title: Genomic occupancies of MLL1 and UTX, and H3K4me3/K3K27me3 histone modifications upon hydrogen peroxide treatment in human HaCaT keratinocytes.

city: Incheon

first: Jangyhun

last: Choi

state: Incheon

address: 5N521, 100 Inha-ro, Michuhol-gu

department: Department of biological sciences

institute: Inha University

summary: ChIP-seq analysis was conducted to investigate the effects of hydrogen peroxide (H2O2) treatment on the occupancy of MLL1 and UTX, and the associated histone modifications in HaCaT cells.

overall_design: Chromatins were prepared from HaCaT cells before and after H2O2 exposure and subjected to immunoprecipitation using antibodies against MLL1, UTX, H3K4me3, and H3K27me3 followed by the next-generation sequencing.

first: Hansol

last: Lee

first: Janghyun


title: Exosomal miRNA profiling in Bcl-w overexpressed U251cells

status: Public on Mar 27 2024

city: Seoul

first: IN HWA

last: BAE

state: --- Select One ---

address: 75 Nowon-ro, Nowon-gu

country: South Korea

institute: Korea Institute of Radiological  & Medical Sciences

summary: Exosomes are cell membrane-derived endoplasmic reticulum measuring 30 to 120 nm, which are secreted from various cells including cancer cells, and consist of lipids, proteins, mRNAs, and microRNAs (miRNAs). Tumor-derived exosomes are involved in tumor progression by delivering various factors to neighboring cells and promoting intercellular communication. MiRNA is a non-coding RNA consisting of 20-24 nucleotides that binds to the 3'UTR region of the target gene with a complementary nucleotide sequence during gene expression to degrade target mRNA or inhibit translation into target protein. In our study, exosomal miRNA profiling was utilized as a crucial technique to analyze the mechanisms of intercellular communication in tumor malignancy

overall_design: We isolated exosomes from the conditioned medium of U251 cells overexpressing vector and Bcl-w. RNA was extracted from isolated exosomes and performed on a miRNA microarray.

first: In

middle: H

last: Bae

first: Jae

middle: Y

first: Hyun

middle: J

last: Seok

first: Dong


title: Chemically induced expansion of type 2 alveolar epithelial cell  promotes regenerative lower airway repair [RNA-seq]

city: Hangzhou

first: Sida

last: Shao

state: Zhejiang

address: 18 Shilongshan Rd, Xihu District

country: China

institute: Westlake University

type: Expression profiling by high throughput sequencing

summary: Type 2 alveolar epithelial cells (AEC2s) are stem cells in the adult lung that contribute to lower airway repair. Agents that promote the selective expansion of these cells might stimulate regeneration of the compromised alveolar epithelium, an etiology defining event in several pulmonary diseases. From a high content imaging screen of the drug repurposing library ReFRAME, we identified that dipeptidyl peptidase 4 (DPP4) inhibitors, widely used type 2 diabetes medications, selectively expand AEC2s and are broadly efficacious in several mouse models of lung damage. Mechanism of action studies revealed that the protease DPP4, in addition to processing incretin hormones, degrades IGF-1 and IL-6, essential regulators of AEC2 expansion whose levels are increased in the luminal compartment of the lung in response to drug treatment. To selectively target DPP4 in the lung with sufficient drug exposure, we developed NZ-97, a locally delivered, lung persistent DPP4 inhibitor that broadly promotes efficacy in mouse lung damage models with minimal peripheral exposure and good tolerability. This work reveals DPP4 as a central regulator of AEC2 expansion and affords a promising therapeutic approach to broadly stimulate regenerative repair in pulmonary disease.

overall_design: To evaluate the effects of DPP4 inhibitors on AEC2 expansion, we carried out RNA sequencing experiments to characterize the human small airway epithelial cells, followed by comparing the transcriptomes of human small airway epithelial cells treated with DMSO, IGF1, sitagliptin, saxagliptin, NVP-728 and TGFβ1.

last: Zhang

first: Gregory

middle: P

last: Specht

first: Shaochen

last: You

first: Shuangwei

last: Li

first: Van

last: Nguyen-Tran

first: Sean

middle: B

last: Joesph

first: Arnab

middle: K

last: Chatterjee

first: Jeffrey

last: Chen

first: Peter

middle: G

last: Schultz

first: Michael

last: Bollong


title: MLL1 histone methyltransferase and UTX histone demethylase functionally cooperate to regulate the expression of NRF2 in response to ROS-induced oxidative stress

first: Jangyhun

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: Increased HIF-2α Activity in the Nucleus Pulposus Causes Mild Degenerative Changes in the Intervertebral Disc in the Aging Mouse Spine

city: Philadelphia

first: Makarand

last: Risbud

address: 1025 Walnut St

country: USA

institute: Thomas Jefferson University

summary:
Transcriptomic analysis of nucleus pulposus (NP) tissues from intervertebral discs of 14- and 24-month-old mice with the conditional postnatal overexpression of HIF-2α.
Hypoxia-inducible factors (HIFs) are essential for the homeostasis of the hypoxic tissues, and therefore, increased activity of the transcription factor HIF-2α is shown to contribute to the pathogenesis of mild disc degeneration in the spine. We examined the transcriptomic profiles of nucleus pulposus cells in control and K19-HIF-2α-dPA overexpression mice using microarrays.

overall_design: Tissues from the nucleus pulposus (NP) were harvested from the intervertebral discs of four K19-HIF-2αdPA control (HIF-2αdPA/dPA) (WT) and four K19-HIF-2αdPA overexpression mice (K19-HIF-2αdPA/dPA) (MUT) at both 14 and 24 months of age. NP tissues were pooled from caudal discs in each animal for RNA extraction and hybridization using Affymetrix microarrays.

first: Shira

middle: N

last: Johnston

first: Maria

last: Tsingas

middle: V


title: RNA expression differences in innate immune response to COVID19 with advancing age.

city: IRVINE

first: Anshu

last: Agrawal

state: CA

address: C-380 MED/SCI

department: Medicine/immunology

institute: University of California Irvine

summary: We investigated differences in RNA expression between aged (65-90 years), middle-aged (41-63 years) and young (21-40 years) in response to COVID 19 to gain insight into the increased susceptibility of the elderly to the virus. To investigate this fresh PBMCs (1 x 106/ml) from the three age groups were stimulated for 24h with 5ug/ml of irradiated COVID19 virus- isolate USA-WA1/2020 obtained from Bei resources (NIAID). Subsequently the cells were collected. Half of the collected cells were stored in DNA/RNA shield for RNA extraction. The rest were used for flow and other studies. Once all samples were collected, they were sent to UCI Genomics Research and Technology Hub, GRTH) for library preparation and sequencing.

overall_design: Blood from various age group subjects were collected using IRB-approved protocols at the University of California, Irvine (UCI). Patient and clinical information was provided to study members as de-identified data elements.

first: Sudhanshu

first: Michelle

middle: T

last: Tran

first: Tara

middle: S

last: Jennings

first: Marlaine

middle: M

last: Soliman

first: Bobby

last: Sasson

first: Farah

last: Rahmatpanah


title: Effects of silencing miR-142-3p on the pathological and physiological functions of cardiac fibroblasts

city: Nanjing

first: Kun

last: Zhao

address: 101Longmian Avenue

institute: Nanjing Medical University

summary: MicroRNAs (miRs), a group of small and non-coding RNAs, negatively regulate gene expression via promoting messenger RNA (mRNA) degradation or blocking mRNA translation. Many miRs have been recognized as biomarkers or possible targets for the diagnosis or therapy of some diseases. Among them, miR-142-3p was involved in the occurrences and progression of various cardiovascular diseases. Previous studies found that miR-142-3p upregulation could ameliorate myocardial ischemia/reperfusion (I/R)-induced transdifferentiation of fibroblasts to myofibroblasts and collagen deposition. miR-142-3p-mediacted autophagy was reported as a novel mechanism towards I/R-induced cardiac injure. Besides, miR-142-3p could mitigate myocardial mitochondrial dysfunction. Thus, it is worth studying whether silencing miR-142-3p may affect the pathological and physiological functions of cardiac fibroblasts.

overall_design: We treated cardiac fibroblasts with NC or miR-142-3p antagomiR (n=3).Briefly, 50nM miR-142-3p antagomir or NC was transfected into CFs using Lipofectamine RNAiMAX (Invitrogen, Carlsbad, CA, USA) following the manufacturers’ instructions.  Then, all samples were used for transcriptome RNA sequencing. Comparative gene expression profiling analysis of RNA-seq data was then performed.


title: Integrative multi-omics analyses to identify the genetic and functional mechanisms underlying ovarian cancer risk regions

city: Los Angeles

middle: Renee

last: Jones

address: 8720 Alden Dv

department: Biomedical Sciences

institute: Cedars-Sinai Medical Center

summary: To identify credible causal risk variants (CCVs) associated with different histotypes of epithelial ovarian cancer (EOC), we performed genome-wide association analysis for 470,825 genotyped and 10,163,797 imputed SNPs in 25,981 EOC cases and 105,724 controls of European origin.  We identified five new histotype-specific EOC risk regions (P-value < 5 x 10-8) and confirmed previously reported associations for 27 risk regions.  Conditional analyses identified an additional 11 signals independent of the primary signal at six risk regions (P-value < 10-5).  Fine mapping identified 4,008 CCVs in these regions, of which 1,452 CCVs were located in ovarian cancer-related chromatin marks with significant enrichment in active enhancers, active promoters, and active regions for CCVs from each EOC histotype.  Transcriptome-wide association and colocalization analyses across histotypes using tissue-specific and cross-tissue data sets identified 86 candidate susceptibility genes in known EOC risk regions and 32 genes in 23 additional genomic regions that may represent novel EOC risk loci (FDR < 0.05).  Finally, by integrating genome-wide HiChIP interactome analysis with TWAS, variant effect predictor, transcription factor ChIP-seq, and motifbreakR data, we identified candidate gene-CCV interactions at each locus. This included risk loci where TWAS identified one or more candidate susceptibility genes (e.g., HOXD-AS2, HOXD8 and HOXD3 at 2q31) and other loci where no candidate gene was identified (e.g., MYC and PVT1 at 8q24) by TWAS. In summary, this study describes a functional framework and provides a greater understanding of the biological significance of risk alleles and candidate gene targets at EOC susceptibility loci identified by GWAS.

overall_design: Fine mapping of risk regions and epigenomic annotation to identify credible causal risk variants (CCVs) at each risk locus. Cell type specific epigenomic enrichment and partitioning heritability analysis and finding expression QTL based approaches to identify candidate susceptibility genes in EOC risk regions and 3D looping analysis to identify gene-CCV interactions at EOC risk loci

first: Simon

last: Coetzee

first: Eileen

middle: O

last: Dareng

first: Pei-Chen

last: Peng

first: Will

last: Rosenow

first: Jonathan

last: Tyrer


title: LINC00115 promotes chemoresistant breast cancer stem-like cell stemness and metastasis through SETDB1/PLK3/HIF1α signaling

city: Shanghai

first: Guoyu

last: Chen

address: Xuhui District Yueyang Road 320

institute: PICB

type: Non-coding RNA profiling by high throughput sequencing


title: Gene expression profiles under oxidative stress conditions in human HaCaT keratinocytes and the derivative cells expressing shRNA against NRF2, MLL1, or UTX.

first: Jangyhun

last: Choi

summary: To determine how transcriptome is altered by knockdown of NRF2, MLL1, or UTX, we performed RNA-sequencing (RNA-seq) analysis of HaCaT cells and its shRNA-expressing derivatives before and after exposure to hydrogen peroxide (H2O2) or cerium oxide nanoparticles (CeO2 NPs).

overall_design: RNA-seq analysis of HaCaT cells and the derivatives following treatment with 100 µM H2O2 or 25 µg/mL CeO2 NPs for 24 hours.

first: Hansol

last: Lee

first: Janghyun


title: LINC00115 promotes chemoresistant breast cancer stem-like cell stemness and metastasis through SETDB1/PLK3/HIF1α signaling [RNA-Seq]

summary: Accumulated data demonstrate that cancer stem-like cell is a key barrier for therapeutic resistance and metastasis in various cancers, including breast cancer, yet the underlying mechanisms are still elusive. Through a genome-wide lncRNA expression profiling, we identified that LINC00115 is robustly upregulated in chemoresistant breast cancer stem-like cells (BCSCs). LINC00115 functions as a scaffold lncRNA to link SETDB1 and PLK3, leading to enhanced SETDB1 methylation of PLK3 at both K106 and K200 in drug-resistant BCSC. PLK3 methylation decreases PLK3 phosphorylation of HIF1α and thereby increases HIF1α stability. HIF1α, in turn, upregulates ALKBH5 to reduce m6A modification of LINC00115, resulting in attenuated degradation of YTHDF2-dependent m6A-modified RNA and enhanced LINC00115 stability. Thus, this positive feedback loop provokes BCSC phenotypes and enhances chemoresistance and metastasis in triple-negative breast cancer. Our findings uncover LINC00115 as a critical regulator of BCSC and highlight potential therapeutic strategies for therapeutic resistance and metastasis in breast cancer.

overall_design: To determine the mechanism by which LINC00115 mediates BCSC properties, we performed RNA-sequencing analysis in MDA-MB-231 PTX-resistant BCSC/WT  and MDA-MB-231 PTX-resistant BCSC/sh115.

first: Fei

last: Luo


title: Circadian transcriptome of pancreatic adenocarcinoma unravels chronotherapeutic targets.

city: Chicago

first: Deepak

last: Sharma

state: Illinois

address: 1653 W Congress Pkwy #12

institute: Rush University Medical Center

summary: Pancreatic ductal adenocarcinoma (PDA) is a lethal cancer characterized by a poor outcome and an increasing incidence. A significant majority (>80%) of newly diagnosed cases are deemed unresectable, leaving chemotherapy as the sole viable option, though with only moderate success. This necessitates the identification of improved therapeutic options for PDA. We hypothesized that there are temporal variations in cancer-relevant processes within PDA tumors, offering insights into the optimal timing of drug administration—a concept termed chronotherapy. In this study, we explored the presence of the circadian transcriptome in PDA using patient-derived organoids (PDOs) and validated these findings by comparing PDA data from TCGA with non-cancerous healthy pancreas data from GTeX. Several PDA-associated pathways (cell cycle, stress response, Rho GTPase signaling) and cancer driver hub genes (EGFR, JUN) exhibited a cancer-specific rhythmic pattern intricately linked to the circadian clock. Through the integration of multiple functional measurements for rhythmic cancer driver genes, we identified top chronotherapy targets and validated key findings in molecularly divergent pancreatic cancer cell lines. Testing the chemotherapeutic efficacy of clinically relevant drugs further revealed temporal variations that correlated with drug-target cycling. Collectively, our study unravels the PDA circadian transcriptome and highlights a potential approach for optimizing chrono-chemotherapeutic efficacy.

overall_design: To investigate the circadian transcriptome of 4 pancreatic cancer cell lines and 6 patient derived pancreatic cancer organoids. Temporal RNA-Seq was carried out at 7 time points (0h, 4h, 8h, 12h, 16h, 20h, 24h) and daily changes in gene expression were quanitifed at the transcriptome-wide level.

first: Darbaz

last: Adnan

first: Mostafa

last: Abdel-Reheem

first: Ron

middle: C

last: Anafi

first: Daniel

middle: D

last: Leary

first: Faraz

last: Bishehsari


title: LINC00115 promotes chemoresistant breast cancer stem-like cell stemness and metastasis through SETDB1/PLK3/HIF1α signaling [lnc RNA-Seq]

overall_design: To determine the roles of lncRNAs in regulating chemoresistant breast cancer stem cell properties,  lncRNA-sequencing was performed in paclitaxel (PTX)-resistant MDA-MB-231 BCSC and non-BCSC.


title: Single-Cell Analysis of Age-Related Changes in Leukocytes of Diabetic Mouse Hindpaws

city: Houston

first: Rajasekaran

last: Mahalingam

state: TX

address: 6565 MD Anderson Blvd

department: Symptom Research

institute: University of Texas MD Anderson Cancer Center

summary: We used single cell RNA sequencing to identify transcriptomic changes in immune cells of the distal limb in diabetic Leprdb/db mice at two different ages that have the potential to contribute to the complications of the distal limb associated with diabetes

overall_design:
Single cell RNA sequencing to identify transcriptomic changes in immune cells of the distal limb in diabetic Leprdb/db mice at two different ages.
Cells were isolated from mice hindpaws and performed fluorescence-activated cell sorting (FACS) to separate the immune cells and then performed scRNAseq

first: James

last: Nichols

first: Hoang

last: Pham

first: Andrew

last: Shepherd


title: Transcriptome analysis of doxorubicin-treated MCF7 breat cancer cells

city: Roma

first: Ivan

last: Arisi

address: viale Regina Elena 295

department: Bioinformatics Facility

country: Italy

institute: European Brain Research Institute

summary: Doxorubicin (DOX) is the most common chemotherapeutic drug used to treat breast cancer(BC), impairing DNA metabolism. We discovered that this drug induces, in breast cancer cells, the selective degradation of mitochondria suggesting that mitophagy could be a pro-survival path induced by DOX, hence favoring drug resistance. We anticipated that BC cells may avoid the effect of drug treatment by enhancing their mitophagy activity. Our goal was here to identify a novel relationship between mitophagy gene expressions and drug resistance in BC cells. This microarray analysis of MCF7 cells was performed to demonstrate a direct modulation of genes encoding key proteins regulating the mitophagy pathway in the cells treated with DOX compared to untreated control cells.

overall_design: A total of n=16 samples were processed. The samples are divided into 2 experimental groups: untreated control samples (n=8) and DOX treated samples (n=8). Samples were treated for 24h with DOX 30 µM.

first: Francesco

last: Naso

first: Krenare

last: Bruqui

first: Valeria

last: Manzini

first: Valerio

last: Chiurchiù

first: Mara

last: D’Onofrio

first: Flavie

last: Strappazzon


title: Transcriptome analysis during VCD exposure-induced POI in mice

city: 兰州市

first: Yi

last: Li

state: 甘肃

address: 甘肃省兰州市城关区东岗西路1号兰州大学第一医院

institute: Lanzhou University

summary: 4-vinylcyclohexene diepoxide (VCD) is a reproductively toxic environmental pollutant that causes follicular failure leading to POIs, which can seriously affect a woman's physical health and fertility. Investigating its pathogenic mechanisms can help provide guidance for the prevention of ovarian impairment and the treatment of POI. We built a mouse model of POI by intraperitoneal injection of VCD into female C57BL/6 mice for 15 days. Then compared it with the control group at two time points, day 15 and day 30, including the comparison of phenotypic characteristics and differences in the transcriptome. We performed a comprehensive analysis of the differential genes identified and validated some key genes by RT-PCR. The results showed that sex hormone levels, follicle number and estrous cycle of VCD-induced POI mice were significantly affected at both day 15 and day 30. Regarding DEGs and enrichment results, the results obtained at day 15 were not as significant as those at day 30. Our results provide a preliminary indication that steroid hormone synthesis, DNA damage repair, and impaired oocyte mitosis play an important part in the process by which VCD affects ovarian function. Maybe it was due to impaired follicular development caused by VCD damage to the primordial follicular pool, and with the progression of time, the ovarian damage was aggravated, and it was gradually difficult to perform normal function.

first: Ruifen

last: He

first: Xue

last: Qin

first: Qinying

last: Zhu

first: Liangjian

last: Ma

first: Xiaolei

last: Liang


title: Gene expression profile at single cell level of isogenic iPSC-derived primitive erythroblasts (RBCs), iPSC-derived definitive RBCs and Fetal liver-derived RBCs

first: Giulia

last: Pavani

state: Pennsylvania

address: 3501 Civic Center Blvd, CTRB 10060-05

institute: Children's Hospital of Philadelphia

summary: In this study, we generated and validated in vitro models to study human embryonic and fetal erythropoiesis using induced pluripotent stem cells (iPSCs).

overall_design: We used distinct differentiation protocols to generate pure embryonic or fetal RBCs from iPSCs and compared them with genetically matched isogenic erythroid cells from a primary fetal liver

first: Paul

last: Gadue


title: Unlocking the power of transcriptomic biomarkers in qualitative and quantitative genotoxicity assessment of chemicals

city: Ottawa

first: Matthew

last: Meier

state: Ontario

address: 251 Sir Frederick Banting Driveway

department: Health Canada

country: Canada

institute: Government of Canada


title: CXXC zinc finger protein 1 (Cfp1) controls cardiomyocyte maturation by modifying histone H3K4me3 of structural, metabolic, and contractile related genes

city: Harbin

first: Changzhu

address: Department of Pharmacology (State Key Laboratory of Frigid Zone Cardiovascular Disease, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy

institute: Harbin Medical University

summary: Cardiomyocyte maturation is the final stage of heart development, and abnormal cardiomyocyte maturation will lead to serious heart diseases. CXXC zinc finger protein 1 (Cfp1) is an important epigenetic factor, which plays an essential role in the development and maturation of multi-lineage cells, while its effect on the maturation of cardiomyocyte remains unclear. This study was performed to explore the potential role of Cfp1 in cardiomyocyte maturation of heart and the underlying mechanisms. Cardiomyocyte-specific Cfp1 knockout (Cfp1-cKO) mice died within 4 weeks of birth. Cardiomyocytes from Cfp1-cKO mice showed an inhibited maturation phenotype in structure, metabolism, contractile function, and cell cycle, accompanied by down-regulation of adult genes and up-regulation of fetal genes. In contrast, cardiomyocyte-specific Cfp1 transgenic (Cfp1-TG) mice and human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) overexpressing Cfp1 showed a more mature phenotype. Mechanistically, deficiency of Cfp1 results in reduced trimethylation on lysine 4 of histone H3 (H3K4me3) modification and formation of ectopic H3K4me3. Moreover, Cfp1 deletion decreased the level of H3K4me3 modification in adult genes and increased the level of H3K4me3 modification in fetal genes. Collectively, Cfp1 modulates the expression of cardiomyocyte maturation related genes by modulating histone H3K4me3 modification, which in turn regulates cardiomyocyte maturation. This study implicates Cfp1 as an important molecule regulating cardiomyocyte maturation, and its dysfunction is strongly associated with cardiac disease.

overall_design: WT and Cxxc1 null hearts are collected to perform high-throughput sequencing.


title: CXXC zinc finger protein 1 (Cfp1) controls cardiomyocyte maturation by modifying histone H3K4me3 of structural, metabolic, and contractile related genes (ChIP-Seq)

overall_design: Two weeks old WT and CXxC1 null hearts were collected for high-throughput sequencing. Each sample was derived from at least three mice.


title: Single cell sequencing data of islets from WT and Npc1KO mice

first: Bei

last: Liu

address: 197 Rui Jin 2nd Road

institute: Ruijin Hospital, Shanghai Jiaotong University School of Medicine

summary: Npc1 is a cholesterol transporter located on lysosomal membrane, and whether it is involved in regulating the function and differentiation of β cells is unclear. To understand molecular basis of the phenotype caused by Npc1 loss in β cells, we isolated islets from 2-week-old WT and Npc1KO mice for single-cell sequencing. We compared the gene expression profiles of different subpopulation of islet cells and found many changes of islet subpopulation and biological pathway occurred in Npc1KO islets.

overall_design: To understand molecular basis of the phenotype caused by Npc1 loss in β cells, we isolated islets from 2-week-old WT and Npc1KO mice, digested the islet into single-cell suspension, and performed single-cell sequencing using 10X Genomics. Our islet samples were divided into two groups, WT and Npc1KO. Every islet suspension sample were digested by the islets of 3 same genotype 2-week-old female mice.

first: B

first: Y

last: Gu


title: MicroRNA profiling in Caco-2BBe1 cells in response to cranberry proanthocyanidin or its metabolites with and without IL-1β

city: Toronto

first: Elena

last: Comelli

address: 1 King's College Circle

department: Nutritional Sciences

institute: University of Toronto

summary: The molecular basis underlying the known anti-inflammatory and anticarcinogenic properties of cranberries is incompletely understood. We investigated the microRNA (miRNA)-modulatory effects of cranberry proanthocyanidin (PAC) and two of its main gut microbial metabolites, 3,4-dihydroxyphenylacetic acid (DHPAA) and 3-(4-hydroxyphenyl)-propionic acid (HPPA), in intestinal cells at homeostasis and in inflammatory conditions. Differentiated Caco-2BBe1 cells were pre-treated with PAC, DHPAA, or HPPA then stimulated with IL-1ß or not. Total RNA was used to profile the expression of 799 miRNAs. PAC, DHPAA, and HPPA generated subsets of shared and distinct miRNA responses. At homeostasis, miRNAs affected by the metabolites, but not by PAC, targeted genes enriched in kinase, Wnt, and growth factor signaling, cell growth and proliferation, apoptosis, and specific cancer pathways. In an inflammatory environment, pre-treatment with PAC and DHPAA, but not HPPA, reversed the expression of 16 and two IL-1ß-induced miRNAs, targeting genes enriched in inflammatory and cancer pathways. These data suggest that in the absence of inflammation, PAC may be reliant on its transformation by the gut microbiota for its miRNA-modulatory effects, while in an inflammatory environment, both PAC and DHPAA counter inflammatory miRNA responses. This work provides a novel mechanism to characterize the bioactivity of cranberry and will inform cranberry utilization in nutritional strategies for the maintenance of intestinal homeostasis.

overall_design: 36 samples were analyzed representing 12 unique treatments (3 biological replicates per treatment);  DMEM with no IL-β stimulation serves as the control vehicle

first: Zoe

last: Lofft

first: Amel

last: Taibi


title: Early-Onset Hearing Loss in Mouse Models of Alzheimer’s Disease correlates to DNA Damage in Cochlea

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

summary:
Alzheimer's disease (AD) is the most common type of dementia and is characterized by cognitive and behavioral impairment that significantly interferes with social functioning. Over the last decade, there has been an increased interest in whether sensory deficiency may be associated with the development of AD. Notably, the relationship between hearing impairment and AD is of great relevance, but still poorly understood. In this study, we found an early-onset hearing loss in 3xTgAD and 3xTgAD/Polβ+/− mouse models. The hearing assessment was measured by auditory brainstem response (ABR) and distortion product otoacoustic emission (DPOAE) recordings. Herein, we report that both 3xTgAD and 3xTgAD/Polβ+/− mice showed increased ABR thresholds between at 16 and 32 kHz at 4 weeks of age, much earlier than any AD behavioral changes. The ABR thresholds were significantly higher in 3xTgAD/Polβ+/− mice than in 3xTgAD mice at 16 kHz, and DPOAE signals were also reduced, indicating that DNA damage may affect hearing impairment in AD. Poly ADP-ribosylation levels and protein expression of DNA damage markers increased significantly and NAD+ levels were reduced in the cochlea of 3xTgAD and 3xTgAD/Polβ+/− mice. Remarkably, we observed the downregulation of phosphoglycerate mutase 2 (PGAM2) in cochlea and a decrease in the number of synaptic ribbons in the presynaptic zones of inner hair cells in 3xTgAD/Polβ+/− mice. We also find that the activity of sirtuin 3 (SIRT3) is downregulated in cochlea, indicative of impaired mitochondrial function. Taken together, hearing impairment may be a potential early marker of AD.  In addition, these findings provide new insights into the mechanism of the relationship between hearing dysfunction and AD and suggest that DNA damage in the cochlea can contributes to the development of early hearing loss of AD.
The hearing assessment was measured by auditory brainstem response (ABR) and distortion product otoacoustic emission (DPOAE) at 4 weeks of age, thereafter whole cochlea and auditory cortex tissue were collected from each mouse (WT, Polβ+/−, 3xTgAD, and 3xTgAD/Polβ+/−) and subjected to total RNA isolation to understand what metabolism-related gene expression changes in cochlea and auditory cortex.

overall_design: We analyzed a total of 24 samples of mouse cochlea and auditory cortex as follows: controls (n=3), PolB+/- (n=3), 3xAD (n=3),  and 3xAD/PolB+/- (n=3). Analysis employed nCounter Advanced Analysis suite of tools.

first: Vilhelm

middle: A

last: Bohr


title: The serum small non-coding RNA (SncRNA) landscape as a molecular biomarker of age associated muscle dysregulation and insulin resistance in older adults.

city: Oxford

first: Elie

last: Antoun

state: United Kingdom

address: Nuffield Department of Medicine

department: CAMS China Oxford Institute (CAMS-COI

country: United Kingdom

institute: University of Oxford

summary:
Small noncoding RNAs (sncRNAs) are implicated in age-associated pathologies, including sarcopenia and insulin resistance (IR). This study aimed to characterise the wider circulating sncRNA transcriptome of older individuals and associations with sarcopenia and IR.
Total RNA was used for sncRNA expression including miRNAs, transfer RNAs (tRNAs), tRNA-associated fragments (tRFs) and piwi-interacting RNAs (piRNAs) was measured in serum from 21 healthy and 21 sarcopenic  women matched for age (mean 78.9 years) and HOMA2-IR from the Hertfordshire Sarcopenia Study. Associations with age, sarcopenia and HOMA2-IR were examined, and predicted gene targets and biological pathways characterised.

overall_design: Comparative small non-coding gene expression profiling analysis of small RNA-seq data from serum of older community dwelling women from the Hertfordshire Sarcopenia Study.

first: Mark

last: Burton


title: Ethoxysanguinarine ameliorates vascular remodeling  by regulating TGF-β1/Smad2/3 signaling pathway in Hypertension：An in vitro and in vivo approach

city: Fuzhou

first: Jun

last: Peng

state: Fujian

address: 1 Qiuyang Road, Minhou Shangjie

department: Academy of Integrative Medicine

institute: Fujian University of Traditional Chinese Medicine

summary: The goals of this study is to compare the differently expressed genes in abdominal aortaof WKY and SHR with or without Ethoxysanguinarine (ETH) treatment. The SHRs (n=12) were randomly divided into 2 groups: SHR, and SHR +ETH (3.5mg/kg/d) groups (n=6 for each group). WKY rats (n=6) were set as control. Rats in WKY and SHR groups were  intragastrically with double distilled water (dd H2O), while rats in  SHR + ETH (3.5mg/kg/d) group were intragastrically with 3.5 mg/kg/d of ETH for 10 weeks.  Then the vascular vessel tissues were used to identify differentially expressed genes among different groups.

overall_design: RNA sequencing was performed with abdominal aortaof rats in 3 groups: WKY, SHR, SHR +ETH (3.5mg/kg/d) treated (n=6 for each group) to identify the differently expressed genes and related pathway.

first: Aling

last: Shen

first: Meizhu

last: Wu

first: Zhi

last: Guo

first: Dawei

last: Lian


title: Intestinal epithelial adaptations to vertical sleeve gastrectomy defined at single-cell resolution

city: Ithaca

first: Kieran

last: Koch-Laskowski

state: NY

address: 618 Tower Road, VRT #T7006

institute: Cornell University

summary: The gut plays a key role in regulating metabolic health. Dietary factors disrupt intestinal physiology and contribute to obesity and diabetes, whereas bariatric procedures such as vertical sleeve gastrectomy (VSG) cause gut adaptations that induce robust metabolic improvements. However, our understanding of these adaptations at the cellular and molecular levels remains limited. In a validated murine model, we leverage single-cell transcriptomics to determine how VSG impacts different cell lineages of the small intestinal epithelium. We define cell type-specific genes and pathways that VSG rescues from high-fat diet perturbation and characterize additional rescue-independent changes brought about by VSG. We show that Paneth cells have increased expression of the gut peptide Reg3g after VSG. We also find that VSG restores pathways pertaining to mitochondrial respiration and cellular metabolism, especially within crypt-based cells. Overall, our study provides unprecedented molecular resolution of VSG’s therapeutic effects on the gut epithelium.

overall_design: Single-cell RNA-sequencing of small intestinal epithelial crypts and villi from three groups of adult male C57BL/6J mice after a 16-week dietary intervention and 5 weeks after surgery: (1) high-fat diet VSG mice, (2) high-fat diet sham mice, and (3) low-fat diet sham mice.

first: Praveen

last: Sethupathy


title: Extracellular matrix derived from dental pulp stem cells promotes osteogenic differentiation of gingival fibroblasts via Wnt and Hippo signaling pathway

city: Bangkok

first: Ajjima

last: Chansaenroj

address: 34 Henri-Dunant Road

department: Anatomy

country: Thailand

institute: Faculty of Dentistry, Chulalongkorn University

summary: This study investigated the efficacy of decellularized ECM derived from human dental pulp stem cells (dECM_DPSCs) and gingival-derived mesenchymal stem cells (dECM_GSCs) as an inductive scaffold for osteogenic differentiation of GSCs.  ECM was constructed from DPSCs and GSCs that were cultured in a growth medium supplemented with L-ascorbic acid (N-ECM) or osteogenic induction medium (OM-ECM). The gene expression profile was examined using a high-throughput RNA sequencing technique.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for GSCs reseeded on N and OM-dECM_DPSCs and GSCs

first: Chatvadee

last: Kornsuthisopon

first: Nunthawan

last: Nowwarote

first: Suphalak

last: Photichailert

first: Sunisa

last: Rochanavibhata

first: Nuttha

last: Klincumhom

first: Benjamin

last: Fournier

first: Thanaphum

last: Osathanon


title: Enhancer infestation drives tumorigenic activation of inactive compartment in Epstein-Barr virus-positive nasopharyngeal carcinoma [RNA-Seq]

city: Chiba

first: Masaki

last: Fukuyo

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

department: Department of Molecular Oncology

country: Japan

institute: Chiba University

summary: We analyzed the gene expressions around the host genomic regions where EBV and host genomic interactions were obsearved in nasopharyngeal carcinoma cell lines.

overall_design: Examination of the gene expressions in nasopharyngeal epithelial cell lines and nasopharyngeal carcinoma cell lines.

first: Harue

last: Mizokami

first: Atsushi

last: Okabe

first: Ruchi

last: Choudhary

first: Masato

last: Mima

first: Bahityar

last: Rahmutulla

first: Motoaki

last: Seki

first: Satoru

last: Kondo

first: Hirotomo

last: Dochi

first: Patrick

last: Tan

first: Tomokazu

last: Yoshizaki

first: Melissa

last: Fullwood

last: Kaneda


title: Enhancer infestation drives tumorigenic activation of inactive compartment in Epstein-Barr virus-positive nasopharyngeal carcinoma [ChIP-Seq]

summary: We analyzed active enhancers of nasopharyngeal epithelial cell lines and nasopharyngeal carcinoma cell lines by performing ChIP-seq on H3K4me1, H3K4me3, and H3K27ac.

overall_design: Examination of active enhancers in nasopharyngeal epithelial cell lines and nasopharyngeal carcinoma cell lines.


title: Enhancer infestation drives tumorigenic activation of inactive compartment in Epstein-Barr virus-positive nasopharyngeal carcinoma [4C-Seq]

summary: We detected the EBV interaction regions and the genomic loops from TSS of PLA2G4A in nasopharyngeal carcinoma cell lines by 4C-seq analysis.

overall_design: Examination of the EBV interaction regions and the genomic loops.


title: Human cytomegalovirus dysregulates neurodevelopmental pathways in cerebral organoids

city: Sydney

first: Susan

last: Corley

state: NSW

address: D26, Kensignton Campus

department: Biotechnology & Biomolecular Sciences

country: Australia

institute: UNSW

summary: This study investigated the viral mechanisms of fetal neural malformation using in vitro human cerebral organoids to model congenital CMV infection

overall_design: Cerebral organoids cultured for 55 days followed by 14 days infection with CMV Merlin were harvested for bulk RNA-sequencing. Four biological replicates of CMV infected cerebral organoids were compared to 4 biological replicates of non-infected cerebral organdies.

first: Ece

last: Egilmezer

first: William

last: Rawlinson


title: Enhancer infestation drives tumorigenic activation of inactive compartment in Epstein-Barr virus-positive nasopharyngeal carcinoma

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

overall_design: Refer to individual Series


title: Sphere cultured biliary tract cancer cell lines SNU245 and SNU1196

city: Seoul

first: Si Young

last: Song

address: 50-1, Yonsei-ro

department: Department of Internal Medicine

institute: Yonsei University College of Medicine

summary:
We analyzed sphere cultured biliary tract cancer cell lines and analysed cancer stem cells asociated-differentially expressed genes by microarray analysis.
biliary tract cancer stem cells(CSCs) associated DEG

overall_design: We performed complementary DNA (cDNA) microarray analysis using adherent and sphere cells from the human biliary tract cancer cell lines SNU1196 and SNU245 to evaluate the unique molecular patterns of BTC CSCs.

first: Si


title: DNA methylation as a therapeutic target in RB1 deficient and neuroendocrine prostate cancer and rational co-targeting with B7-H3 [RNA-Seq 1]

first: Yasutaka

last: Yamada

state: MA

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

department: Urology

institute: Graduate School of Medicine, Chiba University

summary: Aberrant DNA methylation has been implicated as a key driver of prostate cancer lineage plasticity and histologic transformation to neuroendocrine prostate cancer (NEPC). DNA methyltransferases (DNMT) are highly expressed, and global DNA methylation levels are elevated in NEPC. We identified that deletion of DNMT genes decreases expression of neuroendocrine lineage markers and markedly reduced NEPC tumor development and metastasis in vivo. Decitabine, a global DNMT inhibitor, significantly attenuated tumor growth in NEPC patient-derived xenograft (PDX) models, as well as RB1-deficient castration-resistant prostate adenocarcinoma (CRPC) models compared with RB1-proficient CRPC. We further discovered that DNMT inhibition increased expression of B7-H3, an emerging druggable target, via demethylation of B7-H3 CpG islands. We tested DS-7300a, a novel antibody-drug conjugate (ADC) targeting B7-H3, alone and in combination with decitabine. There was potent single agent antitumor activity of DS-7300a in both CRPC and NEPC models bearing high expression of B7-H3. In B7-H3 low models, combination therapy of decitabine plus DS-7300a resulted in a synergistic response. Overall, we report that DNMT inhibition is a novel therapeutic target for NEPC and RB1-deficient CRPC and may sensitize B7-H3-low prostate cancer to the ADC DS-7300a through increasing target expression. NEPC and RB1-deficient CRPC represent prostate cancer subgroups with poor prognosis. The development of novel biomarker-driven therapeutic strategies for this population may ultimately help improve patient outcomes.

overall_design: Three biological replicates were analyzed for each of 3 conditions including wild type (WT) and DNMT1 or DNMT3A knockout.

first: Himisha

last: Beltran


title: DNA methylation as a therapeutic target in RB1 deficient and neuroendocrine prostate cancer and rational co-targeting with B7-H3 [22Rv1sgRB1]

overall_design: Three subcutaneous xenograft model replicates were analyzed in 22Rv1-WT and 22Rv1 sgRB1.


title: DNA methylation as a therapeutic target in RB1 deficient and neuroendocrine prostate cancer and rational co-targeting with B7-H3 [RNA-Seq 2]

summary:
Aberrant DNA methylation has been implicated as a key driver of prostate cancer lineage plasticity and histologic transformation to neuroendocrine prostate cancer (NEPC). DNA methyltransferases (DNMT) are highly expressed, and global DNA methylation levels are elevated in NEPC. We identified that deletion of DNMT genes decreases expression of neuroendocrine lineage markers and markedly reduced NEPC tumor development and metastasis in vivo. Decitabine, a global DNMT inhibitor, significantly attenuated tumor growth in NEPC patient-derived xenograft (PDX) models, as well as RB1-deficient castration-resistant prostate adenocarcinoma (CRPC) models compared with RB1-proficient CRPC. We further discovered that DNMT inhibition increased expression of B7-H3, an emerging druggable target, via demethylation of B7-H3 CpG islands. We tested DS-7300a, a novel antibody-drug conjugate (ADC) targeting B7-H3, alone and in combination with decitabine. There was potent single agent antitumor activity of DS-7300a in both CRPC and NEPC models bearing high expression of B7-H3. In B7-H3 low models, combination therapy of decitabine plus DS-7300a resulted in a synergistic response. Overall, we report that DNMT inhibition is a novel therapeutic target for NEPC and RB1-deficient CRPC and may sensitize B7-H3-low prostate cancer to the ADC DS-7300a through increasing target expression. NEPC and RB1-deficient CRPC represent prostate cancer subgroups with poor prognosis. The development of novel biomarker-driven therapeutic strategies for this population may ultimately help improve patient outcomes.
We performed gene expression profiling analysis using data obtained from PM154 control and decitabine treated PM154 cells.

overall_design: Three biological replicates were analyzed for each of 3 conditions including control and decitabine treated cells.


title: Comprehensive exosomal miRNA profile and construction of ceRNA network in autism spectrum disorder

city: Changsha

first: Sha

last: Zhao

address: No. 86, Ziyuan Road, Yuhua District

institute: Department of Child Healthcare, Hunan Children’s Hospital & University of South China

summary:
Exosomes have been demonstrated to exert momentous roles in autism spectrum disorder (ASD).
In this study, we aimed to make contribution to understanding pathogenesis of ASD and screen for the potential biomarkers associated with the occurrence and development of ASD.

overall_design: Exosomes were extracted from peripheral blood of ten children with ASD and ten normal children. The identification of exosomes was assessed with transmission electron microscopy and Western blot analysis. Then, RNA sequencing was conducted to investigate the exosomal miRNA profile of ASD. The mRNA and circRNA expression profiles of ASD were acquired from GEO database. With identification of differentially expressed mRNAs (DEmRNAs), miRNAs (DEmiRNAs) and circRNAs (DEcircRNAs), a ceRNA regulatory network was constructed. Furthermore, immune cell infiltration in ASD was evaluated.

first: Yan

last: Zhong

first: Fang

last: Shen

first: Xinning

last: Cheng

first: Xiaojuan

last: Qing

first: Jiamin

last: Liu


title: DNA methylation as a therapeutic target in RB1 deficient and neuroendocrine prostate cancer and rational co-targeting with B7-H3 [RRBS]

type: Methylation profiling by high throughput sequencing

overall_design: DNA methylation statuses in prostate cancer xenograft models were analyzed using reduced representation of bisulfite sequencing (RRBS).


title: Histone Deacetylase Complex 1 moderates stress responsiveness of germinating seeds via a histone-1-dependent process [RNA-Seq]

city: Bearsden

first: Pawel

last: Herzyk

address: Wolfson Wohl Cancer Research Centre, Garscube Estate

department: College of Medical, Veterinary and Life Sciences

institute: University of Glasgow

summary:
Plants respond to environmental challenges via a network of signalling pathways. Early responses prevent damage if the stress persists but delay growth in fluctuating conditions. Optimizing these trade-offs requires tunability of plant responsiveness to environmental signals. We have previously shown that Histone Deacetylation Complex 1 (HDC1), which interacts with multiple proteins in histone deacetylation complexes, regulates the sensitivity of Arabidopsis seedlings to salt and ABA, but the underlying mechanism remained elusive. Here we show that knockout of HDC1 enhances transcriptome re-programming prior to growth arrest of salt-treated seedlings and we identify two genes that mediate the effect of salt stress downstream of HDC1. HDC1 attenuates their transcriptional response via a dual mechanism involving H3K9/14 de-acetylation and H3K27 trimethylation. The latter, but not the former, was dependent on the linker histone H1, which interacts with HDC1 via the conserved RXT3 domain. However, a truncated RXT3-like version of HDC1 was not sufficient to recover H3K27me3 deposition in hdc1 suggesting that H1-aided recruitment H3K27 methylation machinery also requires the full-length HDC1-interacting deacetylases. The apparent paradox of repressive marks on stress-induced genes reveals an 'anti-panic' device that employs HDC1 as epigenetic moderator of stress responsiveness offering a leaver to tune stress sensitivity in plants.
To identify genes underpinning salt tolerance in Arabidopsis thaliana and regulated by Histone Deacetylation Complex 1 (HDC1) we performed RNA-sequencing on HDC1 fully complemented line (HDC1c), hdc1-1 knock-out mutant (hdc1-1) and hdc1-1 mutant expressing the HDC1 domain RXT3 (RXT3).
Seedlings were grown for 3 days on control plates and plates supplemented with 100 mM NaCl.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for HDC1c, hdc1-1 and RXT3 seedlings under control and salt conditions.

first: Perella

last: Giorgio

first: Herzyk

last: Pawel

first: Amtmann

last: Anna


title: RNA Sequencing Facilitates Quantitative Analysis of Lupus (MRL/lpr) and Control（MRL/mpj）Mouse Microglia Tanscriptomes

city: Nanjing

first: Han

last: Xiaojuan

state: Jiangsu

address: Zhongshan Road 321

institute: Nanjing Drum Tower Hospital,  The Affiliated Hospital of Nanjing University Medical School

summary: Up to 75% of systematic lupus erythematosus (SLE) patients experience neuropsychiatric (NP) symptoms, called neuropsychiatric SLE (NPSLE), yet the underlying mechanisms remain elusive. Microglia control synaptic pruning during early postnatal brain development. The process in NPSLE remains unclear. Here, we show that microglia-coordinated elimination of synaptic terminals participated in NPSLE in MRL/lpr mice, a lupus-prone murine model. We elucidated that lupus mice developed increased depression- and anxiety-like behaviors and persistent phagocytic microglia reactivation before overt peripheral lupus pathology. Microglial engulfment of synapses explained behavioral disorders. To elucidate the mechanism of synaptic pruning by microglia, we sequenced the gene expression in sorted microglia from both lupus (MRL/lpr) mice and the wild-type (MRL/mpj) controls.

overall_design: RNA sequencing in microglia from control(MRL/mpj) and lupus (MRL/lpr) mice, in triplicate.

first: X

last: Han

first: L

last: Sun


title: DNA methylation as a therapeutic target in RB1 deficient and neuroendocrine prostate cancer and rational co-targeting with B7-H3


title: Coilin and Pol II ChIP-seq in HeLa cells after RPL14 and RPL24 depletion

city: New Haven

first: Karla

last: Neugebauer

state: Connecticut

address: 333 Cedar St

institute: Yale

summary: To investigate location of Cajal bodies (CB) inside the cell nucleus after RPL depletion, we  performed ChIP-seq with an anti-Coilin antibody after siRNA knockdown of RPL14 and RPL24. ChIP-seq revealed a loss of  association of CBs wih snRNA genes and histone genes in histone cluster 1 and 2 upon RPL KD. We also performed Pol 2 ChIP-seq to look at transcription of these gene loci upon RPL knockdown and found decreased Pol II binding along genes.

overall_design: 3 biological replicates of Coilin ChIP seq, Pol II ChIP seq, and input sample after treatment with a non-targeting siRNA (NT), RPL14 siRNA, or RPL24 siRNA

first: Dahyana

last: Escayola


title: Enhancer infestation drives tumorigenic activation of inactive compartment in Epstein-Barr virus-positive nasopharyngeal carcinoma [Hi-C]

first: Masaki

last: Fukuyo

summary: We analyzed the compartment status and chromatin interactions in nasopharyngeal epithelial cell lines and nasopharyngeal carcinoma cell lines by performing Hi-C.

overall_design: Comprehensive chromatin conformational analysis using Hi-C.

first: Harue

last: Mizokami

first: Atsushi

last: Okabe

first: Ruchi

last: Choudhary

first: Masato

last: Mima

first: Bahityar

last: Rahmutulla

first: Motoaki

last: Seki

first: Satoru

last: Kondo

first: Hirotomo

last: Dochi

first: Patrick

last: Tan

first: Tomokazu

last: Yoshizaki

first: Melissa

last: Fullwood

last: Kaneda


title: Non-canonical RNA substrates of Drosha lack many of the conserved features found in primary microRNA stem-loops

city: Fitzroy

first: Mark

last: Chong

state: Victoria

address: 9 Princes Street

institute: St Vincent's Institute of Medical Research

summary: The RNase III enzyme Drosha has a central role in microRNA (miRNA) biogenesis, where it required to release the stem-loop intermediate from primary (pri)-miRNA transcripts. However, it can also cleave stem-loops embedded within messenger (m)RNAs. This destabilizes the mRNA causing target gene repression and has been found to occur primarily in stem cells. While pri-miRNA stem-loops have been extensively studied, such non-canonical substrates of Drosha has yet to characterized in detail. In this study, we employed high-throughput sequencing to capture all polyA-tailed RNAs that are cleaved by Drosha in mouse embryonic stem cells (ESCs). We then compared the features of non-canonical versus miRNA stem-loop substrates. First, these mRNA substrates are less efficiently processed than miRNA stem-loops. Sequence and structural analyses revealed that these substrates are also less stable and more likely to fold into alternative structures than miRNA stem-loops. Moreover, they lack the sequence and structural motifs found in miRNAs stem-loops that are required for precise cleavage. Notably, we discovered a non-canonical Drosha substrate that is cleaved in an inverse manner, which is a process that is normally inhibited by features in miRNA stem-loops. Our study thus provides valuable insights into the recognition of non-canonical targets by Drosha.

overall_design: Investigating noncanonical Drosha cleavage targets and the impact of the cleavage in mouse ESCs.

first: Karen

last: Gu

first: Lawrence

last: Mok

first: Matthew

last: Wakefield


title: Histone Deacetylase Complex 1 moderates stress responsiveness of germinating seeds via a histone-1-dependent process

first: Pawel

last: Herzyk


title: DNA methylation as a therapeutic target in RB1 deficient and neuroendocrine prostate cancer and rational co-targeting with B7-H3 [22Rv1sgCD276]

first: Yasutaka

last: Yamada

overall_design: Two biological replicates were analyzed for each of 2 conditions including wild type (WT) and CD276 knockout.

first: Himisha

last: Beltran


title: Histone Deacetylase Complex 1 moderates stress responsiveness of germinating seeds via a histone-1-dependent process [ChIP-Seq]

summary:
Plants respond to environmental challenges via a network of signalling pathways. Early responses prevent damage if the stress persists but delay growth in fluctuating conditions. Optimizing these trade-offs requires tunability of plant responsiveness to environmental signals. We have previously shown that Histone Deacetylation Complex 1 (HDC1), which interacts with multiple proteins in histone deacetylation complexes, regulates the sensitivity of Arabidopsis seedlings to salt and ABA, but the underlying mechanism remained elusive. Here we show that knockout of HDC1 enhances transcriptome re-programming prior to growth arrest of salt-treated seedlings and we identify two genes that mediate the effect of salt stress downstream of HDC1. HDC1 attenuates their transcriptional response via a dual mechanism involving H3K9/14 de-acetylation and H3K27 trimethylation. The latter, but not the former, was dependent on the linker histone H1, which interacts with HDC1 via the conserved RXT3 domain. However, a truncated RXT3-like version of HDC1 was not sufficient to recover H3K27me3 deposition in hdc1 suggesting that H1-aided recruitment H3K27 methylation machinery also requires the full-length HDC1-interacting deacetylases. The apparent paradox of repressive marks on stress-induced genes reveals an 'anti-panic' device that employs HDC1 as epigenetic moderator of stress responsiveness offering a leaver to tune stress sensitivity in plants.
To identify potential direct targets of HDC1 we isolated nuclei from control and salt-treated HDC1c and hdc1-1 seedlings and performed chromatin immunoprecipitation (ChIP) with an antibody against acetylated lysines 9 and 14 in histone 3 (anti-H3K9K14Ac).

overall_design: To pinpoint possible candidates for a causal link between HDC1 function and salt sensitivity we combined the obtained ChIP-Seq profiles with RNAseq data and extracted genes that showed both stronger transcriptional activation and stronger H3K9K14 hyperacetylation upon salt in hdc1-1 compared to HDC1c.

first: Giorgio

last: Perella

first: Anna

last: Amtmann


title: Long noncoding RNAs expression profiles in granulosa of woman with diminished ovarian reserve based on high-throughput sequencing

city: Jinan

first: li

last: dong

address: No. 42 Wen Hua Xi Road

institute: shandong university of traditional Chinese medcine

summary:
Background: Infertility is one of the major health problems and the third most common disease, and diminished ovarian reserve (DOR) is a common cause of infertility. DOR is defined as decreased number or quality of oocytes in reproductive-age women, but the underlying molecular mechanisms remain unclear. Long noncoding RNAs (lncRNAs) has been recognized to play an important role in physiological and pathological processes of the human body, but it is unknown whether lncRNAs are involved in the development of DOR.
Methods: The ovarian granulosa cells from infertility women with DOR and normal ovarian reserve (NOR) were obtained and subjected to high-throughput sequencing. A comprehensive bioinformatics analysis was conducted to characterize the mRNAs and lncRNAs expression profiles between DOR and NOR women. Then, the sequencing results were validated by selected randomly lncRNAs using real-time quantitative PCR.
Results: A total of 92,853 lncRNAs transcripts were identified between DOR and NOR GCs. Compared with NOR control, 244 lncRNAs were upregulated (53 known and 191 novel) and 222 lncRNAs were downregulated (36 known and 186 novel) in the DOR group. Similarly, 457 differently expressed mRNAs were found between the two groups, with 169 and 288 up- and downregulated respectively. Further functional analysis revealed that differentially expressed genes of mRNA and lncRNA were significantly enriched in various biological processes such as cell adhesion and apoptosis, steroid biosynthesis, and immune system. The results of correlated expression networks between lncRNAs and their predicted target genes uncovered the possible involvement of the thyroid hormone signaling pathway and protein binding, digestion and absorption in the pathogenesis of DOR and showed that SLC16A10 is positively regulated by multiple lncRNAs. In addition, it was verified that the expression patterns of three of the seven selected differentially expressed lncRNAs were consistent with RNA-Seq. Aberrant lncRNAs might be used to develop new diagnostic biomarkers or drugs to target DOR.
Conclusion: This study is the first to elucidate the lncRNA and mRNA expression profiles between NOR and DOR patients in the ovarian granulosa cells using sequencing technology. The lncRNAs identified in this study can potentially be novel diagnostic biomarkers and therapeutic targets for DOR.

overall_design: Expression profiles of lncRNA and mRNA in ovarian granulosa cells from DOR and NOR patients of reproductive age

first: Haicui

last: Wu

first: Fang

last: Lian

first: Li

last: Dong


title: Generation of human excitatory forebrain neurons by cooperative binding of proneural NGN2 and homeobox factor EMX1

city: Stanford

first: Cheen Euong

last: Ang

address: 265 Campus Drive, G3145

institute: Stanford University

summary: We explored NGN2’s molecular chromatin function and its ability to induce specific neuronal programs in the context of different cell states and different transcription factor combinations using a series of single cell and bulk genomic sequencing techniques and epigenomic methods.

overall_design: Examining the effect of chromatin and cofactor expression in Ngn2 binding and outcomes

first: Marius

last: Wernig


title: Potential Roles of IGF2BP3 in Bladder Cancer

city: Nanning

first: Zengnan

last: Mo

state: Guangxi

address: Zhongshan Street

department: Center for Genomics and Personalized Medicine

institute: Guangxi Medical University


title: Potential Roles of IGF2BP3 in Bladder Cancer [m6A-seq]

summary: TCGA data analysis and clinical sample test results showed the IGF2BP3 is highly expressed in bladder cancer and related to tumor metastasis and invasion. RNA sequencing results of clinical bladder tissue from 53 cases showed that the IGF2BP3 expression is related to cell proliferation genes. M6a and RNA sequencing results showed the IGF2BP3 affects the growth, proliferation, and apoptosis of T24 cells, and SpHK1, POMT2, and MRPS18a may be potential targets of IGF2BP3.

overall_design: (1) The TCGA bladder cancer gene expression and the survival data were used to screen the m6A-related RNA-binding protein IGF2BP3. (2) The expression level of the IGF2BP3 in the bladder tissue was detected using immunohistochemistry and reverse transcription-quantitative PCR . (3) The CRISPR/Cas9 was used to construct a T24 stable cell line with the IGF2BP3 knockout, and DNA sequencing and Western blot were used to verify the knockout effect. (4) The MTT test, colony-forming assay, flow cytometry, scratch test, and transwell invasion test were used to detect the changes in the biological function in IGF2BP3 knockout T24 cell lines. (5) The RNA was extracted from the bladder tissue for sequencing to analyze the role of IGF2BP in bladder cancer. (6) The gene expression and the M6a level in T24 knockout IGF2BP3 cells were analyzed using RNA-seq and Merip-seq, and the mechanism of IGF2BP3 in bladder cancer was preliminarily discussed.

first: Yu

last: Ye

first: Rong

last: Huang

first: Xi

last: Wang

first: Caiwang

last: Deng


title: Potential Roles of IGF2BP3 in Bladder Cancer [RNA-Seq]


title: DNA methylation status determines the sensitivity of repeats to restriction by the HUSH-MORC2 complex [ONT whole genome DNA]

status: Public on Mar 26 2024

city: Lund

first: Ninoslav

last: Pandiloski

address: Sölvegatan 17

country: Sweden

institute: Lund University

summary: The human silencing hub (HUSH) complex binds to transcripts of LINE-1 retrotransposons (L1s) and other genomic repeats, recruiting MORC2 and other effectors to remodel chromatin. However, how HUSH and MORC2 operate alongside DNA methylation, a central epigenetic regulator of repeat transcription, remains poorly understood. Here we interrogate this relationship in human neural progenitor cells (hNPCs), a somatic model of brain development that tolerates removal of DNA methyltransferase DNMT1. Upon loss of MORC2 or HUSH subunit TASOR in hNPCs, L1s remain silenced by robust promoter methylation. However, genome demethylation and activation of evolutionarily-young L1s attracts MORC2 binding. Simultaneous depletion of DNMT1 and MORC2 causes massive accumulation of L1 transcripts. We identify the same mechanistic hierarchy at pericentromeric α-satellites and clustered protocadherin genes, repetitive elements important for chromosome structure and neurodevelopment respectively. Our data delineate the independent epigenetic control of repeats in somatic cells, with implications for understanding the vital functions of HUSH-MORC2 in hypomethylated contexts throughout human development.

overall_design:
DNA methylation levels of genes and transposable elements in human neuroepithelial-like stem cells (hNSC) were examined by ONT long-read DNA sequencing in two different conditions: LacZ - CRISPRi (a control targetting a bacterial gene which is not present in the human genome) and MORC2 - CRISPRi.

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title: DNA methylation status determines the sensitivity of repeats to restriction by the HUSH-MORC2 complex [ONT cDNA sequencing]

overall_design: Long transcripts of transposable elements, long, and nested genes were examined with ONT long-read cDNA sequencing in four different conditions: LacZ - CRISPRi (a control targetting a bacterial gene which is not present in the human genome), MORC2 - CRISPRi, TASOR-CRISPRi, and DNMT1-CRISPRcut.


title: RNA-Seq data from the Gastrocneimus muscle of STIM1+/D84G mice.

city: Durham

first: Paul

last: Rosenberg

state: North Carolina

address: Research Drive

department: Medicine

institute: DUMC

summary: The goal of this study is to characterize the genetic changes that occur in muscle of mice carrying a mutant allele for STIM1 (D84G)

overall_design: RNA from muscle of 6-month old female STIM1+/D84G mice was processed for RNA-sequencing.


title: Single-cell RNA-sequencing of human bronchial epithelial organoids infected by four different betacoronaviruses; HCoV-OC43, SARS-CoV, MERS-CoV, and SARS-CoV-2 and mock control.

city: Daejeon

first: Dongbin

last: Park

address: 55, Expo-ro

institute: Institute for Basic Science

summary: We investigated the interactions of four distinct betacoronaviruses; HCoV-OC43, SARS-CoV, MERS-CoV, and SARS-CoV-2 within human bronchial epithelial (HBE) organoids using single-cell RNA sequencing (scRNA-seq) to comprehensively understand betacoronaviruses cellular tropism and the intricate interplay between these cells and the host's immune defense mechanisms.

overall_design: We establish a comprehensive ALI model of the human respiratory system. To compare the infection dynamics of four betacoronaviruses, we investigate cellular tropism, analyze host factor, and identify the shared or virus-specific host responses, using single-cell RNA sequencing and Immunofluorescence.

first: Young

last: Choi


title: Redirecting the pioneering function of FOXA1 with covalent small molecules [ChIP-seq]

city: La Jolla

first: Yuxiang

last: Zhang

state: CA

address: 10550 N. Torrey Pines Rd.

department: Chemistry

institute: The Scripps Research Institute

summary: Pioneer transcription factors (TFs) exhibit a special ability to bind to and open closed chromatin, facilitating engagement by other regulatory factors involved in gene activation or repression. Chemical probes are lacking for pioneer TFs, which has hindered their mechanistic investigation in cells. Here, we report electrophilic small molecules that stereoselectively and site-specifically bind the pioneer TF, FOXA1, at a cysteine (C258) within the forkhead DNA-binding domain. We show that these covalent ligands react with FOXA1 in a DNA-dependent manner and rapidly remodel its pioneer activity in prostate cancer cells reflected in redistribution of FOXA1 binding across the genome and directionally correlated changes in chromatin accessibility. Motif analysis supports a mechanism where the covalent ligands relax the canonical DNA binding preference of FOXA1 by strengthening interactions with suboptimal ancillary sequences in predicted proximity to C258. Our findings reveal a striking plasticity underpinning the pioneering function of FOXA1 that can be controlled by small molecules.

overall_design: ChIP-seq experiments for profiling the impact of stereoprobes treatments on FOXA1 localization in parental 22Rv1 cells or engineered 22Rv1 cells stably expressing Y36C-PHF5A with dox-inducible WT-FOXA1 or C258A-FOXA1 expression.

first: Michael

last: Erb

first: Benjamin

middle: F

last: Cravatt

first: Sang-Joon

last: Won


title: Cryopreservation of cerebrospinal fluid cells preserves transcriptomics integrity for single-cell analysis

city: Charlestown

first: Mahesh Chandra

last: Kodali

department: Neurology

institute: Massachusetts General Hospital / Harvard Medical School

summary: Cerebrospinal fluid (CSF) matrix biomarkers have become increasingly valuable surrogate markers of neuropsychiatric diseases in research and clinical practice. In contrast, CSF cells have been rarely investigated due to their relative scarcity and fragility, and lack of common collection and cryopreservation protocols, with limited exceptions for neurooncology and primary immune-based diseases like multiple sclerosis. The advent of a microfluidics-based multi-omics approaches to studying individual cells has allowed for the study of cellular phenotyping, intracellular dynamics, and intercellular relationships that provide multidimensionality unable to be obtained through acellular fluid-phase analyses. challenges to cell-based research include site to- site differences in handling, storage, and thawing methods, which can lead to inaccuracy and inter-assay variability. In the present study, we performed single-cell RNA sequencing (10x Genomics) on fresh (Samples labeled as FRE) or previously cryopreserved human CSF samples from three alternative cryopreservation methods: Fetal Bovine Serum with Dimethyl sulfoxide (FBS/DMSO, Samples labeled as FBS), FBS/DMSO after a DNase step (a step often included in epigenetic studies, samples labeled as DNA), and cryopreservation using commercially available Recovery©media (Samples labeled as REC). In comparing relative differences between fresh and cryopreserved samples, we found little effect of the cryopreservation method on being able to resolve donor-linked cell type proportions, markers of cellular stress, and overall gene expression at the single-cell level, whereas donor-specific differences were readily discernable. We further, demonstrate the compatibility of fresh and cryopreserved CSF immune cell sequencing using biologically relevant sexually dimorphic gene expression differences by donor. Our findings support the utility and interchangeability of FBS/DMSO and Recovery cryopreservation with fresh sample analysis, providing a methodological grounding that will enable researchers to further expand our understanding of the CSF immune cell contributions to neurological and psychiatric disease.

overall_design: In the present study, we performed single-cell RNA sequencing (10x Genomics) on fresh or previously cryopreserved human Cerebrospinal Fluid Cells using three alternative cryopreservation methods: Fetal Bovine Serum with Dimethyl sulfoxide (FBS/DMSO), FBS/DMSO after a DNase step (a step often included in epigenetic studies), and cryopreservation using commercially available Recovery© media. In comparing relative differences between fresh and cryopreserved samples, we found little effect of the cryopreservation method on being able to resolve donor-linked cell type proportions, markers of cellular stress, and overall gene expression at the single-cell level, whereas donor-specific differences were readily discernable.


title: Redirecting the pioneering function of FOXA1 with covalent small molecules [ATAC-seq]

overall_design: ATAC-seq experiments for profiling the impact of stereoprobes treatments on chromatin accessibility in parental 22Rv1 cells or engineered 22Rv1 cells stably expressing Y36C-PHF5A with doxycycline-inducible WT-FOXA1 or C258A-FOXA1 expression


title: CTCF ChIP-Seq in a panel of 18 cell lines related to ovarian cancer

city: Los Angeles

first: Michelle

last: Jones

address: 8720 Alden Dv

department: Biomedical Sciences

institute: Cedars-Sinai Medical Center

summary: CTCF ChIP-Seq was generated in a panel of 18 ovarian cancer cell lines to identify active regulatory elements in the genome.

overall_design: ChIP-Seq performed in 18 cell lines. Biological replicates were run for all lines other than ES2

middle: R

first: Simon

last: Gayther


title: Dual specificity phosphate 1 (DUSP1) has a key non-invasive predictive marker in preeclampsia

city: Marseille

first: Jonatane

last: Andrieu

address: 14 rue de chanterac

department: Recherche

country: France

institute: ADES EFS CNRS

summary: Preeclampsia (PE) is a multisystem pregnancy complication constituting a major cause of maternal and fetal morbidity and mortality. Factors pointing to a placental origin are the development of the pathology only during pregnancy, and its disappearance in the post-partum period. Our study identified a specific signature of PE including five Gene Ontology clusters including "angiogenesis and differentiation", "cell cycle”, "cell adhesion", "inflammatory response" and "cellular metabolism". Interestingly, we identified DUSP1 as a biomarker of interest in PE. Pregnant women with PE have a higher concentration of DUSP1 in serum in the first trimester of pregnancy compared to healthy donors. Interesting, at a distance from childbirth DUSP1 finds a rate like the control group showing the predictive interest of DUSP1 as a predictive biomarker of PE

overall_design: Here, we aim to identify new early predictive biomarkers based on a transcriptional signature of PE using RNAseq at the time of the event and the disappearance of expression of these markers at a distance from the event in the postpartum

first: Agathe

last: Donet

first: Jean-François

last: Cocallemen

first: Guillaume

last: Charbonnier

first: Noémie

last: Resseguier

first: Julien

last: Paganini

first: Jean-Louis

last: Mège

first: Soraya

last: Mezouar

first: Florence

last: Bretelle


title: Combinatorial miRNA activity is essential for transition of pluripotent cells into dormancy [ivv_sRNA]

city: Munich

first: Francisca

last: Rojas Ringeling

address: Feodor-Lynen-Straße 25, 81377

department: Biochemistry

country: Germany

institute: Ludwig Maximilian University of Munich

summary: Dormancy is a key feature of stem cell function in adult tissues as well as embryonic cells in the context of diapause. The establishment of dormancy is an active process that involves extensive transcriptional, epigenetic, and metabolic rewiring. How these processes are coordinated to successfully transition cells to the resting dormant state is not known. Here we show that microRNA activity, which is normally dispensable for pre-implantation development, is essential for the adaptation of early mouse embryos to the dormant state of diapause. In particular, the pluripotent epiblast depends on miRNA activity, the absence of which results in loss of pluripotency and embryo collapse. Through small RNA profiling of individual embryos and computational integration of miRNA targets, we identified the miRNA-protein network of diapause. Individual miRNA function contributes to combinatorial regulation by the network and the perturbation of the network reduces embryo survival. Without miRNAs, nuclear and cytoplasmic bodies show aberrant expression. We identified the nutrient-sensitive transcription factor TFE3 as an upstream regulator of miRNA biogenesis, linking mTOR activity to miRNA induction. Our results reveal that miRNAs are critical for the transcriptional and structural rewiring of early embryos to establish dormancy.

overall_design: Investigation of miRNAs differential expression in vitro through induced pausing (through mTOR inhibition) and in vivo both through induced pausing and natural diapause.

first: Dhanur

last: Iyer

first: Lambert

last: Moyon

last: Ringeling

first: Chieh-Yu

last: Cheng

first: Lars

last: Wittler

first: Stefan

last: Canzar

first: Annalisa

last: Marsico

first: Aydan

last: Bulut-Karslioglu


title: Combinatorial miRNA activity is essential for transition of pluripotent cells into dormancy [dgcr8_RNA]


title: DNA methylation status determines the sensitivity of repeats to restriction by the HUSH-MORC2 complex [CUT&RUN]

first: Ninoslav

last: Pandiloski

overall_design:
Comparative H3K9me3 and H3K4me3 enrichment analysis of CUT&RUN-seq data for human neuroepithelial like stem cells (hNSCs). The comparison was done between hNSCs lacking MORC2, TASOR, DNMT1 and their respective controls to investigate the changes induced by the removal of the forementioned epigenetic repressors. Additionally, CUT&RUNseq was also employed to explore the occupancy of MORC2.

Comparative H3K4me3 enrichment analysis of CUT&RUN-seq data for human neuroepithelial like stem cells (hNSCs). The comparison was done between hNSCs lacking DNMT1 and DNMT1+MORC2 and their respective controls to investigate the changes induced by the removal of the forementioned epigenetic repressors.


title: Dual-transcriptome of post-germinating Arabidopsis thaliana mutant lines infected by Alternaria brassicicola

city: Angers

first: Jerome

last: Verdier

address: Rue Georges Morel

institute: INRAE / IRHS

summary: We analyzed transcriptome changes from germinating cyp79B2 cyp79B3, qko, and pad3 mutant Arabidopsis seeds. Here were used mutant lines in Col-0 genetic background: a cyp79B2 cyp79B3 double mutant defective in indolic glucosinolate (cyp79B2/B3), a cyp79B2 cyp79B3 myb28 myb29 quadruple mutant defective in indolic and aliphatic glucosinolates (qko), and a camalexin deficient mutant (pad3). Differentially expressed genes were identified at 3, 6 and 10 days after sowing from both the mutant line seeds and from Alternaria brassicicola when inoculated seeds were analyzed.

overall_design: Three replicates of at least 360 mg of seeds at two and three developemental stages using the model pathosystem Arabidopsis thaliana/Alternaria brassicicola

first: Philippe

last: Grappin

first: Mailen

last: Cuadros


title: DNA methylation status determines the sensitivity of repeats to restriction by the HUSH-MORC2 complex

overall_design: Refer to individual Series (listed below).


title: Perfusable adipose decellularized extracellular matrix biological scaffoldco-recellularizedwith adipose-derived stem cellsand L6 promotes functional skeletal muscle regeneration following volumetric muscle loss

city: Beijing

first: Guan

last: Li

email: umemaro@163.com, zzmbysy@sina.com

state: Beijing

address: 49 North Garden Road

institute: Peking University Third Hospital

summary: In this study, we used a recellularization method of perfusing cells into biological scaffolds through vascular pedicles. ASCs and L6 cells were co-seeded into adipose decellularized extracellular matrix (adECM) biological scaffolds. On one hand, this strategy ensures uniform distribution of seeded cells in the scaffold and avoids the formation of non-functional "muscle islands" later. On the other hand, co-seeding of L6 cells and ASCs addresses the issue of low myogenic differentiation potential of ASCs. Subsequently, the recellularized biological scaffold treatment of VML animal experiments showed that the combined recellularization strategy had significantly better muscle regeneration and angiogenesis than the single ASCs recellularization strategy, and the former had better functional recovery of tibialis anterior muscle (TA). Further single cell sequencing analysis found that compared to singly seeded ASCs in biological scaffolds, L6 cells in the combined recellularization induced ASCs to transform into a new subpopulation of cells highly expressing Mki67, CD34 and CDK1 genes, which had stronger ability of oriented myogenic differentiation and formed more mature and larger muscle fibers, significantly restoring TA muscle function.

overall_design: Healthy Sprague Dawley male rats aged 8 weeks were used to establish the tibialis anterior (TA) muscle VML model (n = 10). The right hind leg skin of the rat was incised, and the fascia and muscle were separated. A muscle defect (7 × 10× 3 mm) was excised from TA. Simultaneously, the tissue constructs could be implanted at this point.adECM + ASCs group: The adECM was implanted in the VML defect with ASCs recellularization; adECM+ASCs+L6 group: The adECM was implanted in the VML defect with ASCs+L6 co-recellularization. Both side of the muscle of each rat were removed from the 7day of modeling for snRNA-seq.

first: Yang

last: An

first: Wei

last: Liang

first: Meng

last: Han

first: GUan


title: MicroRNA profiling of Wilms Tumour 1 deleted and induced embryonic stem cells

city: Berhampur

first: Ruthrothaselvi

last: Bharathavikru

state: Odisha

address: IISER Berhampur, Transit Campus

department: Biological Sciences

country: India

institute: Indian Institute of Science Education and Research

summary: We report the microRNA profiles of the mouse embryonic stem cell (E14IV), which have been deleted for tumour suppressor Wilms' Tumour 1 (WT1), and induced with retinoic acid. Additionally, cells that had an inducibe WT1 expression where also used to compare the microRNA  profile during different time points of WT1 induction.

overall_design: Examination of different microRNA profiles in wildtype embryonic stem cells were compared to Wt1 knockout ES cells, retionic acid treated ES cells and Wt1 KO ES cells, and i inducible induction of Wt1 at 12 hour and 24 hour timepoint.

first: Joan

last: Slight

first: Giulia

last: Petrovich

first: Stuart

last: Aitken


title: Chronic viral mimicry induction following p53 loss promotes immune evasion [Mouse RNASeq]

city: Toronto

first: Sajid

last: Marhon

state: ON

address: 101 College Street

institute: Princess Margaret Cancer Centre

summary: Epigenetic therapies that alter DNA- and/or histone modifications facilitate transcription of immunogenic repetitive elements that cull cancer cells through ‘viral mimicry’ responses. Paradoxically, cancer-initiating events that include functional inactivation of canonical tumor suppressor proteins also facilitate transcription of repetitive elements. Contributions of repetitive element transcription towards cancer initiation, and the mechanisms by which cancer cells evade lethal viral mimicry responses during tumor initiation remain poorly understood. In this report, we characterize patient-derived premalignant lesions of the fallopian tube along with syngeneic mouse models of epithelial ovarian cancer to explore the earliest events of tumorigenesis following loss of the p53 tumor suppressor protein. We report that p53 loss disrupts constitutive heterochromatin to permit transcription of immunogenic repetitive elements capable of activating viral mimicry responses. While acute viral mimicry activation diminishes cell fitness, chronic viral mimicry activation following p53 loss promotes epigenetic reprogramming that increases tolerance of cytosolic nucleic acids and diminishes cellular immunogenicity as a pro-survival adaptation. This selection process we describe as ‘viral mimicry conditioning’ can be partially attenuated by the reverse transcriptase inhibitor 3TC to delay spontaneous tumorigenesis. Altogether, these results reveal that viral mimicry conditioning following p53 loss selects for diminished cell immunogenicity to promote immune evasion upon cancer initiation. Disruption of viral mimicry conditioning during cancer initiation may represent a pharmacological target for early cancer interception.

overall_design: RNASeq

first: Charles

last: Ishak

first: Daniel

last: De Carvalho


title: Combinatorial miRNA activity is essential for transition of pluripotent cells into dormancy [ivt_sRNA]

first: Francisca

last: Rojas Ringeling

first: Dhanur

last: Iyer

first: Lambert

last: Moyon

last: Ringeling

first: Chieh-Yu

last: Cheng

first: Lars

last: Wittler

first: Stefan

last: Canzar

first: Annalisa

last: Marsico

first: Aydan


title: Immune Escape of Chronic Myeloid Leukemia in Blast Crisis:  The Cross-over of T cell microRNAs, Metabolism and Exhaustion

status: Public on Mar 25 2024

city: Duarte

first: Hsun

middle: Teresa

last: Ku

address: 1500 E. Duarte Road

department: Translational Research and Cellular Therapeutics

institute: City of Hope

summary: We observed that T cells from patients with blast crisis (BC) chronic myeloid leukemia (CML) lacked miR-142 and were fewer and exhausted compared with those from patients with chronic phase (CP) CML. Accordingly, the BC Mir142−/−BCR/ABL mouse also presented with T lymphopenia compared with the CP Mir142+/+BCR/ABL mouse. The miR-142 deficit impaired thymic differentiation of lymphoid-primed multipotent progenitors (LMPP) into mature T cells and redirected them toward myeloid lineage. The fewer mature T cells that emerged from LMPP differentiation in the BC mouse were enriched with exhausted T effectors. Leukemic blasts-secreted inflammatory cytokines (i.e., IL-6) mediated the miR-142 deficit, which in turn prevented the metabolic reprogramming that allows activated T cells to thrive and expand and promoted expression of the exhaustion marker PD-1. Thus, loss of miR-142 expression ultimately resulted in BC immune escape and disease growth. In fact, immunodeficient mice transplanted with BC CML LSKs and miR-142 KO T cells had shorter survival than those transplanted with BC CML LSKs and miR-142 wild-type T cells. Conversely, BC patient-derived xenograft (PDX) mice receiving autologous T cells and synthetic miR-142 mimic lived longer than those receiving autologous T cells and scramble RNA. Combination of tyrosine kinase inhibitors (TKI) plus synthetic miR-142 and/or PD-1 antibody induced a prolonged survival compared to TKI alone, suggesting that harnessing the host immune system with synthetic miR-142 may provide a novel therapeutic approach for BC CML.

overall_design: T cells (2x105/sample) from the spleen of Mir142+/+BCR-ABL (CP CML, n=8 mice) and Mir142−/−BCR-ABL (BC CML, n=6 mice) (BCR-ABL were induced for three weeks by tet-off) mice were sorted, and total RNA was extracted using the miRNeasy Micro Kit (Qiagen, Valencia, CA). RNA sequencing libraries were prepared with Kapa mRNA HyperPrep kit (Kapa Biosystems) according to the manufacturer's protocol. RNA-seq libraries were sequencing on Illumina NovaSeq6000 with the sequencing length of 2x101bp.

first: Bin

last: Zhang

first: Min-Hsuan

last: Chen


title: High-throughout sequencing of ovarian cancer cells treated with TMPyP4 and H2O2

city: Wenzhou

first: Kejie

state: Zhejiang

address: Chashan

institute: Wenzhou Medical University

summary: The high-throughput sequencing technology was performed after the treatment of human ovarian cancer cells A2780 with TMPyP4 and H2O2 purchased from Sigma-Aldrich, to explore the expression of genes related to cell proliferation, DNA damage and ROS levels of ovarian cancer cells A2780 after the treatment of TMPyP4 and H2O2, and to find an interesting target pathway,HIF-1 signaling pathway.

overall_design: In dark conditions, human ovarian cancer cells A2780 treated with TMPyP4 at the concentration of 5 µM for 72 hours is the TMPyP4 group, A2780 incubated for 46 hours and then treated with H2O2at the concentration of 200 µM for 2 hours and incubated for another 24 hours is the H2O2 group, A2780 treated with TMPyP4 at the concentration of 5 µM for 46 hours and then treated with H2O2at the concentration of 200 µM for 2 hours and incubated with TMPyP4 for another 24 hours is the co-treatment of TMPyP4 and H2O2 group. The experimental design of light conditions is same as dark conditions, with the exception of a 3-minute exposure to 600 nm white light at 48 hours.

first: Feng

last: Lin

first: Xiaohui

last: Zheng


title: DNA methylation status determines the sensitivity of repeats to restriction by the HUSH-MORC2 complex [Bulk RNA-seq]

first: Ninoslav

last: Pandiloski

overall_design: Expression levels of genes and transposable elements in human neuroepithelial-like stem cells (hNSC) was examined by Bulk-RNA sequencing in five different conditions: LacZ - CRISPRi (a control targetting a bacterial gene which is not present in the human genome), TASOR - CRISPRi, MORC2 - CRISPRi, DNMT1 - CRISPRi and DNMT1&MORC2 - CRISPRi.


title: Combinatorial miRNA activity is essential for transition of pluripotent cells into dormancy

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

overall_design: Refer to individual Series


title: Retinoic acid promotes tissue regeneration by resolving stem cell lineage plasticity

city: New York

first: Matthew

last: Tierney

address: 1230 York Ave, Box 300

institute: Rockefeller University

summary: Stem cells upended from their niche upon injury display lineage plasticity, a transient multi-lineage state essential for tissue repair. Employing high-throughput approaches and three-dimensional cultures of hair follicle stem cells (HFSCs), we investigate the signals that govern the transition between homeostatic regeneration and lineage plasticity. We identify retinoic acid (RA) as a master orchestrator of HFSC behavior during these two processes. In the hair follicle, RA signals within defined niches and interacts with WNT and BMP cues to drive hair regeneration. In wounded skin, reduced RA signaling prompts HFSCs to prioritize epidermal re-epithelialization and must be restored to promote hair regrowth. Substantiated in vivo, our findings have profound therapeutic implications for hair growth and for chronic wounds and cancers, where lineage plasticity is unresolved.

overall_design:
scRNA-seq: Mouse skin and hair follicle cells were FACS-purified from AnaVI back skin and submitted for single cell RNA-sequencing using the 10x Genomics platform. In parallel, autologous hair follicle stem cells (HFSCs) were FACS-purified, propagated in culture, and apportioned into 3D cultures as described. Cultured HFSC colonies from each condition were dissociated, multiplexed using TotalSeq-B hashtag antibodies, and submitted for single cell RNA-sequencing using the 10x Genomics platform.

ATAC-seq: Mouse hair follicle stem cells (HFSCs) from wild-type and Sox9-CreER;Rxra-fl/fl;R26-YFP mice were FACS-purified from telogen back skin, propagated in culture, and apportioned into 3D cultures. ATAC-seq was performed as described in Buenrostro et al., 2013.

bulkRNA-seq: Mouse hair follicle stem cells (HFSCs) from wild-type and Sox9-CreER;Rxra-fl/fl;R26-YFP mice were FACS-purified from telogen back skin, propagated in culture, and apportioned into 3D cultures. Cells were collected in Trizol and bulk RNA-seq was performed.

Cut&Run: Mouse hair follicle stem cells (HFSCs) from wild-type and Sox9-CreER;Rxra-fl/fl;R26-YFP mice were FACS-purified from telogen back skin, propagated in culture, and apportioned into 3D cultures. Cells were collected to perform Cut-N-Run experiments for different antibodies.

first: M

first: E

last: Fuchs


title: Peeling back the layers of competitive exclusion using Salmonella as a model

city: Blacksburg

first: John

last: Maurer

state: VA

address: 175 West Campus Dr.

department: School of Animal Sciences

institute: Virginia Tech

summary: An ex vivo system was developed to monitor Salmonella growth, virulence (SPI1 expression) and gene expression (measured by microarray) in response to the permissive and exclusive communities.  Yellow fluorescent protein (yfp) and cyan fluorescent protein (cfp) variants were fused to the rrn growth-dependent promoter and the hilA operon (SPI-1 cell invasion locus), respectively, in Salmonella. Fluorescence associated with the YFP and CFP reporters was used to monitor Salmonella growth and SPI1 virulence gene expression in co-culture with cecal communities ex vivo. The Salmonella reporter strain was grown in dialysis tubing in a simulated cecal medium, ex vivo cecal contents (EVCC), submerged in permissive or exclusive communities, to enable collection of Salmonella cells for study.  Initially, the fluorescent reporters were used to empirically determine the earliest time point at which the exclusive community had the most significant impact on Salmonella growth or virulence expression relative to the permissive community, which was six-hour co-culture of the reporter strain with the communities. Cells were harvested at that time point for gene expression comparisons. Genes within metabolic pathways that were differentially expressed in permissive vs. exclusive communities were subsequently deleted in Salmonella and mutants’ growth dynamics when cocultured with the exclusive community were monitored over 48 hours using a fluorescence plate reader.

platform_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S

overall_design:
Baby chicks administered a fecal transplant from adult chickens are resistant to Salmonella colonization by competitive exclusion. A two-pronged approach was used to investigate the mechanism of this process. First, Salmonella response to an exclusive (Salmonella competitive exclusion product, Aviguard®) or permissive microbial community (chicken cecal contents from colonized birds containing 7.85 Log10 Salmonella genomes/gram) was assessed ex vivo using a S. Typhimurium reporter strain with fluorescent YFP and CFP genes fusions to rrn and hilA operon, respectively. Second, cecal transcriptome analysis was used to assess the cecal communities’ response to Salmonella in chickens with low (<5.85 Log10 genomes/g) or high (>6.00 Log10 genomes/g) Salmonella colonization. The ex vivo experiment revealed reduction in Salmonella growth and hilA expression following co-culture with the exclusive community. The exclusive community also repressed Salmonella’s SPI-1 virulence genes, LPS modification, while the anti-virulence/inflammatory gene avrA was upregulated. Salmonella transcriptome analysis revealed significant metabolic disparities in Salmonella grown with the two different communities. Propanediol utilization and vitamin B12 synthesis was central to Salmonella metabolism co-cultured with either communities; and mutations in propanediol and vitamin B12 metabolism altered Salmonella growth with the exclusive community. There were significant differences in the cecal community, stress response to Salmonella colonization. Cecal community transcripts indicated that antimicrobials were central to the type of stress response detected in the low Salmonella abundance community suggesting antagonism involved in Salmonella exclusion. This study indicates complex community interactions that modulate Salmonella metabolism and pathogenic behavior and reduce growth by antagonism may be key to exclusion.
A six-chip / eleven-sample study using total RNA recovered from Salmonella enterica sv Typhimurium SL1344-derivative YC1104 grown inside dialysis tubing either without any microflora (CTRL), with commercial competitive exclusion product Aviguard outside of the tubing (AV), or with cecal content with high Salmonella load (CECAL35-4) outside of the tubing. Each chip measures the expression level of all Salmonella enterica genes on an oligo array consisting of roughly 380,000 oligos, designed based on the Salmonella typhimurium LT2 (NC_003197.1) and 14028s (CP001363.1: complete genome and CP001362.1: plasmid) genomes, with a moving window of about 12 bases.

middle: J

first: Ying

first: Steffen

last: Porwollik

first: Michael

last: McClelland


title: MicroRNA therapeutics for stratified treatment of Schizophrenia

city: Göttingen

first: Lalit

last: Kaurani

address: Von-Siebold-Straße 3A

institute: DZNE-Göttingen

summary: Schizophrenia (SZ) is a devastating psychiatric illness affecting 1% of the world population. In addition to genetic predisposition, environmental factors contribute to the risk for developing SZ. Such genome environment interactions frequently activate epigenetic and epitranscriptomic mechansims. There are emerging evidence that genetic and environmental risk factors merge at the level of microRNA expression, which are discussed as biomarker and therapeutic target in various disorders including neuropsychiatric diseases. In this study we analyzed the blood microRNAome of healthy individuals and SZ patients via small RNA sequencing. By combining these data with a corresponding analysis of post-mortem human brain tissue, we identify one candidate microRNA that is down-regulated in patients. Moreover, its expression is significantly correlated to disease phenotypes.  Manipulation of this microRNAs in mouse prefrontal cortex causes schizophrenia-like phenotypes. Functional analysis revealed the cellular processes affected by this microRNA and allowed us to develop an arsenal of RNA-based therapeutic approaches that are able to ameliorate molecular disease phenotypes in mouse and human-based cellular systems as well as the behavioral phenotypes. In conclusion, we identify a novel microRNA as target for stratified RNA-therapeutics in schizophrenia.

overall_design: A candidate microRNA knockdown was performed in the adult mouse PFC region as well as in primary microglia, followed by gene expression profiling analysis of RNA-Seq data.

first: Andre

last: Fischer


title: The lipid droplet protein DHRS3 is a regulator of melanoma cell state

first: Eleanor

last: Johns

address: 417 E 68th Street

department: Cancer Biology and Genetics

institute: Memorial Sloan Kettering Cancer Center

summary: Lipid droplets are fat storage organelles composed of a protein envelope and a lipid rich core. Dynamic regulation of this protein envelope underlies differential lipid droplet formation and function in diverse cell types. In melanoma, the ability to form lipid droplets has been linked to tumor progression and metastasis, but it is not known whether lipid droplet proteins play a role in these phenotypes. To address this, we performed proteomic analysis of the lipid droplet envelope in melanoma. We found that proteins expressed in the lipid droplet were differentially enriched in distinct melanoma states, ranging from melanocytic to neural crest like. DHRS3, which is involved in the conversion of all-trans-retinal to all-trans-retinol, is significantly upregulated in the MITFLO/neural crest-like melanoma cell state, and markedly reduced in the MITFHI/melanocytic state. Increased DHRS3 expression is sufficient to drive the MITFHI/melanocytic cells to a more undifferentiated and invasive state. These changes are due to retinoic acid mediated regulation of melanocytic genes through the retinoid X receptors (RXR). Our data demonstrate that melanoma cell state can be regulated by expression of lipid droplet proteins which affect downstream retinoid signaling.

overall_design: To investigate the effects of DHRS3 overexpression on melanoma cell fate we overexpressed DHRS3-V5 in IGR37 human melanoma cells compared to control. We also looked at the effects of 6 hour oleic acid treatment of cells to induce lipid droplet formation in both control and DHRS3-V5 overexpressing IGR37 cells. We then performed bulk RNA-seq to look at the transcriptional changes that occur across these conditions using gene expression profiling analysis. Each condition has 3 replicates

first: Yilun

last: Ma

first: Richard

last: White


title: BCAS2 and hnRNPH1 orchestrate alternative splicing for DNA double-strand break repair and synapsis in meiotic prophase I

first: Liu

last: Jiali

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

department: College of Biological Sciences

institute: China Agricultural University


title: BCAS2 and hnRNPH1 orchestrate alternative splicing for DNA double-strand break repair and synapsis in meiotic prophase I [RNAs-seq]

summary: Understanding the intricacies of homologous recombination during meiosis is crucial for reproductive biology. However, the role of alternative splicing (AS) in DNA double-strand breaks (DSBs) repair and synapsis remains elusive. In this study, we investigated the impact of conditional knockout (cKO) of the splicing factor gene Bcas2 in mouse germ cells, revealing impaired DSBs repair and synapsis, resulting in non-obstructive azoospermia (NOA). Employing crosslinking immunoprecipitation and sequencing (CLIP-seq), we globally mapped BCAS2 binding sites in the testis, uncovering its predominant association with 5' splice sites (5'SS) of introns and a preference for GA-rich regions. Integrating CLIP-seq with RNA-seq, we identified BCAS2 as a key player in the AS of pre-mRNAs, including Spo11, Six6os1, Sycp1, Msh5, Cdk2, Sun2, Stag3, and Spdya, crucial for DSBs repair and synapsis. Notably, BCAS2 exhibited direct binding and regulatory influence on Trp53bp1 and Six6os1 through AS, unveiling novel insights into DSBs repair and synapsis during meiotic prophase I. Furthermore, the interaction between BCAS2, hnRNPH1, and SRSF3 was discovered to orchestrate Trp53bp1 expression via AS, underscoring its role in meiotic prophase I DSBs repair. In summary, our findings delineate the indispensable role of BCAS2-mediated post-transcriptional regulation in DSBs repair and synapsis during male meiosis. This study provides a comprehensive framework for unraveling the molecular mechanisms governing the post-transcriptional network in male meiosis, contributing to the broader understanding of reproductive biology.

overall_design: STRA8+ cell suspensions were isolated and prepared from mouse testes. Total RNA was extracted from STRA8+ cells.

first: Longjie

last: Sun

first: Zheng

last: Lv

first: Chaofan

last: Wang

first: Jiali

last: Liu