title: Epigenetically Down-Regulated BRCA2 through Acetyltransferase KAT2B Increases the Sensitivity of Colorectal Cancer to Olaparib

city: Mannheim

first: Siche

last: Chen

address: Stockhornstrasse 55, 55

department: Dept. of Experimental Surgery - Cancer Metastasis

institute: Medical Faculty Mannheim, Ruprecht-Karls University of Heidelberg

summary: The clinical application of anticancer drugs depends on preclinical models closely recapitulating the molecular profile. We report here the transcriptional profiles of HCT116 (colorectal cancer cells) treated with DMSO or Olaparib for 24 hours. For these two different treatments, also changes of molecule expression are available, which enables their stratification into drug-therapeuticly relevant molecule.

overall_design: Examination of DMSO-treated versus Olaparib-treated colorectal cancer cells from HCT116 cell line representing two treating types in culture.

first: Allgayer

last: Heike


title: Individual Variability in Human Cell Type Transcriptomes and Epigenomes [OM3A]

status: Public on Dec 15 2023

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

type: Methylation profiling by high throughput sequencing

summary: Diversity and individual variability are essential to human cognitive function. Identifying the conserved and variable (epi)genomic signatures of the brain’s cellular components is critical for understanding the neurobiological basis of individual variation in brain function.  We applied single nucleus methylome and transcriptome sequence (snmCT-seq) to neurons from the frontal cortex of 11 adult human donors spanning a range of ages from 23 to 74, including males and females (Broadmann Area BA46). We clustered cells into brain cell types based on methylation features. We then examined the transcriptome and epigenome features in each cell type between and within individual donors. Taking advantage of the multimodal measurements in single cells, we also identified the relation between RNA expression and methylation level.These data with multiomics measurement from donors with sex and age diversity aims to approach the dimension of inter-individual variability.

overall_design: We apply snmCT-seq to identify the transcriptomic and epigenomic features of neurons from individual adult human frontal cortex, including 3 aged male donors (age range 70-71), 3 aged female donors (71-74 years old), 3 young male donors  (25 years old) and 2 young female donors  (23-30 years old). For each donor, 2 chunks of brain tissue were collected and processed separately, to assess within-donor variability. This sample is from chunk A of a 73 years old female.

first: Jofan

last: Chien

first: Anna

last: Bartlett

first: Hanqing

last: Liu

first: Rosa

last: Castanon

last: Nery

first: Bang-An

last: Wang

first: Nick

last: Johnson

first: Julia

last: Osteen

first: M

middle: M

last: Behrens

first: Eran

middle: A

last: Mukamel


title: Cx40 Suppresses Sprouting Angiogenesis In Vitro

status: Public on Dec 14 2023

city: Irvine

first: Christopher

middle: J

last: Hatch

address: 2400 Biological Sciences III

institute: University of California, Irvine

type: Expression profiling by high throughput sequencing

summary: Blood vessels are highly organized and form during development through a series of complex processes that include vasculogenesis, sprouting angiogenesis, and vessel remodeling. Several gap junction proteins (termed connexins, Cx) – including Cx40 (GJA5) – are expressed in  vascular endothelium early during vessel development and are critical for establishment of a healthy vasculature. However, Cx40’s specific role in regulating vessel growth remains uncertain: while previous studies have shown that developmental and cancer-associated neovascularization is reduced in Cx40-knockout mice, Cx40 knockout in zebrafish embryos enhances intersegmental vessel growth. Thus, in the current study, our aim was to identify Cx40’s specific role in sprouting angiogenesis. First, we used a vessel-on-a-chip microphysiological model to confirm Cx40’s overall necessity for microvessel network development. Next, we used the fibrin gel bead assay – a three-dimensional in vitro model of sprouting angiogenesis – to assess Cx40’s necessity for this process. We found that Cx40 knockdown in endothelial cells drives more aggressive sprouting angiogenesis in association with increased endothelial cell proliferation. By contrast, using Electrical Cell-substrate Impedance Sensing (ECIS) we observed no effect of Cx40 knockdown on endothelial cell migration. Lastly, we found that Cx37 (GJA4) is reduced in Cx40- deficient endothelial cells, and that targeted silencing of Cx37 alone produces a more aggressive, hyper-sprouting phenotype compared to control or Cx40 knockdown endothelial cells. Taken together, our data argue that Cx40 plays multiple roles during vessel growth, including to specifically limit sprouting angiogenesis, and that this may occur (at least in part) through regulation of endothelial Cx37 levels.

overall_design: Primary human umbilical vein EC were purchased (Lonza) or isolated in-house as previously described. EC were cultured on gelatinized surfaces in complete EGM2 (Lonza). Cells were plated at ~60% confluence and transfected with 10-30nM scrambled si-Ctrl (Dharmacon or Ambion), or with si-Cx40 or si-Cx37 (Dharmacon SMARTpool) using Lipofectamine 2000 (Sigma) or Lipofectamine RNAiMax (Sigma) according to manufacturers’ protocols. Cells were then allowed to recover for 24-48h prior to functional assays.

first: Edward

middle: K

last: Looker

first: Femke

last: Aan

middle: C

last: Hughes

first: Michelle

middle: L

last: Matter

first: Jennifer

middle: S

last: Fang


title: Individual Variability in Human Cell Type Transcriptomes and Epigenomes [OF3B]

last: Ecker


title: Individual Variability in Human Cell Type Transcriptomes and Epigenomes [OF3A]

last: Chien


title: Reproducible specificity and efficiency of tamoxifen-mediated cre induction across ages

city: Oklahoma City

first: Michael

last: Stout

state: OK

address: 825 N.E. 13th Street

department: Aging and Metabolism

institute: Oklahoma Medical Research Foundation

summary: Temporally controlling cre recombinase through tamoxifen (TAM) induction has many advantages for biomedical research studies. While most projects use TAM induction of mice at early post-natal or adolescence (<2m.o.) ages, age-related neurodegeneration and aging studies can require experimental designs with cre induction in older mice (>12m.o.). While anecdotally reported to be problematic, there are no published comparisons of TAM mediated cre induction at young and older ages. Cx3cr1creERT2 mice for studying microglial were crossed to a floxed NuTRAP reporter to compare cre induction at young (3m.o.) and old (18m.o) ages. Specificity and efficiency microglial labeling was identical at 24m.o. in mice induced with TAM at 3m.o. or 18m.o. of age. Age-related microglial translatomic changes were nearly identical regardless of TAM induction age.  While each cre and flox mouse line should be validated before use, these findings demonstrate that TAM induction of cres can be performed even into older mouse ages.

overall_design: To investigate the effect of different induction ages on the efficiency, specificity, and usefulness of the Cx3cr1-cre;NuTRAP mouse model. We induced mice at early or late ages, and collected both old and young mice. We used RNA sequencing and flow cytometry to compare the effectiveness of recombination, as well as ability to isolate microglial-specific RNA and detect age related changes.

first: Collyn

last: Kellogg

first: Kevin

last: Pham

first: Sunghwan

last: Ko

first: Jillian

last: Cox

first: Adeline

last: Machalinski

first: Mike

last: Beckstead

first: Ana

last: Chucair-Elliott

first: Sarah

last: Ocanas

first: Willard

last: Freeman


title: Molecular and immune changes in tumor draining lymph nodes following node sparing radiotherapy of Non-Small Cell Lung Cancer

city: Toulouse

first: Jonathan

last: KHALIFA

address: IUCT-Oncopole 1 avenue Irène-Joliot Curie

country: France

institute: Institut Universitaire du Cancer de Toulouse - Oncopole

summary: Background: While much progress has been accomplished in the understanding of radiation-induced immune effects in tumors, little is known regarding the mechanisms involved at the tumor draining lymph node (TDLN) level following tumor irradiation. The objective of this retrospective study was to assess the immune and biological changes arising in TDLN upon concurrent chemoradiotherapy of primary non-small cell lung cancer (NSCLC) tumors. Methods: Patients with proved localized (cN0M0) NSCLC, treated by radical surgery plus lymph node dissection with (CRT+) or without (CRT-) neoadjuvant chemoradiotherapy, whereby radiotherapy was targeted on the primary tumor with no significant incidental irradiation of the TDLN station (stations XI or X), were identified. Bulk RNA-Seq of TDLNs was performed and data were analyzed based on differential gene expression (DEG) and gene sets enrichment. Results: Sixteen patients were included and 25 TDLNs were analyzed: 6 patients in the CRT+ group (12 samples) and 10 patients in the CRT- group (13 samples). Overall, 1001 genes were differentially expressed between the two groups (CRT+ and CRT-). Analysis with g-profiler revealed that gene sets associated with antitumor immune response, inflammatory response, hypoxia, angiogenesis, epithelial mesenchymal transition and extra-cellular matrix remodeling were enriched in the CRT+ group, whereas only gene sets associated with B cells and B-cell receptor signaling were enriched in the CRT- group. Unsupervised dimensionality reduction identified two clusters of TDLNs from CRT+ patients, of which one cluster (cluster 1) exhibited higher expression of pathways identified as enriched in the overall CRT+ group in comparison to the CRT- group. In CRT+ cluster 1, 3 out of 3 patients had pathological complete response (pCR) or major complete response (MPR) to neoadjuvant CRT, whereas only 1 out of 3 patients in the other CRT+ cluster (cluster 2) experienced MPR and none exhibited pCR. Finally, pathway comparison to published data from pre-metastatic TDLNs uncovered similarities with CRT+ cluster 1. Conclusion: Neoadjuvant concurrent chemoradiotherapy of the primary tumor in N0 NSCLC patients is associated with distinct microenvironment and immunological patterns in TDLNs as compared to TDLNs from patients with non-irradiated tumors. Our data are in line with studies showing superiority of lymph node sparing irradiation of the primary tumor in the induction of systemic antitumor immunity.

overall_design: Bulk RNA sequencing was performed on 25 human tumor-draining lymph node samples from 16 NSCLC patients.

last: Khalifa

first: Noémie

last: Thébault

first: Françoise

last: Lauzéral-Vizcaino

first: Clara-Maria

last: Scarlata

first: Emma

last: Norkowski

first: Carole

last: Massabeau

first: Julien

last: Mazières

first: Laurent

last: Brouchet

first: Sophie

middle: P

last: Bataille

first: Christelle

last: Casaroli

first: Liza

last: Vaz

first: Etienne

last: Martin

first: Pierre-Benoît

last: Pages

first: Alice

last: Millière

first: Elizabeth

last: Moyal

first: Maha

last: Ayyoub


title: SialidaseNeu3action on GM1 ganglioside is neuroprotective in GM1 Gangliosidosis

city: Bethesda

first: Richard

last: Proia

state: MD

address: 10 Center Drive Room 9D11

department: National Institute of Diabetes and Digestive and Kidney Diseases

institute: National Institutes of Health

summary: GM1 gangliosidosis is a neurodegenerative disorder caused by mutations in theGLB1gene, which encodes lysosomalb-galactosidase. The enzyme deficiency blocks GM1 ganglioside catabolism, leading to accumulation of GM1 ganglioside and asialo-GM1 ganglioside (GA1 glycolipid) in brain. This disease can present in varying degrees of severity, with the level of residualb-galactosidase activity primarily determining the clinical course.Glb1null mouse models, which completely lackb-galactosidase expression, exhibit a less severe form of the disease than expected from the comparable deficiency in humans, suggesting a potential species difference in the GM1 ganglioside degradation pathway. We hypothesized this difference may involve the sialidase NEU3, which acts on GM1 ganglioside to produce GA1 glycolipid. To test this hypothesis, we generatedGlb1/Neu3double knockout (DKO) mice. These mice had a significantly shorter lifespan, increased neurodegeneration, and more severe ataxia thanGlb1KO mice.Glb1/Neu3DKO mouse brains exhibited an increased GM1 ganglioside to GA1 glycolipid ratio compared withGlb1KO mice, indicating that Neu3 mediated GM1 ganglioside to GA1 glycolipid conversion inGlb1KO mice. The expression of genes associated with neuroinflammation and glial responses were enhanced inGlb1/Neu3DKO mice compared withGlb1KO mice. Mouse Neu3 more efficiently converted GM1 ganglioside to GA1 glycolipid than human NEU3 did. Our findings highlight Neu3’s role in ameliorating the consequences ofGlb1deletion in mice, provide insights into NEU3’s differential effects between mice and humans in GM1 gangliosidosis, and offer a potential therapeutic approach for reducing toxic GM1 ganglioside accumulation in GM1 gangliosidosis patients.

overall_design: Compare gene expression profile between Control and DKO mice.

first: Maria

last: Allende

first: Y

middle: T

last: Lee

first: Colleen

last: Byrnes

first: Cuiling

last: Li

first: Galina

last: Tumetova

first: Jenna

middle: Y

last: Bakir

first: Ashley

last: Hirt

first: Elena-Raluca

last: Nicoli

first: Virginia

last: James

first: Jennifer

last: Brodbelt

first: Cynthia

last: Tifft


title: single cell RNAseq of mouse E12.5 fetal ovarian somatic cells

city: Los Angeles

first: Fei-Man

last: Hsu

state: California

address: 610 Charles E Young Dr S

department: MCDB

institute: UCLA

summary: A major technology for generating oocytes by in vitro gametogenesis involves generating ovary models called reconstituted ovaries (rOvaries).  Widespread use of rOvaries depends on the reliable manufacturing of primordial germ cell like cells (PGCLCs) and fetal ovarian somatic cells (FOSCs).  Using  scRNA-seq, we identify that upon thaw, FOSCs are composed largely of Foxl2+ pre-granulosa cells, KRT19+ epithelial cells and Nr2f2+ mesenchymal cells which self-assemble together with PGCLCs into disc-like organoids containing multiple follicles embedded in NR2F2 stroma without an ovarian surface epithelium and no steroidogenic theca.  The absence of an ovarian surface epithelium combined with the small size of GV-oocytes indicates that follicle production in the rOvary corresponds to first-wave folliculogenesis.

overall_design: Ovarian somatic cells for each corresponding lot were obtained from E12.5 mice from ten pregnant female CD1(Charles River, Strain code: 022) mice. Gonads, which included the mesonephros and ovaries, were collected into cell culture plates filled with MEF media on ice. Gonads were transferred into glass plates containing MEF media and mesonephros were removed using surgical blade and fine forceps under a SZX16 (Olympus) microscope. Ovaries were collected into a well of a 4-well plate containing MEF media and DNase I.  Ovaries were washed twice by transferring them into wells containing PBS. Dissociation of ovaries was performed in 0.05% Trypsin for 10 minutes at 37C. MEF media was used to quench and tissues were dissociated by vigorous pipetting. Cells were strained using a 70uM cell strainer and then washed using MEF media. The ovarian somatic cell pellet was then resuspended in MACs Buffer and incubated with the MACs antibodies SSEA1 and CD31 at 4C for 30 minutes. Afterwards labeled cells were washed by adding MACS buffer and spinning for 5 minutes at 1,600rpm. The cell pellet was resuspended in 500uL MACS buffer and then loaded into a MS column held by a MiniMACS™ Separator magnet. Flow through was collected, including the MACS media added for washes. The number of cells collected was counted and aliquots of 300,000 cells per vial were frozen down in Cell Banker 2 at -80C then transferred to Liquid nitrogen storage tanks for long term storage.

first: Amander

last: Clark

first: Enrique

last: Sosa


title: Epigenetics of Yakutia and Central Russia regions

city: Nizhny Novgorod

first: Alena

last: Kalyakulina

address: Gagarin avenue, 23

country: Russia

institute: Lobachevsky State University

summary:
Lobachevsky University DNAm dataset. Whole blood DNA Methylation (EPIC) profiles from healthy samples from two regions: central Russia (131 samples) and Yakutia (114 samples) obtained in the Laboratory of System Medicine for Healthy Aging, Lobachevsky State University of Nizhny Novgorod, Russia
Dataset contains DNAm data from 245 healthy control samples from two regions: central Russia (131) and Yakutia (114). The following characteristics are available for all samples: sex, age, region. Healthy participants in the central Russia region were recruited in 2019–2022. Yakutian participants we recruited in 2022. All measurements were performed at the Laboratory of System Medicine for Healthy Aging, Lobachevsky State University of Nizhny Novgorod, Russia.

overall_design: Genome-wide DNA methylation in whole blood from 245 participants was assessed with the HumanMethylationEPIC BeadChip array

first: Igor

last: Yusipov

first: Elena

last: Kondakova

first: Raisa

last: Zakharova

first: Tatiana

last: Sivtseva

first: Claudio

last: Franceschi

last: Vedunova

first: Mikhail

last: Ivanchenko


title: Spatial gene expression profiling unveils immuno-oncogenic programs of NF1-associated peripheral nerve sheath tumor progression

city: Indianapolis

first: Steven

last: Rhodes

state: IN

address: 1044 W. Walnut St.; Bldg R4, Rm 325

institute: Indiana University

summary: Plexiform neurofibromas (PNF) are benign peripheral nerve sheath tumors (PNST) that arise in persons with neurofibromatosis type 1 (NF1). Despite similar histological appearance, these neoplasms proceed along diverse evolutionary trajectories, with a subset progressing to a devastating form of sarcoma called malignant peripheral nerve sheath tumor (MPNST), the leading cause of premature death in individuals with NF1. Malignant transformation of PNF often occurs through the development of atypical neurofibroma (ANF) precursor lesions characterized by distinct histopathological features and CDKN2A copy number loss. While genomic studies have improved our understanding of key driver events promoting tumor progression, the transcriptional alterations that precede malignant transformation remain poorly understood. Here we resolve gene expression profiles in PNSTs across the neurofibroma-to-MPNST continuum in NF1 patients and genetically engineered mouse models, providing insight into nascent molecular features associated with neurofibroma evolution and transformation. These findings highlight the need for molecular diagnostic tools that augment conventional histopathological criteria to identify neurofibromas at high risk of undergoing malignant transformation, facilitating risk-adapted care.

overall_design: A cohort of n=35 peripheral nerve sheath tumor samples samples was assembled by retrospective review of the Indiana University Pathology archives. Tissues were microdissected from selected regions of interest conforming to consensus diagnostic criteria and subjected to RNA expression profiling across a high-content panel of genes involved in tumor progression, microenvironment, and immune response (PanCancer IO360TM Panel, NanoString Technologies).

middle: D


title: Effect of Bifidobacterium infantis or its secreted byproducts, Bacteroides thetaiotaomicron or heat-killed B. infantis on human colonic epithelial cells transcriptome

city: Seattle

first: Donald

last: Nyangahu

state: Washington

address: 307 Westlake Ave N

institute: Seattle Children's Research Institute

summary:
To investigate bacteria-host interactions in vitro using human colonic epithelial cells. Mature colonic epithelial cells were stimulated with bacteria conditions for 6 hours.
Cells were then lysed and RNA extracted. RNA sequencing was performed on cells stimulated under 6 different conditions (3 replicates per condition).

overall_design: Compare gene expression profile of RNA-seq data of different groups versus B. infantis group.


title: Reconstituted Ovaries Self Assemble without a Surface Epithelium

first: Jonathan

last: DiRusso

address: 615 Charles E. Young Drive

department: Molecular, Cell and Developmental Biology

institute: University of California Los Angeles

summary: Reconstituted Ovaries (rOvaries) represent an important method for in vitro derivation of gametes. The beginning of this process requires differentiation of mouse induced pluripotent stem cells (iPSCs) into Epiblast Like Cells (EpiLCs) followed by 6 days of differentiation as spheres containing PGC-Like Cells (PGCLCs) and somatic cells. Here, we characterize the cells in the differentiated spheres at day 6 of differentiation.

overall_design: 4 biological replicates of day 6 spheres differentiated from EpiLCs induced using 10X genomics

first: Sosa

last: Enrique

first: Espinoza

last: Alejandro

first: Hsu

last: Fei-Man

first: DiRusso

last: Jonathan


title: Effect of Bifidobacterium infantis, Bacteroides thetaiotaomicron or heat-killed B. infantis on murine colonic transcriptome

summary:
To investigate bacteria-host interactions in vivo in a murine model.
Mice were orally gavaged with bacteria at day 7 and 10 of life. The colonic transcriptome was analyzed at day 14 of life.

overall_design: Compare gene expression profile of RNA-seq data of different groups versus B. infantis gavaged group.


title: scRNA-seq analysis of human peripheral blood mononuclear cells collected at the acute HIV-1 infection timepoint

city: Silver Spring

first: Rasmi

last: Thomas

address: 503 Robert Grant Avenue

department: MHRP

institute: Walter Reed Army Institute of Research

summary: To identify host factors associated with HIV-1 control during acute infection, single cell gene expression profiles of immune cells were examined

overall_design: Single cell gene expression profiles of immune cells during acute HIV-1 infection

first: Aviva

last: Geretz

first: Robert

last: Clifford

first: Gautam

last: Kundu

first: Daina

last: Eiser


title: A transcriptomic taxonomy of mouse brain-wide spinal projecting neurons (SmartSeq)

city: Boston

first: Yu

last: Zhang

state: MA

address: 3 Blackfan Street, Room 13060

department: Neurobiology

institute: Boston Childrens Hospital

summary: The brain executes control of nearly all bodily functions via spinal projecting neurons (SPNs) that carry command signals from numerous supraspinal regions to the spinal cord. Despite their physiological and clinical relevance, a comprehensive molecular characterization of SPNs is still lacking. Here, we use retrograde labeling, whole-brain imaging, and high-throughput transcriptional profiling to generate a unified brain-wide anatomic and transcriptomic atlas of adult mouse SPNs at single-cell resolution. We transcriptionally profiled a total of 65,002 SPNs, identified 76 region-specific SPN types, and mapped these types into a companion atlas of the whole mouse brain generated by the Allen Institute for Brain Science within the BRAIN Initiative Cell Census Network (BICCN). This SPN taxonomy reveals a three-component organization of SPNs: (1) molecularly homogeneous excitatory SPNs from the cortex, red nucleus, and cerebellum with somatotopic spinal terminations suitable for point-to-point communication; (2) highly heterogeneous excitatory and inhibitory populations in the reticular formation with broad spinal termination patterns, thus suitable for relaying commands related to the activities of the entire spinal cord; and (3) modulatory neurons expressing slow-acting neurotransmitters and/or neuropeptides in the hypothalamus, midbrain, and reticular formation for gain control of brain-spinal signals. Within each of these components, this atlas revealed additional insights. From components (2) and (3), we discovered a LIM homeobox transcription factor code that parcellates the most transcriptionally complex population, reticulospinal neurons, into five molecularly distinct and spatially segregated populations. For neurons in component (1), we found transcriptional signatures of a subset of SPNs with large soma size and correlated these with fast-firing electrophysiological properties; thus, at least two different cable lines (namely, Pvalb/Kcng4/Spp1 positive and negative) with different electrophysiological properties might underlie the transmission of brain signals to the spinal cord. Together, by integrating the anatomy, molecular identity, and physiological properties, this study establishes a comprehensive taxonomy of brain-wide SPNs and provides insight into the functional organization of SPNs in mediating brain control of bodily functions.

overall_design: Spinal projecting neuron (SPN) nuclei of C57BL6/J mice were retrogradely labeled via injection of recombinant retrograde adeno associated virus (rAAV2/retro-Syn-H2B-fluorescent protein) into multiple segments centering the cervical (GFP) and lumbar (mScarlet) spinal cord of postnatal day 42 C57BL/6J mice. At postnatal day 56, the mice were sacrificed and nuclei were isolated via tissue dissection and dissociation of brain regions containing SPNs (i.e., rostral forelimb area cortex [RFA], primary and secondary motor cortex / primary somatosensory cortex [M1M2S1], secondary somatosensory cortex [S2], hypothalamus [HY], midbrain [MB], cerebellum [CB], pons [PONS], and medulla [MED]). Subsequently, SPNs were enriched via fluorescence activated nucleus sorting. Nuclei were then analyzed with single nucleus RNA sequencing using the 10x genomics and SmartSeq platforms.

first: Carla

last: Winter

first: Anne

last: Jacobi

first: Junfeng

last: Su

first: Leeyup

last: Chung

first: Cindy

last: van Velthoven

first: Zizhen

last: Yao

first: Changkyu

last: Lee

first: Zicong

first: Shuguang

last: Yu

first: Kun

last: Gao

first: Geraldine

last: Salazar

first: Evgenii

last: Kegeles

first: Makenzie

last: Tomihiro

first: Yiming

first: Zhiyun

last: Yang

first: Junjie

last: Zhu

first: Jing

last: Tang

first: Xuan

last: Song

first: Ryan

last: Donahue

first: Qing

last: Wang

first: Delissa

last: McMillen

first: Michael

last: Kunst

first: Ning

first: Kimberly

last: Smith

first: Gabriel

middle: E

last: Romero

first: Michelle

last: Frank

first: Alexandra

last: Krol

first: Riki

last: Kawaguchi

first: Daniel

middle: H

last: Geschwind

first: Guoping

last: Feng

first: Lisa

middle: V

last: Goodrich

first: Yuanyuan

last: Liu

first: Bosiljka

last: Tasic

first: Hongkui

last: Zeng

first: Zhigang

last: He


title: Impact of Olfr78 Knockout on enteroendocrine cells and on colon homeostasis

city: Anderlecht

first: Gilles

last: Dinsart

address: 808 route de lennik

country: Belgium

institute: Université Libre de Bruxelles

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

overall_design: Refer to individual Series


title: Impact of Olfr78 Knockout on enteroendocrine cells and on colon homeostasis [RNA-seq]

summary: The gastrointestinal epithelium constitutes a chemosensory system for microbiota-derived metabolites such as Short Chain Fatty Acids (SCFA). In this study, we investigated spatial distribution of Olfr78, one of the SCFA receptors, in the mouse intestine and studied the transcriptome of colon enteroendocrine cells expressing Olfr78. The receptor is principally detected in the enterochromaffin and L subtypes in the proximal and distal colon, respectively. Using the Olfr78-GFP and VilCre/Olfr78flox transgenic mouse lines, we reveal that loss of epithelial Olfr78 results in impaired enterochromaffin cell differentiation, blocking cells in an undefined secretory lineage state. This is accompanied by reduced defense response to bacteria in colon crypts and mild dysbiosis. Using organoid cultures, we further show that maintenance of enterochromaffin cells involves activation of the Olfr78 receptor via the SCFA ligand acetate. Altogether, this work provides evidence that Olfr78 contributes to colon homeostasis by regulating enterochromaffin cell differentiation.

overall_design: We isolated colon crypts from wildtype and knockout mice to obtain their transcriptome by RNAseq. In addition, we sorted Epcam+ve/GFP+ve cells from colons of heterozygous and homozygous mutants by FACS as well as Epcam+ve/GFP-ve cells.

first: Morgane

last: Leprovots

first: Anne

last: Lefort

first: Frédéric

last: Libert

first: Yannick

last: Quesnel

first: Alex

last: Veithen

first: Gilbert

last: Vassart

first: Sandra

last: Huysseune

first: Marc

last: Parmentier

first: Marie

middle: I

last: Garcia


title: Bulk RNA-seq analysis of control and Dnmt3a conditional knockout (cKO) retinal ganglion cells at 2 days post optic nerve crush

first: Emil

last: Kriukov

address: 20 Staniford St

institute: Schepens Eye Research Institute

summary: Dnmt3a deficiency in retinal ganglion cells promotes axon regeneration in an optic nerve crush mouse model. To investigate the role of Dnmt3a in axon regeneration, retinal ganglion cells isolated from control and retinal ganglion cell-specific Dnmt3a knockout mice at 2 days post-crush were applied for Bulk RNA-seq analysis by NovaSeq platform.

overall_design: Retinal ganglion cells were isolated by magnetic beads from 3 cKO and 3 sex-matched control mice with optic nerve crush. Comparative gene expression profiling analysis of RNA-seq data was performed for all samples.

first: Wai

last: Tai

first: Petr

last: Baranov

first: Dong

middle: F

last: Chen


title: Whole genome bisulfite-seq analysis of control and Dnmt3a conditional knockout (cKO) retinal ganglion cells at 2 days post optic nerve crush

summary: Dnmt3a deficiency in retinal ganglion cells promotes axon regeneration in an optic nerve crush mouse model. To investigate the contribution of Dnmt3a to DNA methylation and axon regeneration, retinal ganglion cells isolated from control and retinal ganglion cell-specific Dnmt3a knockout mice at 2 days post-crush were applied for whole genome bisulfite-seq analysis by Illumina NovaSeq 6000.

overall_design: Retinal ganglion cells were isolated by magnetic beads from 2 cKO and 2 sex-matched control mice with optic nerve crush. Genomic DNA was extracted from the retinal ganglion cells and pooled for each group. Methylation profiling by high throughput sequencing was performed for all samples.


title: Impact of Olfr78 Knockout on enteroendocrine cells and on colon homeostasis [scRNA-seq]

overall_design: We digested mouse colon from one WT and one Olfr78-GFP KO mice to obtain isolated mesenchymal and epithelial cells for the single-cell RNA sequencing.


title: Baffled-flow culture system enables the mass production of megakaryocytes from human embryonic stem cells by enhancing mitochondrial function

city: Beijing

first: Jinhua

last: Qin

address: Taiping Road

country: China

institute: Beijing Institute of Transfusion

summary: Human embryonic stem cells (hESCs) have become an ideal cell source for the ex vivo generation of megakaryocyte (MK) and platelet products for clinical applications. However, an ongoing challenge is to establish scalable culture systems to maximize the yield of stem cell-derived MKs that release platelets. We defined a specific dynamic 3D manufacturing system that could remarkably facilitate megakaryopoiesis and increase the yield of platelet-producing MKs from hESCs within a 12-day induction period. Additionally, an increased number of > 16N ploidy MKs, proplatelets, and platelets were generated from induced cells harvested on day 12 using the specific dynamic culture method. The specific dynamic culture method significantly enhanced endothelium-to-hematopoietic transition and early hematopoiesis. More importantly, MK fate was significantly facilitated in a specific dynamic manner during early hematopoiesis. Mechanistically, this dynamic culture significantly enhanced mitochondrial function via the oxidative phosphorylation pathway and caused differentiation skewing of hESCs toward megakaryopoiesis. We defined a specific dynamic culture system in a baffled-flow manner that enabled the mass production of MKs from hESCs within 12 days. This study can aid in the automatic and scalable production of MKs from stem cells using baffled-flow bioreactors and assist in the manufacturing of hESC-derived MK and platelet products.

overall_design: We performed RNA-Seq and assay to analyse the molecular mechanism of promoting the production of megakaryocytes from human embryonic stem cells in Baffled-flow culture system. RC were manipulated in baffled flasks with agitation. SC, as controls, were manipulated in baffled flasks without agitation.

first: Xumin

last: Wu

first: Bowen

last: Zhang

first: Yanhua

last: Li

first: Xuetao

last: Pei

first: Yan


title: A transcriptomic taxonomy of mouse brain-wide spinal projecting neurons

first: Yu


title: Single nuclei RNA-seq analysis of control and Dnmt3a conditional knockout (cKO) of retinal ganglion cells at 2 days post optic nerve crush.

summary: Dnmt3a deficiency in retinal ganglion cells promotes axon regeneration in an optic nerve crush mouse model. To investigate the role of Dnmt3a in axon regeneration, retinal ganglion cell nuclei were sorted from control and retinal ganglion cell-specific Dnmt3a knockout mice at 2 days post optic nerve crush and applied for single nuclei RNA-seq analysis by 10X Genomics technology.

overall_design: snRNA-seq were performed for retinal ganglion cell nuclei isolated from the retinas of 6 cKO and 6 sex-matched control mice with optic nerve crush, using FACS. Total 8,000~9,000 cells were sequenced to an average of 22,000-30,000 reads/cell per dataset.

first: Kriukov

last: Emil

first: Monavarfeshani

last: Aboozar

last: Wenjun

first: Tai

last: Wai Lydia

first: Baranov

last: Petr

first: Chen

last: Dong Feng


title: By controlling glutathione metabolism, NR0B1 prevents lung cancer cells from going through ferroptosis.

city: Chengdu

first: Xinyue

address: Renmin South Road, Wuhou District,、

institute: Sichuan University

overall_design: Comparative gene expression profiling of RNA-seq data of A549 cells and their KD derivatives (shNR0B1) and OE derivatives (NR0B1 OE).

first: Hao

first: Yuan

last: Yang

first: Yunqiang

last: Liu


title: A Seed Sequence Variant in miR-145-5p causes Multisystem Smooth Muscle Dysfunction Syndrome (MSMDS)

city: boston

first: christian

last: lino cardenas

state: Massachusetts

address: 185 Cambridge st Room 3224

department: cardiology

institute: Massachusetts General Hospital

summary: Multisystem smooth muscle dysfunction syndrome (MSMDS) is a smooth muscle myopathy with major dysfunction in multiple organ systems. Described cases have been exclusively associated with recurrent missense variants at amino acid position 179 in the ACTA2 gene. We describe a patient with multiple major manifestations of MSMDS including steno-occlusive cerebrovascular arteriopathy, prune belly syndrome, gastrointestinal dysmotility, bladder dysfunction, and pupillary hyporeactivity without variation in ACTA2. Whole genome sequencing revealed a single nucleotide variant contained within the seed sequence of MIR145, which encodes the smooth muscle associated microRNA; hsa-miR-145-5p. RNA expression analysis on patient-derived fibroblasts was consistent with actin cytoskeletal dysfunction, and mutant miR-145-5p was unable to mediate cytoskeletal modulation of smooth muscle cells. MSMDS can be caused by a loss-of-function mutation in the smooth muscle differentiation factor, miR-145-5p, the first described non-coding genetic vasculopathy.

overall_design: RNAseq of human fibroblast and primary VSMCs

first: Christian

last: Cardenas

first: David

last: Sweetser

first: Mark

last: Lindsay

first: Patricia

last: Musolino


title: Neurofibromatosis 1 mutation impairs human induced pluripotent stem cell-derived microglia function

city: St Louis

last: Gutmann

state: MO

address: 660 S Euclid Ave

department: Neurology

institute: Washington University in St Louis

summary: Neurofibromatosis type 1 (NF1) is autosomal dominant condition caused by germline mutations in the NF1 gene on chromosome 17. Children with NF1 are prone to the development of multiple nervous system abnormalities, including autism and brain tumors, which could result from the effect of NF1 mutation on microglia function. Using Nf1-mutant mice, we previously identified impaired microglia process extension and phagocytosis resulting from defects in purinergic signaling. To determine whether these abnormalities are also observed in human microglia, we leveraged human induced pluripotent stem cell engineering to generate human microglia-like (hiMGL) cells harboring three different NF1 patient-derived NF1 gene mutations. Both NF1-mutant and isogenic control hiMGL cells express classical microglial markers and exhibit similar transcriptomes and cytokine/chemokine release profiles, NF1-mutant hiMGL cells have defects in P2X receptor activation, phagocytosis and motility. We conclude that NF1 mutation impairs some aspects of microglia function in humans, which could contribute to a subset of the neurological abnormalities seen in children with NF1.

overall_design: To determine whether NF1 mutation had a dramatic effect on human microglia gene expression, we generated at least three independent cultures of CTL and NF1-mutant hiMGL cells (M1 and M3) for bulk RNA sequencing analysis.   To determine whether NF1 mutation had a dramatic effect on human microglia gene expression, we generated at least three independent cultures of CTL and NF1-mutant hiMGL cells (M1 and M3) for bulk RNA sequencing analysis.

first: Leonard

last: Kuhrt

first: Nirmeen

last: Elmadany

first: Edyta

last: Motta

first: Raphaela

last: Fritsche

first: Marina

last: Schnauß

first: Olivia

last: Cobb

first: Ibrahim

last: Efe

first: Sebastin

last: Diecke

first: Marcus

last: Semtner

first: Corina

last: Anastasaki

first: Helmut

last: Kettenmann


title: Dietary supplementation with a novel fish oil enriched in very-long-chain-polyunsaturated-fatty-acids improves cardiometabolic risk factors and retinal function in mice

first: Matthew

last: Brooks

address: 6 Center Dr Bldg 6, Rm 303

department: NEI

institute: NIH

summary: Very-long-chain polyunsaturated fatty acids (VLCPUFA; C24-38) that contain between 5-6 unsaturated double bonds are a unique class of PUFA that are primarily found in the retina, brain and testes. VLCPUFA appear to have important biological roles that cannot be fulfilled by the more common shorter-chain PUFA, but the lack of a suitable dietary source of VLCPUFA have limited research in this field. Typically, fish oils contain only a small amount of VLCPUFA (<1%, w/w), but we were able to produce a fish oil concentrate that contained over 40% by weight of n-3 VLCPUFA, with chain lengths between C24 and C28. A single-dose oral gavage of the VLCPUFA-oil in C57BL/6J mice resulted in a 9-fold increase in plasma levels of C24:5 n-3 by 2 hours. This was followed by a 70% increase in the retinal level of C24:5 n-3  after 8 hours from the gavage.  Long-term (8-week) dietary supplementation with 1% or 5% (w/w) of VLCPUFA-oil in chow diet did not cause any adverse changes in the plasma chemistry profile or evidence of histologic injury to multiple tissues.  It was found to alter the lipid composition of the liver, brain and eye in 11-month-old C57BL/6J mice. The VLCPUFA supplementation also caused favorable cardiometabolic changes by lowering plasma glucose, insulin, cholesterol and triglyceride levels. Furthermore, mice treated with the VLCPUFA oil had improved electroretinography response and visual performance after 15 consecutive days of oral gavage. Transcriptomic analysis of treated mice revealed significant alternation in genes involved in PPAR signaling pathways. Further in vitro studies demonstrated that the VLCPUFA-oil and chemically synthesized C24:5 n-3 are potent agonists for both PPAR-alpha and gamma. In conclusion, the multiple potential beneficial effects of fish-derived VLCPUFA-oil on eye health and cardiometabolic risk in mice support future efforts to develop VLCPUFA-oil into a novel therapy.

overall_design: After mice were fed chow diet supplemented with 0, 1, or 5% VLCPUFA for 8 weeks, total RNA was isolated from liver samples (n = 6/group) using a RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions.  RNA purity and concentration were assessed using a NanoDropTM spectrophotometer (Thermo Fisher Scientific Inc., Waltham, MA, USA).  A 4200 TapeStation System (Agilent Technologies, Santa Clara, CA, USA) was used with RNA screentapes to generate RNA integrity numbers (RIN) for RNA samples. All RNA samples selected for RNA-seq library preparation had a RIN greater than 7. RNA-seq libraries were prepared using a TruSeq Stranded mRNA Sample Prep Kit (Illumina, San Diego, CA, USA). RNA seq data was handled as described previously (Brooks et al., 2019).

first: Zhi-Hong

last: Yang

first: Aruna

last: Gorusupudi

first: Todd

last: Lydic

first: Anupam

last: Mondal

first: Sato

last: Seizo

first: Isao

last: Yamazaki

first: Hideaki

last: Yamaguchi

first: Jingrong

last: Tang

first: Krishna

last: Rojulpote

first: Anna

middle: B

last: Lin

first: Hannah

last: Decot

last: Koch

first: Daniel

last: Brock

first: Zhen-Dan

last: Shi

first: Zu-Xi

last: Yu

first: Milton

last: Pryor

first: Julia

last: Kun

first: Rolf

last: Swenson

first: Anand

last: Swaroop

first: Paul

last: Bernstein

first: Alan

last: Remaley


title: Removal of oxaliplatin- and cisplatin-DNA lesions requires different global genome repair mechanisms that affect their clinical efficacy.

city: Rotterdam

first: Hannes

last: Lans

address: Wytemaweg 80

department: Molecular Genetics

country: Netherlands

institute: Erasmus MC

summary:
The therapeutical efficacy of cisplatin and oxaliplatin depends on the balance between the DNA damage induction and the DNA damage response of tumor cells. Based on clinical evidence, oxaliplatin is administered to cisplatin-unresponsive cancers, but the underlying molecular causes for this tumor specificity are not clear. Hence, stratification of patients based on DNA repair profiling is not sufficiently utilized for treatment selection.
Using a combination of genetic, transcriptomic and imaging approaches, we identified factors that promote global genome nucleotide excision repair (GG-NER) of DNA-platinum adducts induced by oxaliplatin, but not by cisplatin. We show that oxaliplatin-DNA lesions are a poor substrate for GG-NER initiating factor XPC and that DDB2 and HMGA2 are required for efficient binding of XPC to oxaliplatin lesions and subsequent GG-NER initiation. Loss of DDB2 and HMGA2 therefore leads to hypersensitivity to oxaliplatin but not to cisplatin. As a result, low DDB2 levels in different colon cancer cells are associated with GG-NER deficiency and oxaliplatin hypersensitivity. Finally, we show that colon cancer patients with low DDB2 levels have a better prognosis after oxaliplatin treatment than patients with high DDB2 expression. We therefore propose that DDB2 is a promising predictive marker of oxaliplatin treatment efficiency in colon cancer.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for XPCoxa-inactive cells (DLD-1 and Lovo) versus XPCoxa-active (HCT116 and SW480). Colon cancer cells were grown in standard media and after cell expansion, total RNA was isolated in triplicates and analysed for total RNA expression profile. Treatment conditions are not part of this manuscript, which includes only data from untreated WT cells.

first: Jana

last: Slyskova

first: Joana

last: Loizou


title: Modelling Triple A syndrome with functional steroid-producing cells derived from pluripotent stem cells

city: Dresden

first: Gerard

last: Ruiz-Babot

address: Fetchestrasse 74

country: Germany

institute: Uniklinikum Dresden

summary: Generation of cell with the ability to produce glucocorticoids and mineralocorticoids

overall_design: We performed RNA sequencing of control and differentiated samples using steroidogenic factor 1 (SF-1) with or without activation of the PKA signalling.

first: G

first: D

last: Breault


title: Targeting MLKL alleviates neuroinflammation and prevents motor neuron damage in Parkinson’s traits

city: Shanghai

first: Wenqing

last: Gao

address: Songhu Road, Yangpu District

institute: Fudan university

summary: Neuroinflammatory processes are a prominent contributor to the pathology of Parkinson’s disease (PD), characterized by the progressive loss of dopaminergic neurons in the substantia nigra (SN) and deposits of α-synuclein aggregates. MLKL-mediated cell necroptosis might occur in the onset of PD and lead to neuronal dopaminergic degeneration. However, the link between α-synuclein, neuroinflammatory processes, and neurodegeneration in PD remains unclear. Here, our in vitro study indicated that inhibition of MLKL exerted a protective effect against 6-OHDA- and TNF-α-induced neuronal cell death. Furthermore, we created a mouse model (Tg-Mlkl-/-) with typical progressive Parkinson traits by crossbreeding SNCA A53T transgenic mice with MLKL knockout mice. Tg-Mlkl-/ mice displayed dramatically improved motor symptoms and reduced hyperphosphorylated α-synuclein expression. More data suggested that MLKL deficiency protected dopaminergic neurons, blocked neuronal cell death, and attenuated neuroinflammation by inhibiting the activation of the microglia and astrocytes. Single-cell RNA-seq analysis revealed reduced microglial cells and damped neuron death in the SN of the Tg-Mlkl-/- mice. Subcluster analysis identified a unique cell type-specific transcriptome profiling in the MLKL deficiency mice. Thus, MLKL represents a critical therapeutic target for reducing neuroinflammation and preventing dopaminergic neuron degeneration.

overall_design: mRNA profiles of 10-month old Tg-Mlkl+/+ (hA53T α-synuclein mice) and Tg-Mlkl-/- mice (generated by the MLKL KO plus hA53T transgenic mice) in the substantia nigra region

first: Lu

last: Geng

first: Saiyin

last: Hexige

first: Jixi

last: Li


title: Expression data from ageing wt N2 Bristol Caenorhabditis elegans population.

city: Athens

first: Niki

last: Chondrogianni

state: Attiki

address: Leof. Vasileos Konstantinou 48

department: ICB - Institute of Chemical Biology

country: Greece

institute: National Hellenic Research Foundation

summary:
The determination of molecular pathways that are affected with age and lead to increased disease susceptibility is crucial. The nematode has proven an ideal experimental model to study ageing due to significantly conserved genes governing ageing throughout species. Profiling of gene expression levels in ageing wt Caenorhabditis elegans, utilizing a robust Affymetrix microarray platform, resulted in the identification of age-dependent gene expression alterations that characterize the nematode's ageing process.
We used Affymetrix microarrays to detail the global programme of gene expression underlying ageing and identified distinct classes of up- or down-regulated genes during this process.

overall_design: We profiled gene expression levels of wt C. elegans population of three ageing time-points, in biological triplicates for young (Day 1) and middle aged (Day 6) ones and biological duplicates for old worms (Day 12) using the Affymetrix GeneChip™ C. elegans Gene 1.1 ST Array Platform.

first: Tilman

last: Grune

first: Foteini

last: Aktypi


title: Transcriptomes Sequencing  of si-EIF4G2 and si-NC groups in Hep3B cells

city: Hangzhou

first: Shuangshuang

address: Qingchun Road

institute: the first affiliated hospital of Zhejiang University

summary: We transfected siRNA-EIF4G2 and si-NC into Hep3B cells to explore the differentially expressed genes in cells and the affected intracellular signaling pathways after EIF4G2 knockdown

overall_design: There are six samples, three of which are the knockdown group and three of which are the control group

first: Jiajia

last: Shao

first: Yanning

last: Liu

first: Min

last: Zheng


title: Transcriptome analysis and characterization of differential pathways of hMSCs in response to BiFP containing integrin or DDR2 binding motifs creates signals

status: Public on Dec 13 2023

city: Taichung

first: Wei-Chung

last: Cheng

address: No. 91, Hsueh-Shih Road

department: Research Center for Tumor Medical Science

country: Taiwan

institute: China Medical University

summary: To demonstrate the capacity of BiFP with specific integrin or receptor binding motifs for signal creation, three individual hMSCs from distinct sources, such as bone marrow (BM-hMSCs) and dental pulp (DP-hMSCs), were cultured in complete growth medium with BiFP containing integrin α2β1 (GFOGER) or discoidin domain receptors 2 (DDR2, GVMGFO) binding motifs for 48 h, followed by RNA-seq analysis. Gene Ontology (GO) and Gene Set Enrichment Analysis (GSEA) revealed that BiFP containing α2β1 or DDR2 binding motifs enriched different gene sets compared to the same cells treated with peptides not containing the binding motifs (Fig. S6A). These data suggest that BiFP containing integrin or receptor binding motifs creates signals that may play a role in instructing cell fate determination.

overall_design: Three individual hMSCs from distinct sources, such as bone marrow (BM-hMSCs) and dental pulp (DP-hMSCs), were cultured in complete growth medium with 40 uM BiFP containing integrin α2β1 (GFOGER) or discoidin domain receptors 2 (DDR2, GVMGFO) binding motifs for 48 h, followed by RNA-seq analysis. (A) Venn diagram showing overlap (pathway numbers) among gene sets associated with three individual hMSCs. (B) Heat map of top 10 significantly shared signaling pathways and bio-functions by gene set enrichment analysis (GSEA) of RNA-seq data associated with integrin or DDR2 binding motifs creates signals that may play a role in instructing cell fate determination. (C) PI3K/AKT activation pathway in the top 10 significantly reactome pathways from overlap integrin-response genes of DP-hMSCs.

first: Shih-Chieh

last: Hung

first: Tzu-Ya

last: Huang

first: Chiahsin


title: Transcriptome analysis among young and senescent fibroblasts expressing shLuciferase or shFbxo22

city: Minato ku

first: Satotaka

last: Omori

state: tokyo

address: shirokanedai, 4-6-1

country: Japan

institute: the university of Tokyo

summary: We carried out the analysis using human skin fibrobllast HCA2 (MJ90) cells dox-inducible shLuciferase or shFbxo22. Cells were indcued to be senescent cells by treatment with 10 Gy. As a result, Gene set enrichment analysis revealed a significant increase in the expression of lysomal-related and autophagosomal genes in control cells, whereas this gene ontology was not increased in cells depleted of Fbxo22

overall_design: Examination of young and senescent HCA2 cells expressing dox-inducible shLuciferase or shFbxo22.

first: Yoshikazu

last: Johmura

first: Makoto

last: Nakanishi


title: Daily Longitudinal RNAseq Profiling of Rattus Norvegicus Exposed to Liver Toxic Drugs

city: Houston

first: yi

last: chai

address: pgpr

institute: Biostate AI

summary:
Living organisms are intricate systems with dynamic internal processes. Their RNA, protein, and metabolite levels fluctuate in response to variations in health and environmental conditions. Among these, RNA expression is particularly accessible for comprehensive analysis, thanks to the evolution of high throughput sequencing technologies in recent years. This progress has enabled researchers to identify unique RNA patterns associated with various diseases, as well as to develop predictive and prognostic biomarkers for therapy response. Such cross-sectional studies allow for the identification of differentially expressed genes (DEGs) between groups, but they have limitations. Specifically, they often fail to capture the temporal changes in gene expression following individual perturbations and may lead to significant false discoveries due to inherent noise in RNA sequencing sample preparation and data collection.
To address these challenges, our study hypothesized that frequent, longitudinal RNA sequencing (RNAseq) analysis of blood samples could offer a more profound understanding of the temporal dynamics of gene expression in response to drug interventions, while also enhancing the accuracy of identifying genes influenced by these drugs. In this research, we conducted RNAseq on 829 blood samples collected from 84 Sprague-Dawley lab rats. Excluding the control group, each rat was administered one of four different compounds known for liver toxicity: tetracycline, isoniazid, valproate, and carbon tetrachloride. We developed specialized bioinformatics tools to pinpoint genes that exhibit temporal variation in response to these treatments.

overall_design: Following a 3-day acclimatization period for the rats in their new environments, daily blood collection procedures commenced, with the initial day of collection designated as Day 1. A volume of 200µL was consistently drawn for each procedure. This specific volume was strategically chosen to achieve a dual objective: firstly, to gather an adequate amount of biospecimen for both analytical and storage purposes; and secondly, to mitigate any excessive physiological stress or harm to the rats resulting from the phlebotomy process. The determination of this volume took into account the potential cumulative impact of the daily blood collection routine, adhering to protocols sanctioned by the Institutional Animal Care and Use Committee (IACUC). To enhance the reliability of the experimental results and reduce the influence of extraneous variables, all blood draws were scheduled at approximately 10:00am local time each day. Pertinent to the experimental design, selected rats received an intravenous dose of the test drug on either Day 3 or Day 8, roughly 30 minutes prior to the ensuing blood draw. It should be noted that the initial blood specimen obtained post-administration may not fully encapsulate the comprehensive effects of the drug, given the unique pharmacokinetic properties of each compound under investigation. Upon the conclusion of each experimental iteration, liver necropsy samples from the rats were subjected to conventional histopathological analysis.


title: Individual Variability in Human Cell Type Transcriptomes and Epigenomes [OF2B]

city: La Jolla

first: Joseph

middle: R

last: Ecker

address: 10010 North Torrey Pines Road

institute: HHMI-Salk-Institute

summary: Diversity and individual variability are essential to human cognitive function. Identifying the conserved and variable (epi)genomic signatures of the brain’s cellular components is critical for understanding the neurobiological basis of individual variation in brain function.  We applied single nucleus methylome and transcriptome sequence (snmCT-seq) to neurons from the frontal cortex of 11 adult human donors spanning a range of ages from 23 to 74, including males and females (Broadmann Area BA46). We clustered cells into brain cell types based on methylation features. We then examined the transcriptome and epigenome features in each cell type between and within individual donors. Taking advantage of the multimodal measurements in single cells, we also identified the relation between RNA expression and methylation level.These data with multiomics measurement from donors with sex and age diversity aims to approach the dimension of inter-individual variability.

overall_design: We apply snmCT-seq to identify the transcriptomic and epigenomic features of neurons from individual adult human frontal cortex, including 3 aged male donors (age range 70-71), 3 aged female donors (71-74 years old), 3 young male donors  (25 years old) and 2 young female donors  (23-30 years old). For each donor, 2 chunks of brain tissue were collected and processed separately, to assess within-donor variability. This sample is from chunk A of a 73 years old female.

first: Jofan

last: Chien

first: Anna

last: Bartlett

first: Hanqing

first: Rosa

last: Castanon

last: Nery

first: Bang-An

last: Wang

first: Nick

last: Johnson

first: Julia

last: Osteen

first: M

middle: M

last: Behrens

first: Eran

last: Mukamel


title: G3BP1 translocates into mitochondria to impair MCU complex function and promotes NASH progression

city: Nanjing

first: ying

last: zheng

address: 639 Longmian Avenue, Chunhua Street, Jiangning District,

institute: China Pharmaceutical University

summary: Mitochondrial calcium signaling plays a critical role in mitochondrial homeostasis during non-alcoholic steatohepatitis (NASH) progression. Here, we report Ras‐GTPase activating protein SH3 domain‐binding protein 1 (G3BP1), a core protein of stress granule (SG), significantly upregulated in NAFLD/NASH patients, mouse models and palmitic acid-stimulated hepatocytes. Hepatocyte-specific G3BP1 deficiency attenuates NASH in two dietary mouse models. SG and the mitochondrial import protein TOM70 collaboratively mediate the translocation of G3BP1 to the mitochondria. G3BP1 interacts and stabilizes mitochondrial calcium uptake 1 (MICU1) via inhibiting YME1L1-mediated degradation of MICU1, and also impedes MCU complex activity and assembly, leading to mitochondrial calcium overload. Moreover, metabolic stress suppresses TRIM25-mediated K63-ubiquitination of G3BP1 and subsequent SG disassembly. Pharmacological inhibition of G3BP1 impairs the G3BP1-MICU1 interaction and prevents mitochondrial homeostasis imbalance and NASH progression. Collectively, we uncover the significant role of mitochondrial G3BP1 in mitochondrial homeostasis and NASH progression, which provides a potential target for therapeutic interventions.

overall_design: To investigate how G3BP1 affects NASH, we conducted RNA sequencing (RNA-seq) on the livers of G3bp1-HKO and G3bp1-Flox mice that were subjected to a high-fat diet (HFD).

first: Yang

last: Cheng

first: Jingyi

first: Shengtao

last: Ye

first: Yanqiu

last: Zhang

first: Yingrong

last: Leng

first: Ying

last: Zheng

first: Mengmeng

last: He

first: Enyi

last: Wu

first: Lingyi

last: Kong

first: Hao


title: MicroRNAs expression in vulvar lichen sclerosus keratinocytes and fibroblasts: further evidence and possible pathogenetic implications from an observational study

city: Ferrara

first: Cristian

last: Bassi

state: Ferrara

address: Via Fossato di Mortara 70

department: Medicina Traslazionale e per la Romagna

country: Italy

institute: Università di Ferrara

type: Non-coding RNA profiling by high throughput sequencing

summary: It seems established that genetic and epigenetic determinants drive the multifactorial pathogenic processes in vulvar lichen sclerosus (VLS). Aberrant expression of microRNAs (miRNAs) has been observed in a few studies suggesting potential involvement. We aimed to assess the expression of miRNAs both in VLS and in healthy keratinocytes and fibroblasts cultured separately. The differential analysis led to the identification of 171 and 111 microRNAs with an expression difference of at least 1.5-fold between VLS and healthy samples, in keratinocytes and fibroblasts, respectively. More than 80% of the 111 microRNAs identified as differentially expressed in fibroblasts were also found to be differentially expressed in keratinocytes. A number of dysregulated miRNAs are involved in inflammation and fibrotic processes, namely miR-10a-5p and 3p, miR-143-3p and 5p, miR-181a-5p and 3p, miR-181b-5p and 3p, miR-21-3p, miR-146b-5p and miR-29c. Our results showed a clear separation of VLS keratinocytes and fibroblasts from healthy cells in terms of miRNA expression. It is noteworthy that the most dysregulated miRNAs are implicated in inflammatory and fibrotic pathways. It is conceivable that miRNA expression is functional in regulating pathogenetic mechanisms of LS.

overall_design: In this observational study, 5 VLS and 5 healthy skin tissue specimens were used to derive independent keratinocyte and fibroblast cultures.

first: Alessandro

last: Borghi

first: Monica

last: Corazza

first: Lucilla

last: D'Abundo

first: Fernanda

last: Martini

first: Massimo

last: Negrini


title: ChIP-seq in parental and drug-resistant non-small cell lung cancer (NSCLC) cells

city: Shenyang

first: Qiuyue

address: No. 103, Wenhua Road, Shenhe District

institute: Shenyang Pharmaceutical University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Epigenetic regulation is one of the important causes of drug resistance in NSCLC.EZH2 and G9a as epigenetic enzymes play an important role in drug resistance in lung cancer. To further investigate the mechanism of EZH2 and G9a mediating NSCLC drug resistance, we used ChIP-seq to compare the changes of H3K27me3 and H3K9me2, the catalytic substrates of EZH2 and G9a, in parental cells H1299 and cisplatin-resistant cells H1299/CDDP.

overall_design: Chromatin immunoprecipitation sequencing(ChIP-seq) for  H3K27me3 and H3K9me2 in parental cells H1299 and cisplatin-resistant cells H1299/CDDP.


title: Individual Variability in Human Cell Type Transcriptomes and Epigenomes [YF1A]

first: Joseph

last: Ecker

first: Jofan

last: Chien

first: Anna

last: Bartlett

first: Hanqing

last: Liu

first: Rosa

last: Castanon

last: Nery

first: Bang-An

last: Wang

first: Nick

last: Johnson

first: Julia

last: Osteen

first: M

last: Behrens

first: Eran

middle: A


title: Role of the Muscle-Brain-Gut axis in the regulation of skeletal muscle mass II

city: Chuo-ku, Kobe City, Hyogo

first: Yu

last: Hirata

address: 7-5-1 Kusunoki-cho

department: Department of Internal Medicine Division of Diabetes and Endocrinology

institute: Kobe University Graduate School of Medicine

summary: We propose that the Muscle-Brain-Gut axis regulates skeletal muscle mass through the defined mechanism.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for gastrocnemius muscle of immobilized mice.

first: Wataru

last: Ogawa


title: Individual Variability in Human Cell Type Transcriptomes and Epigenomes [OM1A]

overall_design: We apply snmCT-seq to identify the transcriptomic and epigenomic features of neurons from individual adult human frontal cortex, including 3 aged male donors (age range 70-71), 3 aged female donors (71-74 years old), 3 young male donors  (25 years old) and 2 young female donors  (23-30 years old). For each donor, 2 chunks of brain tissue were collected and processed separately, to assess within-donor variability. Data in this series was from chunk A of a 70 years old male.

last: Mukamel


title: Individual Variability in Human Cell Type Transcriptomes and Epigenomes [OF1B]

overall_design: We apply snmCT-seq to identify the transcriptomic and epigenomic features of neurons from individual adult human frontal cortex, including 3 aged male donors (age range 70-71), 3 aged female donors (71-74 years old), 3 young male donors  (25 years old) and 2 young female donors  (23-30 years old). For each donor, 2 chunks of brain tissue were collected and processed separately, to assess within-donor variability.Data in this series was from chunk B of a 73 years old female.


title: ACE2-independent SARS-CoV-2 virus entry through cell surface GRP78 on monocytes - evidence from a translational clinical and experimental approach

city: Muenchen

first: Bing

last: Han

address: Marchioninistrasse 15

summary: SARS-CoV-2 infects host cells via an ACE2/TMPRSS2 entry mechanism. Monocytes and macrophages, which play a key role during severe COVID-19 express only low or no ACE2, suggesting alternative entry mechanisms in these cells. In silico analyses predicted GRP78, which is constitutively expressed on monocytes and macrophages, to be a potential candidate receptor for SARS-CoV-2 virus entry. To confirm the hypothesis, we conducted high-throughput RNA sequence to characterize the role of GRP78 in monocytes function in COVID-19 patients

overall_design:
We then performed gene expression profiling analysis using data obtained from RNA-seq of separated primary monocytes from 4 healthy controls and 4 COVID-19 patients
Comparative gene expression profiling analysis of RNA-seq data for separated monocytes from 4 healthy controls and 4 COVID-19 patients

first: Dominique

last: Moser

first: Tobias

last: Wöhrle

first: Alexander

last: Choukér


title: Sex and Age Impact CD4+ T Cell Susceptibility to HIV In Vitro Through Cell Activation Dynamics [bulk RNA-Seq]

city: Lausanne

first: Paolo

last: Angelino

address: Quartier Sorge, Bâtiment Génopode

department: BCF

country: Switzerland

institute: SIB Swiss Institute of Bioinformatics

summary: Cellular composition and responsiveness of immune system evolve upon ageing and are influenced by biological sex. CD4+ T cells from women living with HIV exhibit decreased viral replication ex vivo compared to men. We thus hypothesized that these findings could be recapitulated in vitro, and infected primary CD4+ T cells with HIV-based vectors pseudotyped with VSV-G or HIV envelopes. We used cells isolated from twenty donors to interrogate the effect of sex and age on permissiveness over a six-day activation kinetics. Our data identified an increased permissiveness to HIV between 24 and 72h post-stimulation. Sex- and age-based analysis at these time points showed increased susceptibility to HIV of cells isolated from males and from donors over 50 years old, respectively. Parallel assessment of surface marker expression revealed higher frequencies of activation markers (CD69, CD25, HLA-DR) and immune check point inhibitors (PD-1 and CTLA-4 in cells from highly permissive donors. Furthermore, positive correlations were identified between CD69, PD-1 and CTLA-4 expression kinetics and HIV expression kinetics. Cell population heterogeneity was assessed by single-cell RNA-Seq analysis and no cell subtype enrichment was identified according to sex. Finally, transcriptomic analyses further highlighted the role of activation in those differences with enriched activation and cell cycle gene sets in men and in older women cells. Altogether, this study brought further evidence about individual features affecting HIV replication at the cellular level and should be considered in latency reactivation studies for HIV cure.

overall_design: To investigate the differences in CD4+ T cells between sexes at different ages, we stimulated (TCR-mediated) primary CD4+ T cells from 10 men and 10 women, then performed RNASeq at 24h and 72h after stimulation. As samples were processed in two batches, two samples (donor B, male, and W, female) were repeated in each batch to allow for identification and correction of batch effects.

first: Ludivine

last: Brandt

first: Raquel

last: Martinez

first: Sara

last: Cristinelli

first: Angela

last: Ciuffi


title: Sex and Age Impact CD4+ T Cell Susceptibility to HIV In Vitro Through Cell Activation Dynamics

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

overall_design: Refer to individual Series


title: Sex and Age Impact CD4+ T Cell Susceptibility to HIV In Vitro Through Cell Activation Dynamics [scRNA-Seq]

overall_design: To investigate the differences in CD4+ T cell subpopulations between sexes, we stimulated (TCR-mediated) primary CD4+ T cells from 2 men and 2 women, then performed sc-RNA-Seq


title: Molecular profiling of lymphatic endothelial cells activation in vitro

city: Firenze

first: Gianluca

last: Mattei

state: FI

address: Via di S. Marta, 3

institute: Università degli Studi di Firenze

summary: The lymphatic vascular system plays a key role in cancer progression. Indeed, the activation of lymphatic endothelial cells (LECs) through the lymphangiogenic process allows the formation of new lymphatic vessels (LVs) that represent the major route for dissemination of solid tumors. This process is governed by a plethora of cancer-derived and microevironmental mediators that strictly activate and control specific molecular pathways in LECs. In this work we used an in vitro model of LEC activation to trigger lymphangiogenesis using a mix of recombinant pro-lymphangiogenic factors (VFS) and a co-culture system with human melanoma cells. Both systems efficiently activated LECs, and under these experimental conditions RNA sequencing was exploited to unveil the transcriptional profile of activated LECs.  Our data demonstrate that both recombinant and tumor cell-mediated activation trigger significant molecular pathways associated with endothelial activation, morphogenesis and cytokine-mediated signaling. In addition, this system provides information on new genes to be further investigated in the lymphangiogenesis process and open the possibility for further exploitation in other tumor contexts where lymphatic dissemination plays a relevant role.

overall_design: RNA-Seq of lymphatic endothelial cells (LEC) activated by a mix of recombinant pro-lymphangiogenic factors and an RNA-Seq of LEC a co-cultured with human melanoma cells. Both systems efficiently activated LECs.

first: Marta

last: Turati

first: Alessia

last: Boaretto

first: Alberto

last: Magi

first: Maura

last: Calvani

first: Roberto

last: Ronca


title: Effect of efferocytosis on the inflammatory response of primary murine macrophages

city: Frankfurt

last: Schmid

address: Theodor-Stern-Kai 7

department: Institute of Biochemistry I

institute: Goethe University Frankfurt

summary: Despite the importance of rapid adaptive responses for an efficient resolution of inflammation, which are commonly regulated on a post-transcriptional and specifically translational level, translational changes caused by efferocytosis remain largely elusive. To gain further insights into such gene regulatory principles, we analyzed translational changes in efferocytic and non-efferocytic bone marrow-derived macrophages (BMDM) in the course of inflammation. Using total RNA-sequencing, we confirmed that efferocytosis induced a pro-resolution signature in LPS-stimulated, inflammatory macropahges. Interestingly though, while LPS-induced transcriptional changes appeared rather small between efferocytic and non-efferocytic macrophages, we observed considerable differences on the level of de novo synthesized proteins. We further identified translationally regulated targets showing reduced translation upon inflammatory stimulation, which was buffered upon efferocytosis. Herein, pro-resolving matrix metallopeptidase 12 (Mmp12) emerged as a novel translationally regulated candidate, which was translationally repressed during early inflammation and increased during the resolution phase. Functionally, the translational repression of Mmp12 was linked to increased spontaneous two-dimensional migration. In summary, we identified the novel translationally regulated target Mmp12 in the context of the resolution of inflammation in primary murine macrophages, which is associated with a modulation of spontaneous migration.

overall_design: total RNA-seq of naive and efferocytic primary mouse macrophages stimulated with LPS/IFNg for 6h (n=2)

first: Silvia

last: Kuntschar

first: Bernhard

last: Brüne


title: Molecular analysis of aging heart in female nonhuman primates.

city: Winston-Salem

first: Jeannie

last: Chan

state: NC

address: Medical Center Boulevard

department: Internal Medicine

institute: Wake Forest School of Medicine

summary:
The goal of this study was to determine the mechanisms underlying age-associated changes in the heart.
Heart samples (n=35) were collected from female baboons aged 7.5 to 22.1 years (human equivalent 30 to 88 years).
RNA-Seq data from these samples were analyzed by weighted-gene correlation network analysis and pathway enrichment.
The results revealed a metabolic shift from catabolic to anabolic pathways, leading to glycosaminoglycan accumulation
in the extracellular matrix of the left ventricle through the hexosamine biosynthetic pathway.

overall_design:
The study included 35 normal female baboons ranging in age from 7.5 to 22.1 years (human equivalent 30 to 88 years).
Heart tissue samples from the left ventricles were collected at necropsy, snap-frozen in liquid nitrogen and stored at -80oC until use.

first: Luis

last: Grilo

first: Peter

middle: W

last: Nathanielsz

first: Laura

last: Cox


title: Circulating miRNA Profiles in COVID-19 Patients and Meta-Analysis: Implications for Disease Progression and Prognosis

city: Monrovia

first: Liangliang

last: Gao

address: 1225 S Shamrock Ave

institute: ChromoLogic

summary: We compared circulating miRNA profiles of hospitalized COVID-positive patients (n = 104, 27 with ARDS) and age and gender matched healthy controls (n = 18) to identify miRNA signatures associated with COVID and COVID-induced ARDS. Meta-analysis incorporating data from published studies and our data was performed to identify a set of differentially expressed miRNAs in 1) COVID-positive patients versus healthy controls as well as 2) severe (ARDS+) COVID vs moderate COVID. Gene ontology enrichment analysis of the genes these miRNAs interact with identified terms associated with immune response, such as interferon and interleukin signaling, as well as viral genome activities associated with COVID disease and severity. Additionally, we observed downregulation of a cluster of miRNAs located on chromosome 14 (14q32) among all COVID patients. To predict COVID disease and severity, we developed machine learning models that achieved AUC scores between 0.88–0.93 for predicting disease, and between 0.62–0.81 for predicting severity, even across diverse studies with different sample types (plasma versus serum), collection methods, and library preparations. Our findings provide network and top miRNA feature insights into COVID disease progression and contribute to the development of tools for disease prognosis and management.

overall_design: Plasma samples were used to obtain miRNA profiles for patients and normal controls

first: Espoir

last: Kyubwa

first: Mark

last: Starbird

first: Jesus

last: de Leon

first: Michelle

last: Nguyen

first: Klaude

last: Rogers

first: Naresh

last: Menon


title: Individual Variability in Human Cell Type Transcriptomes and Epigenomes [OM2A]

first: Joseph

last: Ecker

department: Genomic Analysis Laboratory

first: Jofan

last: Chien

first: Anna

last: Bartlett

first: Hanqing

last: Liu

first: Rosa

last: Castanon

last: Nery

first: Bang-An

last: Wang

first: Nick

last: Johnson

first: Julia

last: Osteen

first: M

last: Behrens

first: Eran

last: Mukamel


title: Epigenetic and Transcriptional regulation of the Human Angiotensinogen Gene by High Salt

city: New Haven

first: Sravan

middle: Kumar

last: Perla

state: CT

address: 333 Cedar Street

department: Pharmacology

institute: Yale University

summary: Hypertension is caused by a combination of genetic and environmental factors. Angiotensinogen (AGT) is a component of RAAS, that regulates blood pressure. The human AGT (hAGT) gene has -6A/-6G polymorphism and -6A variant is associated with human hypertension. In this study, we have investigated the epigenetic regulation of the hAGT gene. To understand transcriptional regulation of the hAGT, we have made transgenic animals containing -6A. We show that HS affects DNA methylation and modulates transcriptional regulation of this gene in liver and kidney. HS increases hAGT gene expression in -6A TG mice. We have observed that the number of CpG sites in the hAGT promoter is decreased after HS treatment. In the liver, four CpG sites are methylated whereas after HS treatment, only two CpG sites observed. In the kidney, five CpG sites are methylated, whereas after HS treatment, only three CpG sites are observed. These results suggest that HS promotes DNA demethylation and increasing AGT gene expression. RT-PCR and immunoblot analysis show that hAGT gene expression is increased after HS treatment. Chip assay has shown that transcription factors bind strongly after HS treatment. RNA-Seq analysis identified differentially expressed genes, canonical pathways, upstream regulators. One of the plausible mechanisms for HS induced up-regulation of the hAGT gene is through IL-6/JAK/STAT3/AGT axis.

overall_design:
To understand the epigenetic and transcriptional regulation of hAGT gene we have made transgenic animals containing -6A.
We gave high salt to mice and collected liver and kidney tissues. We isolated RNA and did RNA Seq analysis in liver and kidney tissues.
We then performed gene expression profiling analysis using data obtained from RNA-seq.
We further identified top canonical pathways, top diseases and functions and upstream regulators by using Ingenuity Pathway Analysis.

first: Ashok

last: Kumar


title: Age and ligand specificity influence the outcome of pathogen engagement on preleukemic and leukemic B cell precursor populations.

city: Vancouver

first: Tanmaya

last: Atre

address: 938 W 28th Ave

country: Canada

institute: BC Children's Hospital Research Institute

summary: Common infections have long been proposed to play a role in the development of pediatric B cell acute lymphoblastic leukemia (B-ALL). However, epidemiological studies report contradictory effects of infection exposure on subsequent B-ALL risk, and no specific pathogen has been definitively linked to the disease. A unifying mechanism to explain the divergent outcomes could inform disease prevention strategies. We previously reported that the pattern recognition receptor (PRR) ligand Poly(I:C) exerted effects on B-ALL cells that were distinct from those observed with other nucleic acid-based PRR ligands. Here, using multiple double-stranded RNA moieties, we show that the overall outcome of exposure to Poly(I:C) reflects the balance of opposing responses induced by its ligation to endosomal and cytoplasmic receptors. This PRR response biology is shared between mouse and human B-ALL and increases leukemia-initiating cell burden in vivo during the preleukemia phase of B-ALL, primarily through TNF-a signaling. The age of the responding immune system further influences the impact of dsRNA exposure on B-ALL cells in both mouse and human settings. Overall, our study demonstrates that potentially pro- and anti-leukemic effects can each be generated by stimulation of pathogen recognition pathways and indicates a mechanistic explanation for the contrasting epidemiologic associations reported for infection exposure and B-ALL.

overall_design: To investigate the effect of Poly (A:U)  on LICs, Eμ-Ret pups were treated with either PBS or Poly(A:U) and LICs were purified 7 days later. RNA-seq was performed on purified LICs from 5 PBS treated and 5 Poly (A:U) treated , Eμ-Ret pups.

first: Ali

last: Farrokhi

first: Samuel

last: Salitra

first: Gregor

last: Reid


title: Micro RNA expression profiling using NanoString technology from IgA Nephropathy patients from Indian cohort.

city: Bengaluru

last: Shankar

address: Mysore Rd, near City Market, New Tharagupet

department: Nephrology

country: India

institute: Institute of Nephrourology, Victoria Hospital Campus, Bengaluru

summary:
The current study makes use of NanoString targeted technology to profile urinary exosomal miRNAs from IgA nephropathy affected patients and corresponding healthy controls.
Circulatory biomarkers were detected for IgA nephropathy from Indian cohort which can be made used for the diagnostic therapy. 14 miRNAs were detected to be related to the disregulation in miRNome of IgA nephropathy patients using lasso feature selection method, out of which multiple miRNAs like hsa.mir.146b.3p, hsa.mir.599 and many more was resulted with high AUROC values >=0.9 efficient in differentiating between healthy controls and IgA nephropathy condition. These markers can be use further in the diagnosis and treatment of IgAN.

overall_design: In total, 10 control and 25 IgN samples were used for the study.

first: Mythri

first: Aditya

last: Shetty

first: N

last: Madhura


title: Gene expression analysis of VMRC-LD cells transfected with siRNA against DRAIC

city: Toyoake

first: Kouhei

last: Sakurai

address: 1-98 Dengakugakubo, Kutsukake-cho

department: Department of Joint Research Laboratory of Clinical Medicine, School of Medicine

institute: Fujita Health University

summary:
DRAIC is a long non-coding RNA, that is involved in various cancer progressions.
We performed gene expression microarray after DRAIC knockdown in VMRC-LCD cells to reveal the potential downstream genes.

overall_design: VMRC-LCD cells were transfected with si-negative control (si-NC) or siRNA no2 against DRAIC (si-DRAIC2), and gene expression microarray was performed.

first: K

first: S

last: Yamada


title: TGF-b1 stimulates lymphatic endothelial cells to produce IL-7 and IL-15, which act as chemotactic factors for breast cancer cells with EMT properties

city: Stockholm

first: Anastasios

middle: Erik

last: Damdimopoulos

state: Huddinge

address: Hälsovägen 7c

department: Department of Biosciences and Nutrition

country: Sweden

institute: Karolinska Institute

summary: The lymphatic system is a major gateway for tumor cell dissemination but the mechanisms of how tumor cells gain access to lymphatic vessels are not completely understood. Breast cancer cells undergoing epithelial-mesenchymal transition (EMT) gain invasive and migratory properties. Overexpression of the cytokine transforming growth factor β1 (TGF-b1), a potent inducer of EMT, is frequently detected in the tumor microenvironment and correlates with invasion and lymph metastasis. Recently, we reported that TGF-b1 stimulated breast cancer cells with EMT properties migrate in a targeted fashion towards the lymphatic system via CCR7/CCL21-mediated chemotaxis, similar to dendritic cells during inflammation. Here, we aimed to identify additional chemotactic factors and receptors that could be involved in this. Through a combination of RNA sequencing analysis, database screening and invasion assays we identified IL-7/IL7R and IL-15/IL15R as pairs of chemokines and chemokine receptors with potential roles in promoting chemotactic migration of breast cancer cells with EMT properties towards the lymphatics. The results warrant studies to further explore their possible roles in lymph metastasis in breast cancer. Moreover, they demonstrate the capacity of TGF-b1 to orchestrate crosstalk between tumor cells and lymphatic endothelial cells.

overall_design: Total RNA was extracted from quadruplicate samples of svLEC cells that were either left untreated or treated for 72 h with 10 ng/ml TGFB1 (R&D Systems, Abingdon, UK), using RNeasy Mini Kit (Qiagen, Valencia, CA) according to the manufacturer´s protocol. Libraries were prepared using TruSeq Stranded mRNA kit (Illumina) and sequenced on the Illumina Nextseq 550 platform, at single end mode and generating 75 bp reads that were mapped to the mouse reference genome (GRCm38/mm10) and Differential Expression Analysis was performed using EdgeR [20].

first: Nikolina

last: Giotopoulou

first: Malgorzata

last: Parniewska

first: Wenyang

last: Shi

first: Wenwen

last: Sun

first: Jonas

last: Fuxe


title: transcriptomic analysis of proliferative or differentiated myoblasts

city: Paris

first: sebastien

last: jacques

address: 24 rue du faubourg saint jacques

department: Genomic

institute: Institut Cochin

summary: Adult skeletal muscle is a plastic tissue that can adapt its size to workload and that can regenerate after demage. Here, we show that RhoA within primary myoblasts is needed for a correct muscle regeneration by controlling satellite cell fusion without affecting their proliferation or their differentiation. Moreover primary cultured myoblast loosing RhoA have no defects in cytoskeleton reorganization however their movement is altered compared to control cells. At the molecular level, we found that RhoA controls the expressions of different genes depending on step of differentiation process, not necessarly already described as implicated in fusion program. These findings unravel the implication of RhoA within satellite cells regulating myoblast fusion in response to demage in order to allow a correct regeneration process.

overall_design: The aim of the analysis is to compare proliferative myoblasts and differentiated myotubes with and wthout RhoA. RhoAfloxed mice were injected or not with tamoxifen in order to delete in vivo RhoA only in satellite cells. Primary myoblast were isolated by RhoAfloxed mice by FACS. The cells isolated by FACS,  proliferate and differentiate in culture. RNA was isolated from primary proliferative myoblast and differentiated myotubes isolated by control or RhoA deleted mice. Microarray analysis will help to understand the molecular pathways involved in fusion defect observed in vivo and in vitro. Isolated RNA from 3 independent control and RhoA-lacking cell cultures were used to perform trasncriptomic arrays. Total Rna was isolated from cells at day0, day1 and day3 of differentiation.

first: Chiara

last: Noviello

first: Athanassia

last: Sotiropoulos


title: Roles of circular RNA in cardiac fibrosis

city: Hwasun, Jeollanam-do

first: Young-Kook

last: Kim

address: 264, Seoyang-ro

department: Department of Biochemistry

country: South Korea

institute: Chonnam National University Medical School

summary: Heart failure is one of the leading causes of death and it often accompanies activation of quiescent cardiac myofibroblasts, which results in cardiac fibrosis and resulting cardiac remodeling. Circular RNA, one form of non-coding RNA discovered recently, is formed by backsplicing of 3’ end to 5’ end of exons and is known to be closely related to the variety of pathophysiological function as well as normal homeostasis. However, its roles in the cardiovascular diseases, especially in cardiac fibrosis, are not fully studied. Circular RNAs (circRNAs) are formed by backsplicing events of 3′ end to 5′ end. To identify circRNA candidates, RNA sequencing (RNA-seq) datasets were obtained from transverse aortic constriction (TAC)-induced hearts. Especially, we were interested in cardiac fibroblast-specific circRNAs that affect its differentiation and cardiac fibrosis. Thus, in the present study, by utilizing RNA sequencing analysis followed by diverse bioinformatic or biochemical studies, we identified and characterized circRNA that may affect the pathologic remodeling of heart.

overall_design: Thoracic aortic constriction (TAC) is established method and is widely used to establish an animal model of pressure overload-induced cardiac hypertrophy and heart failure. Eight-week-old male C57BL/6J mice were anaesthetized by Avertin. The mice were then ventilated and the chest was opened to expose the thymus and aortic arch. A 7-0 silk suture were placed between the innominate and left carotid arteries. A 27-gauge needle put parallel to the transverse aorta and the suture was tied. After ligation, the needle was removed and the rib cage was closed using 4-0 silk suture. As a control, sham mice were subjected to same operation without ligation. One, four, and eight weeks later, the hearts were excised, and the Langendorff perfusion system was used to isolate cardiac fibroblasts and from hearts.

first: Anna

last: Jeong

first: Taewon

last: Kook

first: Woojin

last: Park

first: Hyun


title: RNA sequence of acute lymphoblastic leukemia cells with NRIP1::PDGFRB fusion

city: Tokyo

first: Yosuke

last: Tanaka

address: 5-1-1, tsukiji, Chuo-ku

institute: National Cancer Center Research Institute

summary: Philadelphia chromosome (Ph)-like acute lymphoblastic leukemia (ALL) is a subset of ALL with a high rate of treatment failure. PDGFRB gene fusion is one of the hallmarks of Ph-like ALL. We identified a novel oncogenic PDGFRB fusion gene, NRIP1::PDGFRB, from a pediatric patient with ALL

overall_design: mRNA  from acute lymphoblastic leukemia cells was sequenced by Illumina sequencer.


title: m6A RNA modification of TERRA lncRNA drives R-Loop formation and is required for telomere maintenance in ALT tumors [III]

city: Gothenburg

first: Tanmoy

last: Mondal

state: Västra Götaland

address: Bruna Stråket 16

department: Department of Clinical Chemistry and Transfusion Medicine

institute: University of Gothenburg

summary: Telomerase-negative tumors can maintain telomere length by alternative lengthening of telomeres (ALT) but the mechanism of telomere maintenance in ALT cells is not well understood. A significant portion of the relapse Neuroblastoma (NB) tumors are positive for ALT which suggests better dissecting the ALT mechanism could provide novel therapeutic opportunities. TERRA RNA which is derived from the telomere ends is localized to telomeres in R-loop dependent manner and is essential for telomere maintenance. In the present study, we provide evidence that RNA modification at the N6 position of internal adenosine (m6A) in TERRA RNA by methyl transferase METTL3 is essential for telomere maintenance in ALT cells and loss of TERRA m6A/METTL3 leads to accumulation of DNA damage over telomere. Our data suggest that m6A modification in TERRA RNA is required for R-loop formation and telomere targeting of TERRA. We observed that R-loop enriched TERRA is abundantly m6A modified and m6A mediated recruitment of hnRNPA2B1 to TERRA RNA is essential for R-loop formation. Together our study suggests that m6A-mediated R-loop formation could be a widespread mechanism utilized by other chromatin-interacting lncRNAs. We also show treating ALT positive NB cells with small molecule METTL3 inhibitor leads to compromised telomere targeting of TERRA and accumulation of DNA damage over telomere, suggesting METTL3 inhibition could be a therapeutic opportunity for ALT positive NB.

overall_design: RNA pulldown against TERRA or Luciferase probes (RIP-seq) using Illumina short-read sequencing in U2O-S cells

first: Roshan

last: Vaid

first: Akram

last: Méndez


title: Methylome of 5mC and 5hmC regulated by NEIL2

city: Oslo

first: Mingyi

last: Yang

address: Sognsvannsveien 20

department: Department of Microbiology, Rikshospitalet

country: Norway

institute: Oslo University Hospital

summary: To elucidate the role of DNA glycosylase NEIL2 in regulation of DNA methylome, we performed genome sequencing of epigenetic marker 5mC and 5hmC in genome-wide using enyme-based library methods of TAPS and CAPS. The 5mC and 5hmC profile in CpG contect was further extracted and analysed.

overall_design: Total DNA were isolated from  human cell line HAP1 using a kit of NAxtra magnetic nanoparticles. The samples consisted of Neil2 knockout and wild type cells with 4 replicates in each group. In the pilot study, the sequence depth was about x2-3 genomes. We Comparative 5mC and 5hmC profiling between NEIL2 knockout and control.

first: Magnar

last: Bjørås

first: Adeel

last: Manaf

first: Marco

last: Pannone


title: Single nucleus multiome (RNAseq and ATACseq) of male mouse pituitary

city: Los Angeles

first: Michel

last: Zamojski

address: 8700 Beverly Boulevard

department: Regenerative Medicine Institute

country: USA

institute: Cedars-Sinai Medical Center

summary: We report the single nucleus multiome (RNAseq+ATACseq) of a male mouse pituitary sample. This dataset was generated for supporting the development of a novel computational framework for analyzing gene regulatorty circuitry from single cell multiome datasets. This computational framework extract regulatory circuits consisting of TFs, cis-regulatory sites and target genes by modelling the co-incidence of the RNA levels of the TFs, the chomatin accessibility of the TFs' binding sites and the RNA levels of target genes across single cell. Specifically we identified gonadotrope-specific regulatory circuits under the transcription factor Gata2. These regulatory circuits were validated by male mouse pituitary samples with gonadotrope-conditional knockout of Gata2 previously reported in GSE190066.

overall_design: Single nucleus true multiome (RNAseq and ATACseq) of the pituitary tissue of a male mouse.

first: Zidong

last: Zhang

first: Frederique

last: Ruf-Zamojski

first: Mendelev

last: Natalia

first: Daniel

last: Bernard

first: Stuart

last: Sealfon


title: Transcriptome regulated by NEIL2 in human HAP1 cells

summary: To elucidate the role of DNA glycosylase NEIL2 in transcriptome regulation, we performed RNA sequencing in human HAP1 cells of Neil2 knockout and wild type. The tanscription count was extracted and the differential expressed genes (DEGs) were analysed.

overall_design: Total mRNA were isolated from  human cell line HAP1 using a kit of NAxtra magnetic nanoparticles. The samples consisted of 2 cell types, Neil2 knockout and wild type,  with 8 replicates in each.

first: Mirta

last: Leal de Sousa

first: Junbai

last: Wang


title: Spatial architecture of high-grade glioma reveals tumor heterogeneity within distinct domains

city: Melbourne

first: Joel

middle: Jeffrey Duncan

last: Moffet

state: Victoria

address: 1G Royal Parade

country: Australia

institute: WEHI

summary: High-grade gliomas are aggressive primary brain cancers with poor response to standard regimens, driven by immense heterogeneity. In isocitrate dehydrogenase (IDH) wild-type high-grade glioma (glioblastoma, GBM), increased intra-tumoral heterogeneity is associated with more aggressive disease. Recently, spatial technologies have emerged to dissect this complex heterogeneity within the tumor ecosystem by preserving cellular organization in situ. Here, we construct a high- resolution molecular landscape of GBM and IDH-mutant high-grade glioma patient samples to investigate the cellular subtypes and spatial communities that compose high-grade glioma using digital spatial profiling and spatial molecular imaging. This uncovered striking diversity of the tumor and immune microenvironment, that is embodied by the heterogeneity of the inferred copy- number alterations in the tumor. Reconstructing the tumor architecture revealed brain-intrinsic niches, composed of tumor cells reflecting brain cell types and microglia; and brain-extrinsic niches, populated by mesenchymal tumor cells and monocytes. We further reveal that cellular communication in these niches is underpinned by specific ligand-receptor pairs. This primary study reveals high levels of intra-tumoral heterogeneity in high-grade gliomas, associated with a diverse immune landscape within spatially localized regions.

overall_design: We selected three IDH1-wild type WHO grade 4 glioblastoma (GBM 1-3) and three IDH1-mutant grade 3 astrocytoma (A 1-3) samples for spatial whole transcriptome analysis. Notably, A-1 was re-diagnosed to oligodendroglioma. Regions of interest (ROI) were selected based on histological features, distribution of proliferating tumor cells and regions of tumor bordering on adjacent normal tissue across the six samples. By immunostaining for GFAP, CD45 and Ki67 protein expression, 34 areas of illumination (AOI) representing tumor cells (T, GFAP+), 10 AOIs representing proliferating tumor cells (K, GFAP+Ki67+) and 20 AOIs representing immune cells (I, CD45+) were isolated within each ROI and laser-captured for RNA purification and transcriptome analysis using Digital Spatial Profiling (DSP) on the NanoString GeoMx platform.

middle: J

first: Saskia

last: Freytag

first: Sarah

last: Best

first: Jim

last: Whittle


title: Immunoproteasome function maintains oncogenic gene expression in KMT2a-rearranged leukemia [Cut & Tag]

city: Hannover

first: Tina

middle: M.

last: Schnoeder

address: Carl-Neuberg-Str. 1

institute: Hannover Medical School

summary: Pharmacologic targeting of epigenetic protein complexes has shown significant in vitro responses in AML. Early clinical trials in MLL-rearranged leukemia indicate rather transient responses and development of resistance. In an effort to define functional dependencies of MLL-fusions in acute myeloid leukemia, we identify the catalytic immunoproteasome subunit PSMB8 as an oncogene-specific vulnerability. Genetic and pharmacologic inactivation of PSMB8 results in impaired proliferation of murine and human leukemic cells while normal hematopoietic cells remain unaffected. Disruption of immunoproteasome function results in cellular enrichment of transcription factor BASP1, and consecutive repression of MLL-target genes. Pharmacologic targeting of PSMB8 improves efficacy of Menin-inhibitors, eradicates leukemia in primary human xenografts and shows preserved activity against Menin-inhibitor resistance mutations. This identifies and validates a cell-intrinsic mechanism whereby selectivity of proteostasis results in altered transcription factor abundance and repression of oncogene-specific transcriptional networks. Therapeutic targeting of PSMB8-dependent transcription in combination with Menin-inhibition could thus eradicate AML harboring MLL-rearrangements.

overall_design: Cleavage Under Targets and Tagmentation-sequencing (Cut&Tag-seq) for histone modifications H3K27ac, H3K27me3, H3K4me1 and H3K4me3 in MOLM-13 cells treated with 100nM PR-957 (ONX-0914) or diluent treated controls for 72hours.

first: Nuria

last: Tubío-Santamaría

first: Qirui

first: Florian

last: Perner

last: Heidel


title: Immunoproteasome function maintains oncogenic gene expression in KMT2a-rearranged leukemia

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

overall_design: Refer to individual Series


title: Immunoproteasome function maintains oncogenic gene expression in KMT2a-rearranged leukemia [ATAC-seq]

overall_design: Genome binding/occupancy profiling in MOLM-13 cells after 100nM PR-957 (ONX-0914) treatment or diluent control treatment for 48hours.


title: DGCR8 promotes intestinal regeneration of damaged epithelium in a p53 signaling dependent manner

city: Guangzhou

first: Ye-Guang

last: Chen

address: 190 Kaiyuan Avenue, Guangzhou Science Park, Luogang District

institute: Guangzhou Institutes of Biomedicine and Health,Chinese Academy of Sciences

summary: TO explore role of DGCR8, a essential factor in canonical microRNAs biogenesis, in intestinal epithelial regeneration, we performed gene expression profiling analysis using data obtained from RNA-seq of intestinal organoids, intesitnal stem cells, and crypts from mice following 5-FU administration. To further investigate which microRNA was responsible for intestinal regeneration, we also performed small RNA sequencing with intestinal stem cells and intestinal epithelia cells.

overall_design: Comparative transcriptome profiling analysis of RNA-seq data for intestinal stem cells, intestinal organoids, and crypts from mice following 5-FU administration.

first: Xiyang

last: Wei

first: Shicheng

last: Yu