutes room temperature. Sample slurries were magnetically separated, washed, and incubated with primary antibody diluted in wash buffer containing 0.05% digitonin (Dig Wash) overnight at 4 °C. Slurries were then magnetically separated and washed with Dig Wash three times and then incubated with protein A-MNase (pA-MN, Epicypher 15-1016) for 1 hour at 4 °C. Slurries were magnetically separated and washed, resuspended in 200uL Dig Wash, and placed on an iced heating block. 2uL of 2mM CaCl2 was added to catalyze the pA-MN reaction and digestion. After 45 minutes, one equal volume of Stop Buffer (340mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.05% Digitonin, 0.05 mg/mL glycogen, 5 ug/mL RNase A, 2 pg/mL heterologous spike-in DNA) was added to end the reaction, and sample slurries were then incubated for 30 minutes at 37 °C to release fragments and then magnetically separated. The supernatant was collected, and DNA was purified via phenol-chloroform extraction and ethanol precipitation. Samples were resuspended in molecular-grade water after ethanol precipitation. DNA was quantified with Qubit 2.0 DNA HS Assay (ThermoFisher, Massachusetts, USA) and quality was assessed by Tapestation High sensitivity D1000 DNA Assay (Agilent Technologies, California, USA). Library preparation was performed using the KAPA Hyper Prep kit (Roche, Basel, Switzerland) according to  the manufacturer’s recommendations. Library quality and quantity were assessed with Qubit 2.0 DNA HS Assay (ThermoFisher, Massachusetts, USA), Tapestation High Sensitivity D1000 Assay (Agilent Technologies, California, USA), and QuantStudio ® 5 System (Applied Biosystems, California, USA). Illumina® 8-nt dual-indices were used. Equimolar pooling of libraries was performed based on QC values and sequenced on an Illumina® NovaSeq (Illumina, California, USA) with a read length configuration of 150 paired-end (PE). Antibodies used were anti-BATF2, Rabbit-anti mouse IgG (Jackson ImmunoResearch 315-005-003), and Rabbit anti-H3K27ac (Cell Signaling Technologies 8173T). PE reads were aligned to mm10 using Bowtie2 version 2.4.5. MACS2 version 2.2.7.1 was used to call peaks and CUT&RUN IgG was used as a negative control.
Results: We found binding of BATF2 at cis-elements of ccr5, ifngr2 (interferon gamma receptor 2), ly6c1, and ccl28 genes (Figure 7C). The locations were highly aligned with accessible chromatin positions marked by H3K27ac, suggesting that BATF2 enhanced gene expression in response to infection. The observations were aligned with our RNA-seq analysis of gene expression in WT or Batf2 KO HSCs in the presence or absence of M. avium infection, as ccr5, ifngr2, ly6c1, and ccl28 were more effectively induced in WT compared to Batf2 HSCs during M. avium infection (Figure S5B).
Conclusion: BATF2 interacts with regulatory elements in IFN response genes and facilitates increased expression in response to infection

overall_design: Identify the DNA binding sites for BATF2 in HSCs during M. avium infection

first: Brandon

last: Tran

first: Katherine

middle: Y

last: King


title: Single cell RNA sequencing reveals transcriptional changes of human choroid and retinal pigment epithelium cells during development, in healthy adult and intermediate age-related macular degeneration

city: NEWCASTLE

first: Megan

middle: Saphana Rose

last: Hasoon

address: Newcastle University

institute: Newcastle University

summary: Age related macular degeneration (AMD) is the most prominent cause of blindness in the developed countries. Vision loss in the advanced stages of the disease is caused by atrophy of retinal photoreceptors, overlaying retinal pigment epithelium (RPE) and choroid endothelial cells. The molecular events that underline the development of these cell types from in utero to adult as well as the progression from the asymptomatic, to intermediate and advanced stages AMD are not yet fully understood. We performed single cell RNA-Sequencing (Seq) of human fetal and adult RPE and choroid, profiling in detail all the cell types and elucidating proliferation, differentiation, antigen pathway presentation and immunomodulation events that characterise the first half of human gestation. Our data demonstrate that progression from fetal to adult state is characterised by an increase in expression of genes involved in oxidative stress response and detoxification from heavy metals, suggesting a better defence against oxidative stress in the adult RPE and choroid tissues. Single cell comparative transcriptional analysis between an intermediate AMD patient and unaffected subject revealed specific loss of RPE and melanocytes in the macular region. While the CECs loss was not supported by our single cell RNA-Seq data, pathway enrichment analyses supported the onset of apoptosis in these cells, suggesting that during the course of AMD pathogenesis, endothelial cells are the most likely cell type to atrophy in the macula of AMD patients. Together these finds provide a rich resource for enhancing our understanding the development of RPE and choroid and the role they play in AMD progression and pathogenesis

overall_design: To obtain single cell transcriptome data from developing, and adult RPE and choroid tissue  and identify changes that occur in inetermediate AMD

first: Joseph

last: Collin

first: Darin

last: Zerti

first: Sarah

last: Hammadi

first: Birthe

last: Dorgau

first: Lucy

last: Clarke

first: David

last: Steel

first: Rafiqul

first: Jonathan

last: Coxhead

first: Steven

last: Lisgo

first: Rachel

last: Queen

first: Majlinda

last: Lako


title: FUS-ALS hiPSC-derived astrocytes impair human motor units through both gain-of-toxicity and loss-of-support mechanisms

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

summary: Non-neuronal cells, including astrocytes, play a crucial role in the selective motor neuron pathology in amyotrophic lateral sclerosis (ALS). How astrocytes exactly contribute to the disease is not fully elucidated. Therefore, we characterised human induced pluripotent stem cell (hiPSC)-derived astrocytes from FUS-ALS patients, and incorporated these astrocytes into a human motor unit model to investigate the astrocytic effect on hiPSC-derived motor neuron network and neuromuscular junctions (NMJs). We observed a dysregulation of astrocyte homeostasis, which resulted in a FUS-ALS-mediated increase in reactivity and secretion of pro-inflammatory cytokines. Upon coculture with motor neurons and myotubes, we detected a cytotoxic effect on motor neuron-neurite morphology and outgrowth, as well as on NMJ formation and functionality, which was improved or fully rescued by isogenic control astrocytes. We conclude that mutant astrocytes have both a gain-of-toxicity and loss-of-support function in ALS, ultimately contributing to the disruption of motor neuron homeostasis, intercellular networks and NMJs.

overall_design: FUS-mutant hiPSC-derived astrocytes from two ALS patients and the corresponding CRISPR-Cas9 gene-edited isogenic control lines were analysed in three biological replicate. One biological replicate represents an independent differentiation from iPSC to terminal astrocyte differentiation. Samples were collected at week 4 of astrocyte maturation.

first: Katarina

last: Stoklund Dittlau

first: Rekins

first: Lim

last: De Swert

first: Ludo

last: Van Den Bosch


title: Glycosyltransferase Extl1 promotes CCR7-mediated dendritic cell migration to restrain infection and autoimmunity

city: Shanghai

first: Juan

last: Liu

state: Shanghai

address: 800 Xiangyin Road

institute: Institute of Immunology, Second Military Medical University

summary: This SuperSeries is composed of the SubSeries listed below. The study demonstrate that glycosyltransferase Extl1 plays critical roles in promoting CCR7-mediated DC migration by enhancing CCR7 expression and signaling via HSPG, thus contributing to immune defense against pathogens and prevention of autoimmune diseases.


title: RANK is an independent biomarker of poor prognosis in estrogen receptor-negative breast cancer and functionally contributes to increase tumor aggressiveness

city: Madrid

first: María José

last: Jiménez

state: Madrid

address: C. de Melchor Fernández Almagro, 3

department: Structural Biology

country: Spain

institute: Spanish National Cancer Research Centre

summary: Analyses of genes expression  in estrogen receptor negative, RANK positive,  breast cancer orthoxenografts after in vivo treatment (4 weeks) with RANKL , RANK-Fc or denosumab.

overall_design: Dissociated breast tumor cells mixed 1:1 with Matrigel Basement Membrane (BD Biosciences) were transplanted orthotopically in the inguinal mammary gland of 10/12-week old NSG mice and when tumors reached 5 mm of diameter mice were randomized for mock, h-RANKL (0.75 mg/kg, 4-6 doses, twice per week; Amgen Inc), h-RANK-Fc treatment (10 mg/kg, three times per week; Amgen Inc), denosumab (10 mg/kg, three times per week; XGEVA®). Mice were sacrificed 24 h after the last treatment and RNA extracted from the tumors.

first: Marina

last: Ciscar

first: Maria

last: Jimenez-Santos

first: Eva

last: Gonzalez-Suarez

last: Trinidad


summary: Purpose: mRNAs sequencing of the gene expression differences in LPS-stimulated Extl1-dificient mDC and wild-type mDC. The goals of this study are to investigate the biological effect of glycosyltransferase Extl1 in regulating dendritic cell function.

overall_design: Bone marrow cells from Extl1-dificient and wild-type mice were cultured with GM-CSF and IL-4 for 6 days to generate bone-marrow derived DC (BMDC). BMDC were stimulated with or without  LPS for 12 h and then subjected to RNA seq.

first: Xuetao

last: Cao


summary: The goal of this study is to investigate the role of Extl1 in regulating DC migration and subsequent adaptive immunity in vivo

overall_design: We performed single-cell RNA sequencing (scRNA-seq) analysis of the lymph node cells from wild-type and Extl1-deficient mice post inflammatory challenge with DNFB for 2 days


city: shanghai

first: kun

last: chen

address: No.800 Xiangyin Road, Yangpu District

institute: Zhejiang University

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

overall_design: Refer to individual Series


title: Glycosyltransferase Extl1 promotes CCR7-mediated dendritic cell migration to restrain infection and autoimmunity [treated vs. untreated]

summary: Purpose: mRNAs sequencing of the gene expression differences in CCR7-stimulated mDC. The goals of this study are to investigate the biological effect of glycosyltransferase Extl1 in regulating dendritic cell function.

overall_design: Bone marrow cells from wild-type mice were cultured with GM-CSF and IL-4 for 6 days to generate bone-marrow derived DC (BMDC). BMDC were stimulated with or without CCR7 ligand CCL19 and CCL21 for 12 h


title: Glycosyltransferase Extl1 promotes CCR7-mediated dendritic cell migration to restrain infection and autoimmunity [WT vs. KO]

summary: Purpose: mRNAs sequencing of the gene expression differences in CCR7L-stimulated Extl1-dificient mDC and wild-type mDC. The goals of this study are to investigate the biological effect of glycosyltransferase Extl1 in regulating dendritic cell function.

overall_design: Bone marrow cells from Extl1-dificient and wild-type mice were cultured with GM-CSF and IL-4 for 6 days to generate bone-marrow derived DC (BMDC). BMDC were stimulated with or without CCR7L (CCL19 and CCL21) for 12 h and then subjected to RNA seq.


title: RNA-sequencing to identify differentially expressed mRNAs after knockout of YTHDF2 in granule cells of  mouse hippocampus dentate gyrus

city: Shenzhen

first: Mengru

last: Zhuang

state: Guangdong

address: 1088 Xueyuan Avenue, Nanshan District

institute: Southern University of Science and Technology

summary: To identify differentially expressed mRNAs after knockout of YTHDF2 in granule cells of  mouse hippocampus dentate gyrus, we perfromed RNA-seq. Total RNA from DG deficient in YTHDF2 and the negative control DG were collected and subjected to construct sequencing libraries using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB). After sequencencing, the filtered reads were mapped to the mouse reference genome (GRCm38) using HISAT2 v2.0.5 with default parameters. The resulting bam files were fed to featureCounts v1.5.0-p3 to count the number of RNA-seq reads, which was further normalized to calculate FPKM. Differential expression analysis of two groups (cKO vs NC) (three biological replicates per group) was performed using the DESeq2 package (version 1.20.0). Altogether 779 mRNA were differentially regulated, among which 536 mRNA were upregulated after YTHDF2 KD. This study provides a gene list which shows differentially expressed mRNAs after knockout of YTHDF2 in granule cells of mouse hippocampus dentate gyrus.

overall_design: 3 replicates in each group

first: Fanghao

last: Liang

first: Sheng-Jian

last: Ji


title: Anti-YTHDF2 RIP-Seq to identify YTHDF2 target mRNAs in hippocampus

summary: To identify the target mRNAs of the m6A reader protein YTHDF2 in mouse hippocampus, we carired out anti YTHDF2 RNA Immunoprecipitation (RIP) followed by RNA-sequencencing. Using EZ-Magna RIP™ RNA-Binding Protein Immunoprecipitation Kit (Millipore), RNA from P40 wild type mouse hippocampus was pulled down by rabbit polyclonal anti-YTHDF2 (proteintech) and then sequenced on Illumina Novaseq 6000. The filtered reads were aligned to the mouse reference genome (GRCm38) using BWA mem (v 0.7.12).Then the MACS2 (version 2.1.0) peak calling software was used to identify regions of IP enrichment over background, followed by the motif detected by Homer (Heinz et al., 2010). Peak related genes are then confirmed by PeakAnnotator. Different peak analysis was based on the fold enrichment of peaks of different experiments. A peak was determined as different peak when the odds ratio between two groups was more than 2. Using the same method, genes associated with different peaks were identified. Finally, Biological replicates of anti-YTHDF2 RIP-Seq identified 408 mRNAs transcripts. This study provides gene lists which shows mRNA binding with YTHDF2 in mouse hippocampus.

overall_design: 2 replicates, each containing input and IP samples


title: Photodynamic oncolytic virus therapy for central nervous system malignancies

status: Public on Jan 18 2023

city: Boston

first: Hiroaki

last: Wakimoto

state: MA

address: 185 Cambridge Street, CPZN-3800

department: Neurosurgery

institute: Massachusetts General Hospital

summary: The goal of the study was to determine whether photodynamic oncolytic virus therapy of glioblastoma and malignant meningioma xenografts in mice alters transciptomics associated with efficacy. RNA sequencing was used from tumors treated with PBS, laser, G47delta-KillerRed, and G47delta-KillerRed and laser, which is photodynamic oncolytic virus therapy.

overall_design: RNAseq data for U87 glioblastoma (U) and IOMM-Lee malignant meningioma (I) models. Tumor bearing mice were treated with PBS (1, 2 and 3), laser (4, 5, and 6), G47delta-KillerRed (7, 8, and 9), or G47delta-KillerRed and laser (10, 11 and 12) before RNA extraction. Samples were labeled as CH1, CH2, CH3, CH4, CH5, CH6, CH7, CH8, CH9, CH10, CH11 CH12.

first: Kazuhide

last: Shimizu

first: Joshua

last: Gorham

first: Hiroko


title: Small RNA-sequencing reveals the involvement of microRNA-132 in benzo(a)pyrene-induced toxicity in primary human blood cells

city: RENNES

first: Lydie

last: SPARFEL

address: 2 avenue du Pr Léon Bernard

department: IRSET U1085

country: France

institute: Inserm

summary: Polycyclic aromatic hydrocarbons (PAHs) are widely distributed environmental contaminants, triggering deleterious effects such as carcinogenicity and immunosuppression and peripheral blood mononuclear cells (PBMCs) are among the main cell types targeted by these pollutants. In the present study, we sought to identify the expression profiles and function of miRNAs, gene regulators involved in major cellular processes and recently linked to environmental pollutants, in PBMC-exposed to the prototypical PAH, benzo[a]pyrene (B[a]P). Using small RNA deep sequencing, we identified several B[a]P-responsive miRNAs. Bioinformatics analyses showed that their predicted targets could modulate biological processes relevant to cell death and survival. Further studies of the most highly induced miRNA, miR-132, showed that its up-regulation by B[a]P was time- and dose-dependent and required aryl hydrocarbon receptor (AhR) activation. By evaluating the role of miR-132 in B[a]P-induced cell death, we propose a mechanism linking B[a]P-induced miR-132 expression and CYP1A1 and CYP1B1 mRNA levels, which could contribute to the apoptotic response of PBMCs. Altogether, this study increases our understanding of the roles of miRNAs induced by B[a]P and provides the basis for further investigations into the mechanisms of gene expression regulation by PAHs.

overall_design: 12 independent PBMC cultures each grown in untreated (DMSO) and 2 µM B[a]P-treated conditions for 48 h, were combined in 3 equal pools (with 4 separate blood donors per pool) for each condition. They were then used to isolate 5-15 ng of the small RNA fraction and processed using Qiaseq miRNA library prep kit

first: Rima

last: Souki

first: Jérémy

last: Amossé

first: Valentine

last: Genêt

first: Morgane

last: Le Gall

first: Benjamin

last: Saintpierre

first: Franck

last: Letourneur

first: Anne

last: Maître

first: Christine

last: Demeilliers

first: Eric

last: Le Ferrec

first: Dominique

last: Lagadic-Gossmann

first: Normand

last: Podechard

last: Sparfel


title: Effect of Tormentic Acid on metabolic-associated fatty liver disease in mice

city: Nanning

first: xing

last: lin

address: Shuangyong Road

institute: Guangxi medical university

summary: This study aimed to explored the effects and underlying mechanisms of Tormentic Acid (TA) against metabolic-associated fatty liver disease (MAFLD) in mice. The differentially expressed genes (DEGs) in liver tissue in “Normal VS model ”and “Model VS TA” were identified by RNA-seq.

overall_design: Mouse were randomly devided into three groups, including the normal group, model group and TA group.

first: Xing

last: Lin

first: Yuanyuan

last: Wei

first: Bin

last: Fang

first: Yuhua

last: Xiong