title: Chlamydomonas cells transition through distinct Fe nutrition stages within 48 h of transfer to Fe-free medium

city: Berkeley

first: Sean

middle: D.

last: Gallaher

state: California

address: 176 Stanley Hall, room 408

department: California Institute for Quantitative Biosciences

institute: UC Berkeley

summary: Low iron (Fe) bioavailability can limit the biosynthesis of Fe-containing proteins, which are especially abundant in photosynthetic organisms, thus negatively affecting global primary productivity. Understanding cellular coping mechanisms under Fe limitation is therefore of great interest. We surveyed the temporal responses of Chlamydomonas (Chlamydomonas reinhardtii) cells transitioning from an Fe-rich to an Fe-free medium to document their short- and long-term adjustments. While slower growth, chlorosis and lower photosynthetic parameters are evident only after one or more days in Fe-free medium, the abundance of some transcripts, such as those for genes encoding transporters and enzymes involved in Fe assimilation, change within minutes, before changes in intracellular Fe content are noticeable, suggestive of a sensitive mechanism for sensing Fe. Promoter reporter constructs indicate a transcriptional component to this immediate primary response. With acetate provided as a source of reduced carbon, transcripts encoding respiratory components are maintained relative to transcripts encoding components of photosynthesis and tetrapyrrole biosynthesis, indicating metabolic prioritization of respiration over photosynthesis. In contrast to the loss of chlorophyll, carotenoid content is maintained under Fe limitation despite a decrease in the transcripts for carotenoid biosynthesis genes, indicating carotenoid stability. These changes occur more slowly, only after the intracellular Fe quota responds, indicating a phased response in Chlamydomonas, involving both primary and secondary responses during acclimation to poor Fe nutrition.

overall_design:
Sampling of Chlamydomonas CC-4532 cells cultivated photoheterotrophically (TAP) under Fe-starvation condition (0 uM Fe-EDTA). Samples were collected at multiple timepoints from biological duplicate cultures after washing in TAP medium lacking Fe. Two time courses were collected. A short time course with t=0 (pre-wash), 0 (post-wash), 5, 10, 15, 30, 60, 120, and 240 min. A long time course with t= 0, 0.5, 1, 2, 4, 8, 12, 24 and 48 hours.

Please note that, for long time course, the GSE44611/PRJNA190650 samples were re-used/re-analyzed together with the short time course data:

GSM1087792  C.reinhardtii_Fe_Long_0_hours  SRX245324  SAMN01924672
GSM1087793  C.reinhardtii_Fe_Long_0.5_hours  SRX245325  SAMN01924673
GSM1087794  C.reinhardtii_Fe_Long_1_hours  SRX245326  SAMN01924674
GSM1087795  C.reinhardtii_Fe_Long_2_hours  SRX245327  SAMN01924675
GSM1087796  C.reinhardtii_Fe_Long_4_hours  SRX245328  SAMN01924676
GSM1087797  C.reinhardtii_Fe_Long_8_hours  SRX245329  SAMN01924677
GSM1087798  C.reinhardtii_Fe_Long_12_hours  SRX245330  SAMN01924678
GSM1087799  C.reinhardtii_Fe_Long_24_hours  SRX245331  SAMN01924679
GSM1087800  C.reinhardtii_Fe_Long_48_hours  SRX245332  SAMN01924680

first: Helen

last: Liu

first: Eugen

middle: I

last: Urzica

first: Sabeeha

last: Merchant


title: Endothelial cannabinoid CB1 receptor deficiency reduces arterial inflammation and lipid uptake in response to atheroprone shear stress

status: Public on Apr 04 2024

city: Munich

first: Sabine

last: Steffens

address: Pettenkoferstrasse 9b

department: Clinical Pathobiochemistry

country: Germany

institute: Institute for Cardiovascular Prevention-LMU Klinikum

type: Expression profiling by high throughput sequencing

summary: Peripherally restricted cannabinoid CB1 receptor antagonists without central side effects hold promise for treating metabolic disorders including diabetes and obesity. In atherosclerosis, the specific effects of peripheral CB1 signaling in vascular endothelial cells (ECs) remain incompletely understood.We performed en face in situ hybridization of Cnr1 in murine aortas, revealing a significantly increased expression of the CB1 encoding gene in ECs within atheroprone compared to atheroresistant regions. In vitro, CNR1 was upregulated by oscillatory shear stress in human aortic endothelial cells (HAoECs). Endothelial CB1 deficiency (Cnr1EC-KO) in female mice on atherogenic background resulted in pronounced endothelial phenotypic changes, with reduced vascular inflammation and permeability. This translated into attenuated plaque development with reduced lipid content as well as reduced white and brown adipose tissue mass and liver steatosis. Ex vivo imaging of carotid arteries via two-photon microscopy revealed less DIL-LDL uptake in Cnr1EC-KO. This was accompanied by a significant reduction of aortic endothelial caveolin-1 (CAV1) expression, a key structural protein involved in lipid transcytosis in female Cnr1EC-KO mice. In vitro, pharmacological blocking with CB1 antagonist AM281 reproduced the inhibition of CAV1 expression and LDL uptake in response to atheroprone shear stress in human aortic endothelial cells (HAoECs), which was dependent on cAMP-mediated PKA activation. Conversely, the CB1 agonist ACEA increased DIL-LDL uptake and CAV1 expression in HAoECs. Finally, treatment of atherosclerotic mice with the peripheral CB1 antagonist JD-5037 reduced plaque progression, CAV1 and endothelial adhesion molecule expression in female mice. These results confirm an essential role of endothelial CB1 to the pathogenesis of atherosclerosis.

overall_design: To globally assess the transcriptomic profile regulated by endothelial CB1 signaling

first: Bingni

last: Chen

first: Guo

last: Li

first: Raquel

last: Guillamat-Prats


title: Genomic positioning in LBR and Lamin A K562 knockout cells

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

department: division of Molecular Biology

country: Netherlands

institute: Netherlands Cancer Institute

summary: To probe the functional consequences of nuclear lamina genome association, we made LMNA, LBR, and double LMNA/LBR K562 knockout lines. We first examined the genome interaction changes with nulcear lamina using LMNB1 DamID seq and further assessed the functional consequences of these changes using RNA-seq and repli-seq.

overall_design:
LBR and Lamin A genes were disrupted by frame shift mutations induced by CRISPR cutting in K562 cells. In these cells, genome positioning relative to nuclear locales was determined using DamID. Additionally, functional consequences were determined with RNA-seq and Repli-seq.
Please note that the processed data file generated from both DamID_LMNB1 and DamID_DamControl sample is linked to the corresponding *DamID_LMNB1 sample records.

first: Tom

last: van Schaik

first: Dave

middle: M

last: Gilbert

first: Athanasios

middle: E

last: Vouzas


title: Integrative miRNA networks predict prostate cancer recurrence

status: Public on Apr 05 2024

city: Toronto

first: Shivani

middle: Nainesh

last: Kamdar

state: ON

address: 60 Murray Street

department: Cancer Biology

country: Canada

institute: Sinai Health System (LTRI)

summary: Developing an effective predictor of tumour recurrence is an important challenge in the management of localized prostate cancer. Accurate prediction of disease-free survival is essential for decision-making before or after definitive local therapy, and would allow identification of patients who may derive benefit from adjuvant therapy. Today these decisions are largely based on the clinic-pathologic prognostic factors of tumour size, extent and grade along with serum PSA abundance. MicroRNAs (miRNAs) are promising class of biomarkers to improve patient risk-stratification: they show differential abundance across prostate cancer sub-types and have both oncogenic and tumour-suppressive roles. Here, we report the miRNA abundance profiling of 319 prostate tumours with matching detailed clinical annotation, long-term follow-up and accompanying genetic and epigenetic data including mRNA abundance, copy number alterations, point mutations and methylation. We built a cancer driver-miRNA-target regulatory network to characterize the extent to which genomic, transcriptional and post-transcriptional events contribute to the miRNA abundance architecture. By linking this network with machine-learning we created a multi-modal biomarker that accurately predicts biochemical recurrence after definitive local therapy. We find that combining miRNA information with genetic and epigenetic drivers and clinicopathological parameters improves biomarker accuracy, and quantifies the value of multi-modal biomarkers that exploit the regulatory architecture of gene expression in their development.

overall_design: To explore the miRNA abundance profiles of primary treatment-naïve localized prostate cancers, we first quantified 798 tissue miRNAs in 163 patients diagnosed with low- or intermediate-risk tumours (CPC-GENE cohort; Figure 1; Supplementary Table 1). Median follow-up was 8.38 years, and 65 patients experienced biochemical recurrence (BCR), independent of age (Mann–Whitney test, p = 0.73; Table 1). A second, 156-patient cohort (UHN) was profiled using the same NanoString technology and had a similar clinical distribution as the CPC-GENE cohort, with median follow-up of 5.19 years, and 52 patients experienced biochemical recurrence.

first: Jouhyun

last: Jeon

first: Renu

last: Jeyapala

first: Kathleen

last: Houlahan

first: Michael

last: Fraser

first: Ekaterina

last: Olkhov-Mitsel

first: Christine

last: Hoey

first: Carmelle

last: Cuizon

first: Jessica

last: Ray

first: Michelle

last: Meringer

first: Andrew

last: Loblaw

first: Neil

last: Fleshner

first: Danny

last: Vesprini

first: Alexandre

last: Zlotta

first: Robert

middle: G

last: Bristow

first: Jüri

last: Reimand

first: Theodorus

last: van der Kwast

first: Stanley

middle: K

first: Paul

middle: C

last: Boutros

first: Bharati

last: Bapat


title: Human CD14+ monocytes from rheumatoid arthritis patients before and after a 3-month period of Upadacitinib treatment

city: Madrid

first: Amaya

middle: Rocío

last: Puig Kröger

state: Madrid

address: Dr. Esquerdo 46

department: Immunology

country: Spain

institute: Hospital General Universitario Gregorio Marañón

summary: Janus Kinase (JAK) inhibitors are small molecules that reversibly inhibit JAK activity and their subsequent intracellular signaling and have become the treatment of choice for diseases with an inflammatory or immune basis. We explored the molecular impact of the JAK inhibitor Upadacitinib on the gene expression of human peripheral blood monocytes from three seropositive rheumatoid arthritis patients. The three patients showed disease improvementatthree months follow-up.

overall_design: mRNA profiles of human peripheral blood CD14+ monocytes from rheumatoid arthritis patients at baseline and three months after Upadacitinib treatment

first: Baltasar

middle: L

last: Navarro

first: María

middle: T

last: García-Villanova

first: Isabel

last: Castrejón

middle: P

last: Kröger


title: A common polymorphism in the Intelectin-1 gene influences mucus plugging in severe asthma

city: Denver

first: Nathan

last: Jackson

state: CO

address: 1400 Jackson St.

department: Center for Genes, Environment, and Health

country: USA

institute: National Jewish Health

summary: By incompletely understood mechanisms, type 2 (T2) inflammation present in the airways of severe asthmatics drives the formation of pathologic mucus which leads to airway mucus plugging. Here we investigate the molecular role and clinical significance of intelectin-1 (ITLN-1) in the development of pathologic airway mucus in asthma. Through analyses of human airway epithelial cells we find that ITLN1 gene expression is highly induced by interleukin-13 (IL-13) in a subset of metaplastic MUC5AC+ mucus secretory cells, and that ITLN-1 protein is a secreted component of IL-13-induced mucus.  Additionally, we find ITLN-1 protein binds the C-terminus of the MUC5AC mucin and that its deletion in airway epithelial cells partially reverses IL-13-induced mucostasis. Through analysis of nasal airway epithelial brushings, we find that ITLN1 is highly expressed in T2-high asthmatics, when compared to T2-low children.  Furthermore, we demonstrate that ITLN1 gene expression is significantly reduced and ITLN-1  protein expression is lost through a common genetic variant that is associated with protection from the formation of mucus plugs in T2-high asthma. This work identifies one of the first biomarkers and targetable pathways for the treatment of mucus obstruction in asthma.

overall_design: Bronchial cells were dissociated from the bronchial airway brushes from 2 asthmatic children using Bacillus licheniformis cold active protease (10mg/ml), EDTA (0.5mM), and EGTA (0.5mM) at 4°C with vortex mixing, followed by enzyme neutralization with FBS.  Red blood cell lysis was performed and cells were washed twice in 0.04% BSA/PBS prior to targeted capture for scRNA-seq.

first: Jamie

last: Everman

first: Satria

last: Sajuthi

first: Maude

last: Liegeois

middle: D

first: Erik

middle: H

last: Collet

first: Michael

last: Peters

first: Maurizio

last: Chioccioli

first: Camille

last: Moore

first: Bhavika

middle: B

last: Patel

last: Dyjack

first: Roger

last: Powell

first: Cydney

last: Rios

last: Montgomery

first: Celeste

last: Eng

first: Jennifer

middle: R

last: Elhawary

first: Angel

last: Mak

first: Donglei

last: Hu

first: Scott

last: Huntsman

first: Sandra

last: Salazar

first: Luigi

last: Feriani

first: Ana

last: Fairbanks-Mahnke

first: Gianna

last: Zinnen

first: Cole

last: Michel

first: Joe

last: Gomez

first: Xing

last: Zhang

first: Vivian

last: Medina

first: Hong

middle: W

last: Chu

first: Pietro

last: Cicuta

first: Victor

last: Ortega

first: Nichole

last: Reisdorph

first: Eleanor

last: Dunican

first: Monica

last: Tang

first: Brett

last: Elicker

first: Travis

last: Henry

first: Eugene

last: Bleecker

first: Mario

last: Castro

first: Serpil

last: Erzurum


title: RNA-seq analysis of the young stage ADF, middle stage ADF, and the control worms

city: Kaifeng

first: Shanqing

last: Zheng

address: 1 Jinming Avenue North, Longting District,  School of Basic Medical Sciences, Henan University

country: China

institute: Henan university

summary: NOT PROVIDED; REQUESTED

overall_design: Deep sequencing was employed to generate the mRNA expression profiles of nematodes at the young and middle stages following ADF

first: shanqing

last: zheng


title: Life-long persistence of nuclear RNAs in the mouse brain [Hippocampus]

city: Dresden

first: Tomohisa

last: Toda

address: Tatzberg 41

institute: DZNE

summary: Genomic DNA residing in the nuclei of mammalian neurons can be as old as the organism itself. The life span of non-coding nuclear RNAs, which are critical for proper chromatin architecture and transcription regulation, has not been determined in adult tissues. Here, we report the identification and characterization of nuclear RNAs that do not turn over for at least two years in the adult mouse brain. These long-lived RNAs (LL-RNA) are stably retained in nuclei in a neural cell type-specific manner and are required for the maintenance of heterochromatin. Thus, the remarkable life span of neural cells may depend on both the molecular longevity of DNA for the storage of genetic information but also the extreme stability of RNA for the functional organization of chromatin.

overall_design: To identify long-retained RNAs in the hippocampus, mice were injected with Ethynyluridine (EU) on postnatal days 3-5 and hippocampus tissue was harvested at postnatal day P36. Controls were injected with PBS (vehicle) instead of EU. EU-labelled RNA was purified using Biotin-Click reaction and Streptavidin beads (Life Technologies). To determine background binding, RNA from PBS-treated samples underwent the same pulldown procedure. Total RNA sequencing was performed using Universal Plus Total RNA-Sequencing kit (TECAN).


title: A p53 score derived from TP53 CRISPR/Cas9 HMCLs predicts survival and reveals major role of BAX in BH3 mimetics response [1]

city: Nantes

first: David

last: Chiron

address: 8 quai Moncousu

country: France

institute: CRCI2NA, INSERM_U1307, CNRS_6075, Nantes_Université

summary: In order to establish a strict p53-dependent gene expression profile, p53 negative clones were derived from two TP53+/+ and two TP53-/mut t(4;14) human myeloma cell lines (HMCLs) using CRISPR/Cas9 technology. From the 17 dysregulated genes shared between the 6 clones from the two TP53+/+ myeloma cell lines, we established a 13-gene functional p53 score, involving genes downregulated on p53-silencing. This functional score allowed us to segregate clones, myeloma cell lines and patients’ samples according to the presence or absence of a single or double hit in TP53 gene i.e., chromosomal deletion and/or mutation. The score also distinguished 1,162 cell lines from hematological and solid cancers according to hits in TP53. Moreover, the 13-gene score was predictive of overall survival in two independent cohorts of patients. Among the 13 genes, we showed that p53-regulated BAX expression correlated to, and directly impacted, the MCL1 BH3 mimetic S63845 sensitivity of myeloma cells by modulating the amount of MCL1-BAX complexes. Resistance to cell death induced by p53-silencing was overcome by combining S63845 with venetoclax, although the synergy was significantly lower in p53-deficient versus -proficient clones and patients’ samples. Finally, by using scRNAseq analysis, we further showed in patients’ bone marrow samples that myeloma cells surviving to the BH3 mimetic combination had an about 3-fold lower p53 score. This data established a functional p53 score and showed that p53-mediating BAX expression greatly impacts mitochondria-mediated cell death in myeloma cells.

overall_design: CD138+ cells from patients’ samples were purified and gene expression profile was performed using RNA-Seq (3'SRP)(MM: multiple myeloma, sPCL: secondary plasma cell leukemia, pPCL: primary plasma cell leukemia)

first: Romane

last: Durand

first: Géraldine

last: Descamps

first: Céline

last: Bellanger

first: Christelle

last: Dousset

first: Sophie

last: Maïga

first: Jean-Baptiste

last: Alberge

first: Jennifer

last: Derrien

first: Jonathan

last: Cruard

first: Stéphane

last: Minvielle

first: Nicoletta

last: Libera Lilli

first: Catherine

last: Godon

first: Yannick

last: Le Bris

first: Benoit

last: Tessoulin

first: Martine

last: Amiot

first: Patricia

last: Gomez-Bougie

first: Cyrille

last: Touzeau

first: Philippe

last: Moreau

first: Agnès

last: Moreau-Aubry

last: Pellat-Deceunynck


title: Studies on the biological role of the antifungal protein PeAfpA from Penicillium expansum by transcriptomic profiling

city: Paterna (Valencia)

first: Carolina

last: Ropero-Pérez

state: Comunidad Valenciana

address: Carrer del Catedràtic Agustín Escardino Benlloch, 7

department: Biotechnology

institute: Instituto de Agroquímica y Tecnología de Alimentos (IATA-CSIC)

summary: RNA sequencing evidenced a massive transcriptomic change linked to the onset of PeAfpA production for the wild type strain, which was confirmed in the ΔafpA mutant.  We identified two gene expression clusters putatively involved in PeAfpA function, which correspond to genes induced or repressed with the production of PeAfpA.

overall_design: Comparative gene expression profiling of P. expansum CMP-1 strain and a ΔafpA disruption mutant at time points just before and after PeAfpA production is detected

first: Elena

last: Moreno-Giménez

first: Jose

last: F Marcos

first: Paloma

last: Manzanares

first: Mónica

last: Gandia


title: RpoS acts as a global repressor of virulence gene expression in Escherichia coli O104:H4 and enteroaggregative E. coli

city: Münster

first: Petya

last: Berger

address: Robert-Koch Straße 41

department: Institute of Hygiene

institute: University of Münster

summary: In 2011, in Germany, Escherichia coli O104:H4 caused the enterohemorrhagic E. coli (EHEC) outbreak with the highest incidence rate of hemolytic uremic syndrome. This pathogen carries an exceptionally potent combination of EHEC- and enteroaggregative E. coli (EAEC)-specific virulence factors. Here, we identified an E. coli O104:H4 isolate that carried a single nucleotide polymorphism (SNP) in the start codon (ATG>ATA) of rpoS, encoding the alternative sigma factor S. The rpoS ATG>ATA SNP was associated with enhanced EAEC-specific virulence gene expression. Deletion of rpoS in E. coli O104:H4 Dstx2 and typical EAEC resulted in a similar effect. Both rpoS ATG>ATA and DrpoS strains exhibited stronger virulence-related phenotypes in comparison to wild type. Using promoter-reporter gene fusions, we demonstrated that wild-type RpoS repressed aggR, encoding the main regulator of EAEC virulence. In summary, our work demonstrates that RpoS acts as a global repressor of E. coli O104:H4 virulence, primarily through an AggR-dependent mechanism.

overall_design: We performed strand specific RNA-seq with total RNA isolated from E. coli O104:H4 wild type and rpoS ATG>ATA grown under standard laboratory conditions (LB medium; 37oC; 180 rpm) to logarithmic growth phase (log; OD600 = 0.4- 0.5) and to transition to stationary phase (transition; OD600 = 3.0-3.4). Three biological replicates per strain were included. DESeq2 analysis based on the reads mapped to the E. coli O104:H4 genome was performed to identify examples of differential gene expression.


title: Genome-wide CRISPR/Cas9 screen to uncover  effectors of PRC2 inhibition

city: Shanghai

first: Wei

last: Qi

state: Shanghai

address: B514, L Building

department: School of Life Science and Technology

institute: ShanghaiTech University

summary: The methyltransferase Polycomb Repressive Complex 2 (PRC2), composed of EZH2, SUZ12, and EED subunits, is associated with transcriptional repression via tri-methylation of histone H3 on lysine 27 residue (H3K27me3). PRC2 is a validated drug target, as the EZH2 gain-of-function mutations identified in patient samples drive tumorigenesis. PRC2 inhibitors have been discovered and demonstrated anti-cancer efficacy in clinic. However, their pharmacological mechanisms are poorly understood. MAK683 is a potent EED inhibitor in clinical development. The overall goal of our study is to understand the molecular events leading to tumor regression after PRC2 inhibition. Our study revealed that BMP-ACVR1 signaling pathway as a critical component for the anti-lymphoma efficacy of PRC2 inhibitor.

overall_design: To systematically identify the critical functional effectors that contribute to the anti-lymphoma activity of PRC2 inhibitors, we performed a proliferation-based genome-wide CRISPR/Cas9 knockout screen in the sensitive lymphoma cell WSU-DLCL2.We constructed Cas9 stable-expression cell clone  and transduced it with the human genome-scale CRISPR knockout (GeCKO v2) lentiviral pooled libraries at a low multiplicity of infection (MOI = 0.2) to ensure transduction with only one sgRNA per cell. Then, WSU-DLCL2 cells were cultured in the presence of puromycin for 7 days followed by DMSO or MAK683 (200 nM) treatment for 14 more days. The survival cells were sequenced for the distribution of sgRNAs at days 0 and 14 after drug treatment.

first: Dongdong

last: Liu

first: Zhen

last: Li


title: RNA-seq on DMSO or MAK683 treated cancer cells and xenograft tumor samples

overall_design: We performed RNA-seq, H3K27me3 and H3K4me3 ChIP-seq with spike-in on MAK683-sensitive cancer cells WSU-DLCL2 treated with DMSO or PRC2 inhibitor MAK683 (3 μM for ChIP-seq, 5 μM for RNA-seq). To reveal the ACVR1-independent transcriptome change, we also constructed ACVR1 KO WSU-DLCL2 cell clone, NT and ACVR1 knock out cells that treated with DMSO or MAK683 (5 μM) were also included in the cellular RNA-seq study. Finally, we build WSU-DLCL2 and ACVR1 KO cell-derived xenograft models in mice, and obtained the expression profiles of WSU-DLCL2-derived xenograft tissues (NT or ACVR1 knock out) after treatment with vehicle or 100 mg/kg MAK683 for 28 days.


title: A p53 score derived from TP53 CRISPR/Cas9 HMCLs predicts survival and reveals major role of BAX in BH3 mimetics response [2]

first: David

last: Chiron

overall_design: RNA-seq expression in p53 negative clones derived from two TP53+/+ and two TP53-/mut t(4;14) human myeloma cell lines (HMCLs) treated or not 16H with 10 µM Nutlin3a for NCI-H929 and JIM3 or 2 µM for XG7

first: Romane

last: Durand

first: Géraldine

last: Descamps

first: Céline

last: Bellanger

first: Christelle

last: Dousset

first: Sophie

last: Maïga

first: Jean-Baptiste

last: Alberge

first: Jennifer

last: Derrien

first: Jonathan

last: Cruard

first: Stéphane

last: Minvielle

first: Nicoletta

last: Libera Lilli

first: Catherine

last: Godon

last: Le Bris


title: H3K27me3 and H3K4me3 ChIP-seq on DMSO or MAK683 treated cancer cell

type: Genome binding/occupancy profiling by high throughput sequencing


title: A p53 score derived from TP53 CRISPR/Cas9 HMCLs predicts survival and reveals major role of BAX in BH3 mimetics response

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

overall_design: Refer to individual Series


title: Base editing effectively prevents the early-onset hypertrophic cardiomyopathy in Mybpc3 mutant mice

city: shanghai

first: wu

last: shuo

address: dongchuan road

institute: shanghai jiaotong university

summary: Pathogenic variants in MYBPC3 (myosin-binding protein C3) are the leading cause of genetic hypertrophic cardiomyopathy (HCM). Currently, there is no specific and effective treatment for this disease. Base editing is an emerging modality for treating monogenic diseases; however, its effect on MYBPC3 cardiomyopathy remains unexplored. Mybpc3-R946X/R946X mice developed early-onset left ventricular hypertrophy, systolic dysfunction, ventricular dilatation, and arrythmias. SpRY-ABEmax inefficiently corrected the Mybpc3-R946X mutation. In contrast, SpRY-ABE8e increased the efficiency by 3.6-fold and retained low level off-target editing. In vivo administration of SpRY-ABE8e efficiently corrected Mybpc3-R946X mutation in cardiomyocytes and prevented heart function decline, hypertrophic cardiomyopathy, and ventricular dysfunction. The therapeutic efficacy of SpRY-ABE8e-mediated gene correction surmounted AAV-mediated Mybpc3 gene replacement.Our study unveiled the immense potential of base editing to treat fatal inherited cardiomyopathies and opened a new avenue for the therapeutic managements of inherited cardiac diseases.

overall_design: We generated an HCM mouse model bearing an Mybpc3 premature termination codon (p.R946X) analogous to a common human MYBPC3 pathogenic variant. We developed two base editors, SpRY-ABEmax and SpRY-ABE8e, with broad sgRNA recognition sites for genome correction. We used lentivirus to transduce the base editors to mouse embryonic fibroblasts with Mybpc3 mutation for in vitro assessment. For in vivo therapy, we used adenovirus-associated virus serotype 9 (AAV9) to specifically express the editors in the cardiomyocytes. We measured on- and off-target editing efficiency by high throughput DNA and RNA sequencing.

first: Shuo

last: Wu

first: Ping

last: Yang

first: Zilong

last: Geng

first: Yige

first: Zhizhao

last: Guo

first: Yingmei

last: Lou

first: Shasha

last: Zhang

first: Junhao

last: Xiong

first: Huan

last: Hu

first: William

last: Pu

first: Dan

last: Zhu

first: Yan

first: Bing


title: Merkel cell polyomavirus small tumor antigen contributes to immune evasion by interfering with type I interferon signaling

city: Hamburg

first: Jiabin

last: Huang

address: Martinistr. 52

institute: University Medical Center Hamburg-Eppendorf


title: Merkel cell polyomavirus small tumor antigen contributes to immune evasion by interfering with type I interferon signaling [ChIP-Seq]

summary:
Merkel cell polyomavirus (MCPyV) is linked to Merkel cell carcinoma (MCC), a rare and aggressive skin cancer.
This study investigated the influence of MCPyV T antigens on the host genome using transcriptomics and epigenomics. Results revealed a role for the small Tumor (sT) antigen in subverting type I interferon response and immune evasion, contributing to persistent infection and tumor progression. These findings enhance our understanding of MCPyV pathogenesis and may inform new therapeutic strategies.

overall_design: Use of a lentiviral transduction system to overexpress MCPyV T antigens (large Tumor (LT), small Tumor (sT), and truncated LT (LTtr)) in primary human dermal fibroblasts. Transcriptional profiling to investigate the interaction of T antigens with host cellular gene regulatory processes, focusing on inflammatory cytokines and interferon-stimulated genes (ISGs). Analysis of transcriptional changes induced by T antigens, such as the induction of inflammatory cytokines by both sT and LT, the short-term induction of ISGs by LT, and the stable repression of ISG transcription by sT. Investigation of the balancing effect of sT on immune recognition during the initial phase of infection and its potential role in maintaining a persistent infection. Evaluation of the transcriptional changes when sT is co-overexpressed with LTtr, reflecting the immunogenic feature of MCCs and their ability to attract innate and adaptive immune cells.

first: Ohnezeit

last: Denise

first: Huang

last: Jiabin

first: Fischer

last: Nicole


title: Merkel cell polyomavirus small tumor antigen contributes to immune evasion by interfering with type I interferon signaling [RNA-Seq]


title: Title: RNA-seq analysis of b0-HUDEP2 and HUDEP2 cells following erythroid differentiation

city: Melbourne

first: JIM

last: Vadolas

state: Choose State/Province

address: Wright St, Clayton

country: Australia

institute: Hudson Institute of Medical Research

summary:
Purpose: The goal of this study is to compare the altered transcriptional program (RNA-seq) and cellular adaptation to stress caused by excess a-globin synthesis.
Results: 100bp paired-end polyA-enriched RNA sequencing were performed with a depth of minimum of 20 million read counts per sample. The sequencing library was sequenced on the Illumina HiSeq2500 at Azenta. Raw data then went through read quality assessment by FastQC (version 0.11.5), mapping to the human genome (GRch38) by the STAR aligner and gene-level reads quantification using the Rsubread package.   RNA-seq data analysis identified 1870 upregulated and 1549 down regulated genes on Day 0 (FDR <=0.05) and 1924 upregulated and 1960 down regulated genes on Day 8 (FDR <=0.05). MA plot analysis of differentially expressed genes uncovered an altered transcriptional program favouring γ-globin expression not solely dependent upon the HRI ATF4-BCL11A axis. Instead, we noted attenuated expression of several key γ-globin co-repressors, including SOX6, ZBTB7A, KLF1 and GATA1, which coincided with increased expression of co-activators such as CBFB/NY-FB and GATA2 following erythroid differentiation. Gene Set Enrichment Analysis (GSEA) software was used to determine significantly enriched gene sets. Downregulated DEGs in β0 HUDEP 2 cells in pathways related to haeme metabolism, hypoxia, MTORC1, unfolded protein response and TNFA/NFkB signalling were enriched. Meanwhile, upregulated DEGs in β0 HUDEP-2 cells related to G-protein-coupled receptors (GPCR) signalling, IL-2/STAT5 and hypoxia signalling pathway were also retrieved. Pathways shown to be significantly altered in both β0 HUDEP-2 cells and patient group include apoptosis, MAPK signalling and NFKB pathway thus provided complementary insights in transcriptome profiling.
Conclusions: Our study represents analysis of HUDEP2 transcriptomes, with biologic replicates, generated by RNA-seq technology. The data analysis reported here should provide a framework for comparative investigations of expression profiles.  We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of the cellular adaptation to intrinsic stress caused by excess a-globin synthesis.

overall_design: Erythroid mRNA profiles of b0-HUDEP2and HUDEP2 cells on day 0 and day 8 differentiation.

first: Jim


title: Maternal gestational nutrition perturbs offspring sperm epigenome in sheep [BiSulfite-seq]

city: Gainesville

first: Zongliang

last: Jiang

state: FL

address: 2033 Mowry Rd

department: Animal Sciences

institute: University of Florida

type: Methylation profiling by high throughput sequencing

summary: There is a growing body of evidence that inadequate maternal nutrition during gestation can have immediate and life-long effects on offspring. However, little is known about the reproductive effects of maternal gestational nutrition in offspring males. Here, using a sheep model of poor maternal nutrition (restricted- or over-feeding) during gestation, we found that poor maternal gestational nutrition does not affect semen characteristics (i.e. volume, sperm concentration, pH, sperm motility, sperm morphology) and scrotal circumference in offspring. However, by evaluating associations between poor maternal gestational nutrition and altered small non-cording RNAs (sncRNAs) and DNA methylation in offspring sperm, we demonstrated that poor maternal gestational nutrition alters sperm sncRNA composition and expression. Whole genome bisulfite sequencing further identified genomic regions with increased or decreased DNA methylation in sperm in response to poor maternal gestational nutrition. These findings imply that maternal diet-induced epigenetic errors can accumulate in sperm to worsen developmental outcomes of future generations.

overall_design: Comparative DNA CpG methylation of WGBS data of F1 ram sperm in CON, OVER and RES group.

first: Linkai

first: Giovanna

last: Scatolin


title: Maternal gestational nutrition perturbs offspring sperm epigenome in sheep

type: Non-coding RNA profiling by high throughput sequencing


title: Life-long persistence of nuclear RNAs in the mouse brain [NPCs]

first: Tomohisa

last: Toda

overall_design: To identify long-retained RNAs in quiescent NPCs, in vitro NPCs were labelled with Ethynyluridine (EU) upon induction of quiescence and total RNA was isolated one week after EU administration. Controls were treated with PBS (vehicle) instead of EU. EU-labelled RNA was purified using Biotin-Click reaction and Streptavidin beads. To determine background binding, RNA from PBS-treated samples underwent the same pulldown procedure. Total RNA sequencing was performed using Universal Plus Total RNA-Sequencing kit (TECAN).


title: Gene expression in the mouse cerebral cortex exposed to Bisphenol A (BPA) during development.

city: Kyoto

first: Takeshi

last: Yaoi

address: Kawaramachi-Hirokoji

country: Japan

institute: Kyoto Prefectural University of Medicine

summary: To screen changed gene expression, gene expression microarray analysis was performed in the cerebral cortex at the third postnatal week (P3W) of C57/B6J mice perinatally exposed to BPA (500 ug/kg body/day) .

overall_design: For pregnant mice (n=3) in BPA group, 500 μg/kg of body weight BPA dissolved in 0.01 % ethanol was administered orally daily from E0. In control group (n=3), 0.01 % ethanol was done. From a matched set of male and female littermates at P3W from each dam, cerebral cortices were dissected. Total RNA from each tissues were prepared and analysed.

first: Kyoko

last: Itoh

first: So

last: Tando

first: Shinji

last: Fushiki


title: Neuron-specific chromatin disruption at CpG islands and aging-related regions in Kabuki syndrome mice [NeuN+ hippocampal neurons]

status: Public on Apr 03 2024

city: Baltimore

first: Leandros

last: Boukas

address: 733 North Broadway

institute: Johns Hopkins University

summary: Many Mendelian developmental disorders caused by coding variants in epigenetic regulators have now been discovered. Epigenetic regulators are broadly expressed, and each of these disorders typically exhibits phenotypic manifestations from many different organ systems. An open question is whether the chromatin disruption -- the root of the pathogenesis -- is similar in the different disease-relevant cell types. This is possible in principle, since all these cell-types are subject to effects from the same causative gene, that has the same kind of function (e.g. methylates histones) and is disrupted by the same germline variant. We focus on mouse models for Kabuki syndrome types 1 and 2, and find that the chromatin accessibility abnormalities in neurons are mostly distinct from those in B or T cells. This is not because the neuronal abnormalities occur at regulatory elements that are only active in neurons. Neurons, but not B or T cells, show preferential chromatin disruption at CpG islands and at regulatory elements linked to aging. A sensitive analysis reveals that the regions disrupted in B/T cells do exhibit chromatin accessibility changes in neurons, but these are very subtle and of uncertain functional significance. Finally, we identify a small set of regulatory elements disrupted in all three cell types. Our findings reveal the cellular-context-specific effect of variants in epigenetic regulators, and suggest that blood-derived episignatures may not be well-suited for understanding the mechanistic basis of neurodevelopment in Mendelian disorders of the epigenetic machinery.

overall_design: ATAC-seq in NeuN+ hippocampal neurons from the dentate gyrus in mouse models of Kabuki Syndrome 1, Kabuki Syndrome 2, and wild-type mice

first: Teresa

last: Romeo Luperchio


title: Effect of JAK inhibitors Upadacitinib or Baricitinib on gene expression during human monocyte-derived macrophage differentiation

first: Amaya

last: Puig Kröger

summary: Macrophage phenotypic and functional heterogeneity derives from tissue-specific transcriptional signatures shaped by the local microenvironment. GM-CSF drives the generation of human monocyte-derived macrophages with a potent pro-inflammatory activity upon stimulation. Janus Kinase (JAK) inhibitors are small molecules that reversibly inhibit JAK activity and their subsequent intracellular signaling and have become the treatment of choice for diseases with an inflammatory or immune basis. We explored the molecular impact of blocking GM-CSFR-JAK2-STAT5 axis with the Janus Kinase (JAK) inhibitors Upadacitinib or Baricitinib on the gene expression profile in GM-CSF-primed human monocyte derived macrophages.

overall_design: mRNA profiles of human macrophages differentiated with GM-CSF (GM-MØ) from peripheral blood monocytes in the absence or in the presence of the Janus Kinase (JAK) inhibitors Upadacitinib or Baricitinib. Baricitinib (10nM) and Upadacitinib (10nM or 100nM) were added once-a-day during the 7-day differentiation procedure.

first: Baltasar

last: López Navarro

first: Alicia

last: Sanchez Martín


title: Multiomic Analyses Reveal New Targets of Polycomb Repressor Complex 2 in Schwann Lineage Cells and Malignant Peripheral Nerve Sheath Tumors - RNAseq

city: Minneapolis

first: David

last: Largaespada

state: MN

address: 515 Delaware St SE

department: Department of Pediatrics

institute: University of Minnesota

summary: Background Malignant peripheral nerve sheath tumors (MPNST) can arise from atypical neurofibromas (ANF). Loss of the polycomb repressor complex 2 (PRC2) is a common event. Previous studies on PRC2-regulated genes in MPNST used genetic addback experiments in highly aneuploid MPNST cell lines which may miss PRC2-regulated genes in NF1-mutant ANF-like precursor cells. A set of PRC2-regulated genes in human Schwann cells has not been defined. We hypothesized PRC2 loss has direct and indirect effects on gene expression resulting in MPNST, so we sought PRC2-regulated genes in immortalized human Schwann cells (iHSCs).  Methods We engineered NF1-deficient iHSCs with loss of function SUZ12 or EED mutations. RNA sequencing revealed 1,327 differentially expressed genes to define PRC2-regulated genes. To investigate MPNST pathogenesis we compared genes in iHSCs to consistent gene expression differences between ANF and MPNSTs. Chromatin immunoprecipitation sequencing was used to further define targets. Methylome and proteomic analyses were performed to further identify enriched pathways.  Results We identified potential PRC2-regulated drivers of MPNST progression. Pathway analysis indicates many upregulated cancer-related pathways. We found transcriptional evidence for activated Notch and Sonic Hedgehog signaling in PRC2-deficient iHSCs. Functional studies confirm Notch signaling is active in MPNST cell lines, patient derived xenografts, and transient cell models of PRC2 deficiency.  A combination of MEK and γ-secretase inhibition shows synergy in MPNST cell lines.  Conclusions We report PRC2-regulated genes and potential drivers of MPNSTs. Our findings support the Notch pathway as a druggable target in MPNSTs. Our identification of PRC2-regulated genes and pathways could result in more novel therapeutic approaches.

overall_design: In order to model the progression from atypical neurofibromas to malignant peripheral nerve sheath tumors NF1, SUZ12, and EED were knocked out in immortalized human Schwann cells. RNA-seq was generated for cell lines for all combinations of knockouts for NF1, SUZ12, and EED except that EED and SUZ12 knockouts were mutually exclusive.

first: Minu

last: Bhunia

first: Tyler

middle: A

last: Jubenville


title: PARKIN is not required to sustain OXPHOS function in adult mammalian tissues

city: Lund

first: Markus

last: Ringner

address: Sölvegatan 35

country: Sweden

institute: Lund University

summary: Loss-of-function variants in the PRKN gene encoding the ubiquitin E3 ligase PARKIN cause autosomal recessive early-onset Parkinson’s disease (PD). Extensive in vitro and in vivo studies have reported that PARKIN is involved in multiple pathways of mitochondrial quality control, including mitochondrial degradation and biogenesis. However, these findings are surrounded by substantial controversy due to conflicting experimental data. In addition, the existing PARKIN-deficient mouse models have failed to faithfully recapitulate PD phenotypes. Therefore, we have investigated the mitochondrial role of PARKIN during ageing and in response to stress by employing a series of conditional Parkin knockout mice. We report that PARKIN loss does not affect oxidative phosphorylation (OXPHOS) capacity and mitochondrial DNA (mtDNA) levels in the brain, heart, and skeletal muscle of aged mice. We also demonstrate that PARKIN deficiency does not exacerbate the brain defects and the pro-inflammatory phenotype observed in mice carrying high levels of mtDNA mutations. To rule out compensatory mechanisms activated during embryonic development of Parkin-deficient mice, we generated a mouse model where loss of PARKIN was induced in adult dopaminergic (DA) neurons. Surprisingly, also these mice did not show motor impairment or neurodegeneration, and no major transcriptional changes were found in isolated midbrain DA neurons. Finally, we report a patient with compound heterozygous PRKN pathogenic variants that lacks PARKIN and has developed PD. The PARKIN deficiency did not impair OXPHOS activities or induce mitochondrial pathology in skeletal muscle from the patient. Altogether, our results argue that PARKIN is dispensable for OXPHOS function in adult mammalian tissues.

overall_design: To investigate transcriptional responses induced by PARKIN loss in adult DA neurons we used a strategy to isolate fluorophore-labelled midbrain DA neurons from adult mice. We generated iParkinDA (genotype: Parkin loxP/loxP; +/DatCreERT2) mice allowing the disruption of Parkin by tamoxifen injection at the age of 5-7 weeks. To investigate the efficiency of the inducible knockout system, we used a reporter allele expressing mitochondrially targeted YFP preceded by a loxP-flanked stop cassette (mitoYFP). We also generated control mice containing the mitoYFP allele. We isolated DA neurons for bulk RNAseq analysis at 5 and 40 weeks after tamoxifen injection from both iParkin and control mice. For each time point, we collected both mitoYFP-positive (DA neurons) and mitoYFP-negative cells (mixed cells).

first: Roberta

last: Filograna

first: Katarina

last: Tiklova

last: Ringnér

first: Thomas

last: Perlmann

first: Nils-Göran

last: Larsson


title: Multiomic Analyses Reveal New Targets of Polycomb Repressor Complex 2 in Schwann Lineage Cells and Malignant Peripheral Nerve Sheath Tumors - ChIPseq

overall_design: In order to model the progression from atypical neurofibromas to malignant peripheral nerve sheath tumors NF1, SUZ12, and EED were knocked out in immortalized human Schwann cells. CHIP-seq was generated histone modifications for H3K27me3 and H3K27ac for cell lines for all combinations of knockouts for NF1, SUZ12, and EED except that EED and SUZ12 knockouts were mutually exclusive.


title: Context-Dependent Modification of PFKFB3 in Hematopoietic Stem Cells Promotes Anaerobic Glycolysis and Ensures Stress Hematopoiesis

city: Tokyo

first: Keiyo

last: Takubo

address: 1-21-1 Toyama Shinjuku-ku

department: Department of Stem Cell Biology

institute: National Center for Global Health and Medicine

summary: Metabolic pathways are plastic and rapidly change in response to stress or perturbation. Current metabolic profiling techniques require lysis of many cells, complicating the tracking of metabolic changes over time after stress in rare cells such as hematopoietic stem cells (HSCs). Here, we aimed to identify the key metabolic enzymes that define differences in glycolytic metabolism between steady-state and stress conditions in HSCs and elucidate their regulatory mechanisms. Through quantitative13C metabolic flux analysis of glucose metabolism using high-sensitivity glucose tracing and mathematical modeling, we found that HSCs activate the glycolytic rate-limiting enzyme phosphofructokinase (PFK) during proliferation and oxidative phosphorylation (OXPHOS) inhibition. Real-time measurement of adenosine triphosphate (ATP) levels in single HSCs demonstrated that proliferative stress or OXPHOS inhibition led to accelerated glycolysis via increased activity of PFKFB3, the enzyme regulating an allosteric PFK activator, within seconds to meet ATP requirements. Furthermore, varying stresses differentially activated PFKFB3 via PRMT1-dependent methylation during proliferative stress and via AMPK-dependent phosphorylation during OXPHOS inhibition. Overexpression ofPfkfb3induced HSC proliferation and promoted differentiated cell production, whereas inhibition or loss ofPfkfb3suppressed them. This study reveals the flexible and multilayered regulation of HSC glycolytic metabolism to sustain hematopoiesis under stress and provides techniques to better understand the physiological metabolism of rare hematopoietic cells.

overall_design: 10-week old mice were administered with PBS or 5-FU (150 mg/kg) intraperitoneally 3 times with an interval of 21 days. For 5-FU group, a total of 3000-3500 hematopoietic stem cells (HSCs, CD150+CD48-Lineage-Sca-1+c-Kit+ cells) were isolated 5 days (day 6), and 20 days (day 21) after the first and the third administration of 5-FU. For PBS group, HSCs were isolated 5 days after the first and the third administration of PBS. Untreated fresh HSCs from 2-year-old mice were collected separately. All the samples were subjected to RNA extraction followed by library preparation and RNA-sequencing.

first: Shintaro

last: Watanuki

first: Hiroshi

last: Kobayashi

first: Yuriko

last: Sorimachi

first: Miho

last: Haraguchi

first: Shinpei

last: Tamaki

first: Koichi

last: Murakami

first: Akira

last: Nishiyama

first: Tomohiko

last: Tamura


title: Single-cell RNA sequencing reveals recruitment of the M2-like CCL8high macrophages in Lewis lung carcinoma-bearing mice following hypofractionated radiotherapy

city: Chongqing

first: Yongzhong

last: Wu

state: Chongqing

address: 181 Hanyu Road, Shapingba District

department: Radiation Oncology Center

institute: Chongqing University Cancer Hospital

summary: Tumor-associated macrophages (TAMs) are a crucial factor in reprogramming the tumor microenvironment following radiotherapy. The mechanisms underlying this process remain to be elucidated. We used single cell RNA sequencing (scRNA-seq) to investigate the effects of hypofractionated radiotherapy on macrophages dynamics in a subcutaneous Lewis lung carcinoma (LLC) murine model.

overall_design: The subcutaneous LLC tumors were ioslated 72 hours after  hypofractionated radiotherapy (RT) or mock treatment (NT, 3 tumor samples in 1). Singel-cell suspensions were prepared and analyzed by using scRNA-seq.

first: Haonan

last: Yang

first: Zheng

last: Lei

first: Jiangdong

last: Sui


title: Functionalized nanowires for miRNA-mediated therapeutic programming of naïve T cells

city: Ithaca

first: Andrew

last: Grimson

state: NY

address: 445 Biotechnology Building

department: Molecular Biology & Genetics

institute: Cornell University

summary: Cellular programming of naïve T cells, in contrast to activated T cells, can enhance the efficacy of adoptive T cell therapy. The differentiation of naïve cells into memory T cells impairs adoptive immunotherapy. Most current strategies for ex vivo engineering of T cells require pre-activation of T cells, with CD3/CD28 crosslinking antibodies or cytokines, prior to the delivery of genetic material, and therefore T cells lose the naïve state. Here, using a cationic polymer-functionalized nanowire platform, we pre-programmed the fate of primary, naïve CD8+ T cells to achieve the therapeutic response in vivo. We demonstrate the delivery of single versus multiple microRNAs (miRNAs) to primary naïve mouse and human CD8+ T cells without pre-activation, allowing for T cell programming in user-specific ways, as well as delivery of large, whole lentiviral particles with potential for long-term integration. Because CD8 T cell differentiation is a continuous process where fate decisions require the interplay of multiple miRNAs, we demonstrate how a combination of deletion and overexpression of miR-29 and miR-130 impact ex vivo T cell differentiation fate from the naïve state. The programming of CD8+ T cells using nanowire-delivered co-delivery of miRNAs resulted in the modulation of T cell fitness by altering T cell proliferation, phenotypic and transcriptional regulation, and secretion of effector molecules. Importantly, the in vivo adoptive transfer of murine CD8+ T cells programmed through nanowire-mediated dual delivery of miRNAs provided enhanced immune protection against different types of intracellular pathogens (influenza, Listeria monocytogenes). Nanowires open up therapeutic possibilities for adoptive T cell transfers where the amounts of effector differentiation in CD8+ T cells can be fine-tuned to achieve the therapeutic response in vivo.

overall_design: Splenic CD8 T cells incubated with functionalised Nanowire dually coated with miR-29 ASO and miR-29 mimic or inert controls for 3 days in vitro

first: Kristel

middle: J

last: Mon

first: Sungwoong

last: Kim

first: Zhonghao

last: Dai

first: Jessica

last: West

first: Hongya

last: Zhu

first: Ritika

last: Jain

first: Brian

last: Rudd

first: Ankur

last: Singh


title: Maternal gestational nutrition perturbs offspring sperm epigenome in sheep [ncRNA-seq]

first: Zongliang

last: Jiang

overall_design: Comparative gene expression profiling analysis of sncRNA-seq data for F1 sperm from CON, OVER and RES group.

first: Zhu

last: Linkai

first: Nicole

last: Tillquist


title: Enhanced CLIP (eCLIP) identified differential UPF1 binding sites in mouse neural progenitor cells (NPCs) samples

city: La Jolla

first: Gene

last: Yeo

state: CA

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

summary: As one of the key RNA regulation pathway, the NMD pathway plays a key role in the early brain development. The investigation of UPF1 specific binding transcript in mouse NPCs samples could give us a overall view of potential genes which are subjected to the NMD regulation. Among these genes we could identify how the NMD pathway shapes early mouse brian development.

overall_design: eCLIP-seq with UPF1 specific antibody in mouse NPCs samples

first: JingRong

last: Zhao

first: Steven

last: Blue

last: Yee

first: Sika

last: Zheng


title: The Small Extracellular Vesicle-Mediated Intercellular Transformation of CXCR1Low to CXCR1High Tumor Cells Promotes the Progression of Head and Neck Squamous Cell Carcinoma

city: Beijing

first: Qiaoshi

last: Xu

address: No. 4 Tian Tan Xi Li, Dongcheng District

institute: Beijing Stomatological Hospital, Capital Medical University

summary: The heterogeneity of tumor cells enables cancers to dynamically adapt to microenvironmental stresses during progression. However, the mechanism underlying the transformation and intercellular communication between heterogeneous tumor cells has remained elusive. Here, we report a “contagion model” that mediates intercellular transformation between heterogeneous tumor cells which facilitates tumor progression. Initially identifying heterogeneous expression of CXCR1, a receptor for interleukin-8, in head and neck squamous cell carcinoma (HNSCC) tumor cells. Following interleukin-8-mediated activation, CXCR1High cells transformed CXCR1Low cells into CXCR1High cells through the secretion of small extracellular vesicles (sEVs), which increased the proportion of CXCR1High cells and facilitated tumor progression. Mechanistically, we demonstrate that sEVs derived from interleukin-8-activated CXCR1High cells contain high levels of ATP citrate lyase (ACLY), which acetylates NF-κB p65 and facilitates its nuclear translocation to transcribe CXCR1 in CXCR1Low cells. That process could be inhibited by Bempedoic acid, an FDA-approved ACLY-targeted drug. Taken together, our study reveals an sEV-mediated transformation of CXCR1Low to CXCR1High cells that promotes HNSCC progression. This provides a new paradigm to explain the dynamic changes of heterogeneous tumor cells, and identifies Bempedoic acid as a potential drug for HNSCC treatment.

overall_design:
To investigated the function of IL-8 to HNSCC cell with different CXCR1 expression, we used recombinant human IL-8 to stimulated HN4, HN6 and Cal27 cells.
To investigated the downstream of ACLY, we overexpressed ACLY in HN4, HN6 and Cal27 cells.

first: Zhien

last: Feng

first: Zhengxue

last: Han


title: Multiomic Analyses Reveal New Targets of Polycomb Repressor Complex 2 in Schwann Lineage Cells and Malignant Peripheral Nerve Sheath Tumors - Methylation

first: David

last: Largaespada

type: Methylation profiling by genome tiling array

summary: Background  Malignant peripheral nerve sheath tumors (MPNST) can arise from atypical neurofibromas (ANF). Loss of the polycomb repressor complex 2 (PRC2) is a common event. Previous studies on PRC2-regulated genes in MPNST used genetic addback experiments in highly aneuploid MPNST cell lines which may miss PRC2-regulated genes in NF1-mutant ANF-like precursor cells. A set of PRC2-regulated genes in human Schwann cells has not been defined. We hypothesized PRC2 loss has direct and indirect effects on gene expression resulting in MPNST, so we sought PRC2-regulated genes in immortalized human Schwann cells (iHSCs).   Methods  We engineered NF1-deficient iHSCs with loss of function SUZ12 or EED mutations. RNA sequencing revealed 1,327 differentially expressed genes to define PRC2-regulated genes. To investigate MPNST pathogenesis we compared genes in iHSCs to consistent gene expression differences between ANF and MPNSTs. Chromatin immunoprecipitation sequencing was used to further define targets. Methylome and proteomic analyses were performed to further identify enriched pathways.   Results  We identified potential PRC2-regulated drivers of MPNST progression. Pathway analysis indicates many upregulated cancer-related pathways. We found transcriptional evidence for activated Notch and Sonic Hedgehog signaling in PRC2-deficient iHSCs. Functional studies confirm Notch signaling is active in MPNST cell lines, patient derived xenografts, and transient cell models of PRC2 deficiency.  A combination of MEK and γ-secretase inhibition shows synergy in MPNST cell lines.   Conclusions  We report PRC2-regulated genes and potential drivers of MPNSTs. Our findings support the Notch pathway as a druggable target in MPNSTs. Our identification of PRC2-regulated genes and pathways could result in more novel therapeutic approaches.

overall_design: In order to model the progression from atypical neurofibromas to malignant peripheral nerve sheath tumors NF1, SUZ12, and EED were knocked out in immortalized human Schwann cells. Methylation data was generated for all combinations of knockouts for NF1, SUZ12, and EED except that EED and SUZ12 knockouts were mutually exclusive.

first: Minu

middle: M

last: Bhunia

first: Tyler

last: Jubenville


title: Gene expression changes in Mettl3ed/ed mouse uterus compared to Mettl3f/f mouse uterus on gestational day 4

city: Guangzhou

first: Ji-Long

last: Liu

address: 483 Wushan Rd

institute: South China Agricultural University

summary: We specifically deleted Mettl3 in the epithelium of mouse uterus using the Ltf-Cre driver. To portray the molecular mechanism for Mettl3 function in uterine epithelium, uterine tissues were collected from Mettl3f/f and Mettl3ed/ed mice on gestational day 4 and subjected to RNA-seq analysis.

overall_design: Uterine tissues were collected from Mettl3f/f and Mettl3ed/ed mice on gestational day 4 and subjected to RNA-seq analysis.


title: Neuron-specific chromatin disruption at CpG islands and aging-related regions in Kabuki syndrome mice [CD90.2+ T cells, RNA-seq]

first: Leandros

last: Boukas

overall_design: RNA-seq of T cells (CD90.2+) in mouse models of Kabuki Syndrome 1, Kabuki Syndrome 2, as well as wild-type mice

first: Teresa

last: Romeo Luperchio


title: Activator protein transcription factors coordinate human IL-33 expression from non-canonical promoters in chronic airway disease

city: St Louis

first: Tiandao

last: Li

state: MO

address: 4444 Forest Park Ave

institute: Washington University

summary: Interleukin-33 (IL-33) is a cytokine central to type-2 immune pathology in chronic airway disease. This cytokine is abundantly expressed in the respiratory epithelium and increased in disease, but how this is regulated is undefined. Here we show IL-33 is expressed from multiple promoters in human chronic obstructive pulmonary disease (COPD) and non-canonical promoters mediate production of alternatively spliced isoforms. Transposase-accessible chromatin sequencing (ATAC-seq) performed on cell lines with distinct IL-33 expression levels demonstrated chromatin accessibility as a control point for IL-33 expression. We further discovered that phorbol esters activate non-canonical IL-33 promoters through protein kinase C in airway cells. Transcription factor (TF) binding arrays combined with RNA interference revealed Activator Protein transcription factors as the downstream effectors of non-canonical IL-33 promoter activation. In support of a role for Activator Protein-2 family members in COPD pathogenesis, we found both TFAP2A and TFAP2C are upregulated in disease, with phosphorylated TFAP2C localized to IL-33-positive airway basal cells in COPD lung tissue. This study defines how pioneer transcription factors associated with stemness can drive non-canonical IL-33 promoters and alternative splicing patterns in airway epithelial progenitors. Our work reveals a novel approach for targeting the IL-33 pathway to promote the development of new therapeutics for COPD.

overall_design: To address whether altered chromatin accessibility may be responsible for these different expression patterns of IL33 transcripts, we performed transposase-accessible chromatin sequencing (ATAC-seq) on the HBE-1, Beas2B, and 16HBE14o cell lines to identify peaks within the gene in proximity to the promoters. We compared this to whole lung ATAC-seq data and RNA annotation and mapping of promoters (RAMPAGE) data available through ENCODE.

first: Jennifer

last: Alexander-Brett

first: Bo

last: Zhang

first: Ghandi

last: Hassan


title: HuR promotes triglyceride synthesis and intestinal fat absorption

first: liu

last: cihang

address: Xueyuan Road

institute: Peking University Health Science Center

summary: Triacylglyceride (TAG) synthesis in the small intestine determines the absorption of dietary fat, but the mechanisms underlying are largely unknown. Here, we report that the RNA-binding protein HuR (ELAVL1) promotes TAG synthesis in the small intestine. HuR associates with the 3’UTR of Dgat2 mRNA and the introns 1 of Mgat2 pre-mRNA. Association of HuR with Dgat2 3’UTR stabilizes Dgat2 mRNA, while association of HuR with intron 1 of Mgat2 pre-mRNA promotes the processing of Mgat2 pre-mRNA. Intestinal epithelium-specific HuR knockout reduces the expression of DGAT2 and MGAT2, thereby reducing the dietary fat absorption through TAG synthesis and mitigating high-fat diet (HFD)-induced non-alcoholic fatty liver disease (NAFLD) and obesity. Our findings highlight a critical role of HuR in promoting dietary fat absorption.

overall_design: To investigate HuR binding mRNAs in intestinal fat absorption, we used mouse colon cancer cells CT26. WT for ribonucleoprotein immunoprecipitation assay using anti-endogenous HuR antibody. One input RNA(divided in three), and 3v3 co-immunoprecipitated RNA(IgG and HuR)respectively were used for next-generation sequencing

first: Cihang

first: Yunping

last: Lin

first: Ying

last: Wang

first: Shuyong


title: Desipramine Induces Anti-inflammatory Dorsal Root Ganglion Transcriptional Signatures in the Murine Spared Nerve Injury Model

city: New York

first: Aarthi

last: Ramakrishnan

state: New York

address: 1425 Madison Avenue

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

summary: Monoamine-targeting antidepressants serve as frontline medications for chronic pain and associated comorbidities. While persistent anti-allodynic properties of antidepressants generally require weeks of treatment, several groups have demonstrated acute analgesic effects within hours of administration, suggesting a role in non-mesocorticolimbic pain processing regions such as the peripheral nervous system. To further explore this possibility, after four weeks of spared nerve injury or sham surgeries, we systemically administered desipramine or saline for an additional three weeks and performed whole transcriptome RNA sequencing on injured dorsal root ganglia. Along with alterations in molecular pathways associated with neuronal activity, we observed a robust immunomodulatory transcriptional signature in the desipramine treated group. Cell subtype deconvolution predicted that these changes were associated with A- and C-fibers. Of note, differentially expressed genes from the dorsal root ganglia of DMI-treated, injured mice were largely unique compared to those from the nucleus accumbens of the same animals. These observations suggest that, under peripheral nerve injury conditions, desipramine induces specific gene expression changes across various regions of the nociceptive circuitry.

overall_design: Following four weeks of exposure to tibial spared nerve injury or sham surgeries, animals were treated with desipramine (15 mg/kg i.p. BID) or saline for three weeks.

first: Randal

last: Serafini

first: Li

last: Shen

first: Venetia

last: Zachariou


title: The mouse retinal pigment epithelium mounts an innate immune defense response following retinal detachment

city: Ann Arbor

first: Steven

middle: F

last: Abcouwer

state: MI

address: 1000 Wall Street

department: Ophthalmology and Visual Sciences

institute: University of Michigan

summary: The retinal pigment epithelium (RPE) maintains photoreceptor viability and function, completes the visual cycle, and forms the outer blood-retinal barrier (oBRB). Loss of RPE function gives rise to several monogenic retinal dystrophies and contributes to age-related macular degeneration. Retinal detachment (RD) causes separation of the neurosensory retina from the underlying RPE, disrupting the functional and metabolic relationships between these layers. Although the retinal response to RD is highly studied, little is known about how the RPE responds to loss of this interaction. RNA sequencing (RNAseq) was used to compare normal and detached RPE in the C57BL6/J mouse. The naïve mouse RPE transcriptome was compared to previously published RPE signature gene lists and from the union of these 14 genes (Bmp4, Crim1, Degs1, Gja1, Itgav, Mfap3l, Pdpn, Ptgds, Rbp1, Rnf13, Rpe65, Slc4a2, Sulf1 and Ttr) representing a core signature gene set applicable across rodent and human RPE was derived. Gene ontology enrichment analysis (GOEA) of the mouse RPE transcriptome identified expected RPE features and functions, such as pigmentation, phagocytosis, lysosomal and proteasomal degradation of proteins, and barrier function. Differentially expressed genes (DEG) at 1 and 7 days post retinal detachment (dprd). were defined as mRNA with a significant (padj≤0.05) fold change (FC) of 0.67≥FC≥1.5 in detached versus naïve RPE. The RPE transcriptome exhibited dramatic changes at 1 dprd, with 2297 DEG identified. The KEGG pathways and biological process GO groups related to innate immune responses were significantly enriched. Lipocalin 2 (Lcn2) and several chemokines were upregulated, while numerous genes related to RPE functions, such as pigment synthesis, visual cycle, phagocytosis, andtight junctions were down regulated at 1 dprd. The response was largely transient, with only 18 significant DEG identified at 7 dprd, including upregulation of complement gene C4b. Validation studies confirmed RNAseq results. Thus, the RPE quickly down-regulates cell-specific functions and mounts an innate immune defense response following RD. Our data demonstrate that the RPE contributes to the inflammatory response to RD and may play a role in attraction of immune cells to the subretinal space and the opsonization of orphaned outer segments following RD.

overall_design: Comparative RPE gene expression profiling after approximately 50% retinal detachment from the RPE after 1 and 7 days compared to Naïve.


title: Depolymerization of SUMO chains induces slender to stumpy differentiation in T. brucei bloodstream parasites

city: Armilla

first: Bioinformatics Unit

last: IPBLN-CSIC

state: GRANADA

address: Avda. del Conocimiento, 17. Instituto de Parasitología y Biomedicina Lopez-Neyra. Bioinformática

institute: IPBLN-CSIC

summary: Trypanosoma brucei are protozoan parasites that cause sleeping sickness in humans and nagana in cattle. Inside the mammalian host, a quorum sensing-like mechanism coordinates its differentiation from a slender replicative form into a quiescent stumpy form, limiting growth and virulence. SUMOylation is a reversible post-translational modification that enables dynamic regulation of cellular metabolism by the attachment of SUMO monomer or SUMO polymeric chains. We have found that parasites able to conjugate only SUMO monomers are primed for differentiation. This was demonstrated for monomorphic lines that are normally unable to produce stumpy forms in response to quorum sensing signaling in mice, and also for pleomorphic cell lines in which stumpy cells were observed at unusually low parasitemia levels. SUMO chain mutants showed a stumpy compatible transcriptional profile and better competence to differentiate into procyclics. Our study indicates that SUMO depolymerization may represent a coordinated signal triggered during stumpy activation program.

overall_design: We performed RNA-Seq on parasites isolated from the blood of infected mice at the peak of parasitemia (5 days post-infection, dpi) and performed differential gene expression analyses between WT and SUMO chain mutants

first: Paula

last: Iribarren

first: Lucía

last: Di Marzio

first: María

last: Berazategui

first: Andreu

last: Saura

first: Lorena

last: Coria

first: Juliana

last: Cassataro

first: Federico

last: Rojas

first: Miguel

last: Navarro

first: Vanina

middle: E

last: Alvarez


title: The oxidative stress response highly depends on glucose and iron availability in Aspergillus fumigatus

city: Debrecen

first: Tamas

last: Emri

address: Egyetem ter 1

country: Hungary

institute: University of Debrecen

summary: Pathogens have to cope with oxidative, iron- and carbon-limitation stresses in the human body. To understand how combined iron-carbon limitation alters oxidative stress response, Aspergillus fumigatus was cultured in glucose-peptone or peptone containing media supplemented or not with deferiprone as iron chelator. Changes in the transcriptome in these cultures were recorded after H2O2 treatment. Responses to oxidative stress were highly dependent on the availability of glucose and iron. Out of the 16 stress responsive antioxidative enzyme genes only the cat2 catalase-peroxidase gene was upregulated in more than two culturing conditions. The transcriptional responses observed in iron metabolism also varied substantially in these cultures. Only extracellular siderophore production appeared important regardless to culturing conditions in oxidative stress protection, while enhanced synthesis of Fe-S cluster proteins seemed to be crucial for oxidative stress treated iron-limited and fast growing (glucose rich) cultures. Although pathogens and host cells live together in the same place, their culturing conditions (e.g. iron availability, or occurrence of oxidative stress) can be different. Therefore, inhibition of a universally important biochemical process, like Fe-S cluster assembly, may selectively inhibit the pathogen growth in vivo and represent a potential target for antifungal therapy.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for mycelia of A. fumigatus (Af293 reference strain) on glucose+peptone or on peptone, in the presence of 1 mM deferiprone (DFP) and/or 75 mM H2O2 with three biological replicates.

first: Károly

last: Antal

first: István

last: Pócsi

first: Tamás


title: Gene expression profiling of human colorectal cancer cell lines [Affymetrix]

city: Chapel Hill

first: Yanguang

last: Cao

state: North Carolina

address: 301 Pharmacy Ln

institute: UNC Chapel Hill

summary:
We observed human colorectal cancer cell lines obtained resistance under treatment, and resistant cells switched back to sensitive state when the treatment is withdrawn.
To understand gene expressions change during this process, we performed Affymetrix experiments for parental, R20 (resistant), and W20 (withdrawal treatment) clones for three colorectal cancer cell lines.

overall_design: Parental is the original cell line, and R20 are the cells survived 20 cycles of cetuximab and natural killer cells treatment, W20 cells are the R20 cells cultured without treatment for another 20 cycles.

first: Cao

last: Yanguang

first: Zhou

last: Jiawei


title: Inter-individual variations in circadian misalignment-induced NAFLD pathophysiology in mice

first: Kazuhiro

last: Yagita

address: Kawaramachi-Hirokoji, Kamigyo-ku

institute: Kyoto Prefectural University of Medicine

summary: Pathological consequences of circadian misalignment, such as shift work, show considerable individual differences, but the lack of mechanistic understanding hinders precision prevention to prevent and mitigate disease symptoms. Here, we employed an integrative approach involving physiological, transcriptional, and histological phenotypes to examine inter-individual differences in pathological progression during the pre-symptomatic stage, prior to the development of irreversible diseases under chronic circadian misalignment, using wild-type mice exposed to chronic jet-lag (CJL). We observed that CJL markedly increased the prevalence of hepatic steatosis with pronounced inter-individual differences. Stratification of individual mice based on CJL-induced hepatic transcriptomic signature, validated by histopathological analysis, pinpoints dysregulation of lipid metabolism. Moreover, the period and power of intrinsic behavioral rhythms was found to significantly correlate with CJL-induced gene signatures. Together, our results suggest circadian rhythm robustness of the animals contribute to inter-individual variations in pathogenesis of circadian misalignment-induced diseases, and arise the possibility that these physiological indicators may be available for predictive hallmarks of circadian rhythm disorders.

overall_design: Examination of poly(A)+ enriched RNAs in mouse liver exposed to chronic circadian misalignment in addition to control.  Wild-type male C57BL/6J mice were exposed to chronic jet lag characterized by 8-hour advance every 4 days (referred to as ADV paradigm) for 47 weeks, whereas the control group (LD) were maintained under the normal 12h:12h light-dark condition.

first: Nobuya

last: Koike

first: Yasuhiro

last: Umemura


title: Tumor microenvironment landscapes supporting EGFR-mutant NSCLC are modulated at the single cell interaction level by Unesbulin treatment

city: Segrate

first: Roberta

last: Alfieri

address: Via Fratelli Cervi 93

department: ITB

country: Italy

institute: CNR

summary: Lung cancer is the leading cause of cancer deaths. Lethal pulmonary adenocarcinomas (ADCs) present with frequent mutations in the Epidermal Growth Factor Receptor (EGFR). Genetically-engineered murine models of lung cancer expedited comprehension of the molecular mechanisms driving tumorigenesis and drug response. Here, we systematically analyzed the evolution of tumor heterogeneity in the context of dynamic interactions occurring with the intermingled tumor microenvironment by high resolution transcriptomics. Our effort identified vulnerable tumor-specific epithelial cells, as well as their cross-talk with niche components (endothelial cells, fibroblasts and tumor-infiltrating immune cells), whose symbiotic interface shapes tumor aggressiveness and is almost completely abolished by treatment with Unesbulin, a tubulin binding agent that reduces BMI-1 activity. Simultaneous MRI analysis demonstrated decreased tumor growth, setting the stage for future investigations into the potential of novel therapeutic strategies for EGFR-mutant ADCs.

overall_design: Single cell RNA sequencing (scRNAseq) of lung tissues from EGFR-mutant model mice using InDrops-seq. The dataset includes five samples, each sequenced with distinct index sequences. Upon demultiplexing with these indexes, the dataset includes a total of 17 samples, comprising 2 untreated healthy samples, 2 healthy samples treated with a vehicle, 2 healthy samples treated with Unesbulin, 8 tumor samples treated with a vehicle, and 3 tumor samples treated with Unesbulin.

first: Giorgia

last: Maroni

first: Ivan

last: Merelli

first: Elena

last: Levantini


title: RNA-seq reveals differential gene expression profiles of alveolar type II epithelial cells in young and aged mice lungs

first: Quan

last: Rui

state: Haidian District

address: 10 Tianxiu Road

department: Department of Nutrition and Health

institute: China Agricultural University

summary: Lung aging triggers the onset of various chronic lung diseases, with alveolar repair being a key focus for alleviating pulmonary conditions. The regeneration of epithelial structures, particularly the differentiation from type II alveolar epithelial (AT2) cells to type I alveolar epithelial (AT1) cells, serves as a prominent indicator of alveolar repair. Nonetheless, the precise role of aging in impeding alveolar regeneration and the underlying mechanism remain to be fully elucidated. To elucidate the mechanisms underlying AT2 cell functional decline during lung aging, we employed transcriptomic techniques to explicit the differences in gene expression between AT2 cells of young (3-month old) and old (24-month old) mouse lungs, and revealed correlation between inflammatory factors and genes regulating proliferation and differentiation. Physiological aging-induced chronic inflammation impairs AT2 cell functions, hindering tissue repair and promoting lung disease progression. This study offers novel insights into chronic inflammation's impact on stem cell-mediated alveolar regeneration.

overall_design: To investigate the differential gene expression profile of AT2 cells during lung aging, we extracted primary cells from lung tissues of naturally aged C57/6J mice at 3 months and 24 months of age. Subsequently, flow cytometry was employed to sort CD45- CD31- CD326+ MHCII+ cells, which represent AT2 cells. The RNA-seq data of AT2 cells from these two age groups were analyzed to determine the differences in gene expression between young and old mouse lungs.

first: Rui

last: Quan

first: Yixuan

last: Li


title: Effect of sodium butyrate on rumen epithelial cell proliferation

city: Hangzhou

first: Bin

last: Yang

email: rayyangbin@163.com, binyang@zju.edu.cn

state: Zhejiang

address: No. 866 Yuhangtang Road

department: College of Animal Sciences

institute: Zhejiang University

summary: Promoting rumen development is closely related to the health and efficient growth of ruminants. We investigated the effect of sodium butyrate (SB) on rumen epithelium (RE), and whether the YAP1/TAZ-dependent alteration was involved in the RE developmental process induced by sodium butyrate. In the SB-treated cells, theYAP1/TAZ-dependent changes were not observed. SB increased the expression of genes involved in short-chain fatty acid (SCFA) metabolism, while YAP1/TAZ did not. Thus, SB mediated RE development was not associated with YAP1/TAZ.

overall_design: The RE cells were treated with SB (SB group) or left untreated (Con group) to assess gene expression.

first: Zebang

last: Xu

first: Hongwei

last: Chen

first: Jiakun

last: Wang


title: Effect of YAP1/TAZ on rumen epithelial cell proliferation

summary: Promoting rumen development is closely related to the health and efficient growth of ruminants. In the present study, we aimed to assess the impact of YAP1/TAZ on RE proliferation. The transcriptomic expression was analyzed to investigate the potential regulatory networks. The results indicated that GA promoted RE cell proliferation, while VP disrupted RE cell proliferation. The Hippo, Wnt, and calcium signaling pathways were altered in cells following the regulation of YAP1/TAZ. Upon YAP1/TAZ activation through GA, the CCN1/2 increased to promote RE cell proliferation. While when the YAP1/TAZ was inhibited by VP, the BIRC3 decreased to suppress RE cell proliferation. Thus, YAP1/TAZ may be potential targets for regulating RE cell proliferation. These findings broaden our understanding of the role of YAP1/TAZ and their regulators in RE and offer a potential target for promoting rumen development.

overall_design: GA-017 (GA) and verteporfin (VP) are identified as an efficient activator and inhibitor for YAP1/TAZ, respectively. GA can activate YAP1/TAZ by inhibiting their phosphorylation and promoting their nuclear translocation (Aihara et al., 2022). VP disrupts the YAP1/TAZ-TEA domain transcription factor (TEAD) mediated transcription and suppresses downstream gene expression (Brewer et al., 2021). Thus, the RE cells were treated with either GA (GA group) or VP (VP group), or left untreated (Con group), to assess gene expressions.


title: Maternal oxytocin treatment at birth increases epigenetic age in male offspring

city: Charlottesville

first: Joshua

last: Danoff

state: VA

address: 485 McCormick Road

institute: University of Virginia

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

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus
Microtus ochrogaster

overall_design: Refer to individual Series


title: Integrated transcriptomics and proteomics analysis reveals muscle metabolism effects of dietary Ulva lactuca and ulvan lyase supplementation in weaned piglets

city: Lisboa

first: David

middle: Miguel

last: Ribeiro

state: Lisboa

address: Tapada da Ajuda

department: Secção de Produção Animal

country: Portugal

institute: Instituto Superior de Agronomia

summary: Seaweeds, including the green Ulva lactuca, can potentially reduce competition between feed, food, and fuel. They can also contribute to the improved development of weaned piglets. However, their indigestible polysaccharides of the cell wall pose a challenge. This can be addressed through carbohydrase supplementation, such as the recombinant ulvan lyase. The objective of our study was to assess the muscle metabolism of weaned piglets fed with 7% U. lactuca and 0.01% ulvan lyase supplementation, using an integrated transcriptomics (RNA-seq) and proteomics (LC-MS) approach.

overall_design: Weaned piglets housed in metabolic cages in the context of a nutritional trial

first: Diogo

last: Coelho

first: Mónica

last: Costa

first: Daniela

last: Pires Carvalho

first: Céline

last: Leclercq

first: Jenny

last: Renaut

first: João

last: Bengala Freire

first: André

last: Martinho de Almeida

first: José

last: Mestre Prates


title: Acute effects of  NOAEL-dose of neonicotinoid clothianidin on the gene expression profiles in cerebellum of male mice

city: Toyama

first: Tetsushi

last: Hirano

state: Toyama

address: 2630 sugitani

department: Life Science Research Center

institute: University of Toyama

summary:
The mechanisms of cognitive and learning effects of neonicotinoid pesticides were not fully understood.
We examined the effects of acute exposure to a neonicotinoid pesticide, clothianidin (CLO) on gene expression profiles in the cellebellum of male mice at 10 weeks of age.

overall_design: Mice were orally administrated 50 mg/kg/day of CLO or vehicle for 4 days of rotarod test.

first: Yukako

last: Hara

first: Nobuhiko

last: Hoshi

first: Yoshiaki

last: Tabuchi


title: Single-cell RNA sequencing reveals the landscape of immune cells and the characterization of viral tropism in Japanese encephalitis virus-infected mouse brain

city: wuhan

first: lingen

last: yang

address: Shizishan Street 1

institute: Huazhong Agricultural University

summary: JEV is a neurotropic pathogen that causes lethal encephalitis in humans. The high susceptibility and massive proliferation of JEV in neurons lead to neuronal damage and dramatical inflammation in central nerves system (CNS). However, the mechanisms by which JEV preferentially infects neurons and induces massive neuroinflammation are largely unknown. Here, we found that JEV mainly distributed in cerebral cortex, striatum and thalamus in brain of infected mice, indicating the tissue or cell type bias. Cells in these regions of JEV-infected mice showing different symptoms (mild, moderate and severe) were isolated and subjected to scRNA-seq. 88000 single cells were obtained based on top differentially expressed genes, and 34 clusters and 10 major cell types were identified. As demonstrated by scRNA-seq and flow-cytometry assay, activated microglia cells and infiltrating immune cells including monocyte & macrophage, T cells and NK cells which are responsible for inflammatory response were increased in JEV-infected brain in a symptom severity-dependent manner. Furthermore, the subclusters of these cells and the cell-cell interaction network were analyzed. More communications between individual cells and significant increase in ligand receptor pairs associated with tight junctions, chemokines and antigen-presenting molecules were shown in JEV-infected mouse brain, suggesting upregulation of cellular permeability, inflammation and antiviral response. To identify which subtype(s) of neurons is/are targeted by JEV, 27874 neuronal cells were reclustered to 15 subsets. By analyzing the correlation between the expression of JEV E gene and neuronal genes, we found that Baiap2high neurons are highly permissive to JEV.

overall_design: To understand what are the cell types that enter the CNS from the periphery after Japanese Encephalitis virus (JEV) infection and how are these cells involved in the JEV-induced inflammatory response, we conducted single cell RNA sequencing analysis of brain cell from healthy and JEV infected mice.

first: ling'en


title: Probing liver injury induced by thioacetamide in human in vitro pooled hepatocyte experiments

city: Frederick

first: Himanshu

last: Goel

state: MD

address: 2405 Whittier Drive, Suite 200

institute: Biotechnology HPC Software Applications Institute (BHSAI)

summary: In this study we tested the ability to predict liver injury from in vitro human pooled hepatocyte data after exposure to thioacetamide (24 hour). We selected thioacetamide, a compound extensively used in various studies for its ability to cause liver injury.

overall_design: We treated in vitro multi-donor pooled hepatocytes with saline solution (control), 1.33 mM (low dose) and 12 mM (high dose) for 24 hours to produce different degrees of injury.  Number of repicates were five.

first: Richard

last: Printz

first: Venkat

last: Pannala

first: Mohamed

last: AbdulHameed

first: Anders

last: Wallqvist


title: Targeting Osteosarcoma with Canine B7-H3 CAR T Cells and Impact of CXCR2 Co-Expression on Functional Activity

city: Fort Collins

first: Steven

last: Dow

state: CO

address: 300 W Drake Rd

department: Clinical Sciences

institute: Colorado State University

summary: Abstract. The use of large animal spontaneous models of solid cancers, such as dogs with osteosarcoma (OS), can help develop new cancer immunotherapy approaches, including chimeric antigen receptor (CAR) T cells. Therefore, the goal of the present study was to generate canine CAR T cells targeting the B7-H3 (CD276) co-stimulatory molecule overexpressed by several solid cancers, including OS and glioma in both humans and dogs, and to assess their ability to recognize B7-H3 expressed by canine OS cell lines or by canine tumors in xenograft models. A second objective was to determine whether a novel dual CAR that expressed a chemokine receptor together with the B7-H3 CAR improved the activity of the canine CAR T cells. Therefore, in the studies reported here we examined B7-H3 expression by canine OS tumors, evaluated target engagement by canine B7-H3 CAR T cells in vitro, and compared the relative effectiveness of B7-H3 CAR T cells versus B7-H3-CXCR2 dual CAR T cells in canine xenograft models. We found that most canine OS tumors expressed high levels of B7-H3, whereas levels were undetectable on normal dog tissues. In vitro, both B7-H3 CAR T cells demonstrated activation and OS-specific target killing in vitro, but there was significantly greater cytokine production by B7-H3-CXCR2 CAR T cells. In canine OS xenograft models, little antitumor activity was generated by B7-H3 CAR T cells, whereas B7-H3-CXCR2 CAR T cells significantly inhibited tumor growth, inducing complete tumor elimination in most treated mice. These findings indicated therefore that addition of a chemokine receptor could significantly improve the anti-tumor activity of canine B7-H3 CAR T cells, and that evaluation of this new dual CAR construct in dogs with primary or metastatic OS is warranted since such studies could provide a critical and realistic validation of the chemokine receptor concept.

overall_design: IN the current study we expanded the scope of the original canine B7-H3 CAR T cell studies to evaluate expression of B7-H3 using a larger panel of canine OS tumor cell lines and biopsy tissues.  In addition, these studies conducted in vitro and in vivo characterization of a dual B7-H3 CAR construct co-expressing CXCR2.

first: Jennifer

last: Cao

first: Jessica

last: Lake

first: Renata

last: Impastato

first: Lyndah

last: Chow

first: Luisanny

last: Perez

first: Laura

last: Chubb

first: Jade

last: Kurihara

first: Michael

last: Verneris


title: Age-related increase in the expression of 11β-hydroxysteroid dehydrogenase type 1 in the hippocampus of male rhesus macaques

city: Winston-Salem

first: Kip

last: Zimmerman

state: NC

address: Medical Center Blvd

institute: Wake Forest School of Medicine

summary: The hippocampus is especially susceptible to age-associated neuronal pathologies, and there is concern that the age-associated rise in cortisol secretion from the adrenal gland may contribute to their etiology. Furthermore, because 11β-hydroxysteroid dehydrogenase type 1 (HSD11B1) catalyzes the reduction of cortisone to the active hormone cortisol, it is plausible that an increase in the expression of this enzyme enhances the deleterious impact of cortisol in the hippocampus and contributes to the neuronal pathologies that underlie cognitive decline in the elderly. Rhesus macaques were used as a translational animal model of human aging, to examine age-related changes in gene and protein expressions of (HSD11B1/HSD11B1) in the hippocampus, a region of the brain that plays a crucial role in learning and memory. Older animals showed significantly (p<0.01) higher base-line cortisol levels in the circulation. In addition, they showed significantly (p<0.05) higher hippocampal expression of HSD11B1 but not NR3C1 and NR3C2 (i.e., two receptor-encoding genes through which cortisol exerts its physiological actions). A similar age-related significant (p<0.05) increase in the expression of the HSD11B1 was revealed at the protein level by Western blot analysis. The data suggest that an age-related increase in the expression of hippocampal HSD11B1 is likely to raise cortisol concentrations in this cognitive brain area, and thereby contribute to the etiology of neuropathologies that ultimately lead to neuronal loss and dementia. Targeting this enzyme pharmacologically may help to reduce the negative impact of elevated cortisol concentrations within glucocorticoid-sensitive brain areas and thereby afford neuronal protection.

overall_design: We hypothesized that the expression of HSD11B1 in the hippocampus would show an age-associated increase, both at the mRNA and at the protein level. To test this, we used RNA-seq to compare hippocampal expression of HSD11B1 as well as cortisol-sensitive receptors NR3C1 and NR3C2, in young and old male rhesus macaques. We also used Western blot analysis to examine HSD11B1 protein expression in the same animals.

first: Alejandro

last: Lomniczi

first: Selva

last: Luna

first: Rita

last: Cervera-Juanes

first: Maria

last: Appleman

middle: G

last: Kohama

first: Henryk

last: Urbanski


title: Glutamine antagonist DRP-104 suppresses tumor growth and enhances response to checkpoint blockade in KEAP1 mutant lung cancer

city: New York City

first: Alireza

last: Khodadadi-Jamayran

address: 550 1st Ave, MSB 304

department: Division of Advanced Research Technologies (DART)

institute: New York University, NYU Langone Medical Center

summary: Keap1 mutant lung tumors were injected into mice and once lung tumors formed the mice were treated with anti-PD1, DRP-104, or the combination of the drugs. Immune cells and tumor cells were isolated from the lungs and ExCITE-seq was performed.

overall_design: 2 mice (G1 vs G2) per treatment arm: Isotype + Vehicle (HT4), DRP-104  + Isotype (HT2), anti-PD1 + Vehicle (HT3), and DRP-104 + anti-PD1 (HT1). After 5 days of treatment, immune and tumor cells were analyzed by ExCITE-seq with libraries for gene expression, ADT, and TCR

first: Ray

last: Pillai

first: Sarah

last: LeBoeuf

first: Yuan

last: Hao

first: Aristotelis

last: Tsirigos

first: Sergei

last: Koralov

first: Thales

last: Papagiannakopoulos


title: CORT induced anxiety behaviors via P21-ROS pathway

city: Shanghai

first: Guanhao

last: Wang

address: Siping Road

institute: Tongji University

summary: Anxiety disorders refer to a group of costly psychiatric disorders characterized by feelings of fear, panic and worry and related behavioral disturbances. Up to 275 million people worldwide (4% of the global population) are affected by anxiety disorders, which was ranked 8th of the top 25 leading causes of years lived with disability (YLDs) in 2019. According to a recent article published in the Lancet, the COVID-19 pandemic has led to a substantial rise in prevalence of GAD globally, consequently contributing to an elevated disease burden and a deteriorated economic situation. However, around 50% of patients diagnosed with generalized anxiety disorder (GAD) do not respond to the conventional pharmacological and psychological interventions due to the individual variability. Moreover, the limited accessibility to mental health professionals, the risk of dependence on benzodiazepines and the side effects of selective serotonin reuptake inhibitors (SSRIs) can negatively influence the medication adherence of patients. Hence, there is an urgent need to investigate the underlying pathological mechanisms and develop innovative therapeutic interventions for GAD.

overall_design: Comparative gene expression profiling of RNA-seq data from hippocampus from CORT and Veh mice

first: Jianfeng

last: Lu


title: The modification landscape of P. aeruginosa tRNAs

city: Bethesda

first: Pedro

last: Batista

address: 37 Convent Street Bldg 37

department: National Cancer Institute

institute: National Institutes of Health

summary: RNA modifications have a substantial impact on tRNA function. While modifications in the anticodon loop play an important role in translational fidelity, modifications in the tRNA core influence tRNA structural stability. In bacteria, tRNA modifications play important roles in the stress response and expression of virulence factors. While tRNA modifications are well characterized in a few model organisms, our knowledge of tRNA modifications in human pathogens, such as Pseudomonas aeruginosa is lacking. Here we leveraged two orthogonal approaches to build a reference landscape of tRNA modifications in E. coli, which we used to identify tRNA modifications in P. aeruginosa. We determined conservation for many modifications between the two organisms. We also identified potential sites of tRNA modification in P. aeruginosa tRNA that are not present in E. coli. One of these sites is found at the same positions as acacp3U, a modification previously identified in Vibrio cholerae. Identifying which modifications are present on different tRNAs will uncover the pathways impacted by the different tRNA modifying enzymes, some of which may play roles in determining virulence and pathogenicity.

sample_organism:
Pseudomonas aeruginosa PA14
Escherichia coli BW25113

overall_design: Illumina sequencing of purified RNA reverse transcribed using TGIRT and uniquely barcoded RT primers per each sample, RNA from bacteria grown in varying media conditions.

first: Mariana

last: Mandler

first: Siddhardha

middle: S

last: Maligireddy

first: Wilfried

last: Guiblet

first: Kayla

last: McDonald

first: Christina

last: Fitzsimmons


title: Lupus dermal fibroblasts hyper-respond to inflammatory cytokines and exhibit a pro-fibrotic phenotype to TGF-β in patients with scarring skin disease

first: Lam

last: Tsoi

address: Medical Sciences 1 Bldg. 1301 E. Catherine

institute: University of Michigan

summary: we examined responses to cytokines in dermal fibroblasts from the skin of  SLE patients with CLE and healthy control volunteers to identify the inflammatory phenotype and gene expression profile associated with SLE and scarring CLE lesions.

overall_design: we first compared the inflammatory phenotype in fibroblasts isolated from healthy controls (HC) and from non-lesional skin of SLE patients with CLE to explore differences in gene expression that occur in the disease

first: J

last: Kahlenberg

first: Suzanne

middle: K

last: Shoffner-Beck

first: Lisa

last: Abernathy-Close

first: Johann

last: Gudjonsson

middle: C


title: DNA methylation signatures correlate with response to immune checkpoint inhibitors in metastatic melanoma

city: Wien

first: Gerwin

last: Heller

address: Währinger Gürtel 18-20

department: Medicine I

country: Austria

institute: Medical University of Vienna

summary: DNA methylation profiles were recently proposed to have predictive value in various solid tumors. Therefore, we analyzed DNA methylation profiles of patients with stage IV metastatic melanoma, receiving first-line immune checkpoint inhibitors (ICIs) and correlated those with radiological response (iRECIST). Overall, 81 tissue samples from 71 patients with metastatic melanoma (27 (38.0%) female, 44 (62.0%) male) were investigated; median progression free survival was 8.5 months (0 – 104.1 months) and median overall survival was 30.6 months (0 – 104.1 months), respectively. 29 (40.8%) patients achieved an objective response. DNA methylation analyses revealed signatures correlating with radiological response to ICIs. Based on the 500 mostly differentially methylated genes, three clusters were identified with the majority of responders being in cluster 1 (12/12) and cluster 2 (12/24), and non-responders in cluster 3 (39/45). Our findings indicate that tumor DNA methylation profiling may be used as a predictor for ICI-response in patients with metastatic melanoma.

overall_design: Methylation profiling of responders vs. non-responders to immune checkpoint therapies

first: Julia

last: Ressler

first: Anna

last: Berghoff