title: High targeted integration frequency in human pluripotent stem cells with the CRISPR-Cas12a Ultra system

city: Freiburg

first: Kay

middle: Ole

last: Chmielewski

address: Breisacherstr. 115

department: Institute for transfusion medicine and gene therapy

institute: University clininics Freiburg

summary: The CRISPR-Cas12a platform has attracted interest in the genome editing community because the prototypic Acidaminococcus Cas12a generates a staggered DNA double-strand break upon binding to an AT-rich protospacer-adjacent motif (PAM, 5'-TTTV). The broad application of the platform in primary human cells was enabled by the development of an engineered version of the natural Cas12a protein, called Cas12a Ultra. In this study, we confirmed that CRISPR-Cas12a Ultra ribonucleoprotein complexes enabled allelic gene disruption frequencies of over 90% at multiple target sites in human T cells, hematopoietic stem and progenitor cells (HSPCs), and induced pluripotent stem cells (iPSCs). In addition, we demonstrated for the first time the efficient knock-in potential of the platform in human iPSCs and achieved targeted integration of a GFP marker gene into the AAVS1 safe harbor site and a CSF2RA super-exon into CSF2RA in up to 90% of alleles without selection. Clonal analysis revealed bi-allelic integration in >50% of the screened iPSC clones without compromising their pluripotency and genomic integrity. Thus, in combination with the adeno-associated virus vector system, CRISPR-Cas12a Ultra provides a highly efficient genome editing platform for performing targeted knock-ins in human iPSCs.

overall_design: HSPCs, T-cells and IPSCs were treated with the CPF1 Ultra nuclease

first: Ruba

last: Hammad

first: Jamal

last: Alzubi

first: Manuel

last: Rhiel

middle: O

first: Toni

last: Cathomen


title: Stably-Inverted Apical-Out Human Upper Airway Organoids for SARS-CoV-2 Infection and Therapeutic Testing

status: Public on Feb 09 2024

city: Atlanta

first: Shuichi

last: Takayama

state: GA

address: 950 Atlantic Dr NW

department: Biomedical Engineering

country: USA

institute: Georgia Institute of Technology

type: Expression profiling by high throughput sequencing

summary: Apical-out organoids produced through eversion triggered by extra-organoid extracellular matrix (ECM) removal or degradation are generally small, structurally variable, and limited for viral infection and therapeutics testing. This work describes ECM-encapsulating, stably-inverted apical-out human upper airway organoids (AORBs) that are large (~500 µm diameter), consistently spherical, recapitulate in vivo-like cellular heterogeneity, and maintain their inverted morphology for over 60 days. Treatment of AORBs with IL-13 skews differentiation towards goblet cells and the apical-out geometry allows extra-organoid mucus collection. AORB maturation for 14 days induces strong co-expression of ACE2 and TMPRSS2 to allow high-yield infection with five SARS-CoV-2 variants. Dose-response analysis of three well-studied SARS-CoV-2 antiviral compounds [remdesivir, bemnifosbuvir (AT-511), and nirmatrelvir] shows AORB antiviral assays to be comparable to gold-standard air-liquid interface cultures, but with higher throughput (~10-fold) and fewer cells (~100-fold). While this work focuses on SARS-CoV-2 applications, the consistent AORB shape and size, and one-organoid-per-well modularity broadly impacts in vitro human cell model standardization efforts in line with economic imperatives and recently updated FDA regulation on therapeutic testing.

overall_design: scRNAseq of human bronchial epithelial cell organoids.

first: Jihoon

last: Lee


title: scRNA-seq for stromal Lkb1 deficiency-induced gastrointestinal polyps

city: Shanghai

first: Yijie

last: Huang

state: Shanghai

address: 上海市徐汇区淮海西路241号

department: Cardiology

country: China

institute: Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine

summary: Numerous studies have showed that mesenchymal-specific Lkb1 is sufficient  for the development of PJS-like polyps in mice. However, the cellular origin and component of these Lkb1-associated polyps and underlying mechanisms remain elusive. In this present study, we generated tamoxifen-inducible Lkb1flox/flox;Myh11-Cre/ERT2 mice and performed scRNA-seq to investigate the cellular complexity of gastrointestinal polyps associated with PJS.

overall_design: Polyps tissues from three Lkb1flox/+;Myh11-Cre/ERT2 mice and  normal duodenum tissues of three Lkb1+/+;Myh11-Cre/ERT2 (WT) mice were collected.

first: Zhaohua

last: Cai

first: Yangjing

last: Jiang

first: Min

last: Liang

first: Ben

last: He


title: Comparative transcriptomic analysis of cerebellar astrocytes across developmental stages and brain regions

city: Houston

first: Dongjoo

last: Choi

state: TX

address: 1 baylor plaza

institute: BCM

summary:
To profile gene expression differences in astrocytes in postnatal cerebellar astrocytes .
Comparing cerebellar astrocyte transcriptomes at postnatal days 1, 7, 14, and 28 (P1, P7, P14, and P28),

overall_design: Comparative gene expression profiling analysis of RNA-seq data for FACS purified astrocytes from mouse brain tissue

first: Wookbong

last: Kwon

first: Dong-Joo

first: Benjamin

last: Deneen


title: Surface-associated, motile populations of Pseudomonas aeruginosa gene regulation by Staphylococcus aureus exoproducts

city: Bethesda

first: Anupama

last: Khare

state: MD

address: 37 Convent Drive

institute: National Cancer Institute

summary: Pseudomonas aeruginosa and Staphylococcus aureus are often co-isolated in persistent infections. The goal of this study was to determine how secreted products from S. aureus affect gene expression in surface-associated P. aerguinosa undergoing emergent motility. Therefore, media salts control or S. aureus supernatant was added to agar plates at 25% total volume. P. aeruginosa was inoculated on the agar and gene expression was measured from the leading edge after 17 h incubation using RNA-seq. P. aeruginosa moving on the agar containing S. aureus supernatant had an upregulation in genes involved in intermediate metabolite uptake and a downregulation in heme biosynthesis, response to heat, Type III Secretion System, and aerobic respiration pathways.

overall_design: We collected RNA-seq samples from P. aeruginosa collected from the leading edge on 0.5% or 1.5% (w/v) agar plates containing 25% (v/v) of either media salts control or S. aureus supernatant. RNAprotect (Qiagen) was added to each sample before purification using the Total RNA Purification Plus Kit (Norgen). Genomic DNA was removed using Turbo DNase (Invitrogen) and rRNA was removed using riboPOOLs (siTOOLs Biotech). The cDNA libraries were generated using NEBNext Ultra II Directional Library Kit and amplified with NEBNext index primers (New England Biolabs). Sequencing was performed at the National Cancer Institute Center for Cancer Research Genomics Core.

first: Delayna

last: Warrell

first: Tiffany

last: Zarrella


title: Loss of SLC30A10 manganese transporter alters expression of neurotransmission genes and activates hypoxia-inducible factor signaling in mice

city: Austin

first: Anna

last: Warden

address: 2500 Speedway

institute: University of Texas at Austin

summary: The essential metal manganese (Mn) induces neuromotor disease at elevated levels. The manganese efflux transporter SLC30A10 regulates brain Mn levels. Homozygous loss-of-function mutations in SLC30A10 induce hereditary Mn neurotoxicity in humans. Our prior characterization of Slc30a10 knockout mice recapitulated the high brain Mn levels and neuromotor deficits reported in humans. But, mechanisms of Mn-induced motor deficits due to SLC30A10 mutations or elevated Mn exposure are unclear. To gain insights into this issue, we characterized changes in gene expression in the basal ganglia, the main brain region targeted by Mn, of Slc30a10 knockout mice using unbiased transcriptomics. Compared with littermates, >1,000 genes were upregulated or downregulated in the basal ganglia sub-regions (i.e., caudate putamen, globus pallidus, and substantia nigra) of the knockouts. Pathway analyses revealed notable changes in genes regulating synaptic transmission and neurotransmitter function in the knockouts that may contribute to the motor phenotype. Expression changes in the knockouts were essentially normalized by a reduced Mn chow, establishing that changes were Mn-dependent. Upstream regulator analyses identified hypoxia-inducible factor (HIF) signaling, which we recently characterized to be a primary cellular response to elevated Mn, as a critical mediator of the transcriptomic changes in the basal ganglia of the knockout mice. HIF activation was also evident in the liver of the knockout mice. These results: (1) enhance understanding of the pathobiology of Mn-induced motor disease; (2) identify specific target genes/pathways for future mechanistic analyses; and (3) independently corroborate the importance of the HIF pathway in Mn homeostasis and toxicity.

overall_design: To analyze Mn-induced gene expression changes that may influence motor function in an unbiased manner, we performed Tag-seq analyses in basal ganglia (Caudate Putament, Substantia Nigra, Globus Pallidus) and Liver tissue collected from ~1-month old littermate control or full-body Slc30a10 knockout mice fed regular rodent chow (~84 µg Mn/g chow)

middle: S

first: R

middle: D

last: Mayfield

first: Chunyi

last: Liu

first: Somshuvra

last: Mukhopadhyay


title: IL-10 dampens antitumor immunity and promotes liver metastasis via PD-L1 induction

city: Hamburg

first: Babett

last: Steglich

address: Martinistrasse 52

country: Germany

institute: Universitätsklinikum Hamburg-Eppendorf

summary: Background & Aims: The liver is one of the organs most commonly affected by metastasis. The presence of liver metastasis is reported to be responsible for an immunosuppressive microenvironment and diminished immunotherapy efficacy. Here, we aimed to investigate the role of IL-10 in liver metastasis formation and decipher its therapeutic potential in affecting immunotherapy effectiveness. Methods: To induce spontaneous or forced liver metastasis in mice, murine cancer cells (MC38) or colon tumor organoids were injected into the cecum or the spleen, respectively. Mice with complete and cell-type specific deletion of IL-10- and IL-10Ra were used to identify the source and the target of IL-10 during metastasis formation. Programmed death ligand 1 (PD-L1)-deficient mice were used to test the role of this checkpoint. Flow cytometry was applied to characterize the regulation of IL-10 on PD-L1. Results: We found that Il10-deficient mice and mice treated with IL-10Ra antibodies were protected against liver metastasis formation. Furthermore, by using IL-10 reporter mice, we demonstrated that Foxp3+ regulatory T cells (Tregs) were the major cellular source of IL-10 in liver metastatic sites. Accordingly, deletion of IL-10 in Tregs, but not in myeloid cells, led to reduced liver metastasis. Mechanistically, IL-10 acted on Tregs in an autocrine manner, thereby further amplifying IL-10 production. Furthermore, IL-10 acted on myeloid cells, i.e., monocytes, and induced the upregulation of the immune checkpoint protein PD-L1. Finally, the PD-L1/PD-1 axis attenuated CD8-dependent cytotoxicity against metastatic lesions. Conclusions: Treg-derived IL-10 upregulates PD-L1 expression in monocytes, which in turn reduces CD8+ T-cell infiltration and related antitumor immunity in the context of colorectal cancer (CRC)-derived liver metastasis. These findings provide the basis for future monitoring and targeting of IL-10 in CRC-derived liver metastasis.

overall_design: RNA sequencing of sorted myeloid cells from livers of mice in LysM-Cre IL10R fl/fl vs. LysM-Cre IL10R wt/wt

first: Ahmed

middle: M

last: Shiri

first: Tao

last: Zhang

first: Tanja

last: Bedke

first: Dimitra

last: Zazara

first: Thilo

last: Hackert

first: Nicola

last: Gagliani

first: Anastasios

last: Giannou

first: Samuel

last: Huber


first: Shuichi

last: Takayama

overall_design: Total RNA was isolated from human bronchial epithelial cells (NHBE) grown in 2D as well as 3D organoids in various conditions.

first: Jihoon

last: Lee


title: P5 mouse neocortex

city: Leuven

first: Elia

last: Micoli

address: Herestraat 49

department: VIB - Center for Brain and Disease Research

country: Belgium

institute: VIB - KU Leuven

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

platform_organism:
Mus
Mus musculus

overall_design: Refer to individual Series


title: Spatial transcriptomic data of P5 mouse cortical somatostatin neurons

summary: Probe panel for 94 genes designed using Resolve Biosciences proprietary design software, as reported in table S4 of the manuscript .  Molecular Cartography (100-plex combinatorial single molecule fluorescence in-situ hybridization)

overall_design: P5 brain tissue sections were dissected, fresh frozen and placen on Resolve BioScience slides.After fixation the sections were used for Molecular Cartography. Tissue were primed, followed by overnight hybridization of all the probes specific for the trarget genes.The excess of probes was removed and color development, imaging and decolorization were repeated for multiple cycles to build a unique combinatorial code for every target gene derived from raw images. Samples were imaged on a Zeiss Celldiscoverer 7.

first: Lynette

last: Lim


title: CDCA7-associated global aberrant DNA hypomethylation translates to localized, tissue-specific transcriptional responses [ChIP-seq]

city: Leiden

first: Lucia

last: Daxinger

address: Albinusdreef 2

country: Netherlands

institute: Leiden Univeristy Medica Center

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Disruption of Cell division cycle associated 7 (CDCA7) has been linked to aberrant DNA hypomethylation, but the impact of DNA methylation loss on transcription has not been investigated. Here, we show that CDCA7 is critical for maintaining global DNA methylation levels across multiple tissues in vivo. A pathogenic Cdca7 missense variant leads to the formation of large, aberrantly hypomethylated domains overlapping with the B genomic compartment but without affecting deposition of H3K9 trimethylation (H3K9me3). CDCA7-associated aberrant DNA hypomethylation translated to localized, tissue-specific transcriptional dysregulation that impacted large gene clusters. In brain, we identify CDCA7 as a transcriptional repressor and epigenetic regulator of clustered protocadherin isoform choice. Increased protocadherin isoform expression frequency is accompanied by DNA methylation loss, gain of H3K4 trimethylation (H3K4me3) and increased binding of the transcriptional regulator CCCTC-binding factor (CTCF). Overall, our in vivo work identifies a key role for CDCA7 in safeguarding tissue-specific expression of gene clusters via the DNA methylation pathway.

overall_design: Ultra low input Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for H3K27me3 in E14.5 mouse Cerebrum

first: Maja

last: Vukic

first: Jihed

last: Chouaref

first: Veronica

last: Della Chiara

first: Serkan

last: Dogan

first: Fallon

last: Ratner

first: Jenna

middle: Z

last: Hogenboom

first: Trevor

last: Epp

first: Kallayanee

last: Chawengsaksophak

first: Kelly

middle: K

last: Vonk

first: Cor

last: Breukel

first: Yavuz

last: Ariyurek

first: David

last: San Leon Granado

first: Susan

middle: L

last: Kloet


title: CDCA7-associated global aberrant DNA hypomethylation translates to localized, tissue-specific transcriptional responses [ONT adaptive sampling]

overall_design: Methylation profiling by adaptive sampling target enrichment experiment using Oxford Nanopore Technologies (ONT) long-read sequencing


title: A zinc finger transcription factor enables social behaviors by controlling transposable elements and immune response in prefrontal cortex

city: Richmond

first: Peter

last: Hamilton

state: VA

address: 1217 E Marshall St

department: Anatomy and Neurobiology

institute: Virginia Commonwealth University

summary: The neurobiological origins of social behaviors are incompletely understood. Here we utilized synthetic biology approaches to reprogram the function of ZFP189, a transcription factor whose expression and function in rodent prefrontal cortex was previously demonstrated to be protective against stress-induced social deficits. We created novel synthetic ZFP189 transcription factors including ZFP189VPR, which activates the transcription of target genes and therefore exerts opposite functional control from the endogenous, transcriptionally repressive ZFP189WT. Following viral delivery of these synthetic ZFP189 transcription factors to mouse prefrontal cortex, we observe that ZFP189-mediated transcriptional control promotes mature dendritic spine morphology on transduced pyramidal neurons. Interestingly, inversion of ZFP189-mediated transcription in this brain area, achieved by viral delivery of synthetic ZFP189VPR, precipitates social behavioral deficits in terms of social interaction, motivation, and the cognition necessary for the maintenance of social hierarchy, without other observable behavioral deficits. RNA sequencing of virally manipulated prefrontal cortex tissues reveals that ZFP189 transcription factors of opposing regulatory function have opposite influence on the expression of genetic transposable elements as well as genes that participate in adaptive immune functions. Collectively, this work reveals that ZFP189 function in the prefrontal cortex coordinates structural and transcriptional neuroadaptations necessary for complex social behaviors, and does so by regulating transposable element-rich regions of DNA to control the expression of immune-related genes. Given the evidence for a co-evolution of social behavior and the brain immune response, we posit that ZFP189 may have evolved to augment brain transposon-associated immune function as a way of enhancing an animal’s capacity for functioning in social groups.

overall_design: Bulk RNA sequencing from microdissected mouse prefrontal cortex virally manipulated with different versions of a synthetic transcription factor (ZFP189). DEGs are generated relative to the control vrial treatment. This submission includes two RNA sequencing experiments, one performed 24 hours after viral surgery and one performed 4 days after viral surgery.


title: The effect of valproic acid in BMDMs

city: wuhan

first: Xudong

last: Xie

address: wuhan, 1277, Jiefang avenue

institute: wuhan union hospital

summary: Currently, the clinical role and influence of valproic acid (VPA) on bone homeostasis remains controversial. In the current study, we confirmed that VPA treatment was linked to a decrease in bone mass and bone mineral density (BMD), an effect that is hypothesized to be caused by a VPA-induced elevation in osteoclast formation and activity. RNA-sequencing revealed a prominent increase of miR-6359 expression in VPA-treated osteoclast precursors which has been demonstrated to be responsible for osteoclast differentiation and bone-resorptive activity. VPA-induced miR-6359 upregulation in osteoclast precursors enhanced ROS production by silencing the SIRT3 protein level, followed by activating the MAPK signaling pathways, which promoted osteoclast formation and activity, thereby accelerating bone loss.

overall_design: To define the expression profile associated with VPA treatment, we conducted an RNA sequencing analysis of mRNA from osteoclast precursors (BMDMs) with VPA or vehicle treatment for 48 hours

first: Peng

last: Cheng

first: Liangcong

last: Hu

first: Guohui

last: Liu


title: Maternal Dietary Choline Levels Cause Transcriptome Shift due to Genotype-by-Diet Interaction in Rainbow Trout (Oncorhynchus mykiss)

city: Birmingham

first: Peggy

last: Biga

state: Alabama

address: 902 14th Street South

department: Biology

institute: University of Alabama at Birmingham

summary: The objective of this study was to identify metabolic regulatory mechanisms affected by choline availability in rainbow trout (Oncorhynchus mykiss) broodstock diets associated with increased offspring growth performance. Three customized diets were formulated to have different levels of choline: (a) 0% choline supplementation (Low Choline: 2065 ppm choline), (b) 0.6% choline supplementation (Medium Choline: 5657 ppm choline), and (c) 1.2% choline supplementation (High Choline: 9248 ppm choline). Six all-female rainbow trout families were fed experimental diets beginning 18 months post-hatch until spawning; their offspring were fed a commercial diet. Experimental broodstock diet did not affect overall choline, fatty acid, or amino acid content in the oocytes (p > 0.05), apart from tyrosine (p ≤ 0.05). Offspring body weights from the High and Low Choline diets did not differ from those in the Medium Choline diet (p > 0.05); however, family-by-diet and sire-by-diet interactions on offspring growth were detected (p ≤ 0.05). The High Choline diet did not improve growth performance in the six broodstock families at final harvest (520-days post-hatch, or dph). Numerous genes associated with muscle development and lipid metabolism were identified, including myosin, troponin C, and fatty acid binding proteins, which were associated with key signaling pathways of lipid metabolism, muscle cell development, muscle cell proliferation, and muscle cell differentiation. These findings indicate that supplementing broodstock diets with choline does regulate expression of genes related to growth and nutrient partitioning but does not lead to growth benefits in rainbow trout families selected for disease resistance.

overall_design:
To identify metabolic regulatory mechanisms affected by choline availability in rainbow trout broodstock diets associated with improved offspring growth performance, we fed one of three commercial diets formulated with different levels of choline: Low (2065 ppm choline), Medium (5657 ppm choline), and High (9248 ppm choline).
We then performed gene expressin profiling analysis using data obtained from RNA-seq of 18 rainbow trout sac-fry at 0-days post-hatch (dph) and 14-dph.
Gene expression profiling analysis of RNA-seq data for sac-fry through a main effect of diet and diet-by-broodstock family interaction.

first: Freij

last: Khalid

first: Cleveland

last: Beth

first: Biga

last: Peggy


title: Modulation of apple leaf trancriptome by tomato cutin monomer extract

city: Beaucouzé

first: Matthieu

last: Gaucher

address: 42 rue Georges Morel

department: SPE

country: France

institute: INRAE

summary: Investigation of whole genome gene expression level changes in leaves of apple seedlings (Golden delicious) 3 days after treatment by tomato cutin monomer extract (CME) versus formulation blank (FB). CME is a formulated extract enriched of hydroxy fatty acids from tomato cuticle

overall_design: A total of 6 samples, corresponding to 3 biological replicates (from 3 independent experiments) for each treatment, were used for differential gene expression analysis

first: Sébastien

last: Aubourg

first: Sandra

last: Pelletier

first: Marie-Noëlle

last: Brisset


title: Combined Dietary and Pharmacological Depletion of Polyamines Targets Oncogenic Translation in Neuroblastoma

city: Zurich

first: Sarah

last: Cherkaoui

address: August-Forel-Strasse 51

department: Oncology

country: Switzerland

institute: University Children's Hospital Zurich

summary: Cancer growth is fueled by nutrients obtained from circulation and local biosynthesis. Isolating and exploiting tumoral nutrient dependencies to potentiate current anti-cancer therapies is undergoing active research. We used unbiased metabolomics on patient samples and identified reprogramming of the arginine-proline-glutamine axis in MYCN amplified neuroblastoma. Tumoral acquisition of these non-essential amnio acids, as revealed by stable isotope tracing, was primarily by import, while extra-tumoral deamination of arginine indirectly feeds tumor ornithine via circulation. Dietary depletion of proline and arginine reduced systemic ornithine, the direct precursor of polyamine biosynthesis, and in combination with the clinically approved polyamine biosynthesis inhibitor, difluoromethylornithine, enhanced their depletion to improve survival in a MYCN-driven neuroblastoma mouse model. Mechanistically, ribosome profiling indicated specific translation defects, with ribosomal pausing at adenine-ending codons, to cause reprogramed protein biosynthesis affecting cell cycle and inducing neuronal differentiation. This work provides proof of concept for combined small molecule and nutrient depletion therapy for simultaneous targeting of translation in cancers dependent on external nutrient uptake.

overall_design: Assessment of translation of tumors through ribosome profiling and transcriptomics. Each sample are taken from tumor found from TH-MYCN mice under pharmacological and dietary intervention. Each sample represents a different mouse. Control samples are the mice with a defined control diet (CD) and no pharmacological treatment.

first: George

middle: E

last: Allen

first: Olesya

last: Panasenko

first: Raphael

middle: J

last: Morscher


title: euAP2a, a Key Gene that Regulates Flowering Time with a Novel Mechanism in Peach (Prunus persica)

city: Kearneysville

first: Jianyang

state: WV

address: 2217 Wiltshire Road

institute: USDA-ARS

summary: Spring frost is a growing risk to temperate fruit production as warmer winter conditions can lead to earlier bloom, increasing the chance of damaging cold temperatures. One strategy to minimize the impacts of frost is to breed late-flowering cultivars to avoid the frost risk period. In this study, we analyzed Late-Flowering Peach (LFP) germplasm and showed its floral buds require longer chilling and warming periods during dormancy than the control cultivar, ‘John Boy’ (JB). We identified a 983-bp deletion in an AP2 gene, dubbed euAP2a, present only in LFP but not in 14 other peach genomes analyzed. This mutation eliminates an miR172 binding site, possibly allowing the euAP2a transcript to accumulate preferentially during chilling. These findings together with an early report that a deletion in the same euAP2a causes increasing floral petals, a morphological mark that also occurs in LFP, implies that the 983-bp deletion may contribute to the late-flowering phenotype. Furthermore, RNAseq data revealed that that two chilling- and three warm-responsive co-expression modules, which were collectively composed of 2,931 genes, were differentially activated at four of 13 dormancy stages. This activation was concurrent with a transient, stage-specific down-regulation of euAP2a. However, the mutated euAP2a in LFP did not exhibit the periodic downregulation events observed in JB and the concurrent activation of the five modules, leading to potential loss of activation of two chilling-responsive modules and an 8–12-day delay of three warm-responsive modules, which corresponds to the longer chilling requirement and delayed flowering time in the LFP buds. These findings support euAP2a as a potential regulator to control both floral development and bloom time in peach. Our findings provide important insight into the mechanisms underlying flowering time in peach, as well as a novel regulatory pathway that may operate in other plants. The results provide new insights to facilitate the breeding of new cultivars with late-flowering frost-avoidance traits.

overall_design: Comparison of RNA profiles between 2 peach genotypes with different flowering time

first: Dennis

last: Bennett

first: Mark

last: Demuth

first: Erik

last: Burchard

first: Tim

last: Artlip

first: Chris

last: Dardick

first: Zongrang


first: Shuichi

last: Takayama


title: Single cell RNA Sequencing reveals the cell atlas, communications and  developmental trajectories of Longissimus dorsi in Suhuai piglet

city: NanJing

first: Wei

last: Xiao

state: JiangSu

address: No. 1,Weigang Road,Xuanwu District

institute: NanJing Agricultural University

summary: Single cell RNA sequencing data set of longissimus dorsi muscle of 1-day-old Suhuai pig (boars)

overall_design: Construction of longissimus dorsi muscle cell atlas of 1-day-old Suhuai pig

first: PingHua

last: Li

first: LiMing

last: Hou

first: RuiHua

last: Huang


title: UBE2J1 is the E2 Ubiquitin Conjugating Enzyme Required for Androgen Receptor Degradation

city: Dallas

first: Ping

last: Mu

state: Texas

address: 5323 Harry Hines Blvd.

institute: University of Texas Southwestern Medical Cente

summary:
The Androgen Receptor (AR) is a pivotal protein in human physiology, exerting significant influence on both male and female physiology (PMID: 18434134, 25905231). Functioning as a nuclear transcription factor, AR binds to testosterone, translocates to the nucleus, and subsequently regulates the expression of numerous genes, impacting vital cellular processes such as cell proliferation, differentiation, and apoptosis (PMID: 4810760, 25237629). The prominent role of AR in human physiology is particularly notable in the context of prostate cancer initiation, where aberrant AR signaling has been identified as a key driver in tumorigenesis (PMID: 4810760, 27057074, 37429011). However, despite the considerable success of the current anti-androgen therapeutic approach, it faces the formidable challenge of drug resistance, significantly limiting the clinical outcome for patients and necessitating the urgent development of new therapeutic approaches to overcome resistance (PMID: 26563462, 24881730, 31363002, 35582713). Notably, one key feature of antiandrogen resistance is the sustained or enhanced AR signaling observed in many resistant tumors (PMID: 26563462, 34449248, 23580326), although the underlying molecular mechanisms remain largely unclear. Protein degradation, with ubiquitination at its core, plays a critical role in cell functionality, ensuring the elimination of redundant and harmful proteins (PMID: 16738015, 33634825). This intricate process involves the attachment of small proteins called ubiquitin to target proteins, marking them for degradation. Dysregulation of ubiquitination can lead to the accumulation of oncogenic proteins, contributing to tumorigenesis and therapy resistance in various cancers (PMID: 32296023, 33004065). The degradation of proteins is a complex process that involves the coordination of E1, E2 and E3 enzymes, with E3 enzymes binding to the target protein (PMID: 21111229, 20930542). Logically, research has focused on finding E3s targeting AR for degradation but has overlooked the role that E2s play in the ubiquitination process. In recent years, E2s have been shown to dictate the how and where ubiquitin gets attached in the target protein, dictating the fate of the protein (PMID: 27002219, 19851334). Therefore, finding the E2 involved in the degradation of AR can prove to be essential.
In this study, we conducted an in vivo library screening approach and identified UBE2J1 as the bona fide E2 ubiquitin conjugating enzyme for AR ubiquitination. Our results demonstrated that the frequent loss of UBE2J1 in prostate cancer leads to dysregulated and impaired AR ubiquitination and degradation. Consequently, this promotes the accumulation of AR proteins and confers resistance to antiandrogen treatment in UBE2J1-deficient prostate cancer cells. To address this, we developed an innovative ubiquitination-based AR degrader that effectively restores AR ubiquitination, thereby resensitizing prostate cancer cells to antiandrogen therapy. These findings not only unveil the pivotal role of UBE2J1 as the crucial E2 ubiquitin conjugating enzyme for AR degradation but also shed light on a novel mechanism through which advanced prostate cancer cells upregulate AR protein levels, thereby acquiring resistance to existing antiandrogen therapy. These novel insights hold the potential to inform the development of more effective therapeutic strategies against advanced prostate cancers.

overall_design: Examination of transcriptomic changes in LNCaP/AR prostate cancer cell lines with KO of UBE2J1 genes.


title: Gene expression profile at single cell level of fixed SST expressing neurons from P5 mouse neocortex

first: Elia

last: Micoli

summary: SST expressing neurons are the most diverse cell type in the mouse cortex. We use scRNAseq on fixed tissue to validate the cell type differences described in live cells scRNAseq.

overall_design: Cortical SST expressing neurons were dissociated and isolated by Fluorescence-activated cell sorting (FACS) according to the presence of endogenous GFP reporter and analyzed using scRNAseq.

first: Lynette

last: Lim

first: Clara

last: Milián Alastruey


title: TNIK drives endothelial cell response to viral infection through modulating interferon signaling

first: Tu N

last: Tran

address: 6670 Bertner Ave,

department: Cardiovascular

institute: Houston Methodist Research Institute

summary:
To evaluate the role of TNIK in ECs and in regulation of disturbed flow and laminar flow, we established  Human Aorta (HAECs) from two human donnors in which each target gene has been knocked down of TNIK by siRNA.
We then performed gene expression profiling analysis using data obtained from RNA-seq of two different HAECs witt/without knocking down of TNIK under disturb flow and laminar flow for 24 hours

overall_design: Comparative gene expression profiling analysis of RNA-seq data for HAECs cells (siControl) and its KD derivatives (siTNIK), between HAECs cells (siControl or siTNIK) under disturbed flow or laminar flow

first: Khanh

last: Chau

first: Abishai

last: Dominic

first: Eleanor

last: David

first: Arsany

last: Fahim

first: Dongyu

last: Zhao

first: Kaifu

last: Chen

first: Alan

middle: R

last: Davis

first: Minh

last: Nguyen

first: Guangyu

last: Wang

first: Jun-ichi

last: Abe

first: David

middle: P

last: Huston

first: Nhat-Tu

last: Le


title: Single cell gene expression profiling of prenoplastic cells and myeloid cells during tumour initiation wihin a larval zebrafish model of skin oncogenis driven by inducible HRASG12V

city: Edinburgh

first: Yi

last: Feng

address: 47 Little France Crescent

country: United Kingdom

institute: University of Edinburgh

summary: Tumour initiation begins with a single oncogenic mutation within a single cell, leading to hyperproliferation and clonal expansion. These mutant preneoplastic cells may undergo various fates such as: death, dormancy, benign growth or malignant growth. Whilst further genetic mutations have been linked to progression of preneoplastic cells, even genetically identical preneoplastic cells may undergo different fates. To better understand the phenotypic heterogeneity between genetically identical preneoplastic cells during tumour initiation we have performed single-cell RNA sequencing on preneoplastic cells derived from an inducible larval zebrafish model of skin cancer. Furthermore, inflammation has been identified as a potent driving force in oncogenesis. Macrophages have especially been shown to promote cancer cell growth and progression, whilst neutrophils have the potential to perform either pro- or anti-tumour functions. To study the first responses of myeloid cells following initial oncogenic transformation we also profiled sorted myeloid cells at the single cell level.

overall_design: Preneoplastic cells and myeloid cells were sorted by FACS from transgenic zebrafish larvae, in which the human oncogene HRASG12V is expressed specifically within epidermal keratinocytes following induction with 4OH-Tamoxifen. Induction was carried out at 3dpf. To determine how these preneoplastic cells develop over time within their first day of oncogenic transformation we profiled cells at both 8 and 24 hours post induction. As a control, we also sorted keratinocytes and myeloid cells from time-matched larvae which do not express HRASG12V. Preneoplastic cells and keratinocytes were identified by mCherry fluorescence, whilst myeloid cells were identified by EGFP fluorescence from the following larvae: Tg(krtt1c19e:KALTA44-ERT2; UAS:mCherry-HRASG12V;mpeg1.1:EGFP) and Tg(krtt1c19e:KALTA44-ERT2; UAS:mCherry-CAAX;mpeg1.1:EGFP).

first: Elliot

last: Abigail

first: Ribeiro

middle: B

last: Isabel

first: Beltran

last: Mariana

first: Dobie

last: Ross

first: Henderson

last: Neil

first: Feng

last: Yi


title: The role of Methyl-CpG binding domain 3 (Mbd3) in epileptogenesis

city: Warsaw

first: Kinga

last: Szydlowska

address: Pasteura 3

country: Poland

institute: Nencki Institute of Experimental Biology

summary:
Methyl CpG binding domain 3 (Mbd3) protein belongs to the MBD family of proteins, responsible for reading the DNA methylation pattern. MBD family proteins bind the methyl-CpG domain and are also involved in heterochromatin formation. Mbd3 protein does not have the ability to selectively recognize methyl-CpG islands, however, its characteristic feature is the ability to bind to 5-hydroxymethylcytosine and unmethylated DNA. Little is known about the role of Mbd3 in epilepsy and epileptogenesis. Our previous study (Bednarczyk et al., 2016) showed an increase in levels of NuRD complex proteins, including Mbd3 protein, in the brain of epileptic animals in a rat model of temporal epilepsy induced by electrical stimulation of the amygdala. Amygdala stimulation induced the binding of NuRD complex containing MBD3 to larger number of regions of DNA.
In the present study, we investigated whether the Mbd3 protein is involved in the determination of the seizure threshold. An increase in Mbd3 protein levels was demonstrated in the entorhinal cortex/amygdala in the rat’s brain 4 hours after pentylenetetrazole (PTZ)-induced seizures. No alterations in MBD3 protein levels were detected in hippocampus and somatosensory cortex. No alterations in MBD3 mRNA expression were observed at any time point in any studied brain area.
Reduction of Mbd3 level using AAV vector coding shRNA against Mbd3 injected to the amygdala prolonged the latency time to the onset of an acute seizure in PTZ challenge test indicating increase in seizure threshold. This was accompanied by increased anxiety in the open field test. In the contrast, an overexpression of Mbd3 using AAV decreased anxiety and increased their excitability in the open field test. Moreover Mbd3 overexpression in the amygdala accelerated epileptogenesis in the PTZ-kindling model.
In order to identify the role of Mbd3 protein in the regulation of gene expression, mRNA profiling with RNA-seq was performed in a model of magnesium deficiency-induced epileptiform discharges in vitro. Mbd3 overexpression in vitro induced changes in gene expression in a time- and state-specific manner.
Our data indicate the pro-epileptic properties of the Mbd3 protein in vivo and in vitro.

overall_design: RNAseq samples from neuronal cell culture: control without transfection, AAV transfected cells : AAV-SYN-GFP as a control AAV; AAV-SYN-rMBD3-GFP for Mbd3 overexpression, incubated in standard (medium with Magnesium) and epileptiform (medium without Magnesium) condition, tested in selected time points: 2h, 6h and 24h after induction of epileptiform activity

first: Karolina

last: Nizinska

first: Maciej

last: Olszewski

first: Sandra

last: Binias

first: Dorota

last: Nowicka

first: Bartosz

last: Wojtas

first: Katarzyna

last: Lukasiuk


title: Circadian regulation of genes contributed by rapid RNA turnover in tomato

city: Shanghai

first: Pengfei

last: Xu

address: 800 Dongchuan

institute: Shanghai Jiao Tong University

summary: Large number of genes whose expression cycles are controlled by circadian rhythm. Circadian period and phase changes were positively selected during domestication in tomato. However, the effect of RNA metabolism on circadian gene oscillations remains largely unclear. In this study, we performed transcriptome and degradome termed genome-wide mapping of uncapped and cleavage transcripts (GMUCT) in tomato leaves at 6 time points in one circadian period. Time-series profiling of RNA-seq data revealed 9342 circadian genes, whose functions enriched in multiple types of metabolic process including RNA metabolism. Proportion Uncapped (PU) metric calculated with normalized GMUCT/RNAseq ratio was used to measure general level of RNA degradation. Using this metric, we found 3885 genes whose PU was rhythmically changed, suggesting they were regulated by circadian RNA degradation. These genes with rhythmic PU were significantly enriched in the gene category with high coordination between mRNA abundance oscillation and PU dynamics. Additionally, we identified 2140 genes undergoing co-translational RNA decay (CTRD) with enriched translational termination stalling of 5’ Phosphate end reads. Remarkably, circadian mRNAs with large amplitude tent to be co-translationally decayed. Finally, we found several genes like miR172-targeted AP2, miR398-targeted CSD2 and miR159-targeted MYB125 whose miRNA cleavage efficiency also oscillated in circadian manner. Taken together, these results uncovered the vital roles of RNA metabolism including general RNA degradation, CTRD and miRNA cleavage efficiency in modulating circadian oscillations of RNA abundance.

overall_design: GMUCT and RNA-seq profiling in amture leaves of Tomatos

first: Xu

last: pengfei

first: Zhang

last: YingYing

first: Yu

last: Xiang

first: Shao

last: Wenna


title: Short-term caloric restriction promotes resolution, while weight regain accelerates atherosclerosis in mice

city: New York

first: Emily

last: Brown

state: NY

address: 435 E 30th St

department: Medicine

institute: NYU Langone

summary: While weight loss is highly recommended for obesity, promoting inflammation resolution, >80% of those who lose weight will regain it back, resulting in worsening of disease outcomes (including cardiovascular disease), relative to never having lost weight. However, how weight loss and regain directly influence atherosclerotic inflammation was unknown and investigated in this stud. Using short-term caloric restriction (stCR) in obese mice, we found that weight loss promotes atherosclerosis resolution, independently of plasma cholesterol. Mechanistically, we found that this is partly attributed to a unique subset of macrophage, distinguished by high expression of the antibody receptor Fcgr4, that accumulated in epididymal adipose tissue and plaques with stCR and help to clear necrotic cores. Interestingly, our data suggest that eWAT-derived Fcgr4 macrophages contribute to the clearance of plaque necrotic cores. On the other hand, weight regain achieved by ab libitum feeding following the stCR phase resulted in acceleration of atherosclerosis progression and disappearance of Fcgr4 macrophages from both adipose and plaques. Furthermore, weight regain caused inflammatory reprogramming of bone marrow immune progenitors, retaining hyper-inflammatory capabilities for long periods thereafter.

overall_design: Adipose tissue from calorie restricted mice was digested and cell suspensions from were sorted using BD FACS Aria II SORP. CD45+, CD3-, B220-, Ly6G-, SiglecF-, CD11b+ macrophages were then sorted into either Fcgr4 positive or negative populations using antibodies purchased from BioLegend.

first: Bianca

last: Scolaro

first: Franziska

last: Krauter

first: Marie

last: Petition

first: Cyrus

last: Nikain

first: Michela

last: Garabedian

first: Stephanie

last: Pena

first: Ozlem

last: Tufanli

first: Carmen

last: Hannemann

first: Myriam

last: Aouadi

first: Ada

last: Weinstock

first: Edward

middle: A

last: Fisher


title: Immune dysfunction in COVID-19 Associated Mucormycosis

city: CHANDIGARH

first: KHEM

last: RAJ

state: Chandigarh

address: Deparment of Microbiology, BMS Block-I, PANJAB UNI, PANJAB UNIVERSITY, SECTOR -25

department: Microbiology

country: India

institute: PANJAB UNIVERSITY

summary: The coronavirus pandemic (COVID-19) is associated with secondary bacterial and fungal infections globally. In India, inappropriate use of glucocorticoids, high prevalence of diabetes mellitus and a conducive environment for fungal growth are considered as the main factors for increased incidence of COVID-19 associated mucormycosis (CAM). Few cases of CAM without steroid abuse and normal blood glucose levels were also reported during the pandemic. This study was designed to explore whether altered immune responses due to severe COVID-19 infection predisposes towards development of mucormycosis. The global transcriptome profiling of monocytes and granulocytic cells derived from CAM, Mucormycosis, COVID-19 and healthy control groups were performed to identify the differentially expressed genes (DEGs) involved in dysregulated host immune response towards respective diseased and healthy conditions.

overall_design: The current  study uses an RNA-Sequencing-based approach to obtain the host transcriptome from monocytes and granulocytes to identify the host immune response pathways activated or dysregulated in patients with CAM versus Mucormycosis, COVID-19 disease and healthy control groups. Total RNA was isolated from monocytes and neutrophils and used to prepare libraries for total RNA sequencing. The libraries for all the samples were prepared with paired-end chemistry and a length of 150 bp.  Once the cluster generation was completed, the clustered flow cell was loaded on the Illumina HiSeqX instrument to generate a minimum of 100M raw reads per sample.

first: Manpreet

last: Dhaliwal

first: Valliappan

last: Muthu

first: Arunima

last: Sharma

first: Shivaprakash

last: Rudramurthy

first: Ritesh

last: Agarwal

first: Khem

last: Raj

first: Arunaloke

last: Chakrabarti


title: FOXO3a functions as a transcriptional and co-transcriptional splicing regulator in vascular endothelial cell lines in coronary artery disease

city: Urumqi

first: Zhuo

last: Chen

institute: The First Affiliated Hospital of Xinjiang Medical University

summary: Vascular endothelial cells play an important role in the development of coronary artery disease, their injury leads to coronary heart disease and atherosclerosis. This study aimed to elucidate the role of FOXO3-regulated target gene expression and alternative  splicing in vascular endothelial cell injury in coronary artery disease

overall_design: We constructed a FOXO3A overexpression model in HUVEC cell line, coupled with RNA-seq sequences, to comprehensively reveal the biological function of FOXO3A in HUVEC cell and analyze the alterations of transcriptional profiles upon FOXO3A overexpression and comparative gene expression profiling analysis of RNA-seq data for HUVEC cells and its OE derivatives.

first: Shajidan

last: Abudureyimu

first: Palida

last: Abulaiti

first: Zhi

last: Xing

first: Hui

last: Li

first: Halisha

last: Arkin

first: Ying

last: Gao


title: Defined cellular reprogramming of androgen receptor-active prostate cancer to neuroendocrine prostate cancer [RNA-seq_Nov]

city: Seattle

first: John

last: Lee

state: WA

address: 1100 Fairview Ave N, E2-112

department: Human Biology Division

institute: Fred Hutch Cancer Research

summary: Neuroendocrine prostate cancer (NEPC) arises primarily through neuroendocrine transdifferentiation (NEtD) as an adaptive mechanism of therapeutic resistance. Models to define the functional effects of putative drivers of this process on androgen receptor (AR) signaling and NE cancer lineage programs are lacking. We adapted a genetically defined strategy from the field of cellular reprogramming to directly convert AR-active prostate cancer (ARPC) to AR-independent NEPC using candidate factors. We delineated critical roles of the pioneer factors ASCL1 and NeuroD1 in NEtD and uncovered their abilities to silence AR expression and signaling by remodeling chromatin at the somatically acquired AR enhancer and global AR binding sites with enhancer activity. We also elucidated the dynamic temporal changes in the transcriptomic and epigenomic landscapes of cells undergoing acute lineage conversion from ARPC to NEPC which should inform future therapeutic development. Further, we distinguished the activities of ASCL1 and NeuroD1 from the inactivation of RE-1 silencing transcription factor (REST), a master suppressor of a major neuronal gene program, in establishing a NEPC lineage state and in modulating the expression of genes associated with major histocompatibility complex class I (MHC I) antigen processing and presentation.

overall_design: Bulk RNA-seq was performed on C4-2B cells with different combinations of candidate factors (shRB1, TP53(DN), MYCN, BCL2, SRRM4, ASCL1, NEUROD1) at different timepoints

first: Shan

first: Kai

last: Song

first: Huiyun

last: Sun


title: Defined cellular reprogramming of androgen receptor-active prostate cancer to neuroendocrine prostate cancer [scRNA-seq]

overall_design: Single-cell multiome RNA-seq and ATAC-seq was performed on C4-2B cells 14 days post reprogrammed with various factor combinations


title: Defined cellular reprogramming of androgen receptor-active prostate cancer to neuroendocrine prostate cancer [RNA-seq_Sep]

overall_design: Bulk RNA-seq was performed on C4-2B cells with different combinations of candidate factors (shRB1, TP53(DN), MYCN, BCL2, SRRM4, ASCL1, NEUROD1)


title: Defined cellular reprogramming of androgen receptor-active prostate cancer to neuroendocrine prostate cancer [CUTnRUN]

overall_design: CUT&RUN was performed in reprogrammed C4-2B cells for ASCL1, H3K4me3, H3K4me1, H3K27Ac. Experiments performed in triplicates with an IgG control.


title: Effect of loss of Regnase-1 and Regnase-3 on the transcriptional profile in mouse Lin–Sca1+Kit+ (LSK) cells

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

summary: Regulation of lineage biases in hematopoietic stem and progenitor cells (HSPCs) is pivotal for balanced hematopoietic output. However, little is known about the mechanism behind lineage choice in HSPCs. Here, we show that mRNA decay factors Regnase-1 (Zc3h12a) and Regnase-3 (Zc3h12c) are critical for induction of myeloid lineage priming, restricting lymphoid differentiation in HSPCs. Regnase-1- and Regnase-3-mediated control of mRNA encoding Nfkbiz, a transcriptional and epigenetic regulator, was essential for balancing lymphoid/myeloid lineage output in HSPCs in vivo. Furthermore, single cell-assay for transposase-accessible chromatin sequencing (scATAC-seq) analysis revealed that Regnase-1 and Regnase-3 control the epigenetic landscape on myeloid-related gene loci in hematopoietic stem cells (HSCs) via Nfkbiz. Consistently, an antisense oligonucleotide designed to inhibit Regnase-1- and Regnase-3-mediated Nfkbiz mRNA degradation primed HSCs toward myeloid lineages by enhancing Nfkbiz expression. Collectively, the collaboration between post-transcriptional control and chromatin remodeling by the Regnase-1/Regnase-3-Nfkbiz axis governs lineage priming, instructing HSC lineage specification.

overall_design: LSK cells were single-cell sorted by Fluorescence-activated cell sorting (FACS) from mice competitively transplanted with control and Regnase-1–/–Regnase-3–/– and analyzed by MARS-seq.

first: Takuya

last: Uehata

first: Shinnosuke

last: Yamada

first: Alexis

last: Vandenbon

first: Amir

last: Giladi

first: Adam

last: Jelinski

first: Osamu

last: Takeuchi


title: Defined cellular reprogramming of androgen receptor-active prostate cancer to neuroendocrine prostate cancer

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

overall_design: Refer to individual Series


title: The stem cell-type transcriptome of bioenergy sorghum reveals the spatial regulation of secondary cell wall networks

city: Urbana

first: Amy

last: Marshall-Colon

state: IL

address: 1201 W Gregory Drive

department: Plant Biology

institute: University of Illinois

summary: Bioenergy sorghum is a low-input, drought-resilient, deep-rooting annual crop that has high biomass yield potential enabling the sustainable production of biofuels, biopower, and bioproducts. Bioenergy sorghum’s 4-5 m stems account for ~80% of the harvested biomass. Stems accumulate high levels of sucrose that could be used to synthesize bioethanol and useful biopolymers if information about stem cell-type gene expression and regulation was available to enable engineering. To obtain this information, Laser Capture Microdissection (LCM) was used to isolate and collect transcriptome profiles from five major cell types that are present in stems of the sweet sorghum Wray. Transcriptome analysis identified genes with cell-type specific and cell-preferred expression patterns that reflect the distinct metabolic, transport, and regulatory functions of each cell type. Analysis of cell-type specific gene regulatory networks (GRNs) revealed that unique TF families contribute to distinct regulatory landscapes, where regulation is organized through various modes and identifiable network motifs. Cell-specific transcriptome data was combined with a stem developmental transcriptome dataset to identify the GRN that differentially activates the secondary cell wall (SCW) formation in stem xylem sclerenchyma and epidermal cells. The cell-type transcriptomic dataset provides a valuable source of information about the function of sorghum stem cell types and GRNs that will enable the engineering of bioenergy sorghum stems.

overall_design: 5 individual tissues isolated using laser capture microscopy (LCM), plus bulk stem, 4 replicates each.

first: Jie

last: Fu

first: Brian

last: McKinley

first: Brandon

last: James

first: William

last: Chrisler

first: Lye

last: Markillie

first: Matthew

last: Gaffrey

first: Hugh

last: Mitchell

first: Ka

last: Yu

first: Galya

last: Orr

first: Kankshita

last: Swaminathan

last: Mullet


title: Defined cellular reprogramming of androgen receptor-active prostate cancer to neuroendocrine prostate cancer [scATAC-seq]

first: John

last: Lee

first: Shan

last: Li

first: Kai

last: Song

first: Huiyun

last: Sun


title: CDCA7-associated global aberrant DNA hypomethylation translates to localized, tissue-specific transcriptional responses [snRNA-seq]

city: Leiden

first: Lucia

last: Daxinger

address: Albinusdreef 2

institute: Leiden Univeristy Medica Center

summary: Disruption of Cell division cycle associated 7 (CDCA7) has been linked to aberrant DNA hypomethylation, but the impact of DNA methylation loss on transcription has not been investigated. Here, we show that CDCA7 is critical for maintaining global DNA methylation levels across multiple tissues in vivo. A pathogenic Cdca7 missense variant leads to the formation of large, aberrantly hypomethylated domains overlapping with the B genomic compartment but without affecting deposition of H3K9 trimethylation (H3K9me3). CDCA7-associated aberrant DNA hypomethylation translated to localized, tissue-specific transcriptional dysregulation that impacted large gene clusters. In brain, we identify CDCA7 as a transcriptional repressor and epigenetic regulator of clustered protocadherin isoform choice. Increased protocadherin isoform expression frequency is accompanied by DNA methylation loss, gain of H3K4 trimethylation (H3K4me3) and increased binding of the transcriptional regulator CCCTC-binding factor (CTCF). Overall, our in vivo work identifies a key role for CDCA7 in safeguarding tissue-specific expression of gene clusters via the DNA methylation pathway.

overall_design: 5' Single nuclei RNA-seq (snRNA-seq) on E14.5 mouse Cerebrum

first: Maja

last: Vukic

first: Jihed

last: Chouaref

first: Veronica

last: Della Chiara

first: Serkan

last: Dogan

first: Fallon

last: Ratner

first: Jenna

last: Hogenboom

first: Trevor

last: Epp

first: Kallayanee

last: Chawengsaksophak

first: Kelly

last: Vonk

first: Cor

last: Breukel

first: Yavuz

last: Ariyurek

first: David

last: San Leon Granado

first: Susan

last: Kloet


title: CDCA7-associated global aberranDNA hypomethylation translates to localized, tissue-specific transcriptional responses [WGBS]

type: Methylation profiling by high throughput sequencing

overall_design: Whole Genome Bisulfite sequencing (WGBS) in mouse P21 Spleen


title: Zeb2 drives the formation of CD11c+ atypical B cells to sustain germinal centers that control persistent infection

city: Canberra

first: Xin

last: Gao

state: ACT

address: 131 Garran Rd

country: Australia

institute: The Australian National University

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: CaP-coated Zn-Mn-Li alloys regulate osseointegration via influencing macrophage polarization in the osteogenic environment

city: liaocheng

first: zhaoyong

last: lv

state: shandong

address: dong chang west Road

institute: Liaocheng People's Hospital

summary:
To investigate the mechanism by which Zn alloy scaffold regulates macrophage polarization towards M2, we established RAW264.7 cell lines
We then performed gene expression profiling using data obtained from RNA-seq in macrophages stimulated by three different sets of materials.

overall_design: Differential gene expression profiling of RNA-seq data from RAW264.7 cells stimulated by CaP Zn, CaP Zn0.8Mn, CaP Zn0.8Mn0.1Li alloy scaffolds.

first: Huifen

last: Qiang

first: Zhaoyong

last: Lv


title: CDCA7-associated global aberrantDNA hypomethylation translates to localized, tissue-specific transcriptional responses [H3K9me3_H3K27me3_Spleen]

first: Lucia

last: Daxinger

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for H3K9me3 and H3K27me3 in P21 mouse Spleen

first: Maja

last: Vukic


title: MSH7 confers quantitative variation in pollen fertility and boosts grain yield in maize

city: Beijing

first: Luguang

last: Jiang

state: Beijing

address: No.2 Yuanmingyuan West Road, Haidian, Beijing

institute: China Agricultural University

summary: Fertile pollen is critical for the survival, fitness and dispersal of flowering plants, and directly contributes to crop productivity. Extensive mutational screening studies have been carried out to dissect the genetic regulatory network determining pollen fertility, but we still lack fundamental knowledge about whether and how pollen fertility is controlled in natural populations. We used a genome-wide association study (GWAS) to show that ZmGEN1A and ZmMSH7, two DNA repair-related genes, confer natural variation in maize pollen fertility. Mutants defective in both genes exhibited abnormalities in meiotic or post-meiotic DNA repair, leading to reduced pollen fertility. More importantly, ZmMSH7 underwent selection during maize domestication, and its disruption resulted in a substantial increase in grain yield and protein content for both inbred and hybrid. Overall, our study describes the first systematic examination of natural genetic effects on pollen fertility in plants, providing valuable genetic resources for optimizing male fertility. Moreover, ZmMSH7 may be a potential candidate for simultaneous improvement of grain yield and quality.

overall_design: RNA-seq liabraries were prepared using developing maize seeds (7 DAP and 14 DAP) of zmmsh7-2 and wild-type plants


title: Quantitative analysis of Bckdhaf/f;RIP-Cre and Bckdhaf/f mice eWAT, iWAT and liver transcriptomes

first: Xing

last: Ming

address: Huangpu

department: Department of Endocrine and Metabolic Diseases

institute: Shanghai Jiaotong University School of Medicine

summary:
To explore the underlying mechanism for the regulatory role of branched-chain amino acids (BCAA) catabolism in hypothalamic RIP-Cre neurons to metabolic organs under normal chow diet feeding, we established RIP-Cre neurons selective BCAA catabolic enzyme branched-chain ketoacid dehydrogenase E1 subunit alpha(Bckdha) knockout mice, we conducted RNA sequencing on the inguinal adipose tissue (iWAT), epididymal adipose tissues (eWAT), and liverfrom wild type (WT, Bckdhaf/f) and knockout (KO, Bckdhaf/f;RIP-Cre) mice  (two groups in total). Three biological replicates were performed for each group.
Methods: RNA sequencing (RNA-Seq) and data analysis were performed by Gene Denovo Biotechnology (Guangzhou, China).
Results: In comparison with findings in the Bckdhaf/f group, 393 up-regulated and 214 down-regulated differentially expressed genes (DEGs) were identified in eWAT from Bckdhaf/f;RIP-Cre group . Similarly, 41 up-regulated genes and 152 down-regulated DEGs were identified in iWAT from Bckdhaf/f;RIP-Cre compared to the Bckdhaf/f group. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that DEGs in eWAT were enriched in the categories including all subclass pathways in carbohydrate metabolism class, insulin resistance, PPAR signaling, oxidative phosphorylation, thermogenesis, carbon metabolism, fatty acid metabolism, biosynthesis of amino acids and degenerative disease pathways. Similarly, DEGs in iWATwere clustered in the pathways, including the TCA cycle, pyruvate metabolism, glucagon signaling, glycolysis and gluconeogenesis, and carbon metabolism. These changes indicated broad disturbance in WAT energy metabolism in Bckdhaf/f;RIP-Cre mice. Liver transcriptomes showed minor perturbances in subclasses in lipid metabolism, advanced glycation end products and their receptor (AGE-RAGE), PPAR, estrogen, prolactin signaling pathways. Notably, all 13 mitochondrial DNA encoded mRNA were all significantly down-regulated in eWAT of Bckdhaf/f;RIP-Cre mice, along with nucleus DNA encoded mitochondrial located mRNA.
Conclusions: Our results using RNA-Seq indicated universal defects of mitochondrial gene expression in eWAT and iWAT.

overall_design: iWAT, eWAT, and liver mRNA profiles of 12-week old Bckdhaf/f;RIP-Cre and Bckdhaf/f mice

first: Miaomiao

last: Yuan

first: Xiao

last: Wang


title: TEM1/endosialin/CD248 promotes pathologic scarring and TGF-β activity through its receptor stability in dermal fibroblasts

city: Tainan City

first: Yi-Kai

last: Hong

state: Please select an option below

address: No.1, Daxue Rd., East Dist.

country: Taiwan

institute: National Cheng Kung University

summary:
We established a hypertrophic scar-like animal model using traction force in C57BL/6J mice to demonstrate the crucial mechanistic effect of TEM1 on pathological scarring.
Samples from scar areas in sham and traction groups of Tem1WT/WT and Tem1lacZ/lacZ mice were subjected to RNA sequencing.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for scars in sham and traction groups of Tem1WT/WT and Tem1lacZ/lacZ mice.

first: Chao-Kai

last: Hsu


title: CDCA7-associated global aberrant DNA hypomethylation translates to localized, tissue-specific transcriptional responses [RNA_seq_Spleen]

overall_design: RNA-seq of P21 mouse Spleen

first: Jihed

last: Chouaref

first: Veronica

last: Della Chiara

first: Serkan

last: Dogan

first: Fallon

last: Ratner

first: Jenna

last: Hogenboom

first: Trevor

last: Epp

first: Kallayanee

last: Chawengsaksophak

first: Kelly

last: Vonk


title: Expression data from TH17 cells cultured in the presence or absence of glutamine

city: Taoyaun

first: Chung-Ying

last: Tsai

address: No. 5, Fuxing St., Guishan Dist.

department: Kidney Research Center

institute: Chang Gung Memorial Hospital

summary:
T cell fate and function is closely related to nutrient uptake and utilization. Here we demonstrate that glutamine deprivation switch Th17 cells to Treg cells in a time and dose dependent manner. The finding highlight the critical role of glutamine in T cell fate determination through a metabolic-epigenetic axis.
We performed microarrays to explore the  gene expression pattern of TH17 cells in the presence or absence of glutamine.

overall_design: Naive T cells were cultured in TH17-skewing medium in the presence or absence of glutamine for 3 days. Polarized cells were collected for RNA extraction and hybridization on Affymetrix microarrays.

first: Huang-Yu

last: Yang


title: CDCA7-associated global aberrant DNA hypomethylation translates to localized, tissue-specific transcriptional responses

first: Lucia

last: Daxinger


title: Enhancement of ubiquitination-dependent mitophagy by unconventionally-acting PROTACs

status: Public on Feb 08 2024

city: High Education Mega Center, SCUT, Building B2, Room 404

first: min

last: ma

state: guangzhou

address: Panyu Square

department: medical division

institute: south china university of technology

summary: Enhancing mitophagy, a naturally-occurring cellular process for elimination of damaged mitochondria, holds great promise for the intervention of many human diseases. Proteolysis-targeting chimeras (PROTACs) are heterobifunctional molecules that induce ubiquitination and subsequent proteasome-mediated degradation of a target protein through simultaneously binding to the target protein and an E3 ubiquitin ligase. However, the narrow cavity of the proteasome prevents the degradation of mitochondria. Here we show that the E3 ubiquitin ligase MAP3K1, when recruited to the outer mitochondria membrane (OMM) protein TSPO by our PROTAC-designed molecules (termed “mitophagy-enhancing chimeras”, or MECs), induced extensive K63 ubiquitination of TSPO and other OMM proteins, reminiscent of the PINK1-activated Parkin, without triggering proteasome-mediated degradation of TSPO. Aided by NBR1 and Nur77, this increased K63 ubiquitination of OMM proteins triggered mitophagy exclusively for damaged mitochondria, leading to improved mitochondria function and diminished cellular ROS. With the capability to enhance mitophagy at low nanomolar concentrations, MECs effectively inhibited NLRP3 inflammasome activation, abrogated acetaminophen-induced acute liver injury and mitigated high-fat diet-induced obesity in mice. Our work provided a proof-of-concept for developing unconventionally-acting PROTACs to achieve degradation of damaged mitochondria and possibly other organelles.

overall_design: To assess MEC1 in a chronic disease, we first fed C57Bl/6 mice with either a high-fat diet (HFD) or normal diet (ND) for 2 months to verify the accelerated body weight gain by the HFD feeding, and then randomly divided the HFD mice to a control and a MEC1 treatment group, which received daily intraperitoneal (IP) injection of vehicle and 0.5 mg/kg MEC1, respectively.


title: CDCA7-associated global aberrant DNA hypomethylation translates to localized, tissue-specific transcriptional responses [H3K4me3_brain]

overall_design: Ultra low input Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for H3K4m3  in E14.5  mouse Cerebrum

first: Maja

last: Vukic

first: Cor

last: Breukel

first: Yavuz

last: Ariyurek

first: David

last: San Leon Granado

first: Susan

last: Kloet


title: Multiplexed Assays of Variant Effects (MAVE) of PALB2 single nucleotide variants in exon 10.

city: Rochester

first: Fergus

last: Couch

address: 200 1st ST SW

institute: Mayo Clinic

summary: To validate a high-throughput screening data in human cells using Multiplexed Assays for Variant Effects (MAVE), we performed a high-throughput deep mutational scanning of single nucleotide changes in exon 10 encoding p.G1000 to p.I1037 of the WD40 domain of PALB2 using a cell survival assay in haploid human HAP1 cells. We obtained MAVE scores for 276 single-nucleotide variants, leading to 9 nonsense and 68 synonymous changes, as well as 199 amino acid substitutions. Both variant groups showed an asymmetric distribution that is skewed towards low MAVE scores of nonsense and damaging variants, respectively. These MAVE data included scores for 218 unique single-nucleotide variants, leading to 9 nonsense changes and 209 amino acid substitutions. We observed a good and significant correlation between the outcomes from the MAVE and high-throughput screens (n=179, r=-0,6439, p<0.0001), indicating concordance between the outcomes of high-throughput analysis of PALB2 variants in human and mouse cells.

overall_design: Saturation genome editing was used to introduce variants and the variant count on day 5 and day 20 were measured. The log2 ratio between D5 and D20 was used to measure the variant effects

first: Huaizhi

last: Huang

first: Chunling

last: Hu


title: CDCA7-associated global aberrant DNA hypomethylation translates to localized, tissue-specific transcriptional responses [ATAC-seq]

overall_design: Assay for Transposase accessible chromatin combined with highthroughput sequencing (ATAC-seq) in P21 mouse Spleen

first: Jihed

last: Chouaref

first: Veronica

last: Della Chiara

first: Serkan

last: Dogan

first: Fallon

last: Ratner


title: Early Modulation of the Gut Microbiome by Female Sex Hormones Alters Amyloid Pathology and Microglial Function

city: Chicago

first: Priyam

last: Patel

address: 750 North Lake Shore Drive, Rubloff 11-146

department: Quantitative Data Science Core

institute: Northwestern University

summary: It is well-established that women are disproportionately affected by Alzheimer’s disease (AD).  The mechanisms underlying this sex-specific disparity are not fully understood, but several factors that are often associated-including interactions of sex hormones, genetic factors, and the gut microbiome-likely contribute to the disease's etiology. Here, we have examined the role of sex hormones and the gut microbiome in mediating A amyloidosis and neuroinflammation in APPPS1-21 mice. We report that postnatal gut microbiome perturbation in female APPPS1-21 mice leads to an elevation in levels of circulating estradiol.  Early stage ovariectomy (OVX) leads to a reduction of plasma estradiol that is correlated with a significant alteration of gut microbiome composition and reduction in A pathology.  On the other hand, supplementation of OVX-treated animals with estradiol restores A burden and influences gut microbiome composition. The reduction of A pathology with OVX is paralleled by diminished levels of plaque-associated MGnD-type microglia while estradiol supplementation of OVX-treated animals leads to a restoration of activated microglia around plaques. In summary, our investigation elucidates the complex interplay between sex-specific hormonal modulations, gut microbiome dynamics, metabolic perturbations, and microglial functionality in the pathogenesis of Alzheimer's disease.

overall_design: Total RNA was extracted from the dorsal cerebral cortex using Trizol reagent, as per the protocol by Dodiya et al. [9], and cleaned with the RNAeasy Micro kit (Qiagen). Quality assessment was done with an Agilent Bioanalyzer. RNA-seq library preparations and sequencing were performed using an Illumina HiSeq4000 at The University of Chicago Genomics Core Facility. The data were collected in FASTQ format for bioinformatic analysis.

first: Piyali

last: Saha

first: Julia

last: Michalkiewicz


title: miR-eCLIP of MCF10A cells following treatment with MIR-28 family microRNA mimics

city: New Haven

first: Carson

last: Bryant

state: CT

address: 333 Cedar Street

department: Molecular Biophysics and Biochemistry

institute: Yale University

summary: MIR-28 sibling microRNA mimics (hsa-miR-28-5p or hsa-miR-708-5p) were analyzed by the miR-eCLIP protocol established in Manakov et al. 2022, to determine direct binding targets of these microRNAs in human MCF10A breast epithelial cells.

overall_design: miR-eCLIP experiment was setup and performed by Eclipse Bioinnovations. MCF10A cells were treated with MIR-28 microRNA mimics for 27 h, then UV crosslinked with 254 nm light and collected by scraping. For the MIR-28 treatments, two separate samples were each treated with either hsa-miR-28-5p or hsa-miR-708-5p mimics, then pooled after crosslinking and scraping. siNT and pooled MIR-28 samples were flash frozen and shipped to Eclipse Bioinnovations for miR-eCLIP analysis.


title: Granulocytic myeloid-derived suppressor cell activity during biofilm infection is regulated by a glycolysis-HIF-1α axis I

city: Omaha

first: Sankarasubramanian

last: Jagadesan

state: NE

address: 42end and Emile st

department: Department of Genetics, Cell Biology & Anatomy

institute: University of Nebraska Medical Center

summary: Staphylococcus aureus is a leading cause of biofilm-associated prosthetic joint infection (PJI). A primary contributor to infection chronicity is an expansion of granulocytic myeloid-derived suppressor cells (G-MDSCs) that are critical for orchestrating the anti-inflammatory biofilm milieu. Single-cell sequencing and bioinformatic metabolic algorithms were used to explore the link between G-MDSC metabolism and S. aureus PJI outcome. Glycolysis and the hypoxic response through hypoxia-inducible factor-1 alpha (HIF-1α) were significantly enriched in G-MDSCs. Interfering with both pathways in vivo, using a 2-deoxyglucose nanopreparation and granulocyte-targeted HIF-1α conditional knockout mice, respectively, attenuated G-MDSC-mediated immunosuppression and reduced bacterial burden in a mouse model of S. aureus PJI. In addition, scRNA-seq analysis of granulocytes from PJI patients also showed an enrichment in glycolysis and hypoxic response genes. These findings support the importance of a glycolysis/HIF-1α axis in promoting G-MDSC anti-inflammatory activity and biofilm persistence during PJI.

overall_design: Live CD45+ cells were collected from the soft tissue adjacent to the knee joint of Mrp8CreHif1afl/fl and WT littermates (Mrp8NullHif1afl/fl) at days 3 and 14 post-infection by FACS and prepared for single-cell sequencing using the 10X Genomics platform.

first: Chris

last: Horn

first: Prabhakar

last: Arumugam

first: Cortney

last: Heim

first: Tammy

last: Kielian


title: RNAseq of human tissue culture cells following treatment with MIR-28 family microRNA mimics

summary: The objectives of this study were to investigate the differential RNAseq profiles of nearly-normal human cell lines treated with MIR-28 family microRNA mimics (hsa-miR-28-5p or hsa-miR-708-5p), compared to negative control.

overall_design: To identify polyA+ transcripts that were differentially expressed in MCF10A human breast epithelial cells or hTERT RPE-1 retinal pigment epithelial cells following treatment with MIR-28 family member microRNA mimics, we profiled cellular RNAs by Illumina sequencing. Treatment conditions were a non-targeting siRNA (siNT, negative control), hsa-miR-28-5p microRNA mimic, or hsa-miR-708-5p microRNA mimic (Horizon Discovery/Dharmacon). Cells were seeded at 100,000 cells/well in 6-well plates for 24 h, then transfected with RNAi reagent for 72 h. Total RNA was harvested with TRIzol and purified. The Yale Center for Genomic Analysis prepared 100 bp paired-end libraries for sequencing after polyA+ (oligo dT) selection, and conducted the Illumina sequencing experiments.


title: The P-body protein 4E-T regulates the balance between cell genesis and establishment of the postnatal neural stem cell pool by repressing mRNA translation [4ET_neurosphere]

city: Toronto

first: Adelaida

last: Kolaj

state: Ontario

address: 27 King's College Circle

country: Canada

institute: University of Toronto

summary:
To investigate the targets of 4E-T in postnatal V-SVZ precursors cultured as neurospheres
We performed RNA immunoprecipitations (RIPseq) on neurosphere lysates with anti-4E-T or control anti-IgG antibodies, isolated and sequenced the resulting RNA

overall_design: Neurospheres from the V-SVZ of P7/P8 animals were cultured for 7 days,  and immunoprecipitations were performed using anti-4E-T or anti-IgG control antibodies, and the associated mRNA was isolated


title: Regional Centromere Configuration in the Fungal Pathogens of Pneumocystis Genus

city: Bethesda

first: Ousmane

middle: Hamadoun

last: Cisse

state: MD

address: 10 Center Dr,

institute: National Institutes of Health

sample_organism:
Pneumocystis carinii
Pneumocystis murina

overall_design: Refer to individual Series


title: The P-body protein 4E-T regulates the balance between cell genesis and establishment of the postnatal neural stem cell pool by repressing mRNA translation [4ET_VSVZ]

summary:
To investigate the targets of 4E-T in the postnatal V-SVZ
We performed RNA immunoprecipitations (RIPseq) on V-SVZ lysates anti-4E-T or control anti-IgG antibodies, isolated and sequenced the resulting RNA

overall_design: The SVZ was collected and lysed from P7/P8 CD1 animals, and immunoprecipitations were performed using anti-4E-T or anti-IgG control antibodies, and the associated mRNA was isolated


title: The P-body protein 4E-T regulates the balance between cell genesis and establishment of the postnatal neural stem cell pool by repressing mRNA translation [Cpeb4_VSVZ]

summary:
To investigate the targets of Cpeb4 in the postnatal V-SVZ
We performed RNA immunoprecipitations (RIPseq) on V-SVZ lysates anti-Cpeb4 or control anti-IgG antibodies, isolated and sequenced the resulting RNA

overall_design: The SVZ was collected and lysed from P7/P8 CD1 animals, and immunoprecipitations were performed using anti-Cpeb4 or anti-IgG control antibodies, and the associated mRNA was isolated


title: The P-body protein 4E-T regulates the balance between cell genesis and establishment of the postnatal neural stem cell pool by repressing mRNA translation [Cpeb4_neurosphere]

summary:
To investigate the targets of Cpeb4/Cpeb4-associated transcripts in postnatal V-SVZ precursors cultured as neurospheres
We performed RNA immunoprecipitations (RIPseq) on neurospheres using anti-Cpeb4 or control anti-IgG antibodies, isolated and sequenced the resulting RNA

overall_design: Neurospheres were grown for 7 days, then cells were lysed and immunoprecipitions with either anti-Cpeb4 or anti-IgG were performed, RNA was isolated and sequenced


title: Smooth muscle cell-specific translatome profiling of mouse atherosclerosis uncovers Itih4 as a novel SMC-enriched gene

city: Kuopio

first: Aarthi

last: Ravindran

address: Neulaniementie 2, 70150 Kuopio

country: Finland

institute: University of Eastern Finland

summary: The development of atherosclerosis, a chronic disease characterized by the buildup of plaque in arterial walls, involves the contribution of vascular smooth muscle cells (SMCs) and SMC-derived cells. To better understand the specific role of SMCs in atherosclerosis, a transgenic mouse line expressing EGFP-tagged ribosomal protein L10a (EGFP-L10a) under the SMC-specific αSMA promoter (SMCTRAP mice) was developed, enabling translating ribosome affinity purification followed by sequencing (TRAP-Seq). SMCTRAP mice were crossed with an atherosclerosis model (SMCTRAP-Athero mice). Using TRAP-Seq and bulk RNA-Seq, the aortas of 15-month-old SMCTRAP and SMCTRAP-Athero mice were analyzed to identify atherosclerosis-induced changes in the profiles of SMC ribosome-associated RNA. The results showed high enrichment of known SMC-specific genes in the TRAP fraction, indicating the specificity of the construct. The intersection of SMC-specific genes identified by TRAP-Seq, and atherosclerosis-induced genes identified by bulk RNA-Seq revealed the contribution of SMCs to the expression of several known disease-induced genes, as well as the identification of previously unlinked genes in atherosclerosis that warrant further investigation. These findings provide new insights into the role of SMCs in atherosclerosis and may offer potential targets for future treatments of this chronic disease.

overall_design: Vascular smooth muscle cell ribosome-associated RNA was extracted using immunoprecipitation (IP) enrichment, along with bulk total RNA (Input), from the thoracic aorta of atherosclerosis model (SMCTRAP-Athero) and control mice (SMCTRAP). The extracted RNA was used to identify changes in the SMC ribosome-associated RNA profiles (translatomes) in atherosclerosis.

first: Tiit

last: Örd

first: Minna

middle: U

last: Kaikkonen


title: Meta-analysis of Genome-wide Associations and Polygenic Risk Prediction for Atrial Fibrillation in More Than 180,000 Cases

city: Cambridge

first: Matthew

middle: C

last: Hill

state: MA

address: 75 Aimes Street

institute: Broad Institute of MIT and Harvard

summary: Atrial fibrillation (AF) is the most common abnormality of heart rhythm and is a leading cause of heart failure and stroke. This large-scale meta-analysis of genome-wide association studies (GWAS) increased the power to detect single-nucleotide variant (SNV) associations, and we report more than 350 AF-associated genetic loci. At 139 loci we identified candidate genes related to muscle contractility, cardiac muscle development and cell-cell communication. We next assayed chromatin accessibility by ATAC-seq and histone H3 Lysine 4 trimethylation in stem cell derived atrial cardiomyocytes. We observed a marked increase in chromatin accessibility of our sentinel variants and prioritized genes in atrial cardiomyocytes. Finally, we found that a polygenic risk score (PRS) based on our updated effect estimates improved AF risk prediction compared to the CHARGE-AF clinical risk score and a previously reported PRS for AF. The doubling of known AF risk loci will facilitate a greater understanding of the pathways underlying this heart rhythm disorder.

overall_design: Human pluripotent stem (hPSCs) cells were differentiated to atrial-like cardiomyocytes and subjected to ATAC-seq and H3K4me3 CUT&RUN.

first: Carolina

last: Roselli

first: Patrick

middle: T

last: Ellinor


title: The P-body protein 4E-T regulates the balance between cell genesis and establishment of the postnatal neural stem cell pool by repressing mRNA translation [Ribotag]

summary:
To investigate the translatome of postnatal precursors of the V-SVZ cultured as neurospheres, we employed RiboTag analysis
We performed RiboTag analysis on precursors derived from NestinCreERT2;RPL22HA/HA animals using specific anti-Hemagluttinin antibodies versus non-specific IgG controls

overall_design: Neurospheres were grown for 5 days, tamoxifen was added, and cells were lysed and collected 2.5 days later, immunoprecipitated with either anti-HA or anti-IgG, RNA was isolated and sequenced


title: Transcriptional effects of siRNA-mediated MAFB  knockdown on SARS-CoV-2-infected human M-CSF and GM-derived macrophages.

city: Madrid

first: Angeles

last: Domínguez Soto

address: Ramiro de Maeztu

country: Spain

institute: CSIC

summary:
To investigate the MAFB-dependent genes in the SARS-COV-2 infection on human macrophages, we generated M-CSF and GM-CSF-dependent monocyte-derived macrophages in which MAFB has been knocked down by siRNA and then infected with SARS-CoV-2. Monocytes from three independent donors (0.5 x 106 cells/ml, >95% CD14+ cells) were cultured  in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) at 37°C in a humidified atmosphere with 5% CO2 for 6 days in the presence of GM-CSF or M-CSF, with cytokine addition every two days. Then, monocyte-derived macrophages were transfected with MAFB-specific siRNA or control siRNA, kept in culture for 6 hours, and then were exposed to SARS-CoV-2 (SARS-CoV-2 clinical isolate Gisaid EPI_ISL_1120962, corresponding to ancestral S D614G, at an MOI=1) or uninfected. After 36 hours, cells were lysed and RNA isolated for transcriptional analysis.
We performed gene expression profiling analysis using data obtained from RNA-seq of 3 different donors.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for cells transfected with siMAFB (siMAFB_GM/siMAFB_M) or siControl (siCNT_GM/siCNT_M) exposed or not to SARS-COV-2 (MOI).

last: Soto

first: Maria

last: Colmenares

first: Angel

last: Corbí

first: Miguel

last: Vega


title: Transcriptional effects of SARS-CoV-2 and their VLPs (virus-like particles) on human GM-CSF-derived macrophages

summary:
Analysis of the transcriptional signature of VLPs and SARS-CoV-2-infected human GM-CSF-dependent monocyte-derived macrophages.   Methods: Human Peripheral Blood Mononuclear Cells (PBMC) were isolated from buffy coats from donors over a Lymphoprep gradient according to standard procedures. Monocytes were purified from PBMC by magnetic cell sorting using anti-CD14 microbeads (>95% CD14+ cells). Monocytes from three independent donors (0.5 x 106 cells/ml, >95% CD14+ cells) were cultured  in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) at 37°C in a humidified atmosphere with 5% CO2 and 21% O2 for 7 days in the presence of 1000 U/ml GM-CSF, with cytokine addition every two days. Then, monocyte-derived macrophages were exposed SARS-CoV-2 (SARS-CoV-2 clinical isolate Gisaid EPI_ISL_1120962, corresponding to ancestral S D614G, at an MOI=1), SARS-CoV-2-derived VLPs (MOCK) or nothing (UNT). After 4,12 and 36 hours, cells were lysed and RNA isolated for transcriptional analysis.
We performed gene expression profiling analysis using data obtained from RNA-seq of 4 different donors.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for GM-CSF-derived macrophages infected with SARS-CoV-2 or SARS-CoV-2-derived VLPs


title: Fetal umbilical cord blood CD34+ cells alter proliferation and migration capacities of breast cancer cell lines by direct cell-to-cell interaction: a mechanism of fetal microchimerism?

city: Paris

first: Benjamin

last: SAINTPIERRE

address: 22 Rue Mechain

institute: Inserm

summary: Introduction Fetal microchimerism could be involved in the regulation of breast cancer oncogenesis. CD34+ cells could be of a particular interest as up to 12% of the CD34+ population in maternal blood are of fetal origin. The aim of this research was to analyze the impact of umbilical cord blood (UCB) CD34+ on MCF-7 and MDA-MB-231 breast cancer cell lines. Material and Methods UCB CD34+ cells were obtained from healthy women at full-term delivery. Direct and indirect cultures were grown with MCF-7 and MDA-MB-231 cells. Proliferation, migration, invasion, and transcriptomic analysis of breast cancer cell lines were compared between cultures exposed and non-exposed to UCB CD34+ cells. Interactions between UCB CD34+ and breast cancer cells were analyzed under fluorescent microscopy. Functional analyses were generated with QIAGEN’s Ingenuity Pathway Analysis (IPA) and Gene Set Enrichment Analysis (GSEA). Results Direct contact between UCB CD34+ and breast cancer cell lines induced a reduction in the proliferative capacities of MCF-7 and MDA-MB-231 and diminished the migration abilities of MDA-MB-231 cells. In 3D co-culture, UCB CD34+ cells were attracted by tumor spheroids and incorporated into tumor cells. These cell-to-cell interactions were responsible for transcriptome modifications coherent with observed functional modifications. Among the cytokines secreted by UCB CD34+, INF- was identified as a potential upstream regulator responsible for the molecular modifications observed in transcriptomic analysis of MCF-7 breast cancer cells exposed to UCB CD34+ cells, as was IL-17A in MDA-MB-231 cells. Conclusion Direct cell-to-cell contact induces functional modifications in breast cancer cells. Interactions between UCB CD34+ and breast cancer cells could induce cell fusion and signal transmission via cytokines. Further analysis of direct cell-to-cell interactions should be performed at a molecular level to further understand the potential role of fetal CD34+ cells in breast cancer.

overall_design: After 72h of co-culture assay of MDA-MB-231 or MCF-7 cells with foetal codron derived CD34+ cells, RNA was extracted from the breast cancer cells with QIAGEN RNeasy® Mini Kit (QIAGEN, Hilden, Germany) according to the manufacturer’s instruction.  The RNA samples were stored at -80°C. Sequencing and primary analysis was performed by the GENOM’IC platform (Institut Cochin, Inserm 1016-CNRS 8104- Université Paris Cité).

first: Kamila

last: Kolanska

first: Nathalie

last: Chabbert-Buffet


title: RNA-sequencing analysis reveals the different gene expression in male and female wild type and TECRL knockout mice.

city: Shanghai

first: Shujia

last: Lin

address: No. 355 Luding Road, Shanghai, China

institute: Shanghai Children’s Hospital

summary: Purpose: In previous study, we generated the TECRL knockout mice. The purpose of this study is to indentify the implication function of TECRL on cardiac myocytes in male and female TECRL knockout(TECRL-/-) mice compared with wild type(WT) mice. Methods: Total RNA profiles of 5 males WT mice and 5 males TECRL-/- mice, 3 females WT mice and 7 females TECRL-/- mice were generated by RNA sequencing. The first strand cDNA was synthesized using random hexamer primer and the second strand cDNA synthesis was performed using DNA PolymeraseⅠand RNase H. Results: 1249 genes were identified between TECRL-/- mice and WT mice through RNA-seq analysis. GO analysis and KEGG analysis revealed some pathways, especially lipid metabolism and Ca2+ handling were closedly related to TECRL deficiency.

overall_design: Comparation of transcriptome of heart from 8 weeks male and female wild type(WT) and TECRL-/- mice.

first: Cuilan

last: Hou

first: Shun

last: Chen

first: Lijian

last: Xie

first: Tingting

last: Xiao


title: Exogenous Melatonin RegulatesAlternaria brassicaeReproduction and Pathogenicity in a Dose-Dependent Manner [miRNA_degradome]

status: Public on Feb 07 2024

city: guiyang

first: Tang

last: wenkun

address: Xibei Street

institute: Guizhou University

summary: The development of viroid-elimination technology is an important means to ensure the production of tomatoes. Viroid is an obligate pathogen that can infect the apical meristem cells. The combination of low-temperature therapy and meristem culture is a commonly used method for viroid eradication, but tomatoes cannot withstand long-term low-temperature treatment. This study identified a new HSVd genotype and measured the growth and physiological parameters of diseased tomato “Alisa Craig”. Five HSVd-targeting ds-sRNAs were synthesized to match different regions of the HSVd genome, and their permeability in plants was tested. By screening the types of ds-sRNA and processing duration, the optimal treatment for inhibiting HSVd in diseased tomato shoot terminal was obtained. miRNAs produced by HSVd genome were detected by using miRNA-seq and degradation-seq to verify the occurrence of the ds-sRNA induced HSVd gene silencing. Exogenous ds-sRNA can penetrate all cells including vascular bundles, thin-walled cells, and stem apical meristematic tissues and induced HSVd gene silencing in shoot terminals, leading to the accumulation of miRNAs produced by HSVd in plants.

overall_design: Isolation of vd-sRNAs was strictly conducted according to Kutnjak et al. (2015). 10-50 nt small RNAs were separated. NEBNext®Small RNA Library Prep Set for Illumina kit (E7580L, NEB) was used to construct small RNA libraries according to the manufacturer’s instructions. The libraries were sent for sequencing on an IlluminaHiseq2000 platform (LC-Bio., Hangzhou, China). Three biological replicates were conducted. Reads that shorter than 15 nt were removed since their nonuniquely. Readsfrom each set were mapped to HSVd genome. Thecount and type of genome mapped nonuniquely sRNA reads were thereafter compared among ddH2O and ds-sRNA-H3 36 h fed samples. A confirmatory experiment by degradomeanalysis of ddH2O and ds-sRNA-H3 36 h fed HSVd-infected tomato cuts were conducted according to Navarro et al. (2021) as well. The degradome sequencing was conducted by LC-Bio. One biological replicate for each sample were conducted.

last: Wen-Kun

first: HUANG

last: Ting-Min

first: ZHANG

last: Wan-Ping

first: LI

last: Jing-Wei


title: Exogenous Melatonin RegulatesAlternaria brassicaeReproduction and Pathogenicity in a Dose-Dependent Manner [miRNA]

type: Non-coding RNA profiling by high throughput sequencing


title: A tumor endothelial cell-specific microRNA replacement therapy for hepatocellular carcinoma

city: Kurume

first: Hideki

last: Iwamoto

state: Fukuoka

address: 67 Asahimachi

department: Division of Gastroenterology, Department of Medicine

country: Japan

institute: Kurume University School of Medicine

summary: Current approved anti-angiogenic drugs (AAD) for hepatocellular carcinoma (HCC) inhibit tumor angiogenesis, but affect the hepatic vasculature resulting in adverse effects. Tumor endothelial cells (TECs) differ from normal endothelial cells. In this study, we aimed to detect TEC-specific miRNAs and develop an anti-angiogenic treatment specific for TECs. We established HCC orthotopic mouse models. TEC-specific miRNAs were detected using a microRNA array. Finally, we evaluated the therapeutic effects of the TEC-specific miRNA agonist cocktail. In total, 260 TEC-specific genes were detected. Among the top ten downregulated TEC-specific miRNAs, miR-139-3p and 214-3p were important for the TEC phenotype. The TEC-specific microRNA agonist cocktail showed significant anti-tumor effects by inhibiting tumor angiogenesis without affecting hepatic vasculatures in HCC orthotopic mouse models. Moreover, it significantly downregulated tip-cell sprouting-related genes. We identified two downregulated TEC-specific miRNAs; microRNA replacement therapy, which targets the downregulated TEC-specific miRNAs, is an effective and promising treatment for HCC

overall_design: Gene expression of Tumor endothelial cell isolated from mouse orthotopic hepatoma

first: Takumi

last: Kawaguchi


title: IL-27 regulates the differentiation of follicular helper NKT cells via metabolic adaptation of mitochondria

city: Kisarazu

first: Toshio

last: Kanno

state: Chiba

address: 2-6-7 Kazusa-kamatari

institute: KAZUSA DNA Research Institute

summary:
To investigate transciprtomic landscape changes of Gr-1+ cells after P/A immunization and NKT cells after anti-IL-27 antibody, we isolated Gr-1+ cells on day 1 and 3 after P/A immunization and NKT cells on day 3 after P/A immunization with anti-IL-27 antibody and isotype contorl.
We then performed gene expression profiling analysis of RNA-seq data for Gr-1+ cells on day 0, 1, and 3 after P/A immunization and NKT cells on day 3 after P/A immunization with anti-IL-27 antibody and isotype control. (n=3 per group)

overall_design: See "Materials and Methods".

first: Yasuhiro

last: Kamii

first: Koji

last: Hayashizaki

first: Akio

last: Chiba

first: Taku

last: Ikegami

first: Mitsuru

last: Saito

first: Yukihiro

last: Akeda

first: Toshiaki

last: Ohteki

first: Masato

last: Kubo

first: Kiyotsugu

last: Yoshida

first: Kazuyoshi

last: Kawakami

first: Kazunori

last: Oishi

first: Jun

last: Araya

last: Kuwano

first: Mitchell

last: Kronenberg

first: Yusuke

last: Endo

first: Yuki

last: Kinjo


title: Transcriptome (RNASeq) data of engineered human 293 cell with compromised subcellular NAD availability

city: Bergen

first: Mathias

last: Ziegler

address: Jonas Lies vei 91

country: Norway

institute: University of Bergen

summary: The coenzyme NAD is consumed by signalling enzymes such as poly-ADP-ribose-polymerases (PARPs) and sirtuins. Understanding the mechanisms of aging-associated NAD decline and how cells cope with decreased NAD concentrations requires model systems reflecting chronic NAD deficiency. To evoke compartment-specific over-consumption of NAD, we have engineered cell lines expressing PARP activity in mitochondria, the cytosol, endoplasmic reticulum, and peroxisomes. Additionally, we have engineered cell lines that lack a functional gene for the human mitochondrial transporter SLC25A51 and the NAD biosynthesis enzyme NMNAT3. Isotope-tracer flux measurements and mathematical modelling showed that the lowered NAD concentration limits total NAD consumption kinetically. Moreover, NAD biosynthesis rate and capacity remained unchanged, thereby also precluding an increase of total NAD turnover. The chronic NAD deficiency was surprisingly well tolerated unless the mitochondria were targeted. Oxidative phosphorylation and glycolysis were little affected by NAD over-consumption in the other compartments. Likewise, peroxisomal NAD over-consumption was balanced by mitochondrial NAD decrease to maintain beta-oxidation of very long chain fatty acids in peroxisomes. We propose that subcellular NAD pools are interconnected, with mitochondria acting as a rheostat to facilitate NAD-dependent processes in organelles with excessive consumption.

overall_design:
Human 293 [HEK293] and HeLa S3 cells were stably transfected with vectors encoding fusion proteins composed of enhanced green fluorescent protein (EGFP) and the catalytic domain of human poly-ADP-ribose polymerase 1 (PARP1cd) targeted to the mitochondria, endoplasmic reticulum, cytosol, and peroxisomes under the control of the CMV promoter
Human 293 [HEK293] cells were subjected to CRISPR-Cas9-mediated genome editing targeted against SLC25A51 encoding the human mitochondrial NAD transporter
Human 293 [HEK293] cells were stably transfected with a vector encoding C-terminally FLAG-tagged SLC25A51 under control of the CMV promoter
Human 293 [HEK293] cells were subjected to CRISPR-Cas9-mediated genome editing targeted against NMNAT3 encoding human nicotinamide mononucleotide adenylytransferase 3

first: Marc

last: Niere

first: Øyvind

last: Strømland

first: Christian

last: Dölle