title: Epigenomic profiling of mouse nucleus accumbens at single-cell resolution

first: Parth

last: Bhatia

state: Massachusetts

address: 230 South Huntington Avenue, Apt 1

department: Neurology

institute: Brigham and Women's Hospital

summary: The nucleus accumbens (NAc) is a key brain region involved in reward processing and is linked to multiple neuropsychiatric conditions such as substance use disorder, depression, and chronic pain. Recent studies have begun to investigate persistent changes in NAc gene expression at a single-cell resolution, however, our understanding of the cellular heterogeneity of the NAc epigenomic landscape remains limited. In this study, we utilize single-nucleus assay for transposase-accessible chromatin using high-throughput sequencing (snATAC-seq) to map cell-type-specific differences in chromatin accessibility in the NAc. Our findings not only reveal the transcription factors and putative gene regulatory elements that may contribute to these cell-type-specific epigenomic differences but also provide a valuable resource for future studies investigating epigenomic changes that occur in neuropsychiatric disorders.

overall_design: The nucleus accumbens of 2 8-week old male mice was taken and nuclei were isolated. Single-nucleus ATAC-seq was then performed on these nuclei from 2 biological replicates.

first: P

first: L

last: Yang

first: JXJ

last: Luo

last: Xu

first: W

last: Renthal


title: Expression patterns of white blood cells in response to individual food treatments relative to LPS treatment and untreated in an FPIES subject

status: Public on May 18 2023

city: Ann Arbor

first: Bioinformatics

last: Core

state: MI

address: BRCF Bioinformatics Core, 2800 Plymouth Rd

country: USA

institute: University of Michigan

type: Expression profiling by high throughput sequencing

summary: Total blood white blood cells from two FPIES subjects were treated with 2 foods that were safe for those subjects, 3 foods that were triggers for those subjects, relative to LPS and untreated for each subject

overall_design: Blood was drawn from FPIES subject who was on trigger-food avoidance, the WBCs isolated by ACK buffer RBC lysis, and the WBCs plated in 12-well plate wells, and treated with individual food treatments, LPS or untreated.

first: Mohamad

last: El-Zaatari

first: Charles

middle: F

last: Schuler


title: Immunogenetic metabolomics revealed key enzymes that modulate CAR-T metabolism and function

city: West Haven

first: Sidi

last: Chen

state: CT

address: 850 West Campus Drive

institute: Yale University

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

overall_design: Refer to individual Series


title: Next generation sequencing facilitates quantitative analysis of transcriptional profiling of  Candida albicans SC5314 with H55 treatment or not.

city: Jinan

first: Xueyang

last: Jin

state: Shandong Province

address: No. 44 West Wenhua Road

country: China

institute: Shandong University

summary: mRNA profiles of Candida albicans SC5314 treated with compound H55 and untreated Candida albicans SC5314 were generated by deep sequencing, in triplicate, using Illumina HiSeq X Ten. The sequence reads that passed quality filters were analyzed at the transcript isoform level. qRT–PCR validation was performed using SYBR Green assay. We find that some genes in ergosterol biosynthesis pathaway such as ERG3, ERG6 and ERG9 were upregulated, but HMG1, ERG2 and ERG12 were downregulated. Genes invovled in hyphal growth and adhesion were also accordingly regulated in H55 treated group.

first: Wenqiang

last: Chang

first: Hongxiang

last: Lou


title: Single-cell immunoprofiling of synovial helper T cell of rheumatoid arthritis patients.

city: Chiba

first: Shigeru

last: Tanaka

address: 1-8-1 Inohana

department: Allergy and Clinical Immunology

country: Japan

institute: Chiba University

summary: Rheumatoid arthritis (RA) is a systemic autoimmune disease characterized by chronic destructive arthritis. Although helper T cells are involved in the pathogenesis of RA, the characteristics of synovium-infiltrating CD4+ T cells are still largely unknown. In this study, we investigated synovium-infiltrating helper T cells of rheumatoid arthritis patients

overall_design: scRNA-seq and scVDJ-seq of 4 synovial helper T cells collected from Japanese RA patinets who underwent joint surgery.

first: Hiroshi

last: Nakajima


title: CITED2 is a conserved regulator of deep placentation (Rat III)

city: Kansas City

first: Khursheed

last: Iqbal

state: Kansas

address: 3901 Rainbow Blvd

department: Pathology

institute: University of Kansas Medical Center

summary: Establishment of the hemochorial placentation site requires the exodus of trophoblast cells from the placenta and their transformative actions on the uterine vasculature, which is a critical but poorly understood developmental process. CBP/p300-interacting transactivator with glutamic acid/aspartic acid-rich carboxyl terminal domain 2 (CITED2) is a member of the CITED protein family of co-regulators and has been shown to possess roles in embryogenesis, including placenta development. We examined the involvement of CITED2 in the rat, which exhibits deep hemochorial placentation, a feature it shares with the human. CITED2 is distinctively expressed in the junctional zone compartment of the rat placentation site and in intrauterine invasive trophoblast cells. Homozygous disruption of the rat Cited2 locus resulted in placental and fetal growth restriction and abnormalities in heart and lung development, which are also characteristic of the CITED deficient mouse model. However, other features of the mouse Cited2 null phenotype, including exencephaly, adrenal gland agenesis, and prenatal lethality were not associated with CITED2 deficiency in the rat. Trophoblast-specific lentiviral CITED2 knockdown in the rat yielded a growth arrested placental phenotype. Smaller Cited2 null placentas were associated with a growth restricted junctional zone and coincided with a delay in intrauterine trophoblast cell invasion. Invasive trophoblast cells arise from the junctional zone. Transcriptomes of the junctional zone, the invasive trophoblast cell lineage, and differentiating trophoblast stem cells were affected by CITED2 disruption, as were placental adaptations to hypoxia and exposure to viral mimetics. Evidence for the conservation of CITED2 expression in human placental tissue and conserved actions in invasive/extravillous trophoblast cell development were demonstrated. We conclude that CITED2 is a conserved regulator of deep hemochorial placentation.

overall_design: Rat uterine-placental interface (UPI) tissues were dissected on gd18.5 from heterozygous breeding of Cited2 mutant rats. Dissected UPI compartments from wild type and Cited2 null placentation sites were minced and enzymatically digested into a single cell suspension. Samples were further processed for scRNA-seq by Chromium Single Cell RNA-seq (10X Genomics). 3 wild type and 3 null samples were analyzed.

first: Kuna

last: Marija

first: Michael

middle: J

last: Soares


title: CITED2 is a conserved regulator of deep placentation

sample_organism:
Homo sapiens
Rattus
Rattus norvegicus

platform_organism:
Homo sapiens
Rattus
Rattus norvegicus


title: CITED2 is a conserved regulator of deep placentation (Rat II)

overall_design: Rat placental junctional zone tissues were dissected on gd14.5 from heterozygous breeding of Cited2 mutant rats. Dissected junctional zone compartments from wild type and Cited2 null fetuses were snap-frozen in liquid nitrogen and stored at -80°C until processing for RNA isolation. 4 samples for wild type and 4 samples for null junctional zone tisue was analyzed.

first: Dhakal

last: Pramod


title: CITED2 is a conserved regulator of deep placentation (Human)

overall_design: CITED2 was knocked down in human trophoblast stem cells using lentiviral delivery of shRNA. Following puromycin selection, cells were differentiated for 8 days (Okae et al.) into extravillous trophoblast. Cells were collected and RNA isolated. 3 samples from control knockdown and 3 samples from CITED2 knockdown were analyzed.

first: Dominguez

middle: M

last: Esteban


title: A First-in-Class Pan-Lysyl Oxidase inhibitor impairs stromal remodeling and enhances gemcitabine response and survival in pancreatic cancer

city: Darlinghurst

first: Ruth

last: Pidsley

state: NSW

address: 384 Victoria Street

country: Australia

institute: Garvan Institute of Medical Research

summary: The lysyl oxidase family represents a promising target in stromal targeting of solid tumours due to the importance of this family in cross-linking and stabilising fibrillar collagens, and its known role in tumour desmoplasia. Using small-molecule drug design approaches, we generated and validated PXS-5505, a first-in-class, highly selective and potent pan-lysyl oxidase inhibitor. We demonstrate in vitro and in vivo that pan-lysyl oxidase inhibition decreases chemotherapy-induced pancreatic tumour desmoplasia and stiffness, reduces cancer cell invasion and metastasis, improves tumour perfusion, and enhances the efficacy of chemotherapy in the autochthonous genetically engineered KPC model, whilst also demonstrating anti-fibrotic effects in human PDX models of pancreatic cancer. PXS-5505 is orally bioavailable, safe and effective at inhibiting lysyl oxidase activity in tissues. Our findings present the rationale for progression of the first pan-lysyl oxidase inhibitor aimed at eliciting a reduction in stromal matrix to potentiate chemotherapy in pancreatic ductal adenocarcinoma.

overall_design: Transcriptome analysis of p53_educated cancer-associated fibroblasts (CAFs), isolated from the KPC (PDX1cre, KrasG12D/+,p53R172H/+,Ecad-GFP/+) mouse model of pancreatic ductal adenocarcinoma, assessed by RNASequencing.

first: Shona

last: Ritchie

first: Brooke

last: Pereiera

first: Jess

last: Chitty

first: Paul

last: Timpson

first: Thomas

last: Cox


title: CITED2 is a conserved regulator of deep placentation (Rat I)

overall_design: Rat trophoblast stem cells derived from wild type and Cited2 null blastocyst were differentiated for 12 days, collected and RNA isolated, 3 samples for wild type and 3 samples for null cells.


title: LPS-mediated noncoding RNA IFITM4P promotes malignant progression of oral leukoplakia through nucleocytoplasmic shuttling

city: Shanghai

first: Linjun

last: Shi

address: No. 639, Zhizaoju Road, Shanghai, China

institute: Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University, School of Medicine

summary: To identify the downstream targets of IFITM4P that regulate the proliferation of Leuk-1 cells, we performed RNA sequencing to identify differentially expressed genes.

overall_design: Examination of IFITM4P and Vector in Leuk-1 cells.

first: Hao

last: Jia


title: Histone methyltransferase SETDB1 selectively regulates cortical HTR3A interneuron development and anxiety-like behavior in mice [ChIP-seq]

first: Yan

last: Jiang

address: 131 Dongan rd

department: Institutes of Brain Science

institute: Fudan University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: SETDB1 functioning as a histone H3K9 specific methyltransferase, is critically involved in brain development. Here, we used H3K9me3 and H3K27me3 ChIPseq to study H3K9me3 redistribution and defined enhancer function of elements in genomes of NPCs from ganglionic eminences (GE) in brain-specific Setdb1 conditional knockout mice (Setdb1-Nestin-cKO) and controls at E15.5.

overall_design: H3K9me3 ChIPseq from GE_NPC, 3 animals per genotype; H3K27ac ChIPseq from GE_NPC, 3 animals per genotype.

first: Jiaqi

last: Li

first: Shenghui

last: Zheng


title: Effects of Aflibercept administration at 25 mg per kg body weight in retinas of mice subjected to the oxygen-induced retinopathy protocol [P50]

city: Cambridge

first: Jesus Eduardo

last: Rojo Arias

address: Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Puddicombe Way

department: Wellcome-MRC Cambridge Stem Cell Institute

country: United Kingdom

institute: University of Cambridge

summary:
We aimed at identifying the regulatory network of Aflibercept in the context of pathological neovascularization by using the oxygen-induced retinopathy mouse model as a surrogate of proliferative diabetic retinopathy
Total RNA was collected from entire retinal cups dissected from 50-days old mice subjected to the oxygen-induced retinopathy protocol and subsequently injected with Aflibercept either on postnatal days 13 and 15 (OIR+AFLx2) or on postnatal days 13, 15 and 17. Non-injected OIR littermates (OIR) and age-matched mice housed in normoxic conditions (normoxia) were used as controls.

overall_design: Four treatments were considered, namely normoxic controls, OIR mice, OIR mice injected twice with Aflibercep (OIR+AFLx2), and OIR mice injected three times with Aflibercept (OIR+AFLx3). Each group contained three biological replicates, i.e. three mice. All RNA samples were collected on postnatal day 50. Thus, 12 samples were analyzed in total: 1 time-point, 4 treatments, and 3 replicates per treatment. Each sample consists of total RNA isolated from the 2 whole retinas of 1 mouse pooled together.

first: Jesus

middle: E

first: József

last: Jászai


title: Differentiation and homeostasis of effector Treg cells are regulated by inositol polyphosphates modulating Ca2+ influx

city: Seoul

first: Hyungyu

last: Min

address: 1, Gwanak-ro, Gwanak-gu

country: South Korea

institute: Seoul National University

summary: Activated Foxp3+ regulatory T (Treg) cells differentiate into effector Treg (eTreg) cells to maintain peripheral immune homeostasis and tolerance. T cell receptor (TCR)-mediated induction and regulation of store-operated Ca2+ entry (SOCE) is essential for eTreg cell differentiation and function. However, SOCE regulation in Treg cells remains unclear. Here we show that inositol polyphosphate multikinase (IPMK), which generates inositol tetrakisphosphate and inositol pentakisphosphate, is a pivotal regulator of Treg cell differentiation downstream of TCR signaling. IPMK is highly expressed in TCR-stimulated Treg cells and promotes a TCR-induced Treg cell program. IPMK-deficient Treg cells display aberrant T cell activation and impaired differentiation into RORγt+ Treg cells, and tissue-resident Treg cells. Mechanistically, IPMK controls the generation of higher-order inositol phosphates, thereby promoting Ca2+ mobilization and Treg cell effector functions. Our findings identify IPMK as a critical regulator of TCR-mediated Ca2+ influx and highlight the importance of IPMK in Treg cell-mediated immune homeostasis.

overall_design: Comparing transcriptome of WT and IPMK-deficient Treg cells

first: Rho

middle: H

last: Seong


title: Systematic tethering approach assigns function to RNA binding proteins and identifies UBAP2L as an antagonist to FMRP-mediated translation repression (Neuron_polysome_RNA-seq)

city: La Jolla

first: En-Ching

last: Luo

address: 9500 Gilman St

institute: UCSD

summary: In these FMRP knockout lines we then depleted UBAP2L by lentiviral delivery of two different shRNAs, with a non-targeting shRNA serving as a control.  Then, differentiated all lines to cortical neurons using a directed protocol (Nehme et al., 2018), which is based on a modified version of that of (Zhang et al., 2013)). We then performed polysome profiling by measuring the ratios of transcript levels in polysome factions over inputs

overall_design: RNAseq

first: Gene

last: Yeo


title: Non-pathogenic leaf-colonising bacteria elicit pathogen-like responses in a colonisation density-dependent manner

status: Public on May 17 2023

city: Christchurch, Canterbury

first: Moritz

last: Miebach

state: Canterbury

address: 20 Kirkwood Avenue, University of Canterbury Private Bag 4800

department: School of Biological Sciences

country: New Zealand

institute: University of Canterbury

summary:
Leaves are colonised by a complex mix of microbes, termed the leaf microbiota. Even though the leaf microbiota is increasingly recognised as an integral part of plant life and health, our understanding of its interactions with the plant host is still limited. Here, mature, axenically grown Arabidopsis thaliana plants were spray-inoculated with diverse leaf-colonising bacteria. Whole transcriptome sequencing revealed that four days after inoculation, leaf transcriptional changes to colonisation by non-pathogenic and pathogenic bacteria differed in strength but not in the type of response. Inoculation of plants with different densities of the non-pathogenic bacterium Williamsia sp. Leaf354 showed that high bacterial titers caused disease phenotypes and led to severe transcriptional reprogramming with a strong focus on plant defence.
This SuperSeries is composed of the SubSeries listed below.


title: Natural compounds ursolic acid and digoxin exhibit inhibitory activities to cancer cells in RORγ-dependent and -independent manner

city: Sacramento

first: Hongye

last: Zou

state: CA

address: 4645 2nd Ave, Research III

institute: UC Davis

summary: Natural compounds ursolic acid (UA) and digoxin isolated from fruits and other plants display potent anti-cancer effects in preclinical studies. UA and digoxin have been at clinical trials for treatment of different cancers including prostate cancer, pancreatic cancer and breast cancer. However, they displayed limited benefit to patients. Currently, a poor understanding of their direct targets and mechanisms of action (MOA) severely hinders their further development. We previously identified nuclear receptor RORγ as a novel therapeutic target for castration-resistant prostate cancer (CRPC) and triple-negative breast cancer (TNBC) and demonstrated that tumor cell RORγ directly activates gene programs such as androgen receptor (AR) signaling and cholesterol metabolism. Previous studies also demonstrated that UA and digoxin are potential RORγt antagonists in modulating the functions of immune cells such as Th17 cells. Here we showed that UA displays a strong activity in inhibition of RORγ-dependent transactivation function in cancer cells, while digoxin exhibits no effect at clinically relevant concentrations. In prostate cancer cells, UA down-regulates RORγ-stimulated AR expression and AR signaling, whereas digoxin up-regulates AR signaling pathway. In TNBC cells, UA but not digoxin alters RORγ-controlled gene programs of cell proliferation, apoptosis and cholesterol-biosynthesis.Together, our study reveals for the first-time that UA, but not digoxin, acts as a natural  antagonist of RORγ in the cancer cells. Our finding that RORγ is a direct target of UA in cancer  cells will help select patients with tumors that likely respond to UA treatment.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for C4-2B cells treated by ursolic acid (10µM) or digoxin (100nM) for 24 or 48 hrs, and for HCC70 cells treated by ursolic (5µM or 10µM) for 24 or 48 hrs.

first: Yatian

last: Yang

first: Hong-wu

last: Chen


title: RNA sequencing of Cd44-positive and Cd44-negative livers  isolated from Nf2 - mutant mice

city: Jena

first: Marco

last: Groth

address: Beutenbergstraße 11

department: Core Facility - Next Generation Sequencing

country: Germany

institute: Leibniz Institute on Aging - FLI

summary: Primary liver cancer is the third leading cause of cancer related death worldwide. An increasing body of evidence suggests that the Hippo tumor suppressor pathway plays a critical role in restricting cell proliferation and determining cell fate during physiological and pathological processes in the liver. Merlin (Moesin-Ezrin-Radixin-likeprotein), encoded by the NF2 (neurofibromatosis type 2) gene is an upstream regulator of the Hippo signaling pathway. Targeting of Merlin to the plasma membrane seems to be critical for fulfilling its major tumor-suppressive functions; this is facilitated by interactions with membrane-associated proteins, including CD44 (clusterofdifferentiation44). Indeed, mutations within the CD44-binding domain of Merlin were reported in many human cancers. In this study, we evaluated the relative contribution of CD44- and Merlin-dependent processes to the development and progression of liver tumors. To this end, mice with liver-specific deletion of the Nf2 gene were crossed with Cd44-deleted mice, and subjected to extensive histological, biochemical and molecular analyses. In addition, cells were isolated from mutant livers and subjected to in vitro assays. Deletion of Nf2 in the liver led to substantial liver enlargement and generation of hepatocellular carcinomas (HCCs), intrahepatic cholangiocarcinomas (iCCAs) as well as mixed hepatocellular cholangiocarcinomas. Deletion of Cd44 had no influence on liver size or primary liver tumor development but it significantly inhibited metastasis formation in Nf2-mutant mice. CD44 upregulates expression of integrin β2 and promotes transendothelial migration of liver cancer cells which may facilitate metastatic spreading. Altogether, our results suggest that CD44 may be a promising target for interfering with metastatic spreading of liver cancer.

overall_design: 6 samples in total: 3 samples CD44+/+, 3 samples CD44-/-

first: Monika

last: Hartmann

first: Diana

last: Becker


title: Altered transcriptome in pregnancies initiated by the transfer of an in vitro produced embryo.

city: Blacksburg

first: Fernando

last: Biase

state: VA

address: 175 West Campus Drive

department: School of Animal Sciences

institute: Virginia Tech

summary: Pregnancy loss is a significant problem when embryos produced in vitro are transferred to a synchronized uterus. Currently, mechanisms that underly losses of in vitro produced embryos during implantation are largely unknown. We investigated this problem using cattle (Bos taurus) as a biomedical model of conceptus attachment by analyzing transcriptome data of paired extraembryonic membrane and endometrial samples collected on gestation days 18 and 25, which spans the attachment window in cattle.

overall_design: Pregnancies were initiated by either artificial insemination or the transfer of an embryo proced in vitro, then interrupted on either gestation day 18 or 25 for the collection of samples from the endometrium and conceptus.


title: RNA-sequencing of human neuroblastoma

city: HYderabad

first: Sreedhar

middle: Subbarao

last: Amere

state: Telangana

address: Habsiguda

country: India

institute: CSIR-CCMB

summary: To investigate TRAP-1-dependent alterations in human neuroblastoma

overall_design: We have developed TRAP-1 knockdown and overexpression systems, and the whole cell lysates were processed for RNA-seq analysis

first: Shrikant

middle: P

last: Dharaskar

first: A

middle: S

last: Sreedhar


title: Atorvastatin attenuates diet-induced non-alcoholic steatohepatitis in APOE*3-Leiden mice by reducing hepatic inflammation

city: Leiden

first: Anita

last: van den Hoek

state: Zuid-Holland

address: Zernikedreef 9

department: MHR

country: Netherlands

institute: TNO

summary: Abstract: Patients with metabolic syndrome are often prescribed statins to prevent development of 17 cardiovascular disease. Conversely, data on their effects on non-alcoholic steatohepatitis (NASH) 18 are lacking. We evaluated these effects by feeding APOE*3-Leiden mice a Western-type diet (WTD) 19 with or without atorvastatin to induce NASH and hepatic fibrosis. Besides the well-known plasma 20 cholesterol lowering (-30%) and anti-atherogenic effects (severe lesion size -48%), atorvastatin sig-21 nificantly reduced hepatic steatosis (-22%), the number of aggregated inflammatory cells in the liver 22 (-80%) and hepatic fibrosis (-92%) compared to WTD-fed mice. Furthermore, atorvastatin-treated 23 mice showed less immunohistochemically stained area of inflammation markers. Atorvastatin pre-24 vented accumulation of free cholesterol in the form of cholesterol crystals (-78%). Cholesterol crys-25 tals are potent inducers of the NLRP3 inflammasome pathway and atorvastatin prevented its acti-26 vation, which resulted in reduced expression of the pro-inflammatory cytokines interleukin (IL)-1β 27 (-61%) and IL-18 (-26%). Transcriptome analysis confirmed strong reducing effects of atorvastatin 28 on inflammatory mediators, including NLRP3, NFκB and TLR4. The present study demonstrates 29 that atorvastatin reduces hepatic steatosis, inflammation and fibrosis and prevents cholesterol crys-30 tal formation, thereby precluding NLRP3 inflammasome activation. This may render atorvastatin 31 treatment as an attractive approach to reduce NAFLD and prevent progression into NASH in 32 dyslipidemic patients.

overall_design: The study contains 3 diet groups: Chow, WTD and WTD+Atorvastatin. Female APOE*3-Leiden mice (8-14 weeks old) were fed a semi-synthetic Western-type diet (WTD) for a run-in period of three weeks to start the induction of NASH and fibrosis. From baseline and onward (t = 0-32 weeks), the group was split in two and fed with or without atorvastatin as admixture to the WTD. A healthy reference mice group was kept on a maintenance chow diet. At 32 weeks mice were sacrified and blood and organs were collected for analysis.

first: José

middle: A

last: Inia

first: Geurt

last: Stokman

first: Elsbet

last: Pieterman

first: Martine

middle: C

last: Morrison

first: Aswin

middle: L

last: Menke

first: Lars

last: Verschuren

first: Martien

last: Caspers

first: Martin

last: Giera

first: J

last: Wouter Jukema

first: Hans

last: Princen


title: Distinct molecular profiles for histological subtypes of epithelial ovarian adenocarcinomas

city: Amsterdam

first: Frederike

last: Dijk

address: Meibergdreef 9

institute: AMC

summary: Background: It has been shown that based on gene expression profiles, subgroups within epithelial ovarian cancers (EOC) can be identified. We studied a well characterized series of ovarian carcinomas from patients treated at our institute using gene expression profiling to better define clinically significant subgroups.    Methods: Gene expression profiling was performed using RNA of 90 primary fresh frozen EOC samples representing all histological subtypes and stages (FIGO I-IV). Patients underwent either primary or interval debulking surgery and if indicated taxane-based chemotherapy. Pathology was reviewed for all cased and complete follow-up, including treatment response and recurrences was available for all patients.     Results: Unsupervised and supervised analysis of gene expression data showed distinct subtypes correlating with histology. Mucinous carcinoma was the most distinct subtype based on gene expression profile. No significant differences in gene expression profile between high and low grade serous carcinomas could be observed. No gene expression signatures associated with survival or treatment response could be identified.    Conclusion: Histological subtypes of ovarian adenocarcinomas are characterized by distinct gene expression profiles. In order to find signatures correlated to outcome of treatment it is essential that gene expression profiling studies are performed in histological homogeneous groups.

overall_design: 90 fresh frozen EOC samples representing all histological subtypes (53 high grade serous, 8 low grade serous, 14 undifferentiated, 6 mucinous, 6 enodometrioid en 3 clear cell carcinomas) and all FIGO stages (10 I-IIA and 80 IIB-IV)

first: Marianne

last: Rutten

last: Halfwerk

first: Gerrit

middle: K

last: Hooijer

first: C

middle: D

last: Savci-Heijink

first: Jan

last: Koster

first: Marrije

middle: R

last: Buist

first: Marc

last: van de Vijver

first: Wouter

last: Wegdam

first: Gemma

middle: G

last: Kenter


title: Splicing characterization and isoform switch events in human keratinocytes carrying oncogenes from high-risk HPV-16 and low-risk HPV-84

city: Greenwood

first: Maryam

last: Nasiri Aghdam

state: South Carolina

address: 132 Edinborough Circle

department: Genetics and Biochemistry

institute: Clemson University

summary: To identify the functional differences between LR-HPV and HR-HPV

overall_design: Lentiviral strategies were followed to stablish HaCaT cells with constitutive expression of HPV oncogenes, RNAseq experiments were designed to analyze the transcriptome modulations by each of E5, E6 and E7 oncogenes of HPV-16 and -84 in HaCaT cells.

first: Luis

last: Jave-Suarez

first: Adriana

last: Aguilar-Lemarroy


title: A comparison of the transcriptional profiles of resting NK cells and ex vivo expanded NK cells

city: Busan

first: Yoo-Soo

last: Park

address: Jwadong-gil 40

institute: Dongnam Institute of Radiological & Medical Sciences

summary: NK cells are cytotoxic lymphocytes that play an important role in the innate immune response. The immune response of NK cells was shown under activated conditions. In order to identify such patterns, we performed RNA sequencing to confirm the gene expression profiles in NK cells expanded ex vivo compared to that of resting NK cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for freshly isolated NK cells and after expanded 21 days.

first: E

last: Koh

first: H

last: Lee

first: W

last: Son


title: Comprehensive analysis of rice transcriptome during dehydration and rehydration

city: Chuncheon

first: Dong-Hoon

last: Jeong

state: Gangwon-do

address: Room #8306, Department of Life Science, 1 Hallymdaehak-gil

department: Dept. of Life Science

institute: Hallym University

summary: Drought is a harmful abiotic stress that threatens the growth, development, and yield of rice plants. To cope with drought stress, plants have evolved diverse and sophisticated stress-tolerance pathways by regulating gene expression. Previous genome-wide studies have revealed many rice drought stress-responsive genes that are involved in various metabolism, hormone biosynthesis and signaling pathways, and transcriptional regulation. However, little is known about the regulation of drought-responsive genes during rehydration after dehydration. In this study, we examined the dynamic gene expression patterns in rice seedling shoots during dehydration and rehydration using RNA-seq analysis. To investigate the transcriptome-wide rice gene expression patterns during dehydration and rehydration, RNA-seq libraries were sequenced and analyzed to identify differentially expressed genes (DEGs). DEGs were classified into five clusters based on their gene expression patterns. The clusters included drought-responsive DEGs that were either rapidly or slowly recovered to control levels by rehydration treatment. Representative DEGs were selected and validated using qRT-PCR. In addition, we performed a detailed analysis of DEGs involved in nitrogen metabolism, phytohormone signaling, and transcriptional regulation. In this study, we revealed that drought-responsive genes were dynamically regulated during rehydration. Moreover, our data showed the potential role of nitrogen metabolism and jasmonic acid signaling during the drought stress response. The transcriptome data in this study could be a useful resource for understanding drought stress responses in rice, and may provide a valuable gene list for developing drought-resistant crop plants.

overall_design: Examination of mRNA expression patterns in rice seedling shoots treated with dehydration and rehydration

first: So

middle: Y


title: Combined multidimensional single-cell protein and RNA profiling dissects the cellular and functional heterogeneity of thymic epithelial cells - tuft and non-tuft cells

city: Oxford

first: Adam

last: Handel

address: John Radcliffe Hospital

department: Weatherall Institute of Molecular Medicine

institute: University of Oxford

summary: The network of thymic stromal cells provides essential niches with unique molecular cues controlling T-cell development and selection. Recent single-cell RNA-sequencing studies uncovered a large transcriptional heterogeneity among thymic epithelial cells (TEC) demonstrating a previously unappreciated complexity. However, there are only very few cell markers that allow a comparable phenotypic identification of TEC. Here we deconvoluted by massively parallel flow cytometry and machine learning known and novel TEC phenotypes into novel subpopulations and related these by CITEseq to the corresponding TEC subtypes defined by the cells’ individual RNA profiles. This approach phenotypically identified perinatal cTEC, physically located these cells within the cortical stromal scaffold, displayed their dynamic change during the life course and revealed their exceptional efficiency in positively selecting immature thymocytes. Collectively, we have identified novel markers that allow for an unprecedented dissection of the thymus stromal complexity, the cells physical isolation and assignment of specific functions to individual TEC subpopulations.

overall_design: An ultra-low input RNA-seq experiment generating libraries from UEA+ MHCIIlo CD80- Sca1- CD63- CD117+ CD66a+ (tuft-like TEC) vs. UEA+ MHCIIlo CD80- Sca1- CD63- CD117- CD66a- (non-tuft-like TEC)

first: Fatima

last: Dhalla

first: Fabian

last: Klein

first: Georg

last: Hollander


title: The Oligostilbene Gnetin-H is a Novel Glycolysis Inhibitor that Regulates Thioredoxin Interacting Protein Expression and Synergizes with OXPHOS Inhibitor in Cancer Cells

city: University

first: Ameeta

last: Agarwal

state: MS

address: NCNPR, Room 2049

department: National Center for Natural Products Research

institute: University of Mississippi

summary: Since aerobic glycolysis has been first observed in tumors almost a century ago by Otto Warburg, the field of cancer cell metabolism sparked the interest of scientists around the world as it might offer new avenues of treatments for malignant cells.  Our current study claims the discovery of Gnetin-H (GH) as a novel glycolysis inhibitor that can decrease metabolic activity and lactic acid synthesis and displays a strong cytostatic effect in melanoma and glioblastoma cells.  Compared to most of the other glycolysis inhibitors used in combination with the complex-1 mitochondrial inhibitor Phenformin, GH more potently inhibited cell growth. RNA-Seq with the T98G glioblastoma cell line treated with GH showed more than an 80-fold reduction in Thioredoxin Interacting Protein (TXNIP) expression indicating that GH has a direct effect in regulating a key gene involved in the homeostasis of cellular glucose. GH in combination with Phenformin also substantially enhanced levels of p-AMPK, a marker of metabolic catastrophe. These findings suggest that the concurrent use of the glycolytic inhibitor GH with a complex-1 mitochondrial inhibitor could be used as a powerful tool to induce metabolic catastrophe in cancer cells and reduce their growth.

overall_design: Gene expression profiles of T98G cell line treated with DMSO, 2-Deoxy-2-glucose (DEOX), Phenformin (PHEN), Gnetin-H (GNET), Phenformin + 2-Deoxy-2-glucose (PHDE), or Phenformin + Gnetin-H (PHGN).

first: David

last: Pasco

first: Pier

last: Claudio

first: Shivendra

last: Singh


title: Genome-wide identification of long noncoding RNA in metafemale Drosophila

city: Beijing

first: Lin

last: Sun

address: Xinjiekouwai Street

institute: Beijing Normal University

summary: Metafemale Drosophila is a kind of aneuploidy with three X chromosomes. In this experiment, we performed lncRNA sequencing in metafemale, and revealed the overall characteristics of its lncRNA expression.

overall_design: Comapare the global expression of metafemale and wildtype Drosophila.


title: Restricting synthesis of heterologous phosphoribulokinase and ribulose-1,5-bisphosphatase mitigates byproduct formation during slow growth of engineered low-glycerol-producing Saccharomyces cerevisiae strains

city: Delft

first: Marcel

last: van den Broek

address: Van der Maasweg 9

institute: Delft University of Technology

summary: Background: Anaerobic Saccharomyces cerevisiae cultures require glycerol formation to re-oxidize NADH formed in biosynthetic processes. Introduction of the Calvin-cycle enzymes phosphoribulokinase (PRK) and ribulose-1,5-biphosphate carboxylase/oxygenase (RuBisCO) has been shown to couple re-oxidation of biosynthetic NADH to ethanol production and improve ethanol yield on sugar in fast-growing batch cultures. Since growth rates in industrial ethanol-production processes are not constant, performance of engineered strains was studied in slow-growing cultures.  Results: In slow-growing anaerobic chemostat cultures (D = 0.05 h-1), an engineered PRK-RuBisCO strain produced 80-fold more acetaldehyde and 30-fold more acetate than a reference strain. This observation suggested an imbalance between in vivo activities of PRK-RuBisCO and formation of NADH in biosynthesis. Lowering the copy number of the RuBisCO-encoding cbbm expression cassette from 15 to 2 reduced acetaldehyde and acetate yields by 67% and 29%, respectively. Additional C-terminal fusion of a 19 amino-acid tag to PRK reduced its protein level by 13-fold while acetaldehyde and acetate production decreased by 94% and 61%, respectively, relative to the 15x cbbm strain. These modifications did not affect glycerol production at 0.05 h-1 but caused a 4.6 fold higher glycerol production per amount of biomass in fast-growing (0.29 h-1) anaerobic batch cultures than observed for the 15x cbbm strain. In another strategy, the promoter of ANB1, whose transcript level positively correlated with growth rate, was used to control PRK synthesis in a 2x cbbm strain. At 0.05 h-1, this strategy reduced acetaldehyde and acetate production by 79% and 40%, respectively, relative to the 15x cbbm strain, without affecting glycerol yield. The maximum growth rate of the resulting strain equalled that of the reference strain, while its glycerol yield was 72% lower.   Conclusions: Acetaldehyde and acetate formation by slow-growing cultures of engineered S. cerevisiae strains carrying a PRK-RuBisCO bypass of yeast glycolysis was attributed to an in vivo overcapacity of PRK and RuBisCO. Reducing the capacity of PRK and/or RuBisCO was shown to mitigate this undesirable byproduct formation. Use of a growth-rate-dependent promoter for PRK expression highlighted the potential of modulating gene expression in engineered strains to respond to growth-rate dynamics in industrial batch processes.

overall_design: Comparision of transcription of independent steady-state duplicate cultures of a control (IME324; reference strain lacking PRK-RuBisCO bypass) and a PRK/RuBisCO strain (IMX1489; Δgpd2, non-ox PPP↑, pDAN1-prk, 15x cbbm, GroES/GroEL) in anaerobic C-limited chemostat cultures at 0.05 h-1, 0.1 h-1 and at 0.25 h-1 and in anaerobic N-limited chemostat cultures at 0.1 h-1.

first: Aafke

last: van Aalst

first: Mickel

last: Jansen

first: Robert

last: Mans

first: Jack

middle: T

last: Pronk


title: Development of gene expression signatures in experimental  intracerebral hemorrhage

city: Changsha

first: Zhe

last: Yu

address: Kaifu District, Xiangya Road, No.87

institute: Central South University

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

summary: To identify the potential lncRNA and mRNA post  intracerebral hemorrhage (ICH), we have employed lncRNA microarray expression profiling. 570 mRNAs  and 313 lncRNAs were identified  in the ICH vs sham group .Expression of six mRNA (Saa3, Col10a1, Mmp13, Oxt, Pcdhb6 and Resp18) and lncRNA (ENSMUT00000141700, AK143011, ENSMUT00000128306, AK030988, ENSMUST00000187076 and ENSMUST00000134129) from this signature was quantified by qPCR.

overall_design: Brain samples were dectected at 7 d after ICH.

first: Tao

last: Tang


title: N2-methylguanosine modifications on human tRNAs and snRNA U6 are important for cell proliferation, protein translation and pre-mRNA splicing

city: Göttingen

first: Katherine

last: Bohnsack

address: Humboldtallee 23

institute: University Medical Centre Göttingen

summary:
Modified nucleotides in non-coding RNAs, such as tRNAs and snRNAs, represent an important layer of gene expression regulation through their ability to fine-tune mRNA maturation and translation. Dysregulation of such modifications and the enzymes installing them have been linked to
various human pathologies including neurodevelopmental disorders and cancers. Several methyltransferases (MTases) are regulated allosterically by human TRMT112 (Trm112 in Saccharomyces cerevisiae), but the interactome of this regulator and targets of its interacting MTases
remain incompletely characterized.
Here, we have investigated the interaction network of human TRMT112 in intact cells and identify three poorly characterized putative MTases (TRMT11, THUMPD3 and THUMPD2) as direct partners. We demonstrate that these three proteins are active N2-methylguanosine (m2G) MTases and that TRMT11 and THUMPD3 methylate positions 10 and 6 of tRNAs, respectively. For THUMPD2, we discovered that it directly associates with the U6 snRNA, a core component of the catalytic spliceosome, and is required for the formation of m2G, the last “orphan” modification in U6 snRNA. Furthermore, our data reveal the combined importance of TRMT11 and THUMPD3 for optimal protein synthesis and cell proliferation as well as a role for THUMPD2 in fine-tuning pre-mRNA
splicing.

overall_design: mRNA-seq analysis was performed on polyA-enriched transcripts from wild-type HCT116 cells and HCT116 cells lacking THUMPD2

first: Can

last: Wang

first: Nathalie

last: Ulryck

first: Lydia

last: Herzel

first: Nicolas

last: Pythoud

first: Nicole

last: Kleiber

first: Vincent

last: Guerineau

last: Jactel

first: Chloe

last: Moritz

first: Markus

first: Christine

last: Carapito

last: Touboul

first: Marc

last: Graille


title: Interleukin 21 drives CXCR6+ CD8+ T cell mediators in Autoimmune Checkpoint Inhibitor Thyroiditis

city: Los Angeles

first: Melissa

last: Lechner

address: 10833 Le Conte Ave, CHS 57-154

department: Div of Endocrinology, Diabetes, and Metabolism

institute: UCLA Geffen School of Medicine

summary: Checkpoint inhibitor (ICI) immunotherapy leverages the body’s own immune system to attack cancer cells but leads to unwanted autoimmune side effects in up to 60% of patients. Such immune related adverse events (IrAE) lead to treatment interruption, permanent organ dysfunction, hospitalization and premature death. Thyroiditis is one of the most common IrAE, but the cause of thyroid IrAE remains unknown. To delineate human IRAE pathogenesis, we sampled thyroid tissue from subjects with ICI-thyroiditis and HT. Using single cell RNA sequencing of human thyroid fine needle aspiration (FNA) specimens, we identify CXCR6+ interferon gamma (IFN)+ cytotoxic CD8+ T cells as key contributors to ICI-thyroiditis (IRAE). This is in contrast to the primary role for CD4+ Th17 cells in the pathogenesis of HT (14, 15). Interestingly, we also found a supporting role for IL21-producing CD4+ T follicular (Tfh) and peripheral helper (Tph) cells via the upregulation of CXCR6 and cytotoxic function in CD8+ T cells.

overall_design: This dataset contains a total of 10 single cell transcriptomes (5' and TCR) from human thyroid infiltrating CD45+ immune cells, from 13 individuals with immune checkpoint inhibitor-associated thyroiditis, Hashimoto's thyroiditis, or no thyroid disease, as outlined in the associated manuscript. Specimens were collected by thyroid fine needle aspiration.

first: Zikang

last: Zhou

first: Aline

last: Hoang

last: Huang

first: Jessica

last: Ortega

first: Lauren

middle: N

last: Scott

first: Anushi

last: Patel

first: Rana

last: Yakhshi-Tafti

first: Kristy

last: Kim

first: Willy

last: Hugo

first: Pouyan

last: Famini

first: Alexandra

last: Drakaki

first: Antoni

last: Ribas

first: Trevor

last: Angell

first: Maureen

last: Su


title: DNA Methylome and 3D Chromatin Landscape of Cell Types Across the Mouse Brain [12H]

status: Public on May 19 2023

city: La Jolla

first: Joseph

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

type: Methylation profiling by high throughput sequencing

summary: Illustrating the cellular architecture of the mammalian brain is critical to understanding its diverse functions and complex animal behaviors. With support from NIMH and NINDS as part of the BRAIN Initiative Cell Census Network (BICCN), the Center for Epigenomics of the Mouse Brain Atlas (CEMBA) applied single nucleus methylation sequencing in 117 brain funtional regions across the whole adult male P56 C57BL/6J mouse brain. In each major brain regions, we identified distinct cell clusters and formed them in a hierarchical taxonomy. These clusters include known primary brain cell types and possible sub-types. We use these data to identify the epigenomic characteristics and to define specific regulatory elements for each cell cluster. We integrate the single cell methylome with single cell gene expression and chromatin accessibility profiles from the same brain region to further identify potential enhancers and their corresponding genes for several neuronal cell types. By brain region spacial comparisons, we found spatial specificity among excitatory neuronal clusters within the same cortical layer. We identify brain-region-specific transcription factors that may regulate cortical region development of excitatory neurons. These data define the landscape of cell type and spatial heterogeneity in the mouse brain and the underlining regulatory epigenomic basis.

overall_design: Apply snmC-seq2 to 117 brain functional regions to identify epigenomic landcape of the adult mouse brain, this subseries consists of one single nucleus methylation sequencing experiment of brain region (12H_200730, 12H_200813).

first: Hanqing

last: Liu

first: Anna

last: Bartlett

first: Jacinta

last: Lucero

first: Julia

last: Osteen

first: Jordan

last: Altshul

first: Mia

last: Kenworthy

first: Rosa

last: Castanon

last: Nery

first: Peter

last: Berube

first: Huaming

last: Chen

first: Michael

last: Nunn

first: Jesse

last: Dixon

first: M

last: Behrens


title: PPARg and C/EBPa response to acute cold stress in brown adipose tissue

city: Grand Rapids

first: Ning

last: Wu

address: 333 Bostwick Ave NE

institute: Van Andel Institute

summary: Brown adipose tissue (BAT) has the ability to burn calories as heat. BAT thermogenesis is an attractive way to combat obesity pandemic. However, the transcriptional network resulting in lipid synthesis to oxidation shift during thermogenesis is not completely understood. Here, we report the regulation of two master regulators of adipogenesis, PPARγ and C/EBPα, during acute cold stress in BAT. We found PPARγ dissociated from DNA in a third of its binding sites and these included cebpa enhancers leading to decreased C/EBPα. This dissociation required PPARγ binding to activating ligands, thus modulated by diet. Meanwhile PPARα also detached from DNA, and co-activator PGC1α associated with ERR1 as part of transcriptional network regulating lipid metabolism. Subsequent global replacement of C/EBPα by C/EBPβ and its associated transcriptional machinery was required for upregulation of structural lipid synthesis despite general upregulation of fatty acid oxidation.

overall_design: Various ChIPseq of BAT

first: Althea

last: Waldhart

first: Kin

last: Lau

first: Holly

last: Dykstra

first: Tracey

last: Avequin


title: Effect of small M. tuberculosis RNA MTS1338 on the transcriptome under various stress conditions

city: Moscow

first: Artem

last: Grigorov

address: Ulitsa Miklukho-Maklaya, 16/10

department: Genomics and Postgenomic Technologies

country: Russia

institute: Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry

summary: The study was carried out to study the effect of  small RNA MTS1338 on the M. tuberculosis transcriptome under various stress conditions (low pH, oxidative and nitrosative stress) .

overall_design: Control ("Empty" pMV vector, pMV_E) and overexpressing MTS1338 (1338over) strains of M. tuberculosis were grown to a logarithmic growth stage, then treated with stress conditions according to the described protocol. All experiments were performed in biological triplicates

first: Ostrik

last: Albina

first: Elena

last: Salina

first: Oksana

last: Bychenko

first: Yulia

last: Skvortsova

first: Tatyana

last: Azhikina


title: Influence of Frankincense extract on gene expression in human endometriotic cells

city: Yangsan

first: Ki-Tae

last: Ha

address: Busandaehak-ro 49

institute: Pusan National University

summary: To investigate the anti-endometriotic pathways of frankincense extract.

overall_design: Total RNAs of 12Z cells were used to identify differential gene expression following Frankincense stimulation.

first: Ki

first: Dongryeol

last: Ryu

first: Yunju

last: Jo

first: Minkyoung

last: Cho


title: Effect of depletion of RAD51 on gene expression in Huh7 cells

city: chongqing

first: Pan

last: Mingang

address: No. 1, Medical College Road, Yuzhong District, Chongqing

institute: ChongQing Medical University

summary: To investigate the role of RAD51 in HCC, we established Huh7 cell lines in which RAD51 has been knocked down(KD) by sgRNA,we performed RNA-seq for RAD51-KD Huh7 cells and parental Huh7 cells(control group,sgcon).

overall_design: Gene expression profiling analysis of RNA-seq data for RAD51-KD Huh7 cells and parental Huh7 cells(control group,sgcon).

first: Mingang

last: Pan

first: Jie

last: Xia


title: Next generation sequencing facilitates quantitative analysis of bulk hippocampal tissue in lupus mice.

city: Athens

first: Αnastasia

last: Filia

address: Soranou Efessiou 4

country: Greece

institute: BRFAA

summary: Purpose: Next-generation sequencing (NGS) technology was used to map expression profile of hippocampal tissue in mouse model of Systemic Lupus Erythematosus (SLE). Methods: Total RNA was extracted from total hippocampal tissue using NucleoSpinRNA and mRNA libraries were generated using the Illumina TruSeq Sample Preparation kit. Single-end 100bp mRNA sequencing was performed on Illumina NextSeq500 platform. Quality of sequencing was assessed using FastQC software. Raw reads in fastq format were collected and aligned to the mouse genome (mm10 version) using STAR 2.6 algorithm. Gene quantification was performed using HTSeq and differential expression analysis was performed using edgeR package. Results: We defined hippocampal-specific molecular signatures of the murine lupus transcriptome. Conclusions: By the use of the mouse hippocampal-specific transcriptome and through characterization of hippocampal neurogenesis, we showed that inflammatory mediators induce neuropsychiatric changes in SLE as an early event via the disruption of hippocampal neurogenesis. These data underscore the role of brain inflammation in the pathogenesis of early disease and support the use of immunosuppressants for the management of diffuse NPSLE.

overall_design: New Zealand Black (NZB) female mice were crossed with New Zealand White (NZW) male mice. Female hybrids NZB/W-F1 (n=4-5 at each time-point) were sacrificed with perfusion with PBS at the pre-nephritic stage (3 month) and symptomatic nephritic stage (6 months old where proteinuria is more than 200 mg/dl for 3 consecutive days) of the disease. Bulk hippocampal tissue was extracted. Age-matched female C57BL/6 mice (n=5) were used as controls.

first: Anastasia

first: Dionisios

last: Nikolopoulos


title: Effect of heparan sulafte on adipogenesis

first: Philip

middle: Leo Stefan Maria

last: Gordts

department: CMM

institute: UCSD

summary:
Tro investigate the reason why heperan sulafet control lipid storage in adipocytes.
We then performed gene expression profiling analysis using data obtained from RNA-seq of  3 different cells at two time points.

overall_design:
Comparative gene expression profiling analysis of RNA-seq data forMEF cells and its HS derivatives

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first: Greg

last: Trieger


title: Expression data from RAW264.7 cells infected with wild-type vs srfJ mutant Salmonella enterica serovar Typhimurium

city: Sevilla

first: Francisco

last: Ramos-Morales

state: Sevilla

address: Avda Reina Mercedes, 6

department: Genética

country: Spain

institute: Universidad de Sevilla

summary:
SrfJ is an effector of the type III secretion systems of the Gram-negative intracellular pathogen Salmonella enterica serovar Typhimurium.
To study the effects of this effector on global gene expression in host cells, we have infected murine RAW264.7 macrophages with two strains of Salmonella enterica serovar Typhimurium. The comparison between cells infected with the wild-type strain and cells infected with a srfJ mutant revealed a number of genes that are differentially expressed when SrfJ is present.

overall_design: Two conditions. Each condition replicated three times. Condition 1: RAW264.7 macrophages infected with wild-type strain 14028 of Salmonella enterica serovar Typhimurium. Condition 2: RAW264.7 macrophages infected with srfJ null mutant strain of Salmonella enterica serovar Typhimurium.

first: Joaquín

last: Bernal-Bayard

first: Julia

last: Aguilera-Herce

first: Roberto

last: Balbontín


title: BLM deficiency affects cytotoxicity of temozolomide and olaparib against human glioma cells and induces cellular senescence or polyploidy

city: Warsaw

first: Bartosz

last: Wojtas

address: Pasteura 3

country: Poland

institute: Nencki Institute of Experimental Biology

summary: BLM deficient cells responded differently to the temozolomide and olaparib treatment in comparison to the wild type cells. The double treatment evoked cell cycle arrest, cellular senescence or polyploidy in BLM KO LN229 and LN18 cells, respectively.

overall_design: BLM knock-out and wild type LN18 and LN229 cell lines were used to the experiments.

first: Kamil

last: Wojnicki

first: Agnieszka

last: Kaczmarczyk

first: Bozena

last: Kaminska


title: Localization and pathogenic role of the cysteine protease dentipain in Treponema denticola

city: Tokyo

first: Kazuyuki

last: Ishihara

address: 2-1-14 Kanda-Misakicho, Chiyoda-ku

department: Microbiology

institute: Tokyo Dental College

summary: Treponema denticola is a major etiological agent of chronic periodontis. Dentipain is one of the virulence factors of this microorganism. The localization and function of the protein has yet to be clarified although it has shown to be involved in the virulence of T. denticola. Therefore, this study aimed to characterize the role of dentipain in T. denticola.  To investigate the function of dentipain, dentipain deficient mutant was constructed using an ermFermAM cassette and gene expression profile of the mutant was evaluated by microarray analysis. Growth rate of the dentipain-deficient mutants was smaller than that of the wild-type strain. In the mutant. Thirty-five genes in differentially expressed genes by the microarray analysis annotated as membrane or plasma membrane in gene ontology. Hydrophobicity of the mutant were higher than that of the wild-type strain. These findings suggest that dentipain involved in the surface characteristics and growth of T. denticola.

sample_organism:
Treponema denticola
Treponema denticola ATCC 35405

overall_design: Comparison of 2 strains of T. denticola.  Treponema denticola ATCC 35405 and YM-3 were cultured in TYGVS medium for 24-48 h. Profile of gene expression of T. denticola YM-3 was compared to that of ATCC 35405.

first: Yuri

last: Miyai-Muraia

first: Kazuko

last: Okamoto-Shibayama

first: Toru

last: Sato

first: Yuichiro

last: Kikuchi

first: Eitoyo

last: Kokubu

first: Jan

last: Potempa


title: Trigeminal nerve derived-substance P regulates biological characteristics of limbal stem cells through PI3K-AKT signaling pathway

city: Guangzhou

first: Peipei

last: Xu

address: Duobao road 63

institute: The Third Affiliated Hospital, Guangzhou Medical University

summary: To investigate the function of Substance P- NK1R interaction in the regulation of limbal stem cells, we subconjunctivally injected NK1 receptor antagonist L-733,060 on mice. By RNA sequencing, we found that antagonist injection significantly downregulated PI3K-AKT signaling related genes level. Collectively, our work reveals that Substance P- NK1R interaction is a novel player in limbal stem cells regulation.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for antagonist- injected and control mice limbus.

first: Shuangyong

last: Wang

first: Xiongshi

last: Lin


title: Vaccine-primed CAR T-cells reject antigen-heterogenous tumors via host immunity

city: CAMBRIDGE

first: Duncan

middle: Matthew

last: Morgan

state: MA

address: 500 Main St

department: Koch Institute

institute: MIT

summary:
Chimeric Antigen Receptor (CAR) T-cell therapy effectively treats human cancer, but
loss of the antigen recognized by the CAR poses a major obstacle. We found that in
vivo vaccine boosting of CAR T-cells triggers engagement of the endogenous immune
system to circumvent antigen-negative tumor escape. Vaccine-boosted CAR-T
promoted dendritic cell (DC) recruitment to tumors, increased tumor antigen uptake by
DCs, and elicited priming of endogenous anti-tumor T-cells (antigen spreading). This
process was accompanied by shifts in CAR-T metabolism toward oxidative
phosphorylation and was critically dependent on CAR T-derived IFN-γ. Antigen
spreading induced by vaccine-boosted CAR T enabled a proportion of complete
responses even when the initial tumor was 50% CAR-antigen-negative, and
heterogenous tumor control was further enhanced by genetically amplifying CAR T
IFN-γ expression. Thus, CAR T-cell-derived IFN-γ plays a critical role in promoting
antigen spreading, and vaccine boosting provides a clinically-translatable strategy to
drive such responses against solid tumors.

overall_design: Endogenous CD45.2+ CD4 and CD8 T cells were sorted with fluorescence activated cell sorting (FACS) collectively into 1x RPMI +10%FBS/

first: Leyuan

last: Ma

middle: M

first: Ina

last: Sulkaj

first: Charlie

last: Whittaker

first: Wuhbet

last: Abraham

last: Li

first: Christopher

middle: J

last: Love

first: Darrell

last: Irvine


title: RNA sequencing of LSKs in the bone marrow from irradiated WT and Tespa1-null mice

first: Yukai

last: Lu

address: gaotanyan

institute: Army Medical University

summary: LSKs (lineage-, Sca-1+, c-kit+ cells) in the bone marrow from wild type (WT) and Tespa1-knockout (KO) mice at day 13 after 5.0 Gy irradiation were isolated to explore the differentially expressed genes by RNA-seq.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for LSKs in the bone marrow from irradiated WT and Tespa1-null mice.

first: Lijing

last: Yang


title: RNA sequencing of LSKs in the bone marrow from normal and 5-FU treated WT and Tespa1-null mice

summary: LSKs(lineage-, Sca-1+, c-kit+ cells) in the bone marrow from normal and 5-Fluorouracil (5-FU) treated (Day 9) wild type (WT) and Tespa1-knockout (KO) mice were isolated to explore the differentially expressed genes by RNA-seq.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for LSKs in the bone marrow from normal and 5-FU treated WT and Tespa1-null mice.


title: Far upstream element-binding protein 1 confers lobaplatin resistance via facilitating the arachidonic acid signaling in osteosarcoma

city: Xi'an

first: Qiong

state: Shaanxi

address: Orthopaedic Oncology Institute.Tangdu Hospital, Fourth Military Medical University，569 Xinsi Road, Baqiao District, Xi’an, Shaanxi

institute: Orthopedic Oncology Institute, Department of Orthopedic Surgery, Tangdu Hospital, Fourth Military Medical University

summary:
Purpose: To understand the mechanism of lobaplatin resistance and explore effective strategies for patients with osteosarcoma.
Results: The expression of FUBP1 was remarkably elevated in osteosarcoma cell lines and clinical specimens compared with osteoblast cells and the normal bone. High expression of FUBP1 correlated with more aggressive phenotype and poor prognosis in osteosarcoma patients. Overexpression of FUBP1 confers lobaplatin resistance while inhibition of FUBP1 sensitizes osteosarcoma to lobaplatin cytotoxicity both in vivo and in vitro. Additionally, FUBP1 could regulate the transcription of PTGES, and subsequently activated the arachidonic acid signaling pathway in osteosarcoma cells treated with lobaplatin.   Conclusions: Our investigation provided evidence that FUBP1 represents a potential therapeutic target for patients suffering from osteosarcoma. Targeting FUBP1 and its downstream AA signaling pathway may be a promising strategy to sensitize lobaplatin treatment during osteosarcoma chemoresistance.
Methods: The expression of Far upstream element-binding protein 1(FUBP1) in human osteosarcoma cell lines and patient specimens were determined using Western blotting and Real-time PCR, respectively. 61 human osteosarcoma tissue specimens were analyzed using IHC to investigate the association between the expression of FUBP1 and the clinicopathological data of osteosarcoma patients. CCK8, FACS, clone formation assay, and in vivo animal xenograft model were used to determine the role of FUBP1 in lobaplatin-treating osteosarcoma. ChIP-seq and RNA-seq were performed, and the intersection genes and the enriched signaling pathways were analyzed. Luciferase assay and truncation assay were used to investigate the mechanism of FUBP1 promoting chemoresistance in osteosarcoma.

overall_design: Overall design: mRNA profiles of FUBP1-knockdown osteosarcoma cells and the control osteosarcoma cells were generated by deep sequencing, in triplicate

first: Jin

last: Sun

first: Huan

first: Chenyu

first: Yonghong

last: Wu

first: Yanhua

last: Wen

first: Xiaoyu

last: Zhang

first: Xingguang

last: Ren

first: Zheng

last: Guo

first: Li

last: Gong

first: Wei


title: Expression data from HeLa cells transfected with plasmid expressing Salmonella effector SrfJ or HeLa cells transfected with the empty vector

first: Francisco

last: Ramos-Morales

summary:
SrfJ is an effector of the type III secretion systems of the Gram-negative intracellular pathogen Salmonella enterica serovar Typhimurium.
To study the effects of this effector on global gene expression in host cells, we have expressed SrfJ on human HeLa cells through transient transfection. The comparison with HeLa cells transfected with a plasmid not expressing SrfJ, revealed a number of genes that are differentially expressed when SrfJ is present.

overall_design: Two conditions. Each condition replicated three times. Condition 1: control of HeLa cells transiently transfected with plasmid pcDNA3 without SrfJ. Condition 2: HeLa cells transiently transfected with plasmid pcDNA3 with SrfJ.

first: Joaquín

last: Bernal-Bayard

first: Julia

last: Aguilera-Herce

first: Roberto

last: Balbontín


title: Deep sequencing for mRNA in steatotic/normal liver grafts from patients and rat transplant model

city: Hong  Kong

first: Yueqin

last: ZHU

state: China

address: Sassoon Road

institute: Hong Kong University

summary: To investigate the landscape of alternative splicing events in steatotic liver graft.

sample_organism:
Homo sapiens
Rattus norvegicus

platform_organism:
Homo sapiens
Rattus norvegicus

overall_design: We performed gene alternative splicing event detection by using data obtained from RNA-seq of  28 steatotic/normal liver grafts from patients and 6  steatotic/normal liver grafts from rat transplant model.

first: Kwan

last: Man

first: Kevin

last: Pan Ng

first: Yue

middle: Q

last: Zhu

first: Hui

last: Liu


title: Translocator protein 18 kDa (TSPO) acts as an immune resistance gene involved in the T-cell mediated immune control of glioblastoma

city: Regensburg

last: Lorenz

address: Franz-Josef-Strauß-Allee 11

department: Neuropathology

institute: Regensburg university hospital

summary: Glioblastoma is the most malignant and common type of primary brain tumor with a median survival of less than 21 months. It is particularly resistant to current immunotherapies. Thus, yet unknown mechanisms of immune resistance may be active in glioblastoma. Translocator protein 18 kDa (TSPO) expression is upregulated in glioblastoma and correlates with malignancy and poor prognosis but also with increased immune infiltration. An immunomodulatory role of TSPO in glioblastoma has not been reported. Here, we studied the role of TSPO in the regulation of immune resistance of human glioblastoma cells. We used public bulk and single-cell gene expression data to identify cell types, genes and signalling pathways correlating with TSPO expression. To validate inflammatory triggers and the role of TSPO experimentally, we co-cultured tumor-infiltrating T cells and cytotoxic T cell lines with autologous and antigen-loaded allogeneic, primary brain tumor initiating cells (BTICs). TSPO proficient and deficient BTIC lines and clones were generated through genetic manipulation. Inflammatory factors triggering TSPO expression were determined by ELISA and validated experimentally using blocking antibodies and recombinant proteins. The impact of TSPO on glioblastoma cell resistance against cytotoxic T cells was studied by cytotoxicity assays and by activity analysis of components of the apoptotic cascade. Individual death-inducing pathways suppressed by TSPO were determined using recombinant proteins and TSPO-regulated genes associated with apoptosis resistance were identified by gene expression analysis in TSPO proficient and deficient BTICs and subsequent functional analyses. TSPO expression in glioblastoma cells correlated with cytotoxic T cell infiltration, expression of TNFR and IFNGR, the activity of their downstream pathways, expression of TRAIL receptors and with PD-L1. Coculture of BTICs with tumor-reactive cytotoxic T cells or with T cell-derived factors induced TSPO up-regulation through TNFα and IFNγ. Silencing of TSPO sensitized BTICs against T cell-mediated cytotoxicity. TSPO protected BTICs selectively against TRAIL-induced apoptosis by regulating both intrinsic and extrinsic apoptosis pathways. TSPO regulated the expression of multiple genes associated with apoptosis-resistance of tumors. Among them, we studied the peptidase inhibitors PI3 and SLPI, which sensitized BTICs towards TRAIL-induced apoptosis. Our data revealed that TSPO expression in glioblastoma cells is induced through T cell derived cytokines IFNγ and TNFα. TSPO expression protects glioblastoma cells against cytotoxic T cell attack through the death inducing ligand TRAIL. Our data provided an indication that therapeutic targeting TSPO may be a suitable approach to sensitize glioblastoma to immune cell-mediated cytotoxicity by circumventing tumor intrinsic TRAIL-resistance.

overall_design: BTIC13 and BTIC129 cell lines with shRNA mediated TSPO knockdown (Three biological replicates were analyzed for each of 4 conditions (two primary cell line from different patients ; two shRNA per cell line))

first: Ayse

last: Menevse

first: Laura-Marie

last: Ammer

first: Arabel

last: Vollmann-Zwerenz

first: Lorraine

last: Weidner


title: Transcriptome changes of CD4 T cells in IPMK-deficient mouse

city: Daejeon

first: Seyun

last: Kim

address: Daehak-ro 291

institute: KAIST

summary: To investigate the transcriptomic changes of Th0 or Th17 cells by IPMK, naïve CD4 T cells of Ctrl and IPMK-KO mice were sorted by FACS and differentiated into Th0 or Th17 cells and RNA seq was performed.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Th0 and Th17 cells and its KD derivatives.

first: Chae

last: Yuk

first: Hyun-Woo

last: Jeong


title: DNA Methylome and 3D Chromatin Landscape of Cell Types Across the Mouse Brain [12F-G]

first: Joseph

last: Ecker

institute: HHMI-Salk-Institute

summary: Illustrating the cellular architecture of the mammalian brain is critical to understanding its diverse functions and complex animal behaviors. With support from NIMH and NINDS as part of the BRAIN Initiative Cell Census Network (BICCN), the Center for Epigenomics of the Mouse Brain Atlas (CEMBA) applied single nucleus methylation sequencing in 117 brain funtional regions across the whole adult male P56 C57BL/6J mouse brain. In each major brain regions, we identified distinct cell clusters and formed them in a hierarchical taxonomy. These clusters include known primary brain cell types and possible sub-types. We use these data to identify the epigenomic characteristics and to define specific regulatory elements for each cell cluster. We integrate the single cell methylome with single cell gene expression and chromatin accessibility profiles from the same brain region to further identify potential enhancers and their corresponding genes for several neuronal cell types. By brain region spacial comparisons, we found spatial specificity among excitatory neuronal clusters within the same cortical layer. We identify brain-region-specific transcription factors that may regulate cortical region development of excitatory neurons. These data define the landscape of cell type and spatial heterogeneity in the mouse brain and the underlining regulatory epigenomic basis.

overall_design: Apply snmC-seq2 to 117 brain functional regions to identify epigenomic landcape of the adult mouse brain, this subseries consists of one single nucleus methylation sequencing experiment of brain region (12F_210211, 12F_210218, 12G_210211, 12G_210218).

first: Hanqing

first: Anna

last: Bartlett

first: Jacinta

last: Lucero

last: Osteen

first: Jordan

last: Altshul

first: Mia

last: Kenworthy

first: Rosa

last: Castanon

last: Nery

first: Peter

last: Berube

first: Huaming

last: Chen

first: Michael

last: Nunn

first: Jesse

last: Dixon

first: M

last: Behrens


title: Identification of transcriptional drifts in endothelial cells associated with environmental changes

city: Chicago

first: Luisa

last: Iruela-Arispe

state: IL

address: 303 East Superior Street Simpson Querrey, 8-522

department: Cell and Developmental Biology

institute: Northwestern University

summary:
Purpose: Environmental cues, such as shear stress and heterotypic cell interactions play a critical role in endothelial cell function, yet their unique contributions to the endothelial cell transcriptome remain unclear.
Methods: Using cell preparations from human umbilical cords (ex vivo), we performed individual sample analysis to assess transcriptional drifts associated with environmental changes but independent of sex or background. Global gene expression profiling by RNA-seq, ATACseq, and protein expression by LC-MS distinguished freshly isolated endothelial cells from genetically matched culture (in vitro) samples.
Results: Over 43% of the transcriptome was significantly changed by the in vitro environment. Amongst several signatures, we observed that the expression of TGF-beta and BMP target genes were reduced. In contrast, cytoskeleton-based processes and proliferation-related genes were increased. Subjecting cultured cells to long-term shear stress significantly rescued the expression of approximately 17% of genes including targets of BMP and Notch signaling known to be sensitive to flow. In contrast, co-culture of endothelial cells with smooth muscle cells normalized networks related to cell growth and differentiation, clathrin-vesicle related genes, and recovered targets downstream TGF-beta, recovering approximately 9% of the original in vivo signature.
Conclusions: Our findings highlight specific genes, pathways and functional features of endothelial cells that require contextual information and exposure to physical forces. This transcriptional modulation is important to consider in all paradigms that are focused on understanding the ability of endothelial cells to maintain homeostasis and respond to disease processes.

overall_design: HUVEC mRNA profiles under various culture conditions

first: Yalda

last: Afshar


city: Los Angeles

first: Feiyang

last: Ma

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

institute: UCLA

summary: Environmental cues, such as shear stress and heterotypic cell interactions play a critical role in endothelial cell function, yet their unique contributions to the endothelial cell transcriptome remain unclear. Using cell preparations from human umbilical cords (ex vivo), we performed individual sample analysis to assess transcriptional drifts associated with environmental changes but independent of sex or background. Global gene expression profiling by RNA-seq, ATACseq, and MS/MS directed proteomics distinguished freshly isolated endothelial cells from genetically matched culture (in vitro) samples. Over 43% of the transcriptome was significantly changed by the in vitro environment. Amongst several signatures, we observed that TGF-beta and BMP target genes were reduced. In contrast, cytoskeleton-based processes and proliferation-related genes were increased. Subjecting cultured cells to long-term shear stress significantly rescued the expression of approximately 17% of genes including targets of BMP and Notch signaling known to be sensitive to flow. In contrast, co-culture of endothelial cells with smooth muscle cells normalized networks related to cell growth and differentiation, clathrin-vesicle related genes, and recovered targets downstream TGF-beta, recovering approximately 9% of the original in vivo signature. Our findings highlight specific genes, pathways and functional features of endothelial cells that require contextual information and exposure to physical forces. This transcriptional modulation is important to consider in all paradigms that are focused on understanding the ability of endothelial cells to maintain homeostasis and respond to disease processes.

overall_design: We sought to investigate transcription changes when cells were cultured and cultured with diffenrent cell types.

first: Matteo

last: Pellegrini


title: Gene expression profile at single cell level of splenic antigen specific memory B-cells after immunization with the Fentanyl-VAST vaccine platform

city: Heidelberg

first: Evi P.

last: Vlachou

address: Im Neuenheimer Feld 280

institute: DKFZ

summary: Antigen specific memory B cells are considered as a homogeneous population. Here, we wanted to isolate antigen-specific memory cells from mice in order to both characterize the response to the immunization regimine and identify high-affinity candidate BCRs for expression. For this, we used single cell RNA sequencing (scRNA-seq) to describe the diversity of anti-fentanyl B cells elicited by a fentanyl-immunization platform and identify the different markers for each subbpopulation. We use this appoach to select the switched memory B cell, study their BCR repertoir and identify the BCR sequences from the most potent memory B cells.

overall_design:
Fentanyl specific B cells from mice spleens were isolated by Fluorescence-activated cell sorting (FACS) according to several markers and their specificity for fentanyl and analyzed using scRNAseq.

**Please note that raw data is not provided due to proprietary concerns regarding the raw sequences**

first: Evi

middle: P

first: Gianna

last: Triller

last: Verdi


title: Non-cell autonomous control of liver autophagy via nutrient sensing AgRP neurons

city: Cologne

first: Jens

last: Brüning

address: Gleueler Str. 50

institute: Max Planck Institute for Metabolism Research

summary: Here, we revealed that optogenetic activation of AgRP neurons alters liver transcriptome associated with autophagy, glucose metabolism, lipid metabolism and ß-oxidation.

overall_design: 6mm Optic fibers were placed above the Arcuate Nucleus of adult AgRP-IRES-Cre wt/wt ROSA26 ChR2 fl/wt and AgRP-IRES-Cre tg/wt ROSA26 ChR2 fl/wt mice. Further, mice received either 2 hours or 4 hours of photosimulation in the light cycle in the absence of food.

first: Weiyi

first: Paul

last: Klemm


title: Targetable programs of adult cancer are ontogenically rooted within early specified cell fate trajectories of human pluripotency

city: Hamilton

first: Mickie

last: Bhatia

state: Ontario

address: 1200 Main Street West

department: Stem Cell and Cancer Research Institute (SCC-RI)

country: Canada

institute: McMaster University

summary: Molecular similarities between pluripotency and cancer have recently been underscored by multi-omics campaigns revealing stemness networks that are shared between human pluripotent stem cells (hPSCs) and tumors, as well as tumor types that cluster based on tissue origins. Informed by these in silico studies, we now demonstrate that hPSCs serve as a cellular source to define properties of adult tissue oncogenesis. Single cell deconstruction of hPSCs allowed germ layer primed subsets to be identified that corresponded to lineage specified adult cancers. Functionally, chemical probes that induce hPSC germ layer specification suppressed adult cancer growth, but were restricted to tumors that correspond with shared germ layer origins. For example, metallothioneins induced mesoderm differentiation of hPSC and showed exclusive ability to overcome differentiation block of human leukemia. Our study provides causal evidence for oncogenic reprogramming to define a relationship between pluripotent state and human cancers that can identify covert targets for cancer therapies.

overall_design: Droplet-based single-cell RNA-sequencing of v1H9 transformed H9.

first: Mio

last: NAKANISHI

last: BHATIA


title: Genetically programmed alternative splicing of NEMO mediates an autoinflammatory disease phenotype

city: Bethesda

first: Stephen

last: Brooks

state: MD

address: 50 SOUTH DR, RM 1140

department: Biodata Mining and Discovery Section

institute: NIAMS/NIH

summary: Host defense and inflammation are regulated by the NF-kB essential modulator (NEMO), a scaffolding protein with a broad immune cell and tissue expression profile. Hypomorphic mutations in inhibitor of nuclear factor kappa B kinase regulatory subunit gamma (IKBKG) encoding NEMO typically present with immunodeficiency. Here we characterized a novel pediatric autoinflammatory syndrome in 3 unrelated male patients with distinct X-linked IKBKG germ-line mutations that led to overexpression of a NEMO protein isoform lacking the domain encoded by exon 5 (NEMO-Dex5). This isoform failed to associate with TANK binding kinase 1 (TBK1), and dermal fibroblasts from affected patients activated NF-kB in response to TNF, but not TLR3 or RIG-I-like-receptor (RLR) stimulation when isoform levels were high. By contrast, T cells, monocytes and macrophages that expressed NEMO-Dex5 exhibited increased NF-kB activation and IFN production, and blood cells from these patients expressed a strong interferon and NF-kB transcriptional signature. Immune cells and TNF-stimulated dermal fibroblasts upregulated the inducible IKK protein (IKKi) that was stabilized by NEMO-Dex5, promoting type I IFN induction and antiviral responses. These data reveal how IKBKG mutations that lead to alternative splicing of skipping exon 5 cause a clinical phenotype we name NEMO Deleted exon 5 Autoinflammatory Syndrome (NDAS), distinct from the immunodeficiency syndrome resulting from loss-of-function IKBKG mutations.

overall_design: Examination of novel pediatric autoinflammatory disease by mutational analysis, effect on splicing and gene expression.

first: Younglang

last: Lee

first: Alex

middle: W

last: Weissel

first: Eric

last: Hanson


title: Transcriptiome of ΔPfDNMT parasite during malaria parasite asexual development [DNMT_RNAseq]

city: Tampa

first: JUN

last: MIAO

state: Florida

address: 3720 Spectrum Boulevard, MDC84

department: Internal Medicine

institute: University of South Florida

summary:
Purpose: this study is to analyze the change of overal transcriptome after disruption of DNA methyltransferase (DNMT) in Plasmodium falciparum.
Methods: In this study, the transcriptomes of a PfDNMT gene knockout (KO) parasite line with its wildtype control, its complementation (adding back the DNMT expression by episomal expression of DNMT in the DNMT KO parasite), and overexpression (episomal expression of DNMT in the wildtype parasite) were analyzed by RNAseq. Total RNA were harvested from the asexual parasites at three developmental stages (ring, trophozoite, and schizont) using the Quick-RNA MiniPrep kit (Zymo Research). RNA sequencing libraries were prepared using the KAPA stranded RNA-seq library preparation kit (Roche) with 500 ng RNA from each sample. Illumina adapter sequence removal and quality trimming of reads were performed using Trimmomatic. Only reads that had a minimum length of 50 base pairs were retained. Reads were then mapped to the P. falciparum 3D7 strain reference genome with HISAT2.
Results: Using an optimized data analysis workflow, we mapped about 5 million sequence reads per sample to the malaria parasite genome (pf3D7_V3.0.) and identified 5712 transcripts with high mapping rate at the range between 80% and 95. PfDNMT KO profoundly disturbed the global transcription pattern,especially at trophozoite stage, causing 1732 (30.3%) genes to be differentially expressed at trophozoite.Complementation restored the expression pattern and overexpression of PfDNMT caused nearly 2000 gene ro be differentially expressed at schizont stage.
Conclusions: Collectively, transcriptomic analysis of DNMT KO, complemetation and overexpression shows PfDNMT plays important role in gene regulation.

overall_design: mRNA profiles of 3D7 (WT),  PfDNMT KO, complementation and overexpression were generated by deep sequencing, in triplicate

first: Jun

last: Miao

first: Liwang

last: Cui


title: DNA Methylome and 3D Chromatin Landscape of Cell Types Across the Mouse Brain [12I-13A-13B]

status: Public on May 21 2023

city: La Jolla

first: Joseph

last: Ecker

address: 10010 North Torrey Pines Road

overall_design: Apply snmC-seq2 to 117 brain functional regions to identify epigenomic landcape of the adult mouse brain, this subseries consists of one single nucleus methylation sequencing experiment of brain region (12J_210225, 12J_210304, 13A_190725, 13A_200102, 13B_201203, 13B_201210).

first: Hanqing

last: Liu

first: Anna

last: Bartlett

first: Jacinta

last: Lucero

first: Julia

last: Osteen

first: Jordan

last: Altshul

first: Mia

last: Kenworthy

first: Rosa

last: Castanon

last: Nery

first: Peter

last: Berube

first: Huaming

last: Chen

first: Michael

last: Nunn

first: Jesse

last: Dixon

first: M

last: Behrens


title: Targetable programs of adult cancer are ontogenically rooted within early cell fate trajectories of human pluripotent state [array]

first: Mickie

last: Bhatia

summary: Recognized molecular similarities between pluripotency and cancer have recently been underscored with multi-omics campaigns revealing stemness networks that are shared between human pluripotent stem cells (hPSCs) and tumors, where tumors types cluster based on tissue origins. Informed by these in silico studies, we now demonstrate hPSCs serve as a source of networks that define properties of adult tissue oncogenesis. Single cell deconstruction of hPSCs allowed germ layer primed subsets to be identified that corresponded to lineage specified adult cancers. Chemical probes that induced germ layer differentiation of hPSCs also suppressed adult cancers, but were restricted to tumors of shared origin with germ layer specification. Metallothioneines induced mesoderm differentiation of hPSC with exclusive ability to overcome differentiation block of human leukemia. Our study provides causal evidence for a relationship between pluripotent state and human cancer that defines oncogenic reprogramming and thereby identify covert targets for cancer therapy.

overall_design: Duplicates of each drug treatment were compared to vehicle control (DMSO) for each cell type, also in duplicate.

first: Luca

last: Orlando

first: Yannick

last: Benoit

first: Zoya

last: Shapovalova


title: Mitochondrial DNA and the STING pathway are required for hepatic stellate cell activation

status: Public on May 16 2023

city: New Haven

first: Suyavaran

last: Arumugam

state: Connecticut

address: 300 Cedar Street

institute: Yale University

summary:
The LX2 cells were subjected to TGFβ (5ng/ml) stimulus with or without  STING inhibitor IFM-004490-7 10μM (STINGX) pretreatment.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 3 different groups (Control, TGFβ, STINGX+TGFβ)

overall_design: Comparative gene expression profiling analysis of RNA-seq data for LX2 cells untreated or subjected to TGFβ with or without STINGX pretreatment.

first: Wajahat

last: Mehal


title: Age-induced alterations of granulopoiesis generate atypical neutrophils that aggravate stroke pathology. [scRNA-Seq 2]

city: Milan

first: Giulia

middle: Maria

last: Scotti

state: Milan

address: Viale Rita Levi Montalcini, 1

department: National Facility for Data Handling and Analysis

country: Italy

institute: Fondazione Human Technopole

summary: Stroke in aging leads to a dysregulated emergency granulopoiesis impacting neurological outcome.

overall_design: Comparison of young and aged mice at steady state and after experimental stroke

first: Marco

last: Bacigaluppi

first: Giorgia

last: Gullotta

first: Donatella

last: De Feo


title: Design and deep learning of synthetic B- cell-specific promoters

city: Tianjin

first: Fu

last: Zongheng

address: Yaguan Road 135, Jinnan District, Tianjin, Postcode 300350

institute: Tianjin University

summary: Flexible regulation of gene expression is essential and highly sought for synthetic biology and biotechnology. Designing regulators with specific functions remains a challenge due to the limited understanding of specific regulatory mechanisms. We design and synthesize 23,640 B-cell-specific promoters, following the design-build-test-learn pipeline in synthetic biology. Synthetic promoters exhibit B-cell-specific expression and lead to diverse expression patterns in B-cells. By conducting MPRA testing, we uncovered the factors that influence promoter strength, including core motifs and motif syntax, which shape B-cell-specific promoter strength. Finally, we developed a deep leaning model capable of predicting promoter activity directly from the sequence, and to predict promoter activity for 26,193 variants identified in the global population, indicating that polymorphisms in IgV gene promoters can influence gene expression. Our work helps to decipher the regulatory code in immunoglobulin genes and offers thousands of non-repetitive promoter elements for B-cell engineering.

overall_design: The synthetic promoters were designed to drive the expression of a barcoded green fluorescent protein (GFP) reporter gene, every synthetic promoter drives a reporter gene carrying a unique DNA barcode in its 5’, which allows investigators to quantify the activity of each synthetic promoter by the ratio of its barcode abundances in the output RNA and input DNA.


title: Single-cell transcriptome analysis reveals a cellular immune response in freshwater dark sleeper (Odontobutis potamophila) after infection with Aeromonas veronii

city: Urumqi

first: Zhang

middle: Qing

last: hua

state: Xinjiang

address: Liudao Bay Street

institute: The Second Affiliated Hospital of Xinjiang Medical University

summary: The bacterium Aeromonas veronii is a co-pathogenic species that can negatively impact the health of both humans and aquatic animals. In this study, we used single-cell transcriptome analysis (scRNA-seq) to investigate the effects of infection with A. veronii on head kidney cells and the regulation of gene expression in the dark sleeper (Odontobutis potamophila). scRNA-seq was used to assess the effects of infection with A. veronii in O. potamophila B cells, endothelial cells, macrophages, and granulocytes, and differential enrichment analysis of gene expression in B cells and granulocytes was performed. The analyses revealed a significant increase in neutrophils and decrease in eosinophils in granulocytes infected with A. veronii. Activation of neutrophils enhanced ribosome biogenesis by up-regulating the expression of rps12 and rpl12 to fight against invading pathogens. Crucial pro-inflammatory mediators il1b, ighv1-4, and the major histocompatibility class II genes mhc2a and mhc2dab, which are involved in virulence processes, were up-regulated, suggesting that A. veronii activates an immune response that presents antigens and activates immunoglobulin receptors in B cells. These cellular immune responses triggered by infection with A. veronii enriched the available scRNA-seq data for teleosts, and these results are important for understanding the evolution of cellular immune defense and functional differentiation of head kidney cells.

first: Guoxing

last: Liu

first: Chenxi

last: Zhu

first: Xiaojian

last: Gao

first: You

last: Zheng

first: Xinhai

first: Hucheng

last: Jiang

first: Wanhong

last: Wei

first: Qichen

first: Xiaojun

last: Zhang


title: A distinct CD8+ T cell subset derived from virtual memory T cells causes alopecia areata through innate-like cytotoxicity [scRNA-seq]

first: Su-Hyung

last: Park

address: 291, Daehak-ro, Yuseong-gu

institute: Korea Advanced Institute of Science and Technology

summary: Virtual memory T (TVM) cells are a T-cell subtype that exhibit a memory phenotype without prior exposure to a foreign antigen. Although several recent studies suggest that TVM cells exert anti-viral and anti-bacterial function, pathological roles of TVM cells causing inflammatory diseases have not been studied. Here, we identified a novel CD8+ T-cell subset (CD44s-hiCD49dlo CD8+ T cells), which is originated from TVM cells and can cause a chronic inflammatory disease, alopecia areata (AA). In the skin of alopecic mice, we detected a distinct TVM-cell subpopulation characterized by superior expression of CD44 and features of tissue residency, which was transcriptionally, phenotypically, and functionally distinct from conventional CD8+ TVM cells. Mechanistically, this cell population could be induced from conventional TVM cells by IL-12, IL-15, and IL-18 stimulation. Moreover, the pathological activity of CD44s-hiCD49dlo CD8+ T cells was mediated by NKG2D-depedent innate-like cytotoxicity against target cells, which was further augmented by IL-15 stimulation and triggered the onset of disease. Collectively, our results suggest a new immunological mechanism through which TVM cells can cause chronic inflammatory disease by innate-like cytotoxicity.

overall_design: Comparative gene expression profiling analysis of scRNA-seq data for alopecia areata and naïve mice

first: Joon

last: Seok

first: Sung-Dong

last: Cho


title: A distinct CD8+ T cell subset derived from virtual memory T cells causes alopecia areata through innate-like cytotoxicity

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

overall_design: Refer to individual Series


title: Single-cell transcriptome analysis reveals functional changes in tumor-infiltrating B lymphocytes after chemotherapy in esophageal squamous cell carcinoma

city: Fukuoka

first: Shoichi

last: Nakamura

institute: Kyushu University

summary: Our studies showed that the dynamic change in TIL-Bs functional heterogeneity were involved in the antitumor immune response in ESCC TIME.

overall_design:
We used droplet-based single cell RNA sequencing (scRNA-seq) with 23 samples, including 10 tumor samples, 7 normal samples, 5 normal lymph nodes and 1 metastatic lymph node.
16 Samples were re-analyzed from Series GSE197677. The GSE199619_ESCC_NAC.integrated.rds processed data includes the re-analyzed Samples and Sample ESN08.

first: Kenoki

last: Ohuchida


title: Organized B cell selection sites in cartilaginous fishes reveal the evolutionary foundation of germinal center-based selection.

city: Roslin

first: rose

middle: ruiz

last: daniels

address: The University Of Edinburgh

institute: The University of Edinburgh

summary: The absence of germinal centers (GCs) in cartilaginous fishes lies at odds with data showing nurse sharks can produce robust antigen-specific responses and affinity mature their B cell repertoires. To Investigate this paradox, we performed RNA sequencing on single nuclei, allowing us to characterize the cell types present in the nurse shark spleen, and RNAscope to provide in situ cellular resolution of key marker gene expression following immunization with R-phycoerythrin (PE). We tracked PE to the splenic follicles where it co-localizes with CXCR5high centrocyte-like B cells, surrounded by a peripheral ring of AID+ CXCR4+ centroblast-like B cells, and a population of putative T follicular helper (Tfh) cells. Further, we reveal selection of mutated B cell clones dissected from these follicles. We propose the B cell selection sites identified here represent the evolutionary foundation of GC-based selection, dating back to the jawed vertebrate ancestor.

overall_design: Protocol: A versatile nuclei extraction protocol for single nucleus sequencing in fish species – optimization in various Atlantic salmon tissues

first: Hanover

last: Matz

first: Richard

middle: S

last: Taylor

first: Anthony

last: Redmond

first: Rose

last: Ruiz Daniels

first: Mariana

last: Beltran

first: Neil

middle: C

last: Henderson

first: Daniel

last: Macqueen

first: Helen

last: Dooley


title: A distinct CD8+ T cell subset derived from virtual memory T cells causes alopecia areata through innate-like cytotoxicity [RNA-seq]

overall_design: Comparative gene expression profiling analysis of RNA-seq data for spontaneous and adoptive transferred alopecia areata mice


title: Lipid-anchored Proteasomes Control Membrane Protein Homeostasis

city: hangzhou

first: RUIZHU

last: ZHANG

state: 浙江省

address: Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China 310058

institute: 浙江大学生命科学研究院

summary: As the major protein degradation machinery of eukaryotic cells, the 26S proteasome is generally thought to localize in the nucleus and cytosol. A portion of proteasomes are known to associate with various membrane structures of the cell, the mechanism and biological meaning of which have been elusive. Here we show that N-myristoylation of the proteasome subunit Rpt2 is an evolutionarily conserved determinant of proteasome-membrane interaction. Loss of this modification leads to embryonic lethality in mice, significant reduction of migration ability in MEFs and profound changes in the membrane-associated proteome as determined by SILAC-MS, suggesting a key role of membrane-tethered proteasomes in carrying out compartmentalized protein degradation. And the tumorigenicity is reduced in the oncogene-transformed MEF without modification. Serendipitously, we found that the Rpt2-G2A mutation cell lines confers partial resistance to proteasome inhibitors, such as Bortezomib and MG132. Thus, N-myristoylation of Rpt2 determines the localization and activity of the proteasome at the membrane, which is critical for embryogenesis, cellular homeostasis and tumorigenesis.

overall_design: Total RNA was isolated from immortalized MEFs or 3 pairs (WT and G2A littermates) of E12.5 fetal livers using the Trizol method. Next-generation sequencing was done by   BGI (Shenzhen, China).

first: Ruizhu

first: Shuxian

last: Pan

first: Suya

last: Zheng

first: Yezhang

last: Zhu


title: K29-linked unanchored polyubiquitin chains disrupt ribosome biogenesis and direct ribosomal proteins to the Intranuclear Quality control compartment (INQ)

city: TOULOUSE

first: Benjamin

last: Albert

state: Cedex 9

address: 169 avenue Marianne Grunberg-Manago

department: UMR5077, Bat IBCG

country: France

institute: CNRS

summary: Ribosome assembly requires precise coordination between the production and assembly of ribosomal components. Mutations in ribosomal proteins that inhibit the assembly process or ribosome function are often associated with Ribosomopathies, some of which are linked to defects in proteostasis. In this study, we examine the interplay between several yeast proteostasis enzymes, including deubiquitylases (DUBs), Ubp2 and Ubp14, and E3 ligases, Ufd4 and Hul5, and we explore their roles in the regulation of the cellular levels of K29-linked unanchored polyubiquitin (polyUb) chains. Accumulating K29-linked unanchored polyUb chains associate with maturing ribosomes to disrupt their assembly, activate the Ribosome assembly stress response (RASTR), and lead to the sequestration of ribosomal proteins at the Intranuclear Quality control compartment (INQ). These findings reveal the physiological relevance of INQ and provide insights into mechanisms of cellular toxicity associated with Ribosomopathies.

overall_design: RNA Polymerase II binding was measured in DUB mutants (Wild type (W303), ubp2-Δ, ubp14-Δ, ubp2-Δ ubp14-Δ) using Anti-RNA polymerase II CTD repeat YSPTSPS (phospho S5).

first: Harsha

last: Suresh


title: The effects of different types of sugars on vascular cell diffentiation in a tissue culture system, VISUAL

city: Kobe

first: Yuki

last: Kondo

address: 1-1 Rokkodai-cho, Nada-ku

department: Graduate School of Science

institute: Kobe University

summary:
We established a novel in vitro tissue culture system (named VISUAL), in which xylem and phloem differentiation can be induced with Arabidopsis thaliana cotyledons
To investigate the effects of differenet sugars in VISUAL, we performed GeneChip analysis .

overall_design: Arabidopsis cotyledons cultured with the induction medium containing 5% Glucose (Glc) or Sucrose (Suc) were sampled at 0 , 24 and 48 hours after the induction. Total RNA was extractec from cultured cotyledons.

first: Yukiko

last: Sugisawa


title: Bovine blastocyst like structures derived from stem cell cultures

city: Dallas

first: Carlos

last: Pinzon

state: Texas

address: 5323 Harry Hines Boulevard,  NA5.124

department: Molecular Biology

country: USA

institute: UT Southwestern Medical Center

summary: Understanding blastocyst formation and implantation is critical for improving farm animal reproduction but is hampered by a limited supply of embryos. We developed an efficient method to generate bovine blastocyst-like structures (termed blastoids) via the assembly of trophoblast stem cells and expanded potential stem cells. Bovine blastoids resemble blastocysts in morphology, cell composition, single-cell transcriptomes, and represent an accessible in vitro model for studying bovine embryogenesis.

overall_design: Bovine trophoblast stem cells (TSCs) and bovine and extended pluripotent stem cells (EPSCs),  were aggregated in tFACL+PD and collected at day 4.Single-cell RNA-Seq  was performed using the 10x Genomics Chromium Chip and sequenced by Illumina NextSeq 500/550 sequencing systems.

middle: A

last: Pinzón-Arteaga

first: Yinjuan

last: Wang

first: Yulei

last: Wei

first: Ana

middle: E

last: Ribeiro Orsi