title: Linker histone H1 regulates homeostasis of heterochromatin associated cRNAs [ATAC-seq]

overall_design: ATAC-seq in knockdown for H1 in S2 cells


title: Reshaping the Tumor Microenvironment of KRASG12D Pancreatic Ductal Adenocarcinoma with combined SOS1 and MEK Inhibition for Improved Immunotherapy Response

status: Public on Apr 22 2024

city: Ridgefield

first: Abhishek

last: Kashyap

state: CT

address: 900 Ridgebury Rd

country: USA

institute: Boehringer Ingelheim

type: Expression profiling by high throughput sequencing

summary: KRAS inhibitors have demonstrated exciting pre-clinical and clinical responses, although resistance occurs rapidly. Here, we investigate the effects of KRAS-targeting therapies on the tumor microenvironment using a library of KRASG12D, p53 mutant, murine PDAC-derived cell lines (KPCY) to leverage immune-oncology combination strategies for long-term tumor efficacy. Our findings show that SOS1 and MEK inhibitors (SOS1i+MEKi) suppressed tumor growth in syngeneic models and increased intra-tumoral CD8+ T cells without durable responses. scRNA-sequencing revealed an increase in inflammatory cancer associated fibroblasts (iCAFs), M2 macrophages, and a decreased dendritic cell quality that ultimately resulted in a highly immunosuppressive microenvironment driven by IL6+ iCAFs. Agonist CD40 treatment was effective to revert macrophage polarization and overcome the lack of mature antigen presenting DCs after SOS1i+MEKi therapy. Treatment increased the overall survival of KPCY tumor-bearing mice. The addition of checkpoint blockade to SOS1i+MEKi combination resulted in tumor free mice with established immune memory. Our data suggests that KRAS inhibition affects myeloid cell maturation and highlights the need for combining KRAS cancer-targeted therapy with myeloid activation to enhance and prolong anti-tumor effects.

overall_design: scRNA-seq of mouse subcutaneous KPCY tumors treated with either vehicle control or SOS1 inhibitor plus MEK inhibitor

first: Robert

middle: J

last: Norgard

first: Pratha

last: Budhani

first: Sarah

middle: A

last: O’Brien

first: Youli

last: Xia


title: Linker histone H1 regulates homeostasis of heterochromatin associated cRNAs [DRIP-seq]

status: Public on Apr 23 2024

city: Barcelona

first: Oscar

last: Reina Garcia

state: Barcelona

address: C/Baldiri Reixac 10

department: Biostatistics and Bioinformatics

country: Spain

institute: IRB Barcelona

summary: Chromosomal RNAs (cRNAs) are a poorly understood fraction of cellular RNAs that co-purify with chromatin. Here we show that, in Drosophila, cRNAs constitute a heterogeneous group of RNA species that cover ~28% of the genome. Intriguingly, we found that cRNAs are highly enriched in heterochromatic transcripts. Our results show that heterochromatic cRNAs interact with the hnRNP A/B proteins hrp36 and hrp48 to assemble into RNP particles. We also show that depletion of linker histone dH1, a major component of chromatin, impairs assembly of hrp36 and hrp48 onto heterochromatic cRNAs. Concomitantly, impaired cRNAs assembly induces the accumulation of heterochromatic cRNAs and the formation of unscheduled RNA::DNA hybrids (R-loops). Linker histones H1 are known to regulate chromatin structure and compaction and, indeed, we show that dH1 depletion perturbs chromatin organization, reducing nucleosome occupancy and specifically increasing accessibility and 3D interactions within heterochromatin. These perturbations facilitate annealing of cRNAs to the DNA template, enhancing R-loops formation and cRNAs retention at heterochromatin. Altogether, these results unveil the unexpected contribution of linker histones to RNPs assembly and homeostasis of cRNAs.

overall_design: DNA-RNA immuno precipitation-sequencing (DRIP-seq) for knockdown of hrp36 and hrp48 in S2 cells.

first: Paula

last: Bujosa

last: Reina

first: Adrià

last: Caballé

first: Jordi

last: Bernués

first: Fernando

last: Azorín


title: Nuclear export is a limiting factor in eukaryotic mRNA metabolism

city: Cologne

first: Achim

last: Tresch

state: North Rhine-Westphalia

address: Paul-Schallueck-Str. 10

department: Institute of Medical Statistics and Computational Biology

country: Germany

institute: University of Cologne

summary: The eukaryotic mRNA life cycle includes transcription, nuclear mRNA export and degradation. To quantify all these processes simultaneously, we perform thiol-linked alkylation after metabolic labeling of RNA with 4-thiouridine (4sU), followed by sequencing of RNA (SLAM-seq) in the nuclear and cytosolic compartments. We develop a model that reliably quantifies mRNA synthesis, nuclear export, and nuclear and cytosolic degradation rates on a genome-wide scale. We find that nuclear degradation of polyadenylated mRNA is negligible and nuclear mRNA export is slow, while cytosolic mRNA degradation is comparatively fast. Consequently, an mRNA molecule generally spends most of its life in the nucleus. We also observe large differences in the nuclear export rates of different 3’UTR transcript isoforms. Furthermore, we identify genes whose expression is abruptly induced upon metabolic labeling. These transcripts are exported substantially faster than average mRNAs, suggesting the existence of alternative export pathways. Our results highlight nuclear mRNA export as a limiting factor in mRNA metabolism and gene regulation.

overall_design:
We have performed a SLAM-seq time-series experiment in HeLa-S3 cells, where two replicate samples were taken at t=0, 15, 30, 45, 60, 90, 120 and 180 min after the addition of 500 μM 4sU. After metabolic labeling of RNA, the cells were fractionated to obtain the nuclear and the cytosolic RNA fractions.
To quantify mRNA metabolism, polyadenylated transcripts were captured by targeted sequencing library preparation and sequencing of polyadenylated 3’ ends. Reads were mapped to the human genome using Slamdunk.
We assigned the reads to annotated 3’UTRs. For robustness, we only consider3’UTRs with an average number of at least 30 reads in each cellular compartment and time series experiment.
We performed a refined analysis in which we defined densely covered, highly confined read clusters along the entire genome. We selected  such peaks with robust expression, i.e., at least 30 average counts in each cellular compartment and time-series experiment.

first: Jason

middle: M

last: Müller

first: Katharina

last: Moos

first: Till

last: Baar

first: Kristina

last: Zumer


title: Integrated Enhancer Regulatory Network by Enhancer-Promoter Looping in Gastric Cancer (4C)

city: Chiba

first: Masaki

last: Fukuyo

address: 1-8-1 Inohana, Chuo-ku

department: Department of Molecular Oncology

country: Japan

institute: Chiba University

summary: Enhancer as a cis-regulatory element (CRE), plays a critical role in gene regulation at many stages of cell growth. Meanwhile, enhancers in cancer cells also act as a regulator controlling oncogene transcription. In this study, we did a comprehensive analysis of long-range chromatin interactions, histone modifications, chromatin status, and expressions of two gastric cancer (GC) cell lines, compared with a human normal epithelial cell line. We found that GC-specific enhancers marked by histone modifications in gastric cancer can activate a population of genes including some oncogenes by enhancer-promoter (E-P) interactions. In addition, motif analysis of E-P interacted enhancers showed that three GC-specific TF sequences may regulate enhancer-interacting gene activation. We found MYB which is crucial for GC cellular growth and is activated by TCF7 regulated E-P loop. To validate this mechanism, we applied CRISPRi (dCas9-KRAB) induced transcriptional regulatory element inactivation in our target enhancer, the growth assay resulted in significant inhibition of cell growth in two GC cell lines. In conclusion, we found oncogene activation by aberrant loop formation that contributes to tumorigenesis in GC.

overall_design: Circularized Chromosome Conformation Capture with sequencing (4C-seq) in human gastric cancer cell SNU719 after siCtrl and siTCF7 treatment. Circularized Chromosome Conformation Capture with sequencing (4C-seq) in human gastric cancer cell SNU719 after CRSPRi sgCtrl and sgRNA against MYB enhancer treatment.

first: Tianhui

last: Zhu

first: Atsushi

last: Okabe

last: Kaneda


title: Linker histone H1 regulates homeostasis of heterochromatin associated cRNAs

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Chromosome fusion and programmed DNA elimination shape karyotypes of parasitic nematodes [RNA-seq]

city: Knoxville

first: Jianbin

last: Wang

state: TN

address: 1311 Cumberland Avenue, Ken and Blaire Mossman Building Rm 309

institute: The University of Tennessee

summary: A growing list of metazoans undergo programmed DNA elimination (PDE), where a significant amount of DNA is selectively lost from the genome during development. In some nematodes, PDE leads to the removal of the ends of all germline chromosomes. In several species, PDE also eliminates sequences in the interior of the chromosomes, leading to an increased number of somatic chromosomes. The biological significance of these karyotype changes associated with PDE and the origin and evolution of nematode PDE remain largely unknown. Here, we assembled the single pair of germline chromosomes of the horse parasite Parascaris univalens and compared the karyotypes, gene organization within the chromosomes, and PDE features among ascarids. We show that Parascaris converts an XX/XY sex-determination system in the germline into an XX/XO system in the somatic cells. Comparisons of Ascaris, Parascaris, and Baylisascaris chromosomes suggest that PDE existed in the ancestor of these parasites, and their current distinct germline karyotypes were derived from fusion events of the same ancestral smaller chromosomes. PDE resolves these fused germline chromosomes and restores their pre-fusion karyotypes, leading to alterations in genome architecture and gene expression in the somatic cells. Cytological and genomic analyses further reveal the dynamic organization of the Parascaris germline chromosome during meiosis and a potential function for the satellite DNA and the heterochromatin arms. Overall, our results show that chromosome fusion and PDE have been harnessed in these ascarids to shape their karyotypes that could modulate the organization and functions of the genomes.

overall_design: Sequencing was performed using Parascaris univalens embryos at different developmental stages and different regions of the testis.

first: James

last: Simmons

first: Maxim

last: Zagoskin


title: Chromosome fusion and programmed DNA elimination shape karyotypes of parasitic nematodes [Hi-C]

overall_design: Hi-C was performed using samples from intestines and germlines of both adult male and female Parascaris univalens.


title: Integrated Enhancer Regulatory Network by Enhancer-Promoter Looping in Gastric Cancer (RNA-seq)

overall_design:
To investigate the function of MYB and TCF7 in gastric cancer cells, we obtained MYB and TCF7 knockdown SNU719 and YCC10 gastric cancer cell lines by siRNA and CRISPRi
We then performed gene expression profiling analysis using data obtained from RNA-seq of before and after MYB or TCF7 knockdown in two cell lines (SNU719_siCtrl, SNU719_siMYB, YCC10_siCtrl, YCC10_siMYB; SNU719_siCtrl, SNU719_siTCF7, YCC10_siCtrl, YCC10_siTCF7; SNU719_CRISPRi_sgCtrl, SNU719_CRISPRi_sgMYB-E3, YCC10_CRISPRi_sgCtrl, YCC10_CRISPRi_sgMYB-E3).


title: Chromosome fusion and programmed DNA elimination shape karyotypes of parasitic nematodes [CUT&RUN]

overall_design: CUT&RUN sequencing data for the histone variant CENP-A and histone modifications H3K4me3 and H3K9me3.  Samples are from male and female germlines of Parascaris univalens.

first: Ryan

last: Oldridge


title: Integrated Enhancer Regulatory Network by Enhancer-Promoter Looping in Gastric Cancer (ChIP)

overall_design:
Chromatin immunopreciptation DNA sequencing (ChIP-seq) of H3K27ac, H3K4me1, and TCF7 in human normal gastric epithelial cell GES1 and human gastric cancer cell SNU719 and YCC10; Assay for Transposase-Accessible Chromatin sequencing (ATAC-seq) in human normal gastric epithelial cell GES1 and human gastric cancer cell SNU719 and YCC10; ChIP-seq of H3K27ac in human gastric cancer cell SNU719 and YCC10 after CRISPRi targeted MYB interacted enhancer.

Cleavage Under Targets & Tagmentation (CUT&Tag) of H3K27ac in human gastric cancer cell SNU719


title: Transcriptomic profiling of haloarchaeal denitrification through RNA-Seq analysis

city: San Vicente del Raspeig

first: Jose

middle: María

last: Miralles-Robledillo

state: Alicante

address: Carretera San Vicente S/N

institute: Universidad de Alicante

summary: Denitrification, a crucial biochemical pathway prevalent among haloarchaea in hypersaline ecosystems, has garnered considerable attention in recent years due to its ecological implications. Nevertheless, the underlying molecular mechanisms and genetic regulation governing this respiration/detoxification process in haloarchaea remain largely unexplored. In this study, RNA-sequencing was used to compare the transcriptomes of the haloarchaeon Haloferax mediterranei under oxic and denitrifying conditions, shedding light on the intricate metabolic alterations occurring within the cell such as the accurate control of the metal homeostasis. Furthermore, the investigation identifies several genes encoding transcriptional regulators and potential accessory proteins with putative roles in denitrification. Among these are bacterioopsin transcriptional activators, proteins harbouring a domain of unknown function (DUF2249), and a cyanoglobin. Additionally, the study delves into the genetic regulation of denitrification, finding a regulatory motif within promoter regions that activates numerous denitrification-related genes. This research serves as a starting point for future molecular biology studies in haloarchaea, offering a promising avenue to unravel the intricate mechanisms governing haloarchaeal denitrification, a pathway of paramount ecological importance.

overall_design: Haloferax mediterranei R4 ATCC33500 cells were grown under oxic and denitrifying conditions in media supplemented with nitrate. The aim of this research was to perform comparative transcriptomics (RNA-Seq) to analyse the gene expression changes under denitrifying conditions and identify the metabolic changes of these cells , as well as genes encoding proteins with a potential role in the denitrification pathway .

first: Rosa

last: Martinez-Espinosa

first: Carmen

last: Pire


title: Integrated Enhancer Regulatory Network by Enhancer-Promoter Looping in Gastric Cancer (HiChIP)

overall_design: HiChIP of H3K27ac in human gastric epithelial cell line GES1 gastric cancer cell SNU719 and YCC10


title: Cell-specific regulation of the circadian clock by BMAL1 in the paraventricular nucleus: Implications for regulation of systemic biological rhythms

city: Houston

first: Haichao

last: Wei

state: TX

address: 1825 Pressler St., SRB 637.C

institute: UTHealth

summary: Circadian rhythms are internal biological rhythms driving temporal tissue-specific, metabolic programs. Loss of the circadian transcription factor BMAL1 in the paraventricular nucleus (PVN) of the hypothalamus reveals its importance in metabolic rhythms, but its functions in individual PVN cells are poorly understood. Here, loss of BMAL1 in the PVN results in arrhythmicity of processes controlling energy balance and alters peripheral diurnal gene expression. BMAL1 chromatin immunoprecipitation sequencing (ChIP-seq) and single-nucleus RNA sequencing (snRNA-seq) reveal its temporal regulation of target genes, including oxytocin (OXT), and restoring circulating OXT peaks in BMAL1-PVN knockout (KO) mice rescues absent activity rhythms. While glutamatergic neurons undergo day/night changes in expression of genes involved in cell morphogenesis, astrocytes and oligodendrocytes show gene expression changes in cytoskeletal organization and oxidative phosphorylation. Collectively, our findings show diurnal gene regulation in neuronal and non-neuronal PVN cells and that BMAL1 contributes to diurnal OXT secretion, which is important for systemic diurnal rhythms.

overall_design: PVN regions were dissected from mcie at ZT8 and were pooled for each sample for a total weight of 150mg. Chomatin immunoperciptiation was then carried out on two pooled PVN samples using a BMAL1 specific antibody. Library prep and sequencing was carried out at the Cancer Genomics Core at UTHealth Housgon. BMAL1 binding was validated in both samples from reamining sample by measuring expression of postitive and negative controls via ChIP-qPCR.

first: Rachel

last: Van Drunen

first: Kristin

last: Eckel-Mahan

first: Jiaqian

last: Wu

first: Xian

last: Chen

first: Zhongming

last: Zhao


title: Integrated Enhancer Regulatory Network by Enhancer-Promoter Looping in Gastric Cancer

last: Fukuyo


title: Macrophage epigenetic memories of early life injury drive neonatal nociceptive priming.

city: Cincinnati

first: Michael

last: Jankowski

state: OH

address: 3333 Burnet Ave

department: Anesthesia

institute: Cincinnati Children's Hospital Medical Center


title: Macrophage epigenetic memories of early life injury drive neonatal nociceptive priming. [RNA-Seq]

summary: The developing peripheral nervous and immune systems are functionally distinct from adults. These systems are vulnerable to effects of early life injury which can influence outcomes related to nociception following subsequent injury later in life (i.e. “neonatal nociceptive priming”). The underpinnings of this phenomenon are largely unknown, although critical periods in macrophages can be epigenetically trained by injury. We found that macrophages are both necessary and partially sufficient to drive neonatal nociceptive priming possibly due to a long-lasting epigenetic remodeling of peripheral macrophages. The p75 neurotrophic factor receptor (NTR) was found to be an important effector in regulating this “nociceptive trained immunity”. p75NTR modulates the inflammatory profile and responses of rodent and human macrophages and this “pain memory” was able to be transferred to a naive host to alter sex-specific pain-related behaviors. This study reveals a novel mechanism by which acute post-surgical pain may transition to chronic pain in children.

overall_design: Samples are macrophages isolated from the peritoneum and sorted by LysM+ cells. Groups included naïve P7 isolated, naïve P35 isolated and P35 isolated from animals that had received a hind paw incision at P7.

first: Adam

last: Dourson

middle: P

first: Aditi

last: Paranjpe

first: Omer

last: Donmez


title: Linker histone H1 regulates homeostasis of heterochromatin associated cRNAs [ChIP-seq 1]

first: Oscar

last: Reina Garcia

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for hrp36 and hrp48 in S2 cells.

first: Paula

last: Bujosa

last: Reina

first: Adrià

last: Caballé

first: Jordi

last: Bernués

first: Fernando

last: Azorín


title: Structured and disordered regions of Ataxin-2 contribute differently to the specificity and efficiency of mRNP granule formation

city: Mandi

first: Baskar

last: Bakthavachalu

state: Himachal Pradesh

address: Kamand

department: School of Biosciences and Bioengineering

country: India

institute: Indian Institute of Technology

summary: Ataxin-2 (ATXN2) is a gene implicated in spinocerebellar ataxia type II (SCA2), amyotrophic lateral sclerosis (ALS) and Parkinsonism. The encoded protein is a therapeutic target for ALS and related conditions. ATXN2 (or Atx2 in insects) functions in translational regulation, mRNA stability, and in the assembly of mRNP-granules, a process mediated by intrinsically disordered regions (IDRs). Previous work has shown that the LSm (Like-Sm) domain of Atx2, which mediates translational activation of some target mRNAs, antagonizes mRNP-granule assembly. Here we advance these findings through a series of experiments on Drosophila and human Ataxin-2 proteins. Results of Targets of RNA-Binding Proteins Identified by Editing (TRIBE) experiments indicate that a polyA-binding protein (PABP) interacting, PAM2 motif of Ataxin-2 may be a major determinant of the mRNA content of Ataxin-2 mRNP granules. Co-localization and co-immunoprecipitation analyses show that structured interactions between Ataxin-2 and PABP additionally help determine protein components of Ataxin-2-associated mRNP granules and contribute to Ataxin-2’s association with stress granules. Finally, in vivo experiments in Drosophila indicate that while the Atx2-LSm domain protects against neurodegeneration, structured PAM2- and unstructured IDR- interactions both promote degeneration. Taken together the data: (a) lead to a proposal for how Ataxin-2 interactions are remodelled during different stages of translational control; (b) show how structured and non-structured interactions of Ataxin-2 contribute differently to the specificity and efficiency of RNP granule condensation; and (c) demonstrate that the Ataxin-2 protein contains multiple activities that may respectively prevent or promote neurodegeneration.

overall_design: Elav-Gal4 was used to drive Atx2-ADARcd fusion protein in nervous system and the expression was restricted to adult flies with the use of the temperature sensitive Gal4 inhibitor, GAL80ts. Fly brains were dissected, and mRNA was sequenced using Illumina HiSeq 2500. RNA edits sites were identified using TRIBE pipeline (https://github.com/rosbashlab/TRIBE).

first: Arvind

middle: R

last: Kandi

first: Mani

last: Ramaswami


title: Deletion of cardiac-enriched lncRNA CARDINAL exacerbate TAC induced hypertrophy

city: Los Angeles

first: Yao Wei

last: Lu

state: CA

address: 2011 Zonal Ave

department: Department of Medicine

institute: University of Southern California

summary: Pathological cardiac hypertrophy is featured by enhanced protein synthesis. Translation inhibition is effective in treating cardiac hypertrophy, yet with systematic side effect. We identified a cardiac-enriched LncRNA CARDINAL, when deleted, exacerbate transaortic constriction (TAC) induced hypertrophy.

overall_design: CARDINAL knockout mouse was generated with CRISPR/Cas9 strategy. Cardiac hypertrophy was induced by transverse aortic constriction (TAC) surgery as described previously. Briefly, mice with a body weight of 25-30g were anesthetized with isoflurane (3%–4% isoflurane for induction, 1%–2% isoflurane for maintenance). The chest was shaved and disinfected with alcohol. The chest was opened by left second intercostal thoracotomy. A 26-gauge needle was put on the ascending aorta. The needle and the ascending aorta were tightly ligated together using a 7-0 nylon suture at the transverse aorta, and the 26-gauge needle was removed immediately after ligation. In the sham operation, all procedures were the same except that no ligation was performed. Dissected intercostal space and chest skin were closed using a 6-0 silk suture. Mice genotypes were blinded to the surgeon. Samples were collected 4 weeks post surgery.

first: Yao

middle: W

first: Xin

last: He

first: Da-Zhi

last: Wang


title: AAV9-medated cardiac expression of lncRNA CARDINAL ameliorate TAC induced hypertrophy

summary: Pathological cardiac hypertrophy is featured by enhanced protein synthesis. Translation inhibition is effective in treating cardiac hypertrophy, yet with systematic side effect. We identified a cardiac-enriched LncRNA CARDINAL, when over-expressed in cardiomyocyte using AAV9 driven by cTNT promoter, ameliorate transaortic constriction (TAC) induced hypertrophy.

overall_design: GFP and full-length CARDINAL were separately cloned into ITR-containing AAV plasmid (Penn Vector Core P1967) harboring the chicken cardiac TNT promoter to get pAAV9-cTnT-CARDINAL and pAAV9-cTnT-GFP.AAV9 was packaged in HEK293T cells with AAV9: Rep-Cap and pHelper (pAd deltaF6, Penn Vector Core), then purified and concentrated by gradient centrifugation36. AAV9 titer was determined by quantitative PCR. AAV9 virus (5×109 viral genomes [vg]/g) was injected into postnatal day 1 WT pups by subcutaneous injection. Cardiac hypertrophy was induced by transverse aortic constriction (TAC) surgery as described previously. Briefly, mice with a body weight of 25-30g were anesthetized with isoflurane (3%–4% isoflurane for induction, 1%–2% isoflurane for maintenance). The chest was shaved and disinfected with alcohol. The chest was opened by left second intercostal thoracotomy. A 26-gauge needle was put on the ascending aorta. The needle and the ascending aorta were tightly ligated together using a 7-0 nylon suture at the transverse aorta, and the 26-gauge needle was removed immediately after ligation. In the sham operation, all procedures were the same except that no ligation was performed. Dissected intercostal space and chest skin were closed using a 6-0 silk suture. Mice genotypes were blinded to the surgeon. Samples were collected 4 weeks post surgery. knockout mouse was generated with CRISPR/Cas9 strategy.


title: Macrophage epigenetic memories of early life injury drive neonatal nociceptive priming. [ATAC-Seq]


title: Suppression of inositol pyrophosphate toxicosis and hyper-repression of the fission yeast PHO regulon by loss-of-function mutations in chromatin remodelers Snf22 and Sol1

city: New York

first: Ana

last: Sanchez

state: NY

address: 430 E 67th Street, RRL-865

department: Molecular Biology

institute: Memorial Sloan Kettering Cancer Center

summary: RNA-seq analysis compares gene expression of the snf22∆ and snf22-(D996A-E997A) mutants to the wild-type fission yeast (Schizosaccharomyces pombe).

overall_design: 2 test samples and 1 control sample were processed (each sample has 3 replicate experiments).

first: Beate

last: Schwer

first: Aleksei

last: Innokentev

first: Angad

last: Garg

first: Stewart

last: Shuman


title: Maternal antioxidant treatment prevents behavioural and neurological changes in offspring exposed to prenatal social stress [RNA-seq]

city: Cardiff

first: Hannah

last: Scott

address: Hadyn Ellis Building, Maindy Road

department: UK Dementia Research Institute

country: United Kingdom

institute: Cardiff University

summary: Maternal exposure to social stress during pregnancy is associated with an increased risk of psychiatric disorders in the offspring in later life. How the effects of maternal social stress are transmitted to the developing foetus is unclear. Using a rat model of maternal social stress during pregnancy, we explored the mechanisms by which maternal stress is conveyed to the foetus and the potential for targeted treatment to prevent disease in the offspring. Maternal stress induced oxidative stress in the placenta, but not in the foetal brain, which was prevented by a single administration of nanoparticle-bound antioxidant prior to the stress exposure. Moreover, this antioxidant treatment prevented prenatal stress-induced anxiety-like behaviour in juvenile male offspring, along with neurological and gene expression changes in the offspring brain. In vitro, placental conditioned medium or foetal plasma from stressed pregnancies caused changes to cultured cortical neurons, similar to those observed in the brains of juvenile offspring exposed to prenatal stress, and were found to contain altered levels of extracellular microRNAs but not corticosterone. The present study highlights the crucial role of the placenta, and molecules secreted from the placenta, in foetal brain development and provides evidence of the potential for treatment that can prevent maternal stress-induced foetal programming of neurological disease.

overall_design: RNA sequencing was performed on RNA isolated form frontal cortices of gestational day 20 foetal rats. Dams had been exposed to chronic social stress during pregnancy, while control rats were left undisturbed. Stressed rats had been injected with nanoparticle-bound MitoQ (MitoQ-NP) or saline, while control rats had been injected with saline. For each of the 3 experimental conditions, samples were obtained from 4 independent foetuses (from different dams).

first: Thomas

last: Phillips

first: Ying

last: Sze

first: Alessio

last: Alfieri

first: Mark

middle: F

last: Rogers

first: Charles

last: Case

last: Brunton


title: Precise immuno-fluorescence canceling enables highly multiplexed imaging [scRNA-seq]

status: Public on Apr 21 2024

city: Fukuoka

first: Yasuyuki

last: Ohkawa

address: 3-1-1 Maidashi

institute: Medical Institute of Bioregulation

summary: Cell states are regulated by extrinsic signals from various external factors such as intercellular interactions, and intrinsic gene expression. Although comprehensive cell state profiling has been attempted, it remains simultaneous analysis of signal activation has still been challenging. Multiplexed imaging is a technique acquiring multiple protein information at a single cell level as traditional immunofluorescence. However, the method often compromises resolution, hindering the analysis of intracellular localization dynamics and post-translational modifications of proteins. To address these limitations, we developed an erasable fluorescence method using disulfide linkers to label antibodies. We term these antibodies ‘Precise Emission Canceling Antibodies (PECAbs)’. PECAb allows for high-resolution iterative imaging with minimal non-specific binding. Automation enables our system to achieve reproducible quantitative analysis using 206 antibodies. The resulting quantitative data allow reconstruction of the spatiotemporal dynamics of signaling pathways over both long and short timescales. Additionally, combining this approach with sequential RNA-FISH can effectively classify cells and identify their signal activation states in human tissue. Overall, the PECAb system serves as a comprehensive platform for analyzing complex cell processes, from signal transduction to gene expression.

overall_design:
To investigate the dynamics of gene expression profile during Epithelial Mesenchymal Transition (EMT), human lung carcinoma cell line A549 cells were treated with TGFb and harvested at 0, 0.5, 12, 24, 48 and 96 hours.
We then performed dimensionality reduction with UMAP using dataset obtained from single cell RNA-seq of the TGFb treated A549 cells at 6 time points.

first: Kosuke

last: Tomimatsu

first: Takeru

last: Fujii

first: Kaori

last: Tanaka


title: Precise immuno-fluorescence canceling enables highly multiplexed imaging [RNA-seq]

overall_design: To obtain carcinoma associated geneset from uterus carcinosarcoma tissue, three carcinosarcoma tissues containing different ratios of carcinoma:sarcoma (C:S = 3:7, 1:9 and 0:10) were used.

first: Fujii

last: Takeru

first: Seiichi

last: Mori


title: Gut microbiota rewires host mRNA m6A epitranscriptomic landscape via bile acid metabolism

city: Guangzhou

first: Xiaoyun

last: Wang

state: Guangdong

address: 190 Kaiyuan Avenue, Huangpu

department: Infection and Immunity

country: China

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

type: Methylation profiling by high throughput sequencing

summary: Gut microbiota and their metabolites influence host gene expression and physiological status through diverse mechanisms. Here we investigate how gut microbiota and their metabolites impact host's mRNA m6A epitranscriptome in various antibiotic-induced microbiota dysbiosis models. With multi-omics analysis, we find that the imbalance of gut microbiota can rewire host mRNA m6A epitranscriptomic profiles in brain, liver and intestine. We further explore the underlying mechanisms regulating host mRNA m6A methylome by depleting the microbiota with ampicillin. Metabolomic profiling shows that cholic acids are the main down-regulated metabolites with Firmicutes as the most significantly reduced genus in ampicillin-treated mice comparing to untreated mice. Fecal microbiota transplantations in germ-free mice and metabolites supplementations in cells verify that cholic acids are associated with host mRNA m6A epitranscriptomic rewiring. Collectively, this study employs an integrative multi-omics analysis to demonstrate the impact of gut microbiota dysbiosis on host mRNA m6A epitranscriptomic landscape via cholic acid metabolism.

overall_design: To investigate the influence of gut microbiota on host mRNA m6A epitranscriptome and explore the underlying mechanisms following our previous work, we constructed various gut microbiota dysbiosis mouse models in this study. We treated SPF mice with single antibiotic (ampicillin, gentamicin, metronidazole, neomycin and vancomycin, respectively) via drinking water for 40 days. SPF mice were also treated with an antibiotic cocktail (a mix of the above five antibiotics), and mice treated with distilled water were included in parallel for comparisons. After the model constructions, we collected tissue samples and fecal samples for multi-omics profiling (microbiome, metabolome, m6A epitranscriptome, and proteome) followed by comprehensive data analysis.

first: Meng

last: Yang

first: Jiajun

last: Fan

first: Wei

last: Cheng


title: Gene expression data from acetaminophen-induced toxicity in wild-type and Gα12 knockout mice

city: Seoul

first: Sang Geon

last: Kim

state: Seoul

address: San56-1, Sillim-dong, Kwanak-gu

department: College of Pharmacy

country: South Korea

institute: Seoul National University

summary: Gα12 is an alpha subunit of heterotrimeric G proteins that activates the downstream pathways from G protein-coupled receptor (GPCR) signals. Gα12 overexpression enhances hepatocellular carcinoma (HCC) malignancy, promoting cancer migration and microvascular invasion. Also, it activates hepatic stellate cells (HSCs) and thereby facilitates the progression of liver fibrosis. However, upregulated Gα12 in hepatocytes by acetaminophen (APAP) mechanically has been scarcely explored. This study provides an evaluation of changes in gene expression using liver samples obtained from WT and Gα12KO mice treated with APAP.

overall_design: Examination of RNA expression in mouse livers obtained from WT and Gα12KO treated with vehicle and APAP.

first: Jihoon

last: Tak


title: Transcriptomic profiling of highly- and lowly- metastasizing pancreatic ductal carcinoma cells [mRNAseq shNPTX1]

status: Public on Apr 20 2024

first: Norihiro

last: Yamaguchi

state: Ny

address: 1230 York Avenue, Box 16

department: Systems Cancer Biology

institute: The Rockefeller University

summary: To interrogate transcriptomic changes in highly liver metastatic pancreatic ductal carcinoma cells as relative to their isogenic lowly metastatic cells

overall_design: Comparative gene expression profilling of ex vivo liver metastasizing tumors

first: Gloria

last: Wu

first: Wenbin

last: Mei


title: Transcriptomic profiling of highly- and lowly- metastasizing pancreatic ductal carcinoma cells [mRNAseq in vivo selection]

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Trans-omic Profiling Uncovers Molecular Controls of the Early Human Cerebral Organoid Formation

city: Sydney

first: Carissa

last: Chen

state: NSW

address: 214 Hawkesbury Rd, Westmead

country: Australia

institute: Children's Medical Research Institute

summary: Defining molecular controls that orchestrate human brain development is essential for uncovering the complexity behind neurodevelopment and the pathogenesis of neurological disorders. Due to the difficulties in accessing embryonic and fetal brain tissues, the differentiation of human pluripotent stem cell (hPSC)-derived three-dimensional neural organoids has made it possible to recapitulate this developmental process in vitro and provide a unique opportunity to investigate human brain development and disease. To elucidate the molecular programs that drive this highly dynamic process, here, we generate a comprehensive trans-omic map of the phosphoproteome, proteome, and transcriptome of the initial stages of pluripotency and neural differentiation towards the formation of cerebral organoids. Our integrative analysis uncovers key phospho-signalling events underlying neural lineage differentiation, and their convergence on transcriptional (co-)factors and chromatin remodellers that govern downstream gene regulatory networks (GRNs). Comparative analysis with developing human and mouse embryos using these GRNs demonstrates the fidelity of our early cerebral organoids in modelling embryonic brain development. Finally, we demonstrate biochemical modulation of the AKT signalling as a key molecular switch for controlling human cerebral organoid formation. Our data provides a comprehensive resource to gain insight into the molecular controls in human embryonic brain development and also provide a guide for future development of protocols for human cerebral organoid differentiation.

overall_design: To characterize early human organoid differentiation, we performed bulk and single-cell transcriptomic profiling of differentiating H9 hESC aggregates to the formation of the early neural organoid over a period of 8 days. Timepoints include 0h, 1h, 6h, day 1, day 2, day 4, day 6 and day 8 with 2 replicates per timepoint for bulk RNA-sequencing. Single-cell sequencing was performed on day 8 with one replicate.

first: Scott

last: Lee

first: Milan

last: Fernando

first: Katherine

middle: G

last: Zyner

first: Victoria

last: Nemeruck

first: Emilie

last: Wong

first: Lee

middle: L

last: Marshall

first: Jesse

last: Wark

first: Nader

last: Arymanesh

first: Patrick

last: Tam

first: Mark

middle: E

last: Graham

first: Anai

last: Gonzalez-Cordero

first: Pengyi


title: Gene expression profile of brain tissue from wildtype and GRN knock-out mice treated with an AAV driving expression of PTV-Progranulin in the liver

status: Public on Apr 19 2024

city: South San Francisco

first: Thomas

last: Sandmann

email: genomics@dnli.com, sandmann@dnli.com

state: California

address: 161 Oyster Point Blvd

institute: Denali Therapeutics

summary: PGRN is involved in lysosomal function and is expressed in the brain. Grn knock-out (KO) mice develop several pathologies including lysosomal lipi accumulation, gliosis and neurodegeneration. Here we seek to determine if we can rescue Grn KO pathologies with a peripherally delivered AAV, that targets the liver, and drives expression of full length PGRN fused to a mouse TfR binding scFv (AAV(L):bPGRN. The PGRN fusion protein expressed by this AAV (8D3:PGRN), is brain penetrant. To study this, Grn KO mice were given a single IV injection of either saline or AAV(L):bPGRN at 4 months of age. After 8 months when the mice were 12 months of age, brain samples were collected and bulk RNA sequencing was performed to assess correction of transcriptional changes. Grn wild type (WT) mice treated with saline were also included as a control.

overall_design: We generated AAV(L):bPGRN (L = liver, b = brain-penetrant), a liver-targeting adenovirus (AAV) encoding a fusion protein (8D3:PGRN) consisting of a single chain fragment variable (scFv) antibody recognizing mouse TfR (transferrin receptor) fused to human PGRN (hPGRN). Grn knockout (KO) mice were treated with either an AAV driving expression of 8D3-linked progranulin (AAV(L)-8D3-PGRN) in the liver (n=5) or saline (n=5). As a control, wildtype (WT) animals treated with saline (n=6) were included.

first: M

last: Reich

last: Simon

first: B

last: Polk

first: T

first: G

last: Di Paolo

first: C

last: Haass


title: The cis-regulatory logic integrating spatial and temporal patterning in the vertebrate neural tube

city: London

first: M Joaquina

last: Delas

address: 1 Midland Road

department: Briscoe Lab

institute: The Francis Crick Institute

overall_design: Refer to individual Series


title: Microglia - astrocyte cross-talk in the amyloid plaque niche of an Alzheimer’s disease mouse model as revealed by spatial transcriptomics (Stereo-seq Spatial Transcriptomics)

city: Leuven

first: Bart

last: de Strooper

address: Campus Gasthuisberg, Herestraat 49, bus 602

department: VIB-KU Leuven Center for Brain & Disease Research

country: Belgium

institute: KULeuven

summary: In this study, we characterize the transcriptomic alterations, cellular compositions, and signaling perturbations in the amyloid plaque niche in an AD mouse model using high-resolution spatial transcriptomics (CosMx and Stereo-seq).  We discover a wide heterogeneity in the cellular composition of amyloid plaque niches, marked by an increase in microglial accumulation over time. We profile the alterations of glial cells as they are exposed to plaques, and conclude that the microglial response to plaques is consistent across different brain regions, while the astrocytic response is more heterogeneous. In turn, as the microglial density of plaque niches increases, astrocytes acquire a more neurotoxic phenotype and play a key role in inducing GABAergic signaling and decreasing glutamatergic signaling in neurons of the hippocampus. Taken together, we show that astrocytic signaling around plaque pathology is disrupted with increasing microglial density, which in turn induces an imbalance in synaptic signaling in neurons in the hippocampus.

overall_design: Stereo-seq technology was applied to coronal sections of AppNL-G-F KI and C57BL/6J background mice at 3 and 18 months of age.  Two mixed hemispheres, where one hemisphere is from a WT mouse and the other from an AppNL-G-F mouse, were processed for 3M animals, whilst two full coronal sections were processed for the 18M AppNL-G-F mice, with one full coronal section of an age-matched control. Briefly, 10 µm thick tissue sections were fixed to Stereo-seq chips, with immediately adjacent slides collected for staining. The sections were then stained for ssDNA and imaged to obtain nuclei location information. Tissue sections were then permeabilized and reverse transcription was performed overnight. Afterwards, tissue was digested and cDNA released from the chip. The recovered cDNA was amplified and  fragmented for library construction. PCR products were purified and sequenced on a MGI DNBSEQ-Rx sequencer. Adjacent slides from the Stereo-seq experiments were stained using a standard IHC protocol to visualize reactive astrocytes and amyloid-β plaques. 16-bit fluorescent images of DAPI, 6E10, and GFAP were acquired on a Zeiss Axioscan.Z1 slidescanner. Different FOV were stitched together. The Stereo-seq raw data processing was performed in publicly available SAW pipeline (https://github.com/BGIResearch/SAW). In brief, fastq files were generated using a MGI DNBSEQ-Tx sequencer.Reads  passing QC metrics were aligned to the mm10 reference genome using STAR. Mapped reads with MAPQ > 10 were counted and annotated to their corresponding genes, resulting in a CID-containing expression profile matrix.

first: Anna

last: Mallach

first: Magdalena

last: Zielonka

first: Veerle

last: van Lieshout

first: Yanru

last: An

first: Jia

middle: H

last: Khoo

first: Marisa

last: Vanheusden

first: Wei-Ting

last: Chen

first: Daan

last: Moechars

first: Lorena

last: Arancibia-Carcamo

last: Fiers

last: De Strooper


title: Gut microbiota dysbiosis rewires host mRNA m6A epitranscriptomic landscape via bile acid metabolism

first: Xiaoyun

last: Wang

summary: Gut microbiota and their metabolites influence host gene expression and physiological status through diverse mechanisms. Here we investigate how gut microbiota and their metabolites impact host′s mRNA m6A epitranscriptome in various antibiotic-induced microbiota dysbiosis models. With multi-omics analysis, we find that the imbalance of gut microbiota can rewire host mRNA m6A epitranscriptomic profiles in brain, liver and intestine. We further explore the underlying mechanisms regulating host mRNA m6A methylome by depleting the microbiota with ampicillin. Metabolomic profiling shows that cholic acids are the main down-regulated metabolites with Firmicutes as the most significantly reduced genus in ampicillin-treated mice comparing to untreated mice. Fecal microbiota transplantations in germ-free mice and metabolites supplementations in cells verify that cholic acids are associated with host mRNA m6A epitranscriptomic rewiring. Collectively, this study employs an integrative multi-omics analysis to demonstrate the impact of gut microbiota dysbiosis on host mRNA m6A epitranscriptomic landscape via cholic acid metabolism.

overall_design:
Mice were fed water with different antibiotics to form mouse models with different intestinal flora. MeRIP-seq, Proteome, RNA-seq, 16S rDNA and Metabolome of mouse tissues were used to study the effects of intestinal microbiota and its metabolites on host epigenetic modifications, protein expression, and regulation of gene expression.
The 102 samples in the current dataset are all RNA sequencing datasets.

first: Meng

last: Yang

first: Jiajun

last: Fan

first: Wei

last: Cheng


title: Astrocyte-mediated regulation of BLAWFS1 neurons alleviates risk-assessment deficits in DISC1-N mice

city: Shenzhen

first: Jie

last: Tu

address: 1068 Xueyuan Boulevard, Nanshan, Shenzhen 518055, China

department: The Brain Cognition and Brain Disease Institute (BCBDI)

institute: Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences (CAS)

summary: Assessing and responding to threats is vital in everyday life. Unfortunately, many mental illnesses involve impaired risk assessment, affecting patients, families, and society. The brain processes behind these behaviors are not well understood. We developed a transgenic mouse model (DISC1-N) with a disrupted avoidance response in risky settings. Our study utilized single-nucleus RNA sequencing to uncover a previously undescribed group of glutamatergic neurons in the basolateral amygdala (BLA) marked by WFS1 expression, whose activity is modulated by adjacent astrocytes. These neurons in DISC1-N mice exhibited diminished firing ability and impaired communication with the astrocytes. Remarkably, optogenetic activation of these astrocytes reinstated neuronal excitability via D-serine acting on BLAWFS1 neurons’ NMDA receptors, leading to improved risk-assessment behavior in the DISC1-N mice. Our findings point to BLA astrocytes as a promising target for treating risk assessment dysfunctions in mental disorders.

overall_design: In order to investigate whether cells in the BLA exhibit functional abnormalities that may contribute to this manifestation in pathology, we used snRNA-seq to analyze the transcriptomes of BLA cells in DISC1-N mice.

first: Xinyi

last: Zhou

first: Qian

last: Xiao

first: Yaohui

last: Liu

first: Shuai

first: Xirong

last: Xu

first: Zhigang

last: Zhang

first: Yuchuan

last: Hong

last: Shao

first: Yuewen

first: Yu

first: Liping

first: Fan


title: Analysis of cardiac-enriched lncRNA CARDINAL in TAC induced hypertrophy

first: Yao Wei

last: Lu

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


title: Alveolar Soft Part Sarcoma is driven by ASPSCR1::TFE3-dependent and therapeutically targetable transcriptional programs [ATAC-Seq]

city: Worcester

first: Matthew

last: Hemming

state: MA

address: 364 Plantation Street

institute: UMass Medical School

summary: Alveolar soft part sarcoma (ASPS) is a rare mesenchymal malignancy driven by the ASPSCR1::TFE3 fusion, though the mechanisms by which this oncogenic transcriptional regulator drives cancer growth are poorly understood. Here, we characterize the transcriptional and chromatin landscapes of ASPS tumors and preclinical models, identifying the essential role of ASPSCR1::TFE3 in tumor cell viability by regulating core transcriptional programs including cell proliferation, angiogenesis, and mitochondrial biology. ASPSCR1::TFE3 directly interacts with key epigenetic regulators at enhancers and promoters to support ASPS-associated transcription. Among the effector programs driven by ASPSCR1::TFE3, cell proliferation was driven by high levels of Cyclin D1 expression, and disruption of Cyclin D1/CDK4 signaling led to loss of ASPS proliferative capacity, which when combined with angiogenesis inhibition halted tumor growth in xenografts. These results define the ASPS oncogenic program, mechanisms by which ASPSCR1::TFE3 controls tumor biology, and identify a strategy for therapeutically targeting tumor cell-intrinsic vulnerabilities.

overall_design: To investigate the transcriptional programs in ASPS, we engineered the ASPS-KY cell line to express a degradable ASPSCR1::TFE3 tagged construct and treated with dTAG13, followed by ATAC-seq.


title: ASPSCR1::TFE3 Drives Alveolar Soft Part Sarcoma by Inducing Targetable Transcriptional Programs

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

Alveolar soft part sarcoma (ASPS) is a rare mesenchymal malignancy driven by the ASPSCR1::TFE3 fusion. A better understanding of the mechanisms by which this oncogenic transcriptional regulator drives cancer growth is needed to help identify potential therapeutic targets. Here, we characterized the transcriptional and chromatin landscapes of ASPS tumors and preclinical models, identifying the essential role of ASPSCR1::TFE3 in tumor cell viability by regulating core transcriptional programs involved in cell proliferation, angiogenesis, and mitochondrial biology. ASPSCR1::TFE3 directly interacted with key epigenetic regulators at enhancers and promoters to support ASPS-associated transcription. Among the effector programs driven by ASPSCR1::TFE3, cell proliferation was driven by high levels of cyclin D1 expression. Disruption of cyclin D1/CDK4 signaling led to loss of ASPS proliferative capacity, and combined inhibition of CDK4/6 and angiogenesis halted tumor growth in xenografts. These results define the ASPS oncogenic program, reveal mechanisms by which ASPSCR1::TFE3 controls tumor biology, and identify a strategy for therapeutically targeting tumor cell-intrinsic vulnerabilities.


title: Transcriptomic Diversity of Innate Lymphoid Cells in Human Lymph nodes

city: Milwaukee

first: Subramaniam

last: Malarkannan

state: Wisconsin

address: 8701 Watertown Plank Rd

department: Microbiology & Immunology

institute: Medical college of wisconsin

summary: Presence and functions of ILCs in the human draining lymph nodes (LN) are unknown. Here, we performed single-cell RNA sequencing to unravel the tissue-specific transcriptional profiles of  ILCs  compared them with that of bone marrow (BM) and spleen.

overall_design: Single cells from Lymph nodes, Bone marrow, and Spleen were captured using Multi Tissue Dissociation kit. Then the total innate lymphocyte were isolated using Flourecense activated cell sorting (FACS) according to the presense or acceptance of the CD7 marker.

first: Elaheh

last: Hashemi


title: Alveolar Soft Part Sarcoma is driven by ASPSCR1::TFE3-dependent and therapeutically targetable transcriptional programs [RNA-Seq]

overall_design: To investigate the transcriptional programs in ASPS, we generated RNA-seq samples from tumors and preclinical models. RNA-seq was performed on cell cultures and xenografts following treatment with palbociclib.

first: Hemming

last: Matthew L


title: Alveolar Soft Part Sarcoma is driven by ASPSCR1::TFE3-dependent and therapeutically targetable transcriptional programs [ChIP-Seq]

overall_design: To investigate the transcriptional programs in ASPS, we generated ChIP-seq samples from tumors and preclinical models.


title: Generation of Anterior Eye Cells from hiPSCs in Microfluidic Platforms

city: Izmir

first: Burak

last: Kahveci

address: Izmir

country: Turkey

institute: Izmir Biomedicine and Genome Center

summary: To generate a microfluidic platform to understand micro-physiological features of hiPSC-derived anterior part of the eye, such as mechano-transduction.

overall_design: To understand the transcriptomic profiles of hiPSC-derived ocular structures, we performed the bulk RNA sequencing.

first: Gamze

last: Koçak

first: Sude

last: Uyulgan

first: Elifsu

last: Polatlı

first: Vedat

last: Sarı

first: Ahmet

last: Bursalı

first: Tuba

last: Reçber

first: Emirhan

last: Nemutlu

first: Adil

last: Mardinoğlu

first: Gökhan

last: Karakülah

first: Canan

last: Aslı Yıldırım

first: Sinan

last: Güven


title: C-terminally phosphorylated p27 regulates STAT3 transcriptional activation, inducing gene programs driving mammary duct and cancer stem cell expansion

city: Miami

first: Derek

last: Van Booven

state: FL

address: 1501 NW 10th Ave

institute: University of Miami

summary: While, p27 inhibits cell cycle in normal cells, in most cancers, p27 acquires oncogenic activities when phosphorylated by PI3K-activated kinases at T157 and T198 (p27pTpT). Mechanistically, these oncogenic functions of p27pTpT are poorly understood. Here, we show that p27pTpT promotes cancer stem cell (CSC) expansion through STAT3 both in vitro and in vivo. p27 phosphorylation increased STAT3 recruitment to chromatin to induce CSC self-renewal genes including MYC, the Notch ligand, JAG1, and ANGPTL4. We identify a feed-forward loop in which p27pTpT/STAT3 co-represses the Pyk2 inhibitor, PTPN12. Pyk2 in turn activates STAT3, driving CSCs expansion. p27pTpT is also shown to critically regulate mammary gland development. Mammary transgenic expression of phosphomimetic, cyclin-CDK binding defective p27 (p27CK-DD) increases mammary duct branching morphogenesis and hyperplasia, yielding primary and metastatic breast cancers. This supports a model in which p27pTpT co-regulates STAT3 to drive programs governing stem cell expansion or maintenance in normal and cancer tissues.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for STAT3 in MDA-MB-231-1833 and 1833shp27 cell lins

first: Joyce

last: Slingerland

first: Seyedeh

last: Razavipour


title: The SAGA complex maintains the oncogenic gene expression program in MYCN-amplified neuroblastoma [ChIP-Seq]

city: Cambridge

first: Gabriela

last: Alexe

address: 415 Main St.

department: Computational Biology and Bioinformatics

institute: Broad Institute

summary: Pediatric cancers are frequently driven by fusion or amplification events that result in aberrant transcription factor activity.  As transcription factors themselves remain challenging to target, an emerging therapeutic approach for these cancers is to target epigenetic complexes that help maintain oncogenic transcriptional programs. It is therefore critical to identify the complete set of epigenetic modulators maintaining the oncogenic epigenetic landscape of pediatric cancers. Here, we used functional genomic screens to identify epigenetic complexes critical for viability in cell line models of MYCN-amplified neuroblastoma, a disease of dysregulated development driven by an aberrant oncogenic transcriptional program. We identified multiple genes within the transcriptional coactivator Spt-Ada-Gcn5-acetyltransferase (SAGA) complex as selective dependencies in MYCN-amplified neuroblastoma. Integrating ChIP-seq, ATAC-seq, and RNA-seq with targeted protein-degradation and gene editing tools, we characterized the DNA recruitment sites of the SAGA complex in neuroblastoma, and the consequences of SAGA complex lysine acetyltransferase (KAT) activity loss on histone acetylation and gene expression. We demonstrate that loss of SAGA KAT activity suppresses MYC and MYCN gene expression programs and impairs cell cycle progression. Further, we showed that the SAGA complex is pharmacologically targetable with a KAT2A/KAT2B proteolysis targeting chimera molecule that demonstrated significant activity in vitro and in vivo. Our findings expand our understanding of the histone modifying complexes that maintain the oncogenic transcriptional state in this disease and suggest therapeutic potential for inhibitors of SAGA KAT activity in MYCN-amplified neuroblastoma.

overall_design: Investigate alterations in TADA2B binding after TADA2B loss (degradation dTAG v1 TADA2B vs. DMSO at 6 hours)  in KELLY, NGP and NB1 neuroblastoma cells, one replicate per condition. Investigate alterations in MYCN, H3K27ac and H3K9ac binding after TADA2B loss (degradation dTAG v1 TADA2B vs. DMSO at 6 hours)  in KELLY neuroblastoma cells, one replicate per condition. Investigate alterations in MYCN, H3K27ac and H3K9ac binding after KAT2A/KAT2B targeting (PROTAC GSK-699-1 vs. DMSO at 6 hours)  in KELLY neuroblastoma cells, two replicates per condition.

first: Kimberly

last: Stegmaier


title: The expression profiles of human lymphoma H9 cells after exposure to doxorubicin

status: Public on Apr 18 2024

city: Shanghai

first: ZHU

middle: JIA

last: YAN

address: 197 Ruijin Er Rd

institute: Department of Hematology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine

summary: doxorubicin is commonly used for hematological malignancies. Since some of PTCL patients resistance to dox and die due to refractory disease or relapse, enhanced knowledge about drug response mechanisms is required to improve treatment outcome. we found an increased expression of HDAC3 in T lymphoma H9 cells following dox exprosure, we compared the gene expression profiles of H9 cells pre/post treated with doxorubicin to explore the potential mechanism of the high expression of HDAC3

overall_design: To analyze the differential genes and pathways in H9 cells exposed to doxorubicin, we treated cells with doxorubicin for 6 hour,we then performed gene expression profiling analysis use data obtained from RNA-seq of doxorubicin-treated H9 cells and untreated H9 cells

first: Ke

last: Li

first: Jiong

last: Hu

first: Jiayan

last: Zhu

first: Feng

last: Wang


title: GPR124 regulates murine CNS angiogenesis and blood-brain barrier formation by an intracellular domain-independent mechanism

city: Stanford

first: Kanako

last: Yuki

address: 265 CAMPUS DRIVE

institute: Stanford University

summary: The GPR124/RECK/WNT7 pathway essentially regulates central nervous system angiogenesis and blood-brain barrier (BBB) function. GPR124, a brain endothelial adhesion 7-pass transmembrane protein, associates with membrane RECK, which binds and stabilizes newly synthesized WNT7 for subsequent transfer to Frizzled (FZD) and canonical b-catenin signaling.  GPR124 function remains enigmatic; while its extracellular domain (ECD) is required, the poorly conserved intracellular domain (ICD) appears to be variably required in mammals versus zebrafish, potentially mediated by bridging of the GPR124 and FZD ICDs by intracellular adaptor proteins.  GPR124 ICD deletion mutants impair zebrafish angiogenesis, but paradoxically still mediate WNT7 signaling upon mammalian cell transfection.   We thus further investigated the GPR124 C-terminal ICD by deletion in mice (Gpr124ΔC). Notably, Gpr124ΔC/ΔC mice could be born and did not recapitulate Gpr124-/- embryonic lethal forebrain hemorrhage.  GPR124ΔC protein was inefficiently expressed, resulting in mild, hypomorphic, non-hemorrhagic defects in CNS angiogenesis and BBB function, sparing the cortex and only confined to ganglionic eminences.  Impaired surface expression of GPR124ΔC directly correlated with reduced endothelial WNT signaling, arguing against an intrinsic signaling deficiency. Further, GPR124ΔC and recombinant GPR124 ECD both rescued WNT7 signaling following brain endothelial Gpr124 knockdown. Thus, in mice, the GPR124 essential regulation of WNT7-dependent CNS forebrain angiogenesis and BBB function is exerted by ICD-independent functionality, extending the range of signaling mechanisms used by adhesion 7-pass transmembrane receptors.

overall_design: Comparative gene expression profiling of RNA-seq data for embryonic brain endothelial cells from WT, Gpr124 C-terminal ICD deletion (ΔC/ΔC) and Gpr124 knockout (-/-) mice.

first: Alan

middle: T

last: Tang

first: Mark

last: Kahn

first: Calvin

last: Kuo


title: Desiccation induces varied responses within a soil bacterial genus

city: Irvine

first: Nicholas

middle: C

last: Scales

address: 321 Steinhaus Hall

department: Ecology & Evolutionary Biology

institute: UC Irvine

summary: Nine Curtobacterium strains (three from three clades) were subjected to a lab desiccation experiment with no access to moisture or nutrients to compare between clades. RNA was extracted at days 0, 1, and 32 and sequenced

overall_design: We performed RNAseq on nine bacterial isolates. RNA was extracted and sequenced in triplicate at 3 timepoints

first: Khanh

last: Huynh

first: Claudia

last: Weihe

first: Jennifer

middle: B

last: Martiny


title: Developmental Programming: adipose depot-specific regulation of non-coding RNAs and their relation to coding RNA expression in prenatal testosterone and prenatal bisphenol-A -treated female sheep

city: Ann Arbor

first: Kelly

last: Bakulski

state: MI

address: 1415 Washington Heights

department: Department of Epidemiology

institute: University of Michigan

type: Non-coding RNA profiling by high throughput sequencing

summary: Inappropriate developmental exposure to steroids is linked to metabolic disorders. Prenatal testosterone excess or bisphenol A (BPA, an environmental estrogen mimic) leads to insulin resistance and adipocyte disruptions in female sheep. Adipocytes are key regulators of insulin sensitivity and tissue-specific differences in insulin sensitivity, coupled with adipose depot-specific changes in key mRNAs, were previously observed. We hypothesized that depot-specific changes in the non-coding RNA (ncRNA) regulators of gene expression would prevail to account for the direction of changes seen in mRNAs. Noncoding RNA (lncRNA, miRNA, snoRNA, snRNA) from various adipose depots of prenatal testosterone and BPA-treated animals were sequenced. Adipose depot-specific changes in the ncRNA that are consistent with the depot-specific mRNA expression in terms of directionality of changes and functional implications in insulin resistance, adipocyte differentiation and cardiac hypertrophy were found. Importantly, the adipose depot-specific ncRNA changes were model-specific that were mutually exclusive suggestive of different regulatory entry points in this regulation.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for adipose tissue (subcutaneous, visceral, perirenal , epicardial) samples from control and treated sheep

first: John

last: Dou

first: Soundara

last: Viveka Thangaraj

first: Muraly

last: Puttabyatappa

first: Venkateswaran

last: Ramamoorthi Elangovan

first: Vasantha

last: Padmanabhan


title: Transcriptomic profiling of highly- and lowly- metastasizing pancreatic ductal carcinoma cells

city: New York

first: Norihiro

last: Yamaguchi


title: The SAGA complex maintains the oncogenic gene expression program in MYCN-amplified neuroblastoma

first: Gabriela

last: Alexe


title: KLF5 regulates actin remodeling to enhance the metastasis of nasopharyngeal carcinoma

city: Guangzhou

first: zhenyu

last: yang

address: 651 Dongfeng Road East

institute: Sun Yat-sen University Cancer Center

first: Zhenyu

last: Yang


title: The SAGA complex maintains the oncogenic gene expression program in MYCN-amplified neuroblastoma [ATAC-Seq]

summary: Pediatric cancers are frequently driven by fusion or amplification events that result in aberrant transcription factor activity.  As transcription factors themselves remain challenging to target, an emerging therapeutic approach for these cancers is to target epigenetic complexes that help maintain oncogenic transcriptional programs. It is therefore critical to identify the complete set of epigenetic modulators maintaining the oncogenic epigenetic landscape of pediatric cancers. Here, we used functional genomic screens to identify epigenetic complexes critical for viability in cell line models of MYCN-amplified neuroblastoma, a disease of dysregulated development driven by an aberrant oncogenic transcriptional program. We identified multiple genes within the transcriptional coactivator Spt-Ada-Gcn5-acetyltransferase (SAGA) complex as selective dependencies in MYCN-amplified neuroblastoma. Integrating ChIP-seq, ATAC-seq, and RNA-seq with targeted protein-degradation and gene editing tools, we characterized the DNA recruitment sites of the SAGA complex in neuroblastoma, and the consequences of SAGA complex lysine acetyltransferase (KAT) activity loss on histone acetylation and gene expression. We demonstrate that loss of SAGA KAT activity suppresses MYC and MYCN gene expression programs and impairs cell cycle progression. Further, we showed that the SAGA complex is pharmacologically targetable with a KAT2A/KAT2B proteolysis targeting chimera molecule that demonstrated significant activity in vitro and in vivo. Our findings expand our understanding of the histone-modifying complexes that maintain the oncogenic transcriptional state in this disease and suggest therapeutic potential for inhibitors of SAGA KAT activity in MYCN-amplified neuroblastoma.

overall_design: Investigate chromatin opening in the KELLY neuroblastoma cell line. Three replicates per condition.

first: Kimberly

last: Stegmaier


title: Trem2 Agonist Reprograms Foamy Macrophages to Promote Atherosclerotic Plaque Stability

city: Minneapolis

first: Jesse

last: Williams

state: MN

address: 2101 6th St. SE

department: Dept. Integrative Biology & Physiology

institute: University of Minnesota

summary: To elucidate the impact of Trem2 agonist on aortic gene expression during atherosclerosis.

overall_design: Ldlr-/- mice were fed high fat diet (HFD) for 8 weeks, then began once weekly treatment with Trem2 agonist (AL002a, Antibody 1) or isotype control (Antibody 2) by i.p. injection at 40 mg/Kg per week while being maintained on HFD for an additional 8 weeks. Whole aorta was dissociated by enzymatic digestion, then captured for single cell RNA-sequencing using 10X Chromium 3' kit.

first: Michael

last: Patterson

first: Yingzheng

last: Xu

first: Hannah

last: Hillman


title: Quantifying DNA replication speeds in single cells by scEdU-seq

city: Utrecht

first: Jeroen

last: van den Berg

state: Utrecht

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

summary: In a human cell, thousands of replication forks simultaneously coordinate duplication of the entire genome. The rate at which this process occurs might depend on the epigenetic state of the genome and vary between, or even within, cell types. To accurately measure DNA replication speeds, we developed single-cell 5-ethynyl-2′-deoxyuridine sequencing to detect nascent replicated DNA. We observed that the DNA replication speed is not constant but increases during S phase of the cell cycle. Using genetic and pharmacological perturbations we were able to alter this acceleration of replication and conclude that DNA damage inflicted by the process of transcription limits the speed of replication during early S phase. In late S phase, during which less-transcribed regions replicate, replication accelerates and approaches its maximum speed.

overall_design: Single cell analysis of Replication fork speeds over different treatment and knockouts.

first: Vincent

last: van Batenburg

first: Alexander

last: van Oudenaarden


title: Expression data from AGS cells with Helicobacter pylori infection

city: Chongqing

first: yuan

last: zhuang

address: Gaotanyan Street

institute: Third Military Medical University

summary:
Helicobacter pylori (H. pylori) is a human pathogen that infects almost half of the world’s population. Infection with H. pylori is frequently associated with chronic gastritis and can even lead to gastric and duodenal ulcers and gastric cancer. Although the persistent colonization of H. pylori and the development of H. pylori-associated gastritis remain poorly understood, it is believed that, in gastric mucosa, the modulated gastric epithelial cells (GECs) by H. pylori are key contributors.
We used microarrays to detail the global programme of gene expression in Helicobacter pylori infected-gastric epithelial cell line AGS cells and identified up-regulated genes induced by Helicobacter pylori infection.

overall_design: Gene expressions in WT H. pylori-infected and uninfected AGS cells (MOI=100, 6 h) were compared by microarray (n=3).

first: Geng-Yu

last: Yue

first: Xiao-Lin

first: Wen-Qing

last: Tian

first: Peng

last: Zhu

first: Yu-Gang

last: Liu

first: Jiang-Bo

last: Wu

first: Wan-Yan

last: Chen

first: Pan

last: Wang

first: Jing-Yu

first: Si-Xu

first: Mu-Han

last: Lü

first: Sheng-Qian

first: Tao

first: Ping

last: Cheng

first: Fang-Yuan

last: Mao

first: Yong-Sheng

last: Teng

first: Shou-Lu

last: Luo

first: Jin-Yu

last: Zhang

first: Liu-Sheng

last: Peng

first: Quan-Ming

last: Zou

first: Ya-Ling

last: Liao

first: Shi-Ming

first: Yong-Liang

last: Zhao

first: Hong

last: Zhou

first: Weisan

last: You

first: Rui

last: Xie

first: Yuan

last: Zhuang


title: KLF5 regulates actin remodeling to enhance the metastasis of nasopharyngeal carcinoma [ChIP-seq]

first: zhenyu

last: yang

summary: Transcription factors (TFs) engage in various cellular essential processes including differentiation, growth and migration. However, the master TF involved in distant metastasis of nasopharyngeal carcinoma (NPC) remains largely unclear. Here we show that KLF5 regulates actin remodeling to enhance NPC metastasis. We analyzed the msVIPER algorithm-generated transcriptional regulatory networks and identified KLF5 as a master TF of metastatic NPC linked to poor clinical outcomes. KLF5 regulates actin remodeling and lamellipodia formation to promote the metastasis of NPC cells in vitro and in vivo. Mechanistically, KLF5 preferentially occupies distal enhancer regions of ACTN4 to activate its transcription, whereby decoding the informative DNA sequences. ACTN4, extensively localized within actin cytoskeleton, facilitates dense and branched actin networks and lamellipodia formation at the cell leading edge, empowering cells to migrate faster. Collectively, our findings reveal that KLF5 controls robust transcription program of ACTN4 to modulate actin remodeling and augment cell motility which enhances NPC metastasis, and provide new potential biomarkers and therapeutic interventions for NPC.

overall_design: chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for KLF5 in SUNE-1, C666-1 and HK1 cells

first: Zhenyu

last: Yang

first: Yanfu

first: Denghui

last: Wei

first: Guanqun


title: Next Generation Sequencing Facilitates Quantitative Analysis of EL4+Ctrl and EL4+RGFP966  cells' Transcriptomes in T cells  lymphoma

first: ZHU

last: YAN

summary: We here reported that HDAC3 inhibition induces the infiltration of NK cells in lymphoma and enhances their cytotoxicity by promoting the secretion of CXCL12 from lymphoma cells. RNA-seq analysis of EL4 cells treated with or without RGFP966 showed that chemokine signaling was significantly enriched in the HDAC3 inhibitor-treated group. And the expression of CXCL12 in mRNA and protein level were increased. ATF3 overexpression decreased the mRNA level of CXCL12 in lymphoma cells and reduced CXCL12 transcription can be reversed by HDAC3 inhibition in H9 cells. To sum up, targeting HDAC3 promoted the secretion of CXCL12 by inhibiting ATF3’s transcriptional activity.

overall_design:
to analysis the differiational genes and pathways in EL4+Ctrl and EL4+RGFP966 lymphoma cells,we treated cells with vehicle or HDAC3 inhibitors (RGFP966)
we then performed gene expression profiling analysis use data obtained from RNA-seq of EL4 cells treated with vehicle or RGFP966

first: Ke

last: Li

first: Jiong

last: Hu

first: Jiayan

last: Zhu

first: Feng

last: Wang


title: KLF5 regulates actin remodeling to enhance the metastasis of nasopharyngeal carcinoma [RNA-seq]

overall_design: To investigate whether KLF5 augments cell motility by tuning actin remodeling and lamellipodia formation in NPC, we generated KLF5-KD HONE-1 cell line which KLF5 has been knocked down by siRNA. Gene expression profiling analysis was performed using data from RNA-seq of KLF5-KD and control HONE-1 cells.


title: Condensin I folds the C. elegans genome [RNA-seq]

city: Bern

first: Peter

last: Meister

state: Schweiz

address: Baltzerstrasse 4

department: Institute of Cell Biology

country: Switzerland

institute: University of Bern

summary: Structural Maintenance of chromosomes (SMC) complexes, cohesin and condensins, have been named after their roles during meiosis and mitosis. Recent data in mammalian cells and Drosophila have described the additional role of cohesin for genome folding into loops and domains during interphase. However, determinants of genome folding in holocentric species remain unclear. Using high resolution chromosome conformation capture, we show that overlapping large-scale nuclear localization and small-scale epigenomic states compartmentalize the C. elegans genome. By systematically and acutely inactivating each SMC complex, we observe that in contrast to other studied systems, cohesin creates small loops, while condensin I has a major role in genome folding: its inactivation causes genome-wide decompaction, chromosome mixing, loss of loops and TAD structures and reinforcement of fine-scale epigenomic compartments. Counter-intuitively, removal of condensin I and its X-specific variant condensin IDC from the X chromosomes led to the formation of a loop compartment coinciding with a subset of previously characterized loading sites for condensin IDC and bound by the X-targeting complex SDC. While transcriptional changes were limited for all autosomes upon cohesin and condensin II inactivation, removal of condensin I/IDC from the X chromosome led to transcriptional up-regulation of X-linked genes demonstrating that a sustained role for condensin IDC in gene regulation. Finally, while condensin I inactivation leads to reduced lifespan, we show that this reduction is due to X-specific gene upregulation rather than global genome decompaction.

overall_design: In this study, a total of 40 samples were analysed that comprise of 9 different strains in which different SMC complexes were inactivated and their controls. Each strain/condition has 3-4 biological replicates.

first: Moushumi

last: Das

first: Jennifer

last: Semple

first: Janik

last: Scotton

first: Ahrmad

last: Annan

first: Julie

last: Campos


title: Single-Cell RNA-sequencing of lung mesenchymal cells at multiple time points after bleomycin injury

city: San Francisco

first: Tatsuya

last: Tsukui

address: 555 Mission Bay Blvd South, 282

department: Medicine

institute: UCSF

summary: Mesenchymal cells (CD31-, CD45-, EpCAM-, Ter119-) were collected for 10x Genomics Chromium Single Cell v3.1 scRNA-seq from the lungs of Scube2-CreER/Rosa26-tdTomato double homozygous mice on day 0 , 7, 14, 21 after bleomycin treatment.

overall_design: Scube2-CreER, Rosa26-tdTomato double homozygous mice were treated with tamoxifen for two weeks. Bleomycin treatment was performed 2 weeks after the last tamoxifen treatment. Three biological replicates from day 0 (non-bleomycin-treated), 7, 14, and 21 samples were collected on the same day and tamoxifen/bleomycin treatment was scheduled accordingly to the collection day.  After harvesting and dissociating left lungs, mesenchymal cells were enriched by magnetic negative selection with anti-CD31, CD45, EpCAM and Ter119-biotin antibodies (1:200) and Dynabeads MyOne Streptavidin T1 (40 ul / sample, Invitrogen). After magnetic negative selection, cells were stained with Streptavidin-APC/Cy7 (1:200) and DAPI (0.1 ug/ml). Approximately 2 x 10^5 lineage-APC/Cy7-negative cells were sorted for each sample. The sorted cells were counted and labeled with oligonucleotide tags for multiplexing using 10x Genomics 3’ CellPlex Kit.  Tag assignment was as follows; day 0 (301, 302, 303), day 7 (304, 305, 306), day 14 (307, 308, 309), and day 21 (310, 311, 312). All 12 samples were pooled and 30,000 cells / lane were loaded onto 4 lanes of Chromium Next GEM Chip (10x Genomics). Chromium Single Cell 3’ v3.1 (10x Genomics) reagents were used for library preparation according to manufacturer’s protocol. The libraries were sequenced on Illumina NovaSeq 6000 S4 flow cell.

first: Dean

last: Sheppard


title: Fibroblasts as an in vitro model of circadian genetic and genomic studies: A temporal analysis (RNA-Seq)

status: Public on Apr 17 2024

city: Los Angeles

first: Marcelo

last: Francia

address: 1771 Beloit Avenue, Unit 204

department: Neuroscience

institute: University of California, Los Angeles

summary: Bipolar disorder (BD) is a heritable disorder characterized by shifts in mood that manifest in manic or depressive episodes. Clinical studies have identified abnormalities of the circadian system in BD patients as a hallmark of underlying pathophysiology. Fibroblasts are a well-established in vitro model for measuring circadian patterns. We set out to examine the underlying genetic architecture of circadian rhythm in fibroblasts, with the goal to assess its contribution to the polygenic nature of BD disease risk. We collected, from primary cell lines of 6 healthy individuals, temporal genomic features over a 48 hour period from transcriptomic data (RNA-seq) and open chromatin data (ATAC-seq). The RNA-seq data showed that only a limited number of genes, primarily the known core clock genes such as ARNTL, CRY1, PER3, NR1D2 and TEF display circadian patterns of expression consistently across cell cultures. The ATAC-seq data identified that distinct transcription factor families, like those with the basic helix-loop-helix motif, were associated with regions that were increasing in accessibility over time. Whereas known glucocorticoid receptor target motifs were identified in those regions that were decreasing in accessibility. Further evaluation of these regions using stratified linkage disequilibrium score regression (sLDSC) analysis failed to identify a significant presence of them in the known genetic architecture of BD, and other psychiatric disorders or neurobehavioral traits in which the circadian rhythm is affected. In this study, we characterize the biological pathways that are activated in this in vitro circadian model, evaluating the relevance of these processes in the context of the genetic architecture of BD and other disorders, highlighting its limitations and future applications for circadian genomic studies

overall_design:
To identify broad circadian genetic features on a circadian in vitro fibroblast model, we stablished skin fibroblast primary cell cultures from 6 healthy, control individuals
We then performed gene expression profiling analysis using data obtained from RNA-seq of the 6 different cell lines at 13 time points.
We analyzed temporal changes in gene expression for these fibroblast cells.

first: Merel

last: Bot

first: Toni

last: Boltz

first: Juan

last: De la Hoz

first: Marco

last: Boks

first: Rene

last: Kahn

first: Roel

last: Ophoff


title: The SAGA complex maintains the oncogenic gene expression program in MYCN-amplified neuroblastoma [RNA-Seq]

first: Gabriela

last: Alexe

overall_design: Investigate alterations in gene expression after TADA2B loss (degradation dTAG v1 TADA2B vs. DMSO at 6 hours, 24 hours, and 72 hours; CRISPR TADA2B knock-out vs. control at 7 days and 12 days) and after KAT2A/KAT2B loss (GSK-699-1 vs. DMSO at 6 hours, 24 hours, and 72 hours) in KELLY neuroblastoma cells. Three replicates per condition.

first: Kimberly

last: Stegmaier


title: Condensin I folds the C. elegans genome [Hi-C]

first: Peter

last: Meister

overall_design:
To optimise the protocol, wild type strains were tested first. Once the protocol was established, Hi-C was performed on 6 different strains including the control. All the strains used in this study have two biological replicates.
HiC on entire animals, following cleavage of cohesin's kleisins COH-1 and SCC-1. Two biological repeats, sequenced on a iSeq and Novaseq

first: Anja

last: Haemmerli

first: Todor

last: Gitchev

first: Julien

last: Mozziconacci


title: Condensin I folds the C. elegans genome [Ribo-Zero-seq]

overall_design: There are 4 samples analysed in this study which comprises of 4 different strains, including the control.

first: Moushumi

last: Das

first: Jennifer

last: Semple


title: Fibroblasts as an in vitro model of circadian genetic and genomic studies: A temporal analysis (ATAC-Seq)

overall_design:
To identify broad circadian genetic features on a circadian in vitro fibroblast model, we stablished skin fibroblast primary cell cultures from 6 healthy, control individuals
We then performed gene expression profiling analysis using data obtained from ATAC-seq of the 6 different cell lines at 13 time points.
We analyzed temporal changes in gene expression for these fibroblast cells.


title: An immunohistochemical atlas of necroptotic pathway expression

first: Isabella

last: Kong

state: New York

address: 1300 York Ave

institute: Weill Cornell Medicine

summary: Necroptosis is a lytic form of regulated cell death reported to contribute to inflammatory diseases of the gut, skin and lung, as well as ischemic-reperfusion injuries of the kidney, heart and brain. However, precise identification of the cells and tissues that undergo necroptotic cell death in vivo has proven challenging in the absence of robust protocols for immunohistochemical detection. Here, we provide automated immunohistochemistry protocols to detect core necroptosis regulators – Caspase-8, RIPK1, RIPK3 and MLKL – in formalin-fixed mouse and human tissues. We observed surprising heterogeneity in protein expression within tissues, whereby short-lived immune barrier cells were replete with necroptotic effectors, whereas long-lived cells lacked RIPK3 or MLKL expression. Local changes in the expression of necroptotic effectors occurred in response to insults such as inflammation, dysbiosis or immune challenge, consistent with necroptosis being dysregulated in disease contexts. These methods will facilitate the precise localisation and evaluation of necroptotic signaling in vivo.

overall_design: Mice were given free access to drinking water or driking water supplemented with antibiotics. 6 days later their spleen and ileum were harvested for RNAseq analyses.

first: Andre

last: Samson

first: James

last: Murphy

middle: Y


title: Germinal Center Cytokines Driven Epigenetic Control of Epstein-Barr Virus Latency Gene Expression

city: Boston

first: Yifei

last: Liao

state: Massachusetts

address: 181 Longwood Ave, 8th Floor

institute: Brigham and Women's hospital

summary: Epstein-Barr virus (EBV) persistently infects 95% of adults worldwide and is associated with multiple human lymphomas that express characteristic EBV latency programs used by the virus to navigate the B-cell compartment. Upon primary infection, the EBV latency III program, comprised of six Epstein-Barr Nuclear Antigens (EBNA) and two Latent Membrane Protein (LMP) antigens, drives infected B-cells into germinal center (GC). By incompletely understood mechanisms, GC microenvironmental cues trigger the EBV genome to switch to the latency II program, comprised of EBNA1, LMP1 and LMP2A and observed in GC-derived Hodgkin lymphoma. To gain insights into pathways and epigenetic mechanisms that control EBV latency reprogramming as EBV-infected B-cells encounter microenvironmental cues, we characterized GC cytokine effects on EBV latency protein expression and on the EBV epigenome. We confirmed and extended prior studies highlighting GC cytokine effects in support of the latency II transition. The T-follicular helper cytokine interleukin 21 (IL-21), which is a major regulator of GC responses, and to a lesser extent IL-4 and IL-10, hyper-induced LMP1 expression, while repressing EBNA expression. However, follicular dendritic cell cytokines including IL-15 and IL-27 downmodulate EBNA but not LMP1 expression. CRISPR editing highlighted that STAT3 and STAT5 were necessary for cytokine mediated EBNA silencing via epigenetic effects at the EBV genomic C promoter. By contrast, STAT3 was instead necessary for LMP1 promoter epigenetic remodeling, including gain of activating histone chromatin marks and loss of repressive polycomb repressive complex silencing marks. Thus, EBV has evolved to coopt STAT signaling to oppositely regulate the epigenetic status of key viral genomic promoters in response to GC cytokine cues.

overall_design: GM12878 or Mutu I cells were treated with cytokines or mock treated. Cells were collected for RNA extraction, library preparation and sequencing.

first: Jinjie

last: Yan

first: Nina

last: Beri

first: Lisa

last: Giulino-Roth

first: Ethel

last: Cesarman

first: Benjamin

last: Gewurz


title: Jagged2 targeting in lung cancer activates anti-tumor immunity via Notch-induced functional reprogramming of tumor-associated macrophages

city: Tampa

first: Paulo

last: Rodriguez

state: Florida

address: 3011 W. Holly Drive, MRC, 2067

institute: H. Lee Moffitt Cancer Center

summary: Signaling through Notch receptors intrinsically regulates tumor cell development and growth. However, whether Notch ligands on cancer cells impact anti-tumor immunity remains unclear. We demonstrate that deletion of Notch ligand Jagged2, but not Jagged1, in lung cancer cells attenuates tumor growth and activates anti-tumor T cell responses. Jagged2 deletion in cancer cells incites intra-tumor accumulation of macrophages with elevated capacity to uptake, process, and present antigens. Also, transfer of Jagged2KO tumors-related macrophages into mice provokes lymphocyte-mediated anti-tumor actions, while macrophage ablation in mice restores Jagged2KO tumor growth. Jagged2 deletion on lung tumors induces Notch ligands DLL1/4, which signal through Notch1-2 on macrophages to stimulate IRF4-driven anti-tumor responses. Intercepting DLL1/4 in tumors or IRF4 in myeloid cells blunts macrophage expansion and reinstates Jagged2KO tumor growth. Therapeutically, anti-Jagged2 treatments restrict tumor growth and augment immunotherapy effectiveness. Findings elucidate how cancer cell Jagged2 promotes immune-evasion and identify Jagged2-targeting immunotherapy to activate anti-tumor immunity.

overall_design: Lewis Lung Carcinoma (LLC) GFP cells with either Scramble or sgRNA for JAG2 (JAG2KO) were injected into the flanks of mice. At endpoint, mice were euthanized and tumors were collected, dissociated with Liberase, and stained with CD45 and DAPI. 400,000 GFP+/CD45-/DAPI-cells were flow sorted  directly into RLT Lysis Buffer. Using the QIAGEN RNeasy kit, RNA was extracted and submitted for RNAseq.

first: Darwin

last: Chang

first: Xiaoqing

last: Yu

first: Timothy

last: Shaw


title: Effects of Essential 8 (E8) media additives polyethylene glycol (PEG) and Heparin sodium salt (HS) on the pluripotency and oncogenes

status: Public on Apr 16 2024

city: Beachwood

first: Trailhead

last: Biosystems

state: Ohio

address: 23215 Commerce Park Rd

institute: Trailhead Biosystems Inc

summary:
Manuscript Name: "Addressing Bioreactor hiPSC Aggregate Stability, Maintenance and Scaleup Challenges Using a Design of Experiment Approach"
Evaluation of core pluripotent genes showed that expression levels were similar between samples with a clear indication of a primed phenotype. In addition, we evaluated several well-known oncogenes notable TP53, MYC, NANOGP8, EEF1A2 and KLF4 were expressed with similar transcript levels between samples, though KLF4 had low overall expression. It was observed that a few genes indicative of forward differentiation were expressed with TSR genes TDGF1, LEFTY1 and IL17RC and the trophectodermal genes KRT8 and TEAD4 showing comparable expression levels. Expression of the primary primitive streak gene NODAL was observed at low transcript levels in both samples. Examining the top differentially expressed genes we noted that there were several genes involved in ectodermal differentiation and some key signaling pathway components that were significantly downregulated in response to the presence of PEG and HS. Down-regulated ectodermal genes included SOX1, OLIG3, LHX5 and OTX2 as well as some less known ones. The pathways most downregulated were the TGFβ family as suggested by BMP2 and BMP4 down regulation, though the previously mentioned levels of TDGF1, LEFTY1 and NODAL remained consistent to cultures lacking additives. Wnt family signaling components down regulated were Wnt4, FRZB, FZD5 and FRZ8. Also a decreased in retinoic acid signaling components were noted as indicated by decreased CYP26A1, CYP26C1, DHRS3 and CRABP2 transcript levels.

overall_design: To investigate the function of polyethylene glycol (PEG) and Heparin sodium salt (HS) in providing aggregate stability and growth while maintaining an equal of better pluripotency maintenance in comparison to the control medium (E8) on induced pluripotent stem cells (iPSCs).

first: Haneen

last: Yehya

first: Sofija

last: Raudins

first: Roshan

last: Padmanabhan

first: Jan

last: Jensen

first: Michael

last: Bukys


title: Analysis of intestinal epithelial cell responses to Cryptosporidium highlights the temporal effects of IFN-γ on parasite restriction

city: Philadelphia

first: Ryan

last: Pardy

state: PA

address: 380 South University Ave

department: Pathobiology

institute: University of Pennsylvania

summary: The production of IFN-γ is crucial for control of multiple enteric infections, but its impact on intestinal epithelial cells (IEC) is not well understood. Cryptosporidium parasites exclusively infect epithelial cells and the ability of interferons to activate the transcription factor STAT1 in IEC is required for parasite clearance. Here, the use of single cell RNA sequencing to profile IEC during infection revealed an increased proportion of mid-villus enterocytes during infection and induction of IFN-γ-dependent gene signatures that was comparable between uninfected and infected cells. These analyses were complemented by in vivo studies, which demonstrated that IEC expression of the IFN-γ receptor was required for parasite control. Unexpectedly, treatment of Ifng-/- mice with IFN-γ showed the IEC response to this cytokine correlates with a delayed reduction in parasite burden but did not affect parasite development. These data sets provide insight into the impact of IFN-γ on IEC and suggest a model in which IFN-γ signalling to uninfected enterocytes is important for control of Cryptosporidium.

overall_design: Single-cell RNA sequencing (scRNA-seq) data were generated in this study. Intestinal epithelial cells and intraepithelial lymphocytes were isolated form the ileum of the small intestine for two mice per group, which were pooled following removal of dead cells and prior to processing for scRNA-seq. For the C57BL/6 dataset, mice were uninfected, or infected with 50,000 oocysts of mouse-adapted C. parvum (maCp) for 4 or 10 days. For the IFNg KO dataset, mice were infected with 50,000 oocysts of maCp and on day 5 post-infection, groups of infected and uninfected mice were treated with either PBS or IFNg. 12 hours post-treatment, mice were euthanized for processing and scRNA-seq.

middle: D

first: Katelyn

last: Walzer

first: Bethan

last: Wallbank

first: Jessica

last: Byerly

first: Keenan

last: O'Dea

first: Ian

middle: S

last: Cohn

first: Breanne

last: Haskins

first: Justin

last: Roncaioli

first: Eleanor

middle: J

last: Smith

first: Gracyn

last: Buenconsejo

first: Boris

last: Striepen

first: Christopher

last: Hunter


title: Jagged2 targeting in lung cancer activates anti-tumor immunity via Notch-induced functional reprogramming of tumor-associated macrophages [scRNA-seq]

first: Paulo

last: Rodriguez

overall_design: Lewis Lung Carcinoma (LLC) cells with either Scramble or sgRNA for JAG2 (JAG2KO) were injected into the flanks of mice. At endpoint, mice were euthanized and tumors were collected, dissociated with Liberase, and stained with CD45 and PI. 600,000 CD45+/PI- cells were sorted and resuspended into 300uL 0.04% BSA PBS. 10,000 cells were encapsulated and processed for 10x scRNA sequencing. Files contained are filtered to remove barcodes with no cells encapsulated.

first: Darwin

last: Chang

first: Xiaoqing

last: Yu

first: Timothy

last: Shaw


title: IL-12 drives the diferentiation of human T follicular regulatory cells [RNA-seq]

first: Emily

last: Shields

state: Pennsylvania

address: 3400 Civic Center Blvd

summary: T follicular regulatory (Tfr) cells can counteract the B cell-helper activity of T follicular helper (Tfh) cells and hinder the production of antibodies against self-antigens or allergens. A mechanistic understanding of the cues initiating the differentiation of T regulatory (Treg) cells into Tfr cells, which is instrumental for the therapeutic manipulation of diseases associated with a Tfr cell imbalance, is still missing. Despite their opposed roles, Tfr and Tfh cell differentiation appears to be controlled by partially overlapping signals, including TCR stimulation and costimulatory molecules. However, it is still unknown if cytokines that have been shown to control the biology of human Tfh cells, including IL-12 and activin A, can influence the differentiation of Tfr cells. To address this question, we evaluated the impact of these two cytokines on the in vitro differentiation of Tfr cells. Herein, we report a role for IL-12 and down stream Stat4 chromatin binding in driving, on activated Treg cells, the induction of molecules that belong to the Tfr cell program, including CXCR5, PD-1, BCL6 and ICOS meanwhile preserving Tfr regulatory function.

overall_design: RNA-seq profiling in vivo (naïve Tregs from cord blood and tonsil-derived Tfrs) and in vitro (activated Tregs from cord blood +/- IL12) samples

first: Roberto

last: Bonasio

first: Michela

last: Locci

first: Segovia

last: Atencio-Garcia

first: Diana

last: Castano


title: IL-12 drives the diferentiation of human T follicular regulatory cells

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

overall_design: Refer to individual Series


title: Single nuclei RNA sequencing of PVN tissue across day and night

city: Houston

first: Yulin

last: Dai

state: TX

address: 7000 fannin, suite 600

department: School of Biomedical Informatics

institute: University of Texas health science center at Houston

summary: To examine the transcriptional landscape of the paraventricular nucleus of the hypothalmus across 24-hrs day and night we carried out snRANseq on PVN tissue harvested at two antiphase timepoints, ZT8 and ZT20

overall_design: Single nuclei isolation for the single nuclei RNA-seq analysis was performed on five pooled PVN tissues dissected from male C57Bl6 mice aged 10-12 weeks at two time points, ZT8 and ZT20.

first: Rachel

last: Van Drunen

first: Kristin

last: Eckel-Mahan


title: The role of MEIOC at the transition from mitosis to meiosis during mammalian spermatogenesis [scRNA]

city: Cincinnati

first: Maria

middle: M.

last: Mikedis

state: OH

address: 240 Albert Sabin Way

institute: Cincinnati Children's Hospital Medical Center

summary: We investigated how MEIOC affects testicular germ cells at the transition from mitosis to meiosis. We used single cell RNA sequencing (scRNA-seq) to identify and analyze the germ cells present in the P15 testis.

overall_design: Wild-type and Meioc KO testes from P15 pups analyzed using scRNAseq.

middle: M


title: Effects of deletioin of cholesterol efflux genes Abca1 and Abcg1 on other gene expressions in macrophages

city: St. Louis

first: Ryo

last: Terao

state: MO

address: 517 S. Euclid Ave

department: Ophthalmology & Visual Sciences

institute: Washington University School of Medicine in St. Louis

summary: ATP binding cassette subfamily member 1 (ABCA1) and G1 (ABCG1) are cholesterol efflux transporter to prevent excess intracellular cholesterol accumulation. We here report the deletion of Abca1 and Abcg1 results in the significant increased expression of Cd38, a multi-faceted ectoenzyme with NADase activity.

overall_design: To investigate the effect of the deletion of Abca1 and Abcg1 on macrophages, bone marrow (BM) cells isoleted from the sex-matched littermate of Abca1/Abcg1 flox/flox and Abca1/Abcg1 flox/flox LysM-Cre mice were collected. Bone marrow derived macrophages (BMDM) were obtained by differentiating from BM cells.

first: Rajendra

last: Apte

first: Mitsukuni

last: Yoshida


title: G6PD and ACSL3 are synthetic lethal partners of NF2 in Schwann cells

status: Public on Apr 24 2024

city: Heidelberg

first: Aurelio

middle: A

last: Teleman

address: Im Neuenheimer Feld 580

institute: German Cancer Research Center (DKFZ)

summary: Neurofibromatosis Type II is a genetic condition caused by loss of the NF2 gene, resulting in activation of the YAP/TAZ pathway and recurrent growth of benign tumors from Schwann cells, the glia of the peripheral nervous system. Unfortunately, no pharmacological therapy is currently available for NFII. Here, we undertake a genome-wide CRISPR/cas9 screen to search for synthetic-lethal genes that, when inhibited, cause death of NF2 mutant cells but not NF2 wildtype cells. We thereby identify ACSL3 and G6PD as two synthetic-lethal partners for NF2. We find that NF2 mutant Schwann cells are vulnerable to G6PD inhibition because they have low levels of ME1. G6PD and ME1 redundantly generate cytosolic NADPH needed by cells to fight oxidative stress. Lack of either one of the two is compatible with cell viability, but down-regulation of both leads to Schwann cell death. Since genetic deficiency for G6PD is tolerated in the human population, this raises the possibility that G6PD could be a pharmacological target for NFII.

overall_design: A pooled sgRNA library as transduced into NF2-WT and NF2-KO Schwann cells, and sgRNA representation was sequenced at the start of the experiment, and after 7 passages, to assay the effect of genes on cell viability and proliferation.

first: Kyrkou

last: Athena

first: Teleman

last: Aurelio


title: Effects of selective elimination of senescent cells on RPE/choroid complex in mice with subretinal drusenoid deposits

summary: The target deletion of ATP binding cassette subfamily member 1 (ABCA1) and G1 (ABCG1) in myeloid cells leads to subretinal drusenoid deposits in mice (Abca1/g1 -m/-m). We here report the selective elimination of p16-positive cells results in the significant eduction in myeloid markers, pro-inflammatory cytokines and prostaglandin biosynthetic enzymes.

overall_design: INK-ATTAC mice are transgenic mice expressing FKBP-caspase 8 fusion protein under INK4a promoter. p16Ink4a-positive senescent cells can be effectively ablated by the administration of AP20187 which dimerizes the fusion protein and selectively induce apoptosis of p16-positive senescent cells.To ablate p16Ink4a-positive cells, Abca1/g1 -m/-m; INK-ATTAC mice were treated with intraperitoneal injection of AP20187 every other day for 3 months. RPE/choroid complex samples were collected from eyes.