title: RNA-seq analysis of chemotherapy resistance in esophageal squamous cell carcinoma

city: Shijiazhuang

first: Yuchen

last: Wang

state: Hebei

address: No.12, Jiankang Road

institute: The Fourth Hospital of Hebei Medical University

summary: Esophageal cancer presents significant challenges due to limited treatment options and poor prognosis, particularly in advanced stages. Dysregulated long non-coding RNAs (lncRNAs) are implicated in cancer progression and treatment resistance. This study investigated the roles of dysregulated lncRNA, identified through lncRNA-seq, and its downstream target gene  in esophageal squamous cell carcinoma（ESCC).

overall_design: In order to investigate the molecular mechanism of different sensitivity of esophageal squamous cell carcinoma to chemotherapy, we performed incrNA-seg to detect the differentially expressed IncRNA in esophageal squamous cell carcinoma tissues between chemotherapy-sensitive and chemotherapy-resistant groups. To comprehensively explore LncRNA and its downstream molecules in ESCC, cell functions including cell viability, cell proliferation and flow cytometry analysis were examined after interference and overexpression of differential IncRNA.

first: Yingying

first: Jinze

last: Zhang

first: Zhihua

last: Shi

first: Junfeng

last: Liu


title: The Functional Roles of HDAC1 and HDAC2 in Neurodevelopment of the Mouse Brain

status: Public on Oct 01 2024

city: Shanghai

first: Yunli

last: Xie

state: Shanghai

address: 131 Dong'an Road, Shanghai

department: Institutes of Brain Science

country: China

institute: Fudan University

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

summary: In this study, we explored the roles of histone deacetylases HDAC1 and HDAC2 in the developmental dynamics of the mouse brain. We discovered that these epigenetic regulators, HDAC1/2, are crucial in mediating the transition from neural epithelial cells (NEs) to radial glial cells (RGCs). To probe the epigenomic influence of HDAC1/2 on cortical development, we utilized a suite of techniques including RNA sequencing (RNA-seq), single-cell RNA sequencing (scRNA-seq), and H3K27ac Cleavage Under Targets and Tagmentation (CUT&Tag) in both wild-type (WT) and HDAC1/2-deficient brain samples. Our analysis identified a significant dysregulation of numerous transcription-related genes in the HDAC1 and HDAC2 mutant brains. These findings underscore the critical role of HDAC1/2 as epigenetic modulators in the NE-to-RGC transition.

overall_design: For all expresiments cells from embryonic mouse brains were isolated from control and HDAC1/2 cKO mice were collected. Single cell sequencing library were prepared using 10x Genomics Chromium Single Cell 3`v3 assays.For bulk RNA-seq, Mouse embryonic for brains were isolated from E13.5,E14.5,E15.5 and E16.5 embryos. Total RNAs were extracted using Trizol reagent and applied for RNA sequencing subsequently. And H3K27ac Cleavage Under Targets and Tagmentation (CUT&Tag) in both wild-type (WT) and HDAC1/2-deficient brain samples.

first: Yue

last: Zhu

first: Yunyun

last: Huang


title: Drosha loss drives pineoblastoma by upregulating Ccnd2 [smallRNAseq of normal brain, Drosha tumor, and pineal gland

status: Public on Oct 03 2024

city: Dallas

first: Kenneth

middle: S

last: Chen

state: TX

address: 5323 Harry Hines Blvd

department: Pediatrics

country: USA

institute: UT Southwestern

type: Non-coding RNA profiling by high throughput sequencing

summary: Mutations in the microRNA processing genes DICER1 and DROSHA drive childhood cancers such as pineoblastoma, a brain tumor that resembles undifferentiated precursors of the pineal gland. To understand how microRNAs regulate proliferation of these progenitors, we developed a mouse model of pineoblastoma by ablating Drosha or Dicer1 in the developing pineal gland. The tumors that arise in these models resemble proliferative, undifferentiated embryonic progenitors. They are marked by loss of microRNAs, including the let-7 family, and de-repression of let-7 target genes. One upregulated let-7 target gene is the oncofetal transcription factor Plagl2, which activates expression of key pro-growth genes Igf2 and Ccnd2, and we show that small molecules targeting these two drivers block tumor growth. Thus, our results demonstrate that tumors driven by loss of microRNA processing may be therapeutically targeted by inhibiting downstream drivers of proliferation.

overall_design: We used small RNA sequencing in IPDrosha tumor, matched normal brain, and age-matched normal pineal glands, to identify microRNAs expressed in each tissue and lost in IPDrosha tumors.

first: Claudette

middle: R

last: Fraire

first: Kavita

last: Desai

first: Lindsay

last: Mendyka

first: Uma

last: Obalaparum

first: Teja

last: Sebastian

first: Veena

last: Rajaram


title: Effect of RBN-2397, paclitaxel and their combination on ovarian cancer cell biology.

first: W. Lee

last: Kraus

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

summary: PARP7 (TiPARP), a mono (ADP-ribosyl) transferase (MART) was found to target α-tubulin proteins in ovarian cancer cells, enhancing their growth and migration. RBN-2397 is a potent inhibitor that selectively acts on PARP7. Here, we show that RBN-2397 treatment leads to the stabilization of microtubules in ovarian cancer cells, namely α-tubulin, mimicking what was previously observed with PARP7 knockdown. When treated with RBN-2397, we observe a decrease in growth and migration of ovarian cancer cells and, interestingly, the effect is intensified upon adding the microtubule stabilizing chemotherapeutic agent, paclitaxel. Mutating the site of α-tubulin MARylation by PARP7 similarly results in α-tubulin stabilization and decreased cell migration in the presence of paclitaxel when the tubulin network is further stabilized. In sum, we demonstrate that PARP7 inhibition decreases α-tubulin MARylation resulting in its stabilization, and ultimately leading to decreased ovarian cancer cell proliferation and migration. Finally, we show that combining PARP7 inhibitor and paclitaxel results in a more robust inhibition of aggressive ovarian cancer phenotypes. Collectively, this study highlights the potential of targeting PARP7 in combination with established chemotherapeutic agents to enhance treatment efficacy for ovarian cancer.

overall_design: RNA seq of OVCAR4 and OVCAR3 cell lines treated with DMSO, PARP7 inhibitor, taxol and combination.

first: Alexandra

middle: N

last: Spirtos

first: Marwa

middle: W

last: Aljardali

first: Sneh

last: Koul

first: Jayanthi

last: Lea

first: Cristel

middle: V

last: Camacho

first: W

middle: L


title: Effect of regorafenib, anti-PD1, and anti-CD40 agonist in Head and Neck Squamous Cell Carcinoma [4NQO_model]

city: Taipei

first: Chia-Lang

last: Hsu

address: No. 7, Zhongshan S. Rd.

department: Department of Medical Research

country: Taiwan

institute: National Taiwan University Hospital

summary: Regorafenib presented an antitumor activity in HNSCC mouse model and delayed the tumorigenesis of the 4NQO-indued oral mouse model. By tumor-infiltration lymphocytes isolation and RNA-seq analysis, the immunity-related function was activated by regorafenib. We approved that regorafenib can determine the macrophage polarization toward M1 inflammatory macrophages by suppressing the production of certain cytokines such as plasminogen activator inhibitor-1 (PAI-I) from tumor cells. Also, Regorafenib suppresses secretion of PAI-1 from ex vivo cultures of human HNSCC organoids.

overall_design: We performed RNA-seq on tumors from HNSCC mouse model and 4NQO-indued oral mouse model with the treatment of vehicle control, regorafenib, anti-PD1, and regorafenib + anti-PD1

first: Y

middle: H

middle: M

last: Lee

first: D

last: Ou

first: C

middle: T

last: Tang


title: SART3 is a Novel Rme2s Reader

city: Houston

first: Bin

last: Liu

address: 1515 Holcombe BLVD

department: epigenetics and molecular carcinogenesis

institute: University of Texas MD Anderson Cancer Center

summary: Arginine methylation is a ubiquitous post-translational modification involved in many biological processes such as transcription, cell signaling and RNA splicing. Tudor domains by far are the major effector domain family for arginine methylation mark recognition. Here we characterize SART3 as a novel selective reader for symmetric dimethylarginine (Rme2s) marks. SART3 harbors a series of HAT (Half-a-TPR) repeats that are aromatic-rich, and it is this region that binds Rme2s motifs. An analysis of the reported structure of the HAT repeats of SART3 identified a putative aromatic cage that potentially “read” the Rme2s-modified motifs, and the key aromatic residues required for Rme2s recognition were identified. We further confirm that this Rme2s reader ability is important for SART3-mediated RNA splicing. Together, our studies revealed that the evolutionarily conserved SART3 HAT domain was a novel reader of Rme2s mark involved in RNA splicing.

overall_design: Hela SART3-KO was restored with SART3 wild-type(WT) or mutants(Y112A, W377A), total RNA was harvested for RNA-seq analysis

first: Mark

last: Bedford

first: Yalong

last: Wang


title: Targeting Cyclin Y Inhibits STAT3 Activation to Enhance Radiosensitivity via Down-regulation of RRM2 in Lung Cancer

city: Wuhan

first: Zhi

middle: Wei

state: Hubei

address: No.13, Aviation Road, Baofeng Street, Qiaokou District

institute: HuaZhong University of Science and Technology

summary: Purpose: Radioresistance is a main reason for the recurrence and metastasis of lung cancer. Cyclin Y is involved in normal physiological processes such as cell proliferation, growth and metabolism, as well as in the development of certain cancers. However, the function and mechanism of Cyclin Y in lung cancer are still unclear.Methods: Lung cancer cell lines were subjected to Cyclin Y knockdown using small interfering RNA (siRNA), and their growth and proliferation were assessed in vitro. Comet assay, γH2AX/Rad51 foci formation assay and clonogenic cell survival assay were performed to assess DNA damage and the DNA repair capacity. SgRNA transfection was applied to construct cell lines with stable Cyclin Y knockdown. Xenograft mouse models were used to validate the findings in vivo. RNA sequencing (RNA-seq) analysis was conducted to clarify the downstream target genes of Cyclin Y. Western blotting was employed to measure protein expression.Results: Cyclin Y was overexpressed in lung cancer, correlating with poor prognosis. Cyclin Y knockdown inhibited cell growth and proliferation, increased DNA damage, inhibited DNA damage repair and increased radiosensitivity in vitro and in vivo. RNA-seq analysis was used to reveal RRM2 as a downstream target gene of Cyclin Y. Cyclin Y depletion down-regulated the protein and mRNA levels of RRM2, leading to reduced STAT3 phosphorylation. Rescue experiments demonstrated that the effect of Cyclin Y on lung cancer was mediated partially by RRM2.Conclusions: We revealed for the first time that targeting Cyclin Y inhibits tumorigenesis and promotes radiosensitivity in lung cancer partially through the RRM2-STAT3 signaling pathway.

overall_design: RNA sequencing (RNA-seq) analysis was conducted to clarify the downstream target genes of Cyclin Y, which we use siRNAs to knock down in A549 cells.

first: Zhiwei

first: Xiaorong

last: Dong

first: Shuangbin

last: Xu


title: Git2 deficiency promotes MDSCs recruitment in intestine  and ameliorates necrotizing enterocolitis.

city: shanghai

first: huijuan

last: le

address: kongjiang road

department: School of Medicine

institute: Shanghai Jiaotong University

summary: Necrotizing enterocolitis (NEC) is a life-threatening gastrointestinal  disease in newborns. Myeloid-derived suppressor cells (MDSCs) play an important role in immunosuppressive function and ameliorate NEC. G protein-coupled receptor kinase-interacting protein 2 (GIT2) has been implicated in multiple immune processes. Our study demonstrates that Git2 deficiency in mice can promote MDSCs recruiment in intestine. This data will reveal that the mechanism of MDSCs' intestinal gathering in Git2-knockout mice compares to wilde type mice.

overall_design: Intestinalepithelialcells (IEC) from Git2-knockout mice and wild type mice. All included samples are enteroid from 12 days mice.

first: Huijuan

last: Le


title: Genome-wide chromatin profiles of ZNF395

city: Singapore

first: Xiaosai

last: Yao

address: 60 Biopolis Street, Genome, #02-01

country: Singapore

institute: Genome Institute of Singapore

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

overall_design: Refer to individual Series


title: Inflammatory gene expression in livers undergoing ex situ normothermic perfusion is attenuated by leukocyte removal from the perfusate

city: Cambridge

first: Kasra

last: Bahadori

state: Cambridge

address: Francis Crick Avenue

department: Medicine

country: United Kingdom

institute: University of Cambridge

summary:
ABSTRACT:
Background.
Ex situ normothermic perfusion (ESNP) is a method to evaluate and potentially recondition organs before transplantation. However, increased expression of inflammatory molecules, including by tissue-resident immune cells, may occur during the perfusion process, potentially negating the beneficial effects of perfusion.

Methods.
We used RNA sequencing to assess gene expression in 31 livers undergoing ESNP, including 23 donated after circulatory death (DCD) and 8 donated after brain death. In 7 DCD livers, a leucocyte filter was added to the circuit during perfusion. Biopsies were available for transcriptomic assessment in all cases at the start of perfusion and at varying time points postperfusion.

Results.
During ESNP in DCD livers, we observed an increase in proinflammatory, profibrinolytic, and prorepair pathway genes. SERPINE1, encoding plasminogen activator inhibitor-1, was among the genes most significantly upregulated during perfusion in DCD livers, potentially promoting fibrin clot persistence in vasculature. We also found increased expression of monocyte and neutrophil recruiting chemokine and proinflammatory cytokine transcripts during ESNP, but several prorepair molecules, including thymic stromal lymphopoietin, were also upregulated. In both DCD and donation after brain death livers, interferon-gamma response genes were enriched, whereas oxidative phosphorylation genes decreased in organs with high perfusate alanine transaminase, a biomarker associated with adverse clinical outcomes. The inclusion of a leukocyte filter in the perfusion circuit mitigated the induction of inflammation/immune pathway genes during perfusion and was associated with enrichment in oxidative phosphorylation genes.

Conclusions.
Leukocyte removal during ESNP abrogates transcriptional changes that are associated with unfavorable clinical outcomes, potentially benefiting human livers undergoing ESNP.

overall_design:
experiment1: Comparative gene expression profiling analysis of RNA-seq data of DCD (donation after circulatory death) liver biopsies taken pre and post machine perfusion.
experiment2: Comparative gene expression profiling analysis of RNA-seq data of DCD (donation after circulatory death) liver biopsies taken pre and post machine perfusion with the addition of a leukocyte filter.
experiment3: Comparative gene expression profiling analysis of RNA-seq data of DCD (donation after circulatory death) liver biopsies of pre-perfusion samples with a raised 2h perfusate alanine transaminase levels
experiment4: Comparative gene expression profiling analysis of RNA-seq data of DBD (donation after brainstem death) liver biopsies of pre-perfusion samples with a raised 2h perfusate alanine transaminase levels

first: Colin

middle: Y

first: John

last: Ferdinand

first: Mia

last: Cabantous

first: Andrew

last: Butler

first: Foad

middle: J

last: Rouhani

first: Christopher

last: Watson

first: Menna

last: Clatworthy


title: Genome-wide chromatin profiles of ZNF395 [RNA-seq]

summary: Hypoxia signaling induced by VHL deficiency fuels growth but also poses immense metabolic stress to clear cell renal cell carcinomas (ccRCCs). Tumor cells depend on glutamine as the primary source of tricarboxylic acid (TCA) anaplerosis. Hypoxia-inducible factor alpha (HIFα) governs glycolysis but does not directly regulate glutamine metabolism; instead, the factor responsible for orchestrating glutamine metabolism and mitochondrial adaptations to hypoxia remains elusive. We now show that ZNF395 is a hypoxia-responsive factor that regulates glutamine metabolism in the mitochondria. ZNF395 is activated by a HIF2α-modulated super-enhancer but plays non-redundant functions from HIF2α. Specifically, ZNF395 facilitates the transcription of enzymes essential for glutaminolysis, including glutaminase (GLS) and isocitrate dehydrogenase 2 (IDH2). Functionally, ZNF395 depletion results in reduced TCA intermediates and their derivatives, including amino acids, glutathione and pyrimidine nucleotides. In addition, ZNF395 depletion diminishes mitochondrial respiration; restoration of complex I function rescues the effects of ZNF395 depletion. Our study underscores the coordinated role of HIFα and ZNF395 in shaping metabolic adaptations in response to hypoxia in VHL-deficient ccRCCs.

overall_design: Comparison of transcriptomic changes with and without ZNF395 shRNA-mediated knockdown

first: Bin

last: Teh


title: Effect of phosphorus deficiency on gene expression of sorghum roots

city: beijing

first: jiayang

last: shi

address: No.1 House, West Beichen Road

institute: University of Chinese Academy of Sciences

summary: To verify whether phosphorus deficiency can induce sorghum to produce and secrete SLs, we conducted RNA-sequencing (RNA-seq) analyses in sorghum plants grown under phosphorus deficiency conditions; to verify which genes induced by SL treatment, we conducted RNA-sequencing (RNA-seq) analyses in sorghum plants grown under SL treatment.

overall_design: Transcriptome analysis profiles in sorghum roots of phosphorus deficiency and MOCK were generated by RNA-seq;Transcriptome analysis profiles in sorghum roots of GR245DS and MOCK were generated by RNA-seq. GR245DS is one of the synthetic strigolactone analogues.

first: Qi

last: Xie

first: Feifei

last: Yu

first: Jiayang

last: Shi


title: KDM6A Regulates Immunogenicity of Multiple Myeloma  (ChIP-seq)

city: Gainesville

first: Alberto

last: Riva

state: FL

address: 2033 Mowry Rd

department: ICBR

institute: University of Florida

summary: We created isogenic mutiple myeloma and mouse embryonic fibroblast cell lines disrupted for KDM6A using CRISPR editing and Cre-mediated deletion. To detect KDM6A we inserted a dual HA tag sequence into the C-terminal of KDM6A by CRISPR-mediated  editing. We also created one isogenic cell line harboring a jmjD-dead KDM6A where 2 amino acids essential for KDM6A enzymatic activity, H1146 and E1148 , were replaced with alanine residues

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for KDM6A, HA epitote and the histone modifications H3K27me3, H3K27ac, H3K4me1 in KDM6A knock out and JmjD-dead cell lines.

first: Jonathan

middle: D

last: Licht

first: Daphné

last: Dupéré-Richer


title: Molecular basis of Urostyle development

first: Gayani

last: Senevirathne

state: MA

address: 11 Divinity Avenue

department: Human Evolutionary Biology

institute: Harvard University


title: Skin transcriptome analysis in Brangus cattle under heat stress

city: La Plata

first: Leónidas

middle: Hernán

last: Olivera

state: Buenos Aires

department: IGEVET

country: Argentina

institute: CONICET-UNLP

summary: Heat stress is a major factor that negatively affects animal welfare and production systems. Livestock should adapt to tropical and subtropical areas and to meet this, composite breeds have been developed. This work aimed to evaluate gene expression profiles in the skin of Brangus cattle under heat stress using a case-control design, and to correlate this with skin histological characteristics. Two groups of bulls were set using rectal temperature as a criterion to define stress conditions: stressed (N=5) and non-stressed (N=5) groups. Skin transcriptomics was performed and correlations between breed composition, phenotypic and skin histological traits were evaluated. Results showed 4,309 differentially expressed genes (P < 0.01), 2,113 downregulated and 2,196 upregulated. Enrichment and ontology analyses revealed 132 GO terms and 67 pathways (P < 0.01), including thermogenesis, glycolysis, gluconeogenesis, mitochondrial activity, antioxidant and immune response, and apoptosis. The identity of the terms and pathways indicated the diversity of mechanisms directed to relieve the animals´ suffering, acting from simple passive mechanisms (conduction, convection and radiation) to more complex active ones (behavioural changes, evaporation, vasodilation and wheezing). Furthermore, significant differences between phenotypic and skin histological traits and correlations between pairs of traits suggested a direction towards heat dissipation processes. In this sense, number of vessels was positively correlated with number of sweat glands (P < 0.001) and both were positively correlated with zebuine genetic content (P < 0.05 and P < 0.01, respectively), gland size was positively correlated with epidermal thickness and negatively with hair length (P < 0.05), and epidermal thickness was negatively correlated with gland-epidermis distance (P < 0.0005). These results support the notion that response to heat stress is physiologically complex, producing significant changes in the expression of genes involved in several biological pathways, while the animal’s ability to face it depends greatly on their skin features.

overall_design: Transcriptomic profile of skin in Brangus cattle under heat stress conditions and and control animals (case-control design)

first: Paulo

middle: A

last: Cecco

first: Marianela

last: Balbi

first: Martín

last: Bonamy

first: Andrés

last: Muñoz

first: Hernán

first: Guillermo

last: Giovambattista

first: María

middle: E

last: Fernández


title: Genome-wide epigenetic reprogramming during chick embryonic development

city: Toyonaka

first: Takamasa

last: Ito

state: Osaka

address: 1-1 Machikaneyama

department: Biological Science

country: Japan

institute: Osaka University

summary: In mice, genome-wide DNA methylation is actively erased at the onset of fertilisation, followed by remethylation in epiblasts after implantation, leading to inactive chromatin formation as a preliminary step to somatic cell differentiation, and then demethylation again during primitive streak formation and the determination of primordial germ cells (PGCs). This sequence of DNA methylation changes is accompanied by dynamic epigenetic reprogramming, including nuclear structure, histone modification, and intranuclear re-localisation of chromosomes, during totipotency acquisition of the fertilised egg and germline development. Here we show that in the avian strain White Leghorn of Gallus gallus domesticus, global reprogramming of DNA methylation and histone modifications, as seen in mice, is induced during primitive streak formation but then reaches an almost basal state in somatic cells during later embryogenesis unlike mice. Avian chromosomes are subdivided into large and genetically less functioning macrochromosomes (MACs) and gene-rich microchromosomes (MICs), of which remarkable karyotypic composition is evolutionarily conserved from cartilaginous fish to reptiles. We found that these MACs undergo reprogramming that involves particularly active DNA demethylation and removal of trimethylation at lysine 9 of histone H3, leading to activation of the MAC-linked HOXA and HOXD gene clusters that control morphogenesis. We show here that the erasure of genome-wide epigenetics may not only have an important function to initiate differentiation into three germ layers via primitive streak formation, as seen in mice but may also provide a basis for the acquisition of new epigenetics required to regulate morphogenesis during late chicken embryonic development.

overall_design: ChIP-seq data for H3K9me3, H3K27me3, and H3K4me2 from HH27 chicken embryos and DT40 cells

first: T

first: A

last: Hayashi

first: Y

last: Asano

first: S

last: Ishihata

first: M

last: Atsuta

last: Hori

last: Misu

first: C

last: Obuse

first: K

last: Ikeo

last: Matsuda

last: Fukagawa

last: Tada


title: Molecular basis of Urostyle development [RNA-seq]

first: Gayani

last: Senevirathne

summary:
Evolutionary novelties entail the origin of morphologies that enable new functions. These features can arise through changes to gene function and regulation. One important noveltyis the fused rod at the end of the vertebral column in anurans, the urostyle. This feature is composed of a coccyx and an ossifying hypochord, and both structures ossify during metamorphosis.
These experiments reveal that the coccyx and hypochord have two different molecular signatures. ATAC-seq data reveals potential regulatory regions that are observed in proximity to candidate genes identified from RNA-seq.

overall_design: We used Laser Capture Micro-dissection of these identified tissues and subjected them to RNA-seq and ATAC-seq analyses at three developmental stages (during tadpole metamorphic climax) in tadpoles of Xenopus tropicalis.

first: Neil

last: Shubin


title: Comprehensive profiling and targeting of BCL-2 family members in nasopharyngeal carcinoma

city: Parkville

first: Alesha

last: Thai

state: VIC

address: Department of Medical Oncology, 305 Grattan St

country: Australia

institute: Peter MacCallum Cancer Centre

summary: Nasopharyngeal carcinoma (NPC) is among a small number of solid tumors that are caused by the Epstein-Barr virus (EBV). Recently, BH3 mimetics, a novel class of drugs that inhibit pro-survival proteins of the BCL-2 family, have demonstrated clinical anti-cancer efficacy in hematological malignancies and are being investigated for use in solid tumors. There is known dysregulation of pro-survival pathways, particularly, the intrinsic apoptotic pathway during EBV infection of B cells suggesting NPC may be driven by the same pathways, and thus sensitive to BH3 inhibition. Using immunohistochemistry, we examined the expression of BCL-2 family of proteins (BCL2, MCL1 and BCLxL) in 174 NPC from patients treated with curative intent as well as five NPC cell lines. We subsequently evaluated the anti-tumor efficacy of three BH3 mimetics (ABT-199, ABT-737 and S63845) in NPC cells alone or in combination with cisplatin, a commonly used cytotoxic agent in NPC treatment. BCL-2 was highly expressed in NPC tumors and cells. Despite this, BCL2 inhibition, or BH3 monotherapy was not effective. However, marked sensitivity was observed with the combination S63845 (targeting MCL-1) and cisplatin in NPC43, which had high expression of MCL-1. This combination resulted in upregulation of pro-apoptotic tBID suggesting a priming role of cisplatin and apoptotic potentiation through MCL-1 inhibition. Flow cytometry studies and RNA sequencing of NPC43 cells treated with the combination of cisplatin with S63845 and untreated cells showed death by apoptosis and upregulation in stress response and DNA damage pathways. Our study suggests that combining BH3 mimetics with cisplatin could be an effective treatment strategy for NPC and warrants further investigation

overall_design: RNA was extracted and processed using the Nanostring nCounter platform from 69 human NPC samples collected from patients undergoing curative treatment with radiotherapy with or without chemotherapy. There are no duplicates.

first: Richard

last: Young

first: Mathias

last: Bressel

first: Gemma

last: Kelly

first: Nenad

last: Sejic

first: Sai

last: Tsao

first: Anna

last: Trigos

first: Danny

last: Rischin

first: Benjamin

last: Solomon


title: miR-324 regulates both osteoblast and osteoclast differentiation and function to control bone homeostasis

city: NEWCASTLE UPON TYNE

first: David

address: Centre For Life

institute: Newcastle University

summary: microRNAs are non-coding RNAs which modulate the expression of other RNA molecules. One microRNA can target many transcripts, allowing each microRNA to play key roles in many biological pathways. miR-324 is a microRNA previously implicated in bone and cartilage maintenance, defects of which result in common age-related diseases, such as osteoporosis or osteoarthritis (OA).  Cartilage damage was increased in both surgically and ageing-induced OA however changes in the cartilage transcriptome were minimal, with few miR-324 predicted targets dysregulated. However, in vivo micro-computed tomography and histology demonstrated that global miR-324-null mice had an increase in bone mineral density, trabecular thickness and cortical thickness, with many parameters increasing with age. The bones of the miR-null mice also had decreased osteocytes numbers and lipid droplets. In vivo TRAP staining revealed a decrease in osteoclasts with histomorphometry demonstrating an increased rate of bone formation in miR-324-null mice.  Ex vivo assays revealed that the high bone mass phenotype of the miR-324-null mice resulted from increased osteoblast activity and decreased osteoclastogenesis. RNA-seq and qRT-PCR followed by miR-324 target prediction and validation in osteoblasts, bone marrow macrophages and osteocytes, revealed that the osteoclast fusion regulator Pin1 was a miR-324 target in the osteoclast lineage, Hoxa9 and Samd5 were osteocyte target genes and the master osteogenic regulator Runx2 was a target of miR-324-5p in osteoblasts, the in vitro overexpression of which recapitulated the increased osteogenesis and decreased adipogenesis phenotype observed in vivo.  These data point to important roles of miR-324 in skeletal biology. Elucidation of pathways regulated by miR-324 offers promise for the treatment of bone diseases such as osteoporosis.

overall_design: Medial knee cartilage caps were dissected from individual mice (five per genotype; wild-type and miR-324-null). Tissue was washed three times with sterile DPBS, placed in cryogenic vials and immediately frozen in liquid nitrogen. For grinding, the tissue was placed in an autoclaved chamber with a ball (Retsch, Verder Scientific UK Ltd, UK) and 250µl QIAzol lysis reagent (QIAGEN, Manchester, UK). The chambers were transferred to Retsch MM200 mixer mill and tissue ground at vibration frequency of 25 Hz for 90 seconds. To this was added an additional 250µl QIAzol lysis reagent and the mixture transferred to an RNase free tube and incubated at room temperature for 5 minutes. 100µl of chloroform was added and the sample vortexed for 15 s, incubated at room temperature for 10 minutes then centrifuged at 12,500 x g at 4oC for 5 minutes. The upper RNA containing aqueous phase was transferred into a new Eppendorf and RNA and miRNA were purified using a mirVana™ miR Isolation Kit (Ambion, ThermoFisher Scientific, Loughborough, UK) followed by DNAse treatment (DNA-free™ DNA Removal Kit, Invitrogen, ThermoFisher Scientific) following the manufacturer's protocol.

first: Dan

last: Hayman

first: Matt

last: Barter

first: Jamie

last: Soul

first: Hua

last: Lin


title: miR-324 regulates both osteoblast and osteoclast differentiation and function to control bone homeostasis II

summary: microRNAs are non-coding RNAs which modulate the expression of other RNA molecules. One microRNA can target many transcripts, allowing each microRNA to play key roles in many biological pathways. miR-324 is a microRNA previously implicated in bone and cartilage maintenance, defects of which result in common age-related diseases, such as osteoporosis or osteoarthritis (OA). Cartilage damage was increased in both surgically and ageing-induced OA however changes in the cartilage transcriptome were minimal, with few miR-324 predicted targets dysregulated. However, in vivo micro-computed tomography and histology demonstrated that global miR-324-null mice had an increase in bone mineral density, trabecular thickness and cortical thickness, with many parameters increasing with age. The bones of the miR-null mice also had decreased osteocytes numbers and lipid droplets. In vivo TRAP staining revealed a decrease in osteoclasts with histomorphometry demonstrating an increased rate of bone formation in miR-324-null mice. Ex vivo assays revealed that the high bone mass phenotype of the miR-324-null mice resulted from increased osteoblast activity and decreased osteoclastogenesis. RNA-seq and qRT-PCR followed by miR-324 target prediction and validation in osteoblasts, bone marrow macrophages and osteocytes, revealed that the osteoclast fusion regulator Pin1 was a miR-324 target in the osteoclast lineage, Hoxa9 and Samd5 were osteocyte target genes and the master osteogenic regulator Runx2 was a target of miR-324-5p in osteoblasts, the in vitro overexpression of which recapitulated the increased osteogenesis and decreased adipogenesis phenotype observed in vivo. These data point to important roles of miR-324 in skeletal biology. Elucidation of pathways regulated by miR-324 offers promise for the treatment of bone diseases such as osteoporosis.

overall_design: Rib cages were dissected from individual mice (four per genotype; wild-type and miR-324-null). Tissue was digested with collagenase as described previously (PMID: 32660984) to release the cells (costal chondrocytes). RNA was extracted from the cells using trizol/mirVana miRNA Isolation Kit (Thermo Fisher Scientific), following the manufacturer’s protocol to isolate total RNA.


title: Dissecting a regenerative role of il11a as a mitogenic and pro-fibrotic factor in the adult zebrafish heart

city: Madison

first: Kwangdeok

last: Shin

state: Wisconsin

address: 1111 Highland Ave ZN 3, 4451 WIMR II

department: Cell and Regenerative Biology

institute: University of Wisconsin Madison

summary: We found that il11a induction in adult zebrafish hearts can initiate regeneration programs, including cardiomyocyte (CM) prolifeartion and vascularization, even in the absence of injury. However, we also found that chronic il11a induction results in collagen deposition in the cortical layer of the ventricle. In conclusion, our studies unveil the regenerative roles of Il11 signaling and provide a potential strategy of dual treatment to improve heart repair.

overall_design: Uninjured hearts RNA profiles of adult control and il11a overexpression zebrafish at 7 days post tamoxifen treatment (dpt)

first: Junsu

last: Kang


title: Genome-wide chromatin profiles of ZNF395 [ChIP-seq]

first: Xiaosai

last: Yao

overall_design: ChIP-seq against eGFP-tagged ZNF395 in A498 and 786-O cells


title: Molecular basis of Urostyle development [ATAC-seq]

first: Gayani

last: Senevirathne

first: Neil

last: Shubin


title: Gene expression analysis of porcine granulosa cells treated in virtro with sulforaphane or follicle stimulating hormone

city: Nanjing

first: Jiaqi

last: Zhou

address: NO.1 WeiGang

institute: Nanjing Agricultural University

summary: FSH is considered as the most critical regulatory factor for follicle growth and development. It is widely acknowledged that exogenous administration of FSH can effectively stimulate ovulation.However, these techniques have several drawbacks such as high cost and detrimental effects on hormone balance and embryo implantation.Sulforaphane (SFN) is a naturally occurring compound that belongs to the isothiocyanate group, which is predominant in cruciferous vegetables.Our previous research demonstrated SFN could inhibit hypoxia-evoked apoptosis in porcine GCs. Intriguingly, SFN exhibits a biphasic dose-response, stimulating cell growth at low doses in various mammalian cells. Therefore,to investigate the functional implications of sulforaphane  in the regulation of granulosa cell proliferation, we conducted a  gene expression profiling analysis using RNA-seq data, comparing SFN to follicle stimulating hormone (FSH).

overall_design: Gene expression profiling analysis of RNA-seq data for porcine granulosa cells with SFN, FSH and control treatment.

first: Zhou

last: Jiaqi

first: Liu

last: Honglin

first: Shen

last: Ming


title: M1 Macrophages cause cardiac arrhythmia in an in vitro hiPSC coculture model of inflammation-induced atrial fibrillation

city: Leiden

first: Thomas

last: Hutschalik

address: Galileiweg 8

country: Netherlands

institute: Ncardia Services B.V.

summary: Atrial fibrillation (AF) has an estimated prevalence of 1.5–2%, making it the most common cardiac arrhythmia. The mechanisms that cause and sustain AF are still not completely understood. An association between AF and systemic as well as local inflammatory processes has been reported, however, the exact mechanisms underlying this association have not been established. While it is understood that tissue resident macrophages can influence cardiac electrophysiology, the effects of activated pro-inflammatory macrophages have not been described yet. This study investigated the pro-arrhythmic effects of activated macrophages (M1) on human induced pluripotent stem cell (hiPSC)-derived atrial cardiomyocytes (aCM), to propose a mechanistic link between inflammation and AF. Two hiPSC lines from healthy individuals were differentiated to aCMs and M1 macrophages. Electrophysiology characteristics of M1 and aCM cocultures were analysed for beat rate irregularity, electrogram amplitude and conduction velocity. M1 cocultures resulted in a significant increase in beat rate irregularity and decrease in electrogram amplitude compared to other conditions tested, including aCMs treated with activated M1 supernatant, which did not produce an increase in irregularity. Conduction analysis further showed significantly lower conduction homogeneity in M1 cocultures. Immunosuppression through glucocorticoids significantly decreased beat irregularity in aCM+M1 cocultures compared to vehicle. RNA sequencing performed in aCMs, revealed downregulation of various ion channels (SCNA5, KCNA5, ATP1A1), as a result of the M1 coculture. Electrophysiology related transcription changes were reversed by glucocorticoid treatment. This study establishes a causal relationship between M1 activation and the development of subsequent atrial arrhythmia, documented as irregularity in spontaneous electrical activation in aCM cocultured with activated macrophages. Further, beat rate irregularity could be alleviated using anti-inflammatory steroidal glucocorticoids. These results strongly support the relevance of the proposed hiPSC-derived coculture model and point at macrophage mediated inflammation as a potential AF mechanism.

overall_design: For bulk RNA sequencing hiPSC-derived atrial cardiomyocytes (aCM) from 2 healthy donor lines in coculture with isogenic hiPSC-derived M1 macrophages (m1) were investigated. 4 conditions were analyzed: aCM only, aCM+M1 conditioned medium, aCM+M1 and aCM+M1+ 10 µM Hydrocortisone. All samples were seeded on fibronectin coated (1:100) 24 well Cellstar plates (Greiner) with 500,000 aCM per well and 125,000 M1 added to cocultures. Medium (PCM, 500 ul per well) was added according to M1 maturation/activation medium change schedule (as described before), with non-activated conditions having no added GM-CSF, LPS and IFN-γ. Hydrocortisone addition was performed as previously described in the manuscript. For conditioned medium samples, 125 ul supernatant from M1 monocultures (24 well plate, 500,000 cells/well in 0.5 mL PCM) was added to appropriate samples. Addition was performed 2 hours prior to cell collection. On d8, cells were detached using TrypLe-Express (Gibco) and single cell suspensions generated. M1 cells in coculture suspensions were removed through CD14 magnetic bead cell sorting (CD14 Microbeads human, MS column, MiniMACS kit, all Miltenyi) according to manufacturer’s protocol. aCM cell populations were stored at -80°C and used for RNA extraction (as previously described). Bulk RNA-seq was performed on RNA samples by SingleCellDiscoveries. Count data was analyzed using R-studio (R-studio, PBC , Boston, USA) and Deseq2. P values were analyzed using Wald test, with a P value <0.05 regarded as significant. Genes were annotated for ontologies using clusterProfiler and DOSE.

first: Hutschalik

last: Thomas

first: Matsa

last: Elena


title: Effect of regorafenib, anti-PD1, and anti-CD40 agonist in Head and Neck Squamous Cell Carcinoma [HNSCC_model]

first: Chia-Lang

last: Hsu

summary: Regorafenib presented an antitumor activity in HNSCC mouse model and delayed the tumorigenesis of the 4NQO-indued oral mouse model. By tumor-infiltration lymphocytes isolation and RNA-seq analysis, the immunity-related function was activated by regorafenib. We approved that regorafenib can determine the macrophage polarization toward M1 inflammatory macrophages by suppressing the production of certain cytokines such as plasminogen activator inhibitor-1 (PAI-I) from tumor cells. Also, Regorafenib suppresses secretion of PAI-1 from ex vivo cultures of human HNSCC organoids.

overall_design: We performed RNA-seq on tumors from HNSCC mouse model and 4NQO-indued oral mouse model with the treatment of vehicle control, regorafenib, anti-PD1, and regorafenib + anti-PD1

first: Y

last: Chen

last: Lee

first: D

last: Ou

first: C

last: Tang


title: The Nucleolar Remodeling is Required for the of Mouse Fibroblasts Reprogramming to iPSC

city: Harbin

first: Yuchen

last: Sun

state: Heilongjiang

address: Baojian road 157

department: Department of histology and embryology

institute: Harbin Medical University


title: Analysis of rectal transcriptome in ulcerative colitis (UC) patients who received tofacitinib

city: New York

first: Kyungku

last: Jang

state: NY

address: 430 East 29th Street

department: Microbiology

institute: New York University

summary: The gold of this study is to identify genes that differentially expressed in rectum of ulcerative colitis patients who are responisve to tofacitinib compared with the patients who are refractory to the drug. This study may help to identify preditive markers to determine tofacitinib responders prior to the treatment.

overall_design: We enrolled 48 UC patients for this project and collected rectum pinch biospies during colonoscopy at the baseline (week 0, before tofacitinib treatment) and end of study (week 24, after tofacitinib treatment). RNA-seq was performed using RNA isolated from the biopsies .

first: Kyung

middle: K

first: Defne

last: Ercelen

first: Chaoting

first: Jordan

last: Axelrad

first: Ken

last: Cadwell


title: The MicroRNAmiR-223constrains Colitis-associated tumorigenesis by limiting myeloid cell infiltration and Chemokine expression

city: Maynooth

first: Eoin

last: McNamee

state: Co Kildare

address: Rm 2.19 Bioscience bldg

department: Biology

country: Ireland

institute: Maynooth University

summary: Aberrant intestinal inflammation plays a critical role in the development of colitis-associated colorectal cancer (CAC), yet the mechanisms behind this progression are not clearly defined. While altered microRNA (miRNA) expression is observed in CAC, it is unclear how myeloid-specific microRNA’s impact on the inflammatory process that underpins the continuum from Ulcerative colitis (UC) to tumorigenesis. Here we used the Azoxymethane-Dextran Sodium Sulfate (AOM-DSS) (10mg/kg) model of CAC on miR-223-/y and WT mice, with an overall aim of identifying differences in their expression profiles following AOM/DSS treatment.

overall_design: To investigate the effects of miR-223 on the development of colitis associated colorectal cancer, we used miR-223-/y and C57BL/6J mice treated with azoxymethane(AOM)/dextran sodium sulfate(DSS) (10mg/kg). Total RNA was extracted from colonic tissue and gene expression analysis was performed on RNA-seq results.

first: Eóin

first: Ciara

last: Flynn

first: Gary

last: Markey

first: Viola

last: Dengler

first: Charlotte

last: Farrelly

first: Holger

last: Eltzschig

first: Joanne

middle: C

last: Masterson

first: Glenn

last: Furuta


title: The Nucleolar Remodeling is Required for the of Mouse Fibroblasts Reprogramming to iPSC [ATAC-Seq]

overall_design: Comparative gene expression profiling analysis of ATAC-seq data for 4F2A cells(+DOX,48h) that treated by DMSO or CX-5461 for 1 hour at reprogramming begainning.

first: Lei

last: Lei


title: KDM6A Regulates Immunogenicity of Multiple Myeloma  (ATAC-seq)

first: Alberto

last: Riva

summary: We created isogenic mutiple myeloma cell lines disrupted for KDM6A using CRISPR-mediated editing.

overall_design: We performed ATAC-seq to understand how KDM6A regulates DNA accessibility

first: Jonathan

last: Licht

first: Daphné

last: Dupéré-Richer


title: Transcriptome and chromosome accessibilty profile of HPMCs treated with high glucose containing culture medium

city: xi'an

first: guangbo

last: tang

address: xianning road

institute: xi'an jiaotong university

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

overall_design: Refer to individual Series


title: KDM6A Regulates Immunogenicity of Multiple Myeloma (RNA-seq)

summary: We created isogenic mutiple myeloma and mouse embryonic fibroblast cell lines disrupted for KDM6A using CRISPR editing and Cre-mediated deletion.

overall_design: We performed gene expression profiling analysis using data obtained from RNA-seq from 4 different cell lines. We also obtained RNA-seq from 1 isogenic cell line with and without IFN-alpha.


title: KDM6A Regulates Immunogenicity of Multiple Myeloma


title: Transcriptome and chromosome accessibilty profile of HPMCs treated with high glucose containing culture medium [RNA-Seq]

summary: RNA-seq and ATAC-seq were performed on HPMCs treated with high glucose containing culture medium

overall_design: HPMCs were incubated with control or high glucose containing medium for 5 days, and used for sequencing library constraction

first: Qiong

last: Song

first: Guangbo

last: Tang


title: miR-BART1-3p inhibits proliferation and invasion of gastric cancer cells by regulating STAT3/pSTAT3 and PI3K/AKT/pAKT signaling pathways

city: Fuzhou

first: Shun

last: Hu

state: Fujian

address: Chazhong Road

department: Department of Pathology

institute: The First Affiliated Hospital of Fujian Medical University

summary:
[Aim] EBVaGC accounts for about 10% of gastric cancer and has a better prognosis than EBVnGC, but its molecular mechanism is still unclear. We investigated the role of EBV-miR-BART1-3p in the occurrence and development of EBVaGC by applying bioinformatics methods, high-throughput sequencing, in vitro experiments, target gene screening and verification, differential gene protein interaction network and gene regulatory network construction.
[Materials and Methods] The data set GSE51575 was normalized, and the outlier samples were deleted. Finally, gene expression profiles of 11 EBVaGC and 14 EBVnGC tumor tissues and non-tumor control tissues were obtained. Differential gene function analysis was performed, and molecular regulatory network was constructed. The mRNA expression levels of SNU-719 (EBV-positive gastric cancer cell line), AGS, AGS-NC (EBV-negative gastric cancer cell line) and AGS-OE (lentivirus-transfected miR-BART1-3p overexpression cell line) were detected by high-throughput next-generation sequencing technology, and differential gene expression characteristics were analyzed. To investigate the effect of miR-BART1-3p overexpression on mRNA expression level of gastric cancer cells and construct the protein interaction network of differential genes and the regulatory network of miR-BART1-3p gene. DIANA-MR micro-T, miRnada, miRDB, TarBase v.8, and ViRBase online databases were used to predict the target genes of miR-BART1-3p and GO enrichment analysis of target gene function was performed. Real-time fluorescence quantitative PCR was used to detect the expression levels of miR-BART1-3p and target genes in SNU719, AGS-OE and AGS gastric cancer cells. The effects of overexpression of EBV-miR-BART1-3p on proliferation, apoptosis, invasion, and migration of gastric cancer cells were investigated by CCK-8, cell cloning, cell scratch and Transwell.
[Results] By analyzing the gene expression profile of the GSE51575 dataset, we found that EBVaGC up-regulated the expression of immune cell membrane protein receptors and chemokine family, and was involved in inducing tumor immunity, suggesting a better prognosis. EBVnGC significantly up-regulated the expression of AURK, BUB1B, CCNA2 and CDC20, suggesting the risk of malignant progression and recurrence. High-throughput next-generation sequencing of SNU719 and AGS to detect differences in gene expression revealed that EBVaGC cells (SNU719) up-regulated the expression of genes that inhibit malignant progression as well as potential tumor immunotherapy targets. These results are consistent with those found in the GSE51575 dataset. Fifteen miR-BART1-3p target genes, including FAM168A, TET3, HBP1, ZBTB5, ATXN7L3, KMT5C, SPARC and BMF, were predicted and screened by online tools. After the overexpression of miR-BART1-3p in AGC(EBVnGC) cells, the proliferation, migration, and invasion ability were significantly inhibited, and the signaling pathway promoting tumor progression was also limited in activation.
[Conclusions] The overexpression of miR-BART1-3p may inhibit the proliferation and invasion and migration of gastric cancer cells by inhibiting the activation of STAT3/ pSTAT3 and PI3K/AKT signaling pathways and may become a target for the treatment of EBVaGC, which is worthy of further study.

overall_design: Through the high-throughput sequencing laboratory of Shanghai Shengong Bioengineering Co., LTD., library construction was conducted to detect the gene expression profiles of SNU719, AGS-OE (miR-BART1-3p overexpressed gastric cancer cells) and AGS-NC, and the differentially expressed genes and the associated genes of miR-BART1-3p in gastric cancer were obtained.

first: Xiqian

last: Cai

first: Li

last: Mu

first: Feng

last: Gao

first: Zhenzhen

last: Zhang

first: Ke

last: Zheng

first: Guoping

last: Li

first: Caihong

last: Ren

first: Xiangna

last: Chen

first: Sheng


title: Role of Fibulin-V (FibV) in disturbed flow induced arterial stiffening and atherosclerosis

city: Atlanta

first: Luke

last: Brewster

state: GA

address: 101 Woodruff Circle

department: Surgery

institute: Emory University

summary: The mechanisms of arterial stiffness (independent cardiovascular risk factor) are not well understood. Here, we investigated the role of Fibulin V in arterial stiffness and remodeling in response to disturbed blood flow.

overall_design: In vivo animal model of d-flow was used to investigate how knockdown of Fibulin V (FibV KO) influences arterial stiffness/remodeling and atherosclerosis.  Briefly, Partial Carotid ligation was performed on the left common carotid artery of the mouse while the right common carotid artery was left untouched. Induction of disturbed blood flow was confirmed by ultrasound.  One-day post ligation, the carotid arteries were explanted and the RNA extraction was performed to investigate the global changes in gene expression using illumina microarray.

first: Sandeep

last: Kumar

first: Feifei


title: YAP overcomes restriction of translation induced by nutrient deprivation through restoration of mTORC1 activity

city: Daejeon

first: Daehee

last: Hwang

address: Yuseong-gu, Daehak-ro 291 Basic Science Bldg. (E6-6) #413

department: Biological Sciences

country: South Korea

institute: Korea Advanced Institute of Science and Technology


title: Time-dependent gene expression patterns in injured brains of WT and LRRK2 G2019S mice.

city: Suwon

first: Jiawei

last: An

state: Kyunggi-do

address: 206, World cup-ro

institute: Ajou University

summary: The effects of the LRRK2 G2019S (GS) mutation on brain injury and recovery from injury were examined by comparing time-dependent gene expression patterns in injured brains of WT and GS mice, beginning 6 h after injury to almost complete repair 15 days later. Brain injury was induced by stereotaxic injection of ATP, a component of damage-associated molecular patterns (DAMPs), into the striatum.

overall_design: We performed gene expression profiling analysis using data obtained from RNA-seq of injured brains of WT and LRRK2 G2019S mice at 4 time points.

first: Haijie

last: Yang

first: Sang Myun

last: Park

first: Yong - Joon

last: Chwae

first: Eun - Hye

last: Joe


title: mRNA-seq of wild-type or ZUFSP knockout THP1 cells after vesicular stomatitis virus infection

city: Beijing

first: Ming

last: Kuang

address: Xueyuan Road 38 #, Haidian District

institute: Peking University

summary:
To investigate the function of ZUFSP in immune response, we established ZUFSP knockout cell lines in which ZUFSP gene has been knockdown by sgRNA.
We then performed gene expression profiling analysis using data obtained from RNA-seq of WT or ZUFSP knockdown THP1 cells with or without VSV infection

overall_design: Comparative gene expression profiling analysis of RNA-seq data for  WT or ZUFSP knockdown THP1 cells that were infected by VSV for 0 or 6 hours.

first: Tianyi

last: Liu


title: High-Fructose Corn Syrup Promotes Proinflammatory Macrophage Activation via ROS-Mediated NF-κB Signaling and Exacerbates Colitis in Mice

city: wuhan

first: wang

middle: li

last: ping

address: Jiefang Avenue, Jianghan District, Wuhan City, Hubei Province

institute: Department of Clinical Laboratory, Union Hospital, T ongji Medical College

summary: we focused on HFCS and found that HFCS aggravates colitis by altering the intestinal immune microenvironment. Our data demonstrate that short-term consumption of HFCS upregulates the proportion of macrophages in IBD mice but not in healthy mice. HFCS promotes proinflammatory cytokine production through reactive oxygen species (ROS)-mediated nuclear factor-κB (NF-κB) signaling. Our work unveils the important role of macrophages in HFCS-induced exacerbation of colitis and reveals the mechanism of how HFCS immunologically aggravates IBD.

overall_design: mRNA profiles of RAW264.7 cells and HFCS-treated RAW264.7 cells

first: Liping

last: Wang

first: Tiantian

last: Ji

first: Ye

last: Yuan

first: Zheng

first: Lin


title: Triptolide sensitizes cancer cells to nucleoside DNA methyltransferase inhibitors through inhibition of DCTPP1 mediated cell-intrinsic resistance [RNA-Seq]

city: Baltimore

first: Roshan

last: Chikarmane

state: Maryland

address: 30 W Biddle Street, Apt 1103B

department: Pharmacology

institute: Johns Hopkins University

summary: We show that high DCTPP1 expression was associated with cell-intrinsic resistance to nucleoside DNMT inhibition, and that triptolide and its analogs could overcome this resistance.

overall_design: mRNA profiles of DU145 treated with the DNMT inhibitor decitabine alone or in combination with triptolide

first: Liu

last: Jianyong

first: Chikarmane

last: Roshan

first: Steinberg

last: Ruchama

first: Nelson

middle: G

last: William

first: Yegnasubramanian

last: Srinivasan


title: Triptolide sensitizes cancer cells to nucleoside DNA methyltransferase inhibitors through inhibition of DCTPP1 mediated cell-intrinsic resistance [Array]

type: Methylation profiling by genome tiling array

first: Jianyong

first: Ruchama

last: Steinberg

first: William

last: Nelson

first: Srinivasan

last: Yegnasubramanian


title: Extracellular vesicles derived from synovial inflammatory macrophages induce the onset of osteoarthritis in a FMRP-selectively sorted manner

status: Public on Sep 30 2024

city: shanghai

first: shu

middle: I

last: zhao

address: Road siping 1239

institute: Tongji University

summary: Osteoarthritis (OA) is an aging-related degenerative joint disease without effective therapeutic. In the early stage of OA, mild synovitis has been proven to induce normal cartilage lesions. However, the mechanism is poorly defined. Here, we identified that the extracellular vesicles (EVs) derived from synovial inflammatory macrophages regulate the autophagy function of chondrocytes, acting as the dominant inducer of the onset of cartilage degeneration in normal and OA joints. Mechanistically, the active transfer of miR-155-5p via EVs from synovial inflammatory macrophages to chondrocytes accelerates cartilage degeneration by suppressing GSK 3β/mTORC1 axis-mediated autophagy function during OA progression.

overall_design: To explore the underlying mechanism by which synovial inflammatory macrophages aggravate cartilage damage in OA progression, the miRNA expression in EVs derived from synovial macrophages between sham and OA rats was examined. As BM-derived macrophages contributed to the pool of synovial macrophages during OA progression, the CD45+ and CD11b+ monocytes from BM cells between sham and OA rats were sorted. Then the sorted monocytes were induced to M0 (presented synovial macrophages in the sham model) and M1 polarization (presented synovial inflammatory macrophages in the OA model), separately. The Agilent Rat miRNA Microarray, Release 21.0 (8*15K, Design ID: 070154) were used to investigated. The microarray has 758 probes for mature miRNAs of rats.

first: Shu

last: Zhao

first: Jun

last: Xu


title: Therapeutic inhibition of METTL3/miR-146a-5p-guided NOTCH pathway suppresses bladder cancer progression

city: Shanghai

first: Minfeng

last: Shu

state: State...

address: No.131 Dongan Road II Xuhui district

institute: Fudan University

summary: Bladder cancer characterized by RNA methylation abnormalities and NOTCH pathway dysregulation exhibits high recurrence that remains the major obstacle for bladder cancer treatment. Targeting methyltransferase-like 3 (METTL3) and NOTCH signal is a potential strategy to block bladder cancer progression. However, the underlying mechanisms by which METTL3-manipulated NOTCH signal and its effect on bladder cancer tumorigenesis remain to be clarified. Here we showed that METTL3-guided m6A modification methylated pri-miR-146 at the flaking sequence, which was responsible for the pri-miR-146 maturation. Furthermore, NUMB/NOTCH2 axis was identified as the functional downstream target signal that mediated the pro-survival role of miR-146a-5p in bladder cancer cells. Therapeutically, the polypeptide melittin was demonstrated to induce apoptosis of bladder cancer cells in a METTL3-dependent manner. Importantly, METTL3 and miR-146a-5p were positively correlated with recurrence and poor prognosis of bladder cancer patient. Our studies indicate that METTL3/miR-146a-5p/NUMB/NOTCH2 axis could be a potential therapeutic target for recurrent bladder cancer treatment and METTL3 acts as a fate determinant that controls sensitivity of bladder cancer cells to melittin treatment.

overall_design: Examination of miRNAs in T24 bladder cancer  cells treated with or without melittin

first: Rucheng

last: Yan

first: Weiwei

last: Dai

first: Ruixin

last: Wu

first: Houbao

last: Huang


title: RNA_Seq of recipients mice with Klebsiella and Lactobacillus

first: Yiyangzi

last: Ma

address: No.145 Shandong Rd, Huangpu District

institute: Renji Hospital;PUMC

summary: We transplanted Klebsiella and Lactobacillus to germ free C57/B6J mice. All of the recipients mice were male. Here we report the intestine mRNA profiles of recipients mice with  Klebsiella and Lactobacillus.

overall_design: Intestine mRNA profile of recipients mice with Klebsiella and Lactobacillus.


title: Triptolide sensitizes cancer cells to nucleoside DNA methyltransferase inhibitors through inhibition of DCTPP1 mediated cell-intrinsic resistance

first: Roshan

last: Chikarmane


title: Transcriptome and chromosome accessibilty profile of HPMCs treated with high glucose containing culture medium [ATAC-Seq]

first: guangbo

last: tang

first: Qiong

last: Song

first: Guangbo

last: Tang


title: Effects of Pd1 targeted myeloid deletion on brain development

first: Jianwei

last: Jiao

state: Beijing

address: 1 Beichen West Road

department: State Key Laboratory of Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

summary: During early brain development, the nervous system continues to evolve and improve, and cells in different stages contact and connect to form a unique nervous system network. Various cross-talk between cell populations is the key to neurological homeostasis. Communication between astrocytes and myeloid cells affects brain function. Programmed cell death protein 1 (PDCD1), also known as PD-1 or CD279 (differentiation cluster 279), is a member of the immunoglobulin gene superfamily. Here, we investigated the loss of PD-1 in myeloid cells results in abnormal development of the nervous system. Specific ablation of PD-1 affects myeloid cell proliferation and subtype classification. At the stage of astrogenesis onset, the astrocyte proliferation ends, and the continuous development, the results of immunofluorescence staining with different astrocyte markers show that astrocytes-related genes were highly expressed in PD-1f/flysMCre mice. PD-1f/flysMCre mice exhibited more outgoing, less anxious, and a more extroverted mode of exploration in behavioral tests. The specific ablation of PD-1 increases the expression of CXCL1 through the NF-κB signaling pathway. It reaches the brain and interacts with CXCR2 on astrocytes, promoting astrocyte proliferation. Our results not only reveal an important regulatory role of PD-1 in myeloid cells on astrocytes but also provide some theoretical basis and ideas for the study of myeloid and brain axis

overall_design: To investigate the function and mechanism of PD-1 in the cerebral development, we estibalished conditional knockout mice and isolated myeloid cells from fetal liver to obtain RNA- seq of wild type and conditional knockout mice. Specifically, Agilent 2100 Bioanalyze was used to quality controlled and quantified. then, mRNA was converted to cDNA and bound the library. RNA-sequencing analysis was used by the Illumina HiSeq 2500 platform in Annoroad Genomics.

first: Jie

last: Qin

first: Fen

last: Ji


title: DNMT3a-mediated methylation of TCF21/hnRNPA1 aggravates liver fibrosis by regulating the NF-κB signaling pathway

city: Hefei

first: liangyun

last: li

address: 81 Meishan Road

institute: Anhui Medical University

summary: Hepatic fibrosis is caused by liver damage as a consequence of wound healing response. Recent studies have shown that hepatic fibrosis could be effectively reversed, partly through regression of activated hepatic stellate cells (HSCs). Transcription factor 21 (TCF21), a member of the basic helix-loop-helix (bHLH) transcription factor, is involved in epithelial-mesenchymal transformation in various diseases. However, the mechanism by which TCF21 regulates epithelial-mesenchymal transformation in hepatic fibrosis has not been elucidated. In this research, we found that hnRNPA1, the downstream binding protein of TCF21, accelerates liver fibrosis reversal by inhibiting the NF-κB signaling pathway. Furthermore, the combination of DNMT3a with TCF21 promoter results in TCF21 hypermethylation. Our results suggest that DNMT3a regulation of TCF21 is a significant event in reversing hepatic fibrosis. In conclusion, this research identifies a novel signaling axis, DNMT3a-TCF21-hnRNPA1, that regulates HSCs activation and liver fibrosis reversal, providing a novel treatment strategy for hepatic fibrosis.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for 5-mC methylated  in quiescent LX-2 Cells (q-LX-2) and activated LX-2 Cells (a-LX-2).

first: Liangyun

last: Li

first: Shaoxi

last: Diao

first: Zixiang

last: Chen

first: Jintong

last: Zhang

first: Wei


title: Synthesis of 2'-formamidonucleoside phosphoramidites for suppressing the seed-based off-target effects of siRNAs

city: Bunkyo-ku

first: Seongjin

last: An

state: Tokyo

department: Graduate School of Frontier Science

institute: The University of Tokyo

summary:
To investigate effects of siRNA with 2'-formamidonucleoside phosphoramidites (2'-FA) modifications on genome-wide off-target, we analyzed gene expression profile of HeLa cells transfected by their siRNAs.
Gene expression profiling

overall_design: Total RNAs were extracted from HeLa cells transfected by mock, unmodified, or 2'-formamidonucleoside phosphoramidites (2'-FA)  modified siRNA and performed microarray analysis.

first: Kumiko

last: Ui-Tei


title: The Nucleolar Remodeling is Required for the of Mouse Fibroblasts Reprogramming to iPSC [RNA-Seq]

first: Yuchen

last: Sun

institute: Harbin Medical University

overall_design: Comparative gene expression profiling analysis of RNA-seq data for 4F2A cells(+DOX,48h) that treated by DMSO or CX-5461 for 1 hour at reprogramming begainning.

first: Lei

last: Lei


title: Integrating multi-omics data to identify key functional variants affecting feed efficiency in pigs

city: 武汉

first: jahui

last: sun

state: 湖北

address: 湖北省武汉市

institute: 华中农业大学

summary: Optimizing feed efficiency through the feed conversion ratio (FCR) is paramount for economic viability and sustainability. In this study, we integrated RNA-seq, ATAC-seq, and genome-wide association study (GWAS) data to investigate key functional variants associated with feed efficiency in pigs. Identification of differentially expressed genes in the duodenal and muscle tissues of low- and high-FCR pigs revealed that pathways related to digestion of dietary carbohydrate are responsible for differences in feed efficiency between individuals. Differential open chromatin regions identified by ATAC-seq were linked to genes involved in glycolytic and fatty acid processes. GWAS identified 211 significant single nucleotide polymorphisms associated with feed efficiency traits, with candidate genes PPP1R14C, TH, and CTSD. Integration of duodenal ATAC-seq data and GWAS data identified six key functional variants, particularly in the 1500985–1509676 region on chromosome 2. In those regions, CTSD was found to be highly expressed in the duodenal tissues of pigs with a high feed conversion ratio, suggesting its role as a potential target gene. Overall, the integration of multi-omics data provided insights into the genetic basis of feed efficiency, offering valuable information for breeding more efficient pig breeds.

overall_design: In this study, we utilized six Large White pigs, three with extremely high FCR values and three with extremely low FCR values. These pigs were raised on the same commercial farm under similar conditions and fed the same diet. All pigs were euthanized at 180 days of age after an overnight fasting period. Muscle and duodenal samples were collected and stored at -80°C for subsequent experiments. The sampling procedures received approval from the Ethics Committee of Huazhong Agricultural University. RNA-seq analysis was conducted on samples from three pigs with the highest FCR levels and three with the lowest FCR levels. In addition, ATAC-seq analysis was performed on samples from two pigs with extremely high FCR levels and two with extremely low FCR levels

first: Xiaolong

last: Qi

first: Kui

first: Liangliang

last: Fu

first: Xinyun

first: Yue

last: Xiang

first: Jiahui

first: Guojian

last: Ma

first: Xueting

last: Dai

first: Yuan

last: Meng

first: Chong

first: Yan

first: Qiulin

last: Zhao

first: Jingjin

first: Saixian

first: Zhuqing

last: Zheng


title: Synthesis of 2'-formamidonucleoside phosphoramidites for suppressing the seed-based off-target effects of siRNAs [RNA-seq]

first: Seongjin

summary: To investigate effects of siRNA with 2'-formamidonucleoside phosphoramidites (2'-FA) modifications on genome-wide off-target, we analyzed gene expression profile of HeLa cells transfected by their siRNAs.

overall_design: Total RNAs were extracted from HeLa cells transfected by mock, unmodified, or 2'-formamidonucleoside phosphoramidites (2'-FA)  modified siRNA and performed RNA-seq.

first: Kumiko


title: Whole blood RNA biomarkers for predicting survival in non-human primates following thoracic radiation

city: Bethesda

first: Uma

last: Shankavaram

state: MD

address: 9000 Rockville Pike

department: NCI

institute: NIH

summary: We conducted a comprehensive transcriptome analysis of whole blood from male and female nonhuman primates (rhesus macaque (Macaca mulatta)) that received upper thoracic radiation. A Varian CLINAC 21EX linear accelerator was used (6 MV Linear Accelerator (Linac)). Body Weight Range: 3.5 to 5 kg (at initial physical exam). Age Range: 3 to 5 years (at initial physical exam).

overall_design: Rhesus macaques were randomly assigned to a group, either receiving 9.8 Gy or 10.7 Gy to whole thoracic lung irradiation, with weight and biological sex being factored into distribution. 6 male and 6 female were placed in the 9.8 Gy group and 8 male and 8 female were placed in the 10.7 Gy group. Dose rate of 600 ± 10 cGy/min using the linear accelerator in an anterior-posterior (AP) and posterior-anterior (PA) technique. Animals were housed in a temperature- and humidity-controlled environment with a target temperature between 19-29C and target humidity 30 and 70%. PMI LabDiet® Fiber-Plus® Monkey Diet 5049 biscuits were be provided two times per day and fresh drinking water was provided ad libitum. Veterinary care including analgesics (tramadol 1-4mG given twice daily beginning on post irradiation Day 4 and continuing through Day 25) and anti-inflammatory drugs (Dexamethasone administered IM using the following regimen: 1.0 mg/kg BID in animals who displayed tachypnea) were provided after radiation injury. Whole blood draws were performed Day -2, then every three days post-irradiation through Day 30, Days 40, 50 and 60, then every 30 ± 3 days thereafter.

first: Jared

last: May

first: Shannon

last: Martello

first: Sunita

last: Chopra

first: Molykutty

last: Aryankalayil


title: Understanding the impact of PROM1 alternative splicing on the development and maturation of human photoreceptors

city: Newcastle upon Tyne

first: Graham

last: Smith

address: Framlington Place

department: Bioinformatics Support Unit

institute: Newcastle University

summary: Alternative splicing (AS) is a crucial mechanism contributing to proteomic diversity, which is highly regulated in tissue-specific and development-specific patterns. Retinal tissue exhibits one of the highest levels of AS. In particular, photoreceptors have a distinctive AS pattern involving the inclusion of microexons not found in other cell types. PROM1 whose encoded protein Prominin-1 is located in photoreceptor outer segments (OSs), undergoes exon 4 inclusion from the 12th post-conception week of human development through adulthood. Exon 4 skipping in PROM1 is associated with late-onset mild maculopathy, however its role in photoreceptor maturation and function is unknown. In this study retinal organoids, a valuable model system, were employed in combination with phosphorodiamidate morpholino oligos (PMOs) to assess the role of exon 4 AS in the development of human retina. Our data demonstrate that 55% skipping of PROM1 exon 4 resulted in decreased Prominin-1 expression by 40%, detectable photoreceptor cilium defects and impaired transport of specific OS proteins in cone photoreceptors, such as cone opsin. Transcriptomic and Western blot analyses revealed decreased expression of cone, inner segment and connecting cilium basal body markers, and increased expression of genes associated with stress response and the ubiquitin-proteasome system, and downregulation of autophagy. Together these data indicate that cones may be more sensitive to PROM1 exon 4 skipping, corroborating the pathogenesis of late-onset mild maculopathy. Importantly, the use of retinal organoids provides a valuable platform to study AS and unravel disease mechanisms in a more physiologically relevant context, opening avenues for further research and potential therapeutic interventions.

overall_design: Gene expression profiling by RNA-seq of PMO-Treated ROs after 4 weeks (n=3). ROs were treated at day 180 of differentiation with either PROM1-PMO, PMO1 (targeting exon 4) or Ctrl-PMO (SC) and incubating for 4 weeks, adding a fresh dose of PMO every week.

first: Marina

last: Moya Molina

first: Birthe

last: Dorgau

first: Emily

last: Flood

first: Stef

last: Letteboer

first: Esben

last: Lorentzen

first: Jonathan

last: Coxhead

middle: R

first: Ronald

last: Roepman

first: Sushma

last: Nagaraja Grellscheid

first: Lyle

last: Armstrong

first: Majlinda

last: Lako


title: The Role of Hexokinases in Epigenetic Regulation: Insights from Altered Expression of Hexokinases and Chromatin Stability

city: Minneapolis

first: Quinn

last: Dickinson

state: MN

address: 100 Church Street SE

institute: University of Minnesota

summary: Hexokinases (HXKs) are the key enzymes regulating glycolysis in cells. Overexpression of HXKs has been linked to numerous types of cancers and targeting HXKs has been suggested as a potential strategy of cancer therapy. How these abnormal HKs express affect epigenetics and gene expression is less understood. In this study, we artificially altered the HXKs expression level and test its impact on the parental nucleosome transfer process, a key replication coupled-epigenetic inheritance process, in yeast cells. Our result suggests the altered HXKs expression level has little effect on the parental nucleosome assembly and chromatin instability. However, 2- Deoxy-D-glucose(2DG), a HXK inhibitor, treatment cells show increased chromatin instability.

overall_design: Strand specific chip analysis at replication forks for hexokinase 2 deletion and expression strains of yeast

first: Srinivasu

last: Karri

first: Jing

last: Jia

first: Haiyun

last: Gan

first: Zhiquan

last: Wang

first: Yibin

last: Deng

first: Chuanhe

last: Yu


title: An endophytic Magnaporthaceae species reduces take-all disease in wheat through the induction of cell-wall mediated defence response pathways

city: Harpenden

first: Daniel

last: Smith

state: Hertfordshire

address: West Common

department: IDE

institute: Rothamsted Research

summary: A comparison of Chinese Spring wheat to infection by the pathogenic fungi Gaeumannomyces tritici and G. hyphopodioides (not known as a wheat pathogen) at three time points

overall_design: In-planta RNAseq during Chinese Spring (CS) wheat infection at three time points by the pathogenic fungi Gaeumannomyces tritici and G. hyphopodioides (not known as a wheat pathogen)

first: Tania

last: Chancellor

first: Dan

first: Wanxin

last: Chen

first: Eudri

last: Venter

first: Kirstie

last: Halsey

first: Gail

last: Canning

first: Kim

last: Hammond-Kosack

first: Javier

last: Palma-Guerrero


title: Effect of miR-33 supression in hepatocytes in NAFLD

city: New Haven

first: PABLO

last: FERNANDEZ-TUSSY

state: CT

address: 10 amistad street, 420C

department: Comparative Medicine

institute: Yale University

summary: We perform RNAseq in NAFLD livers from WT and miR-33-AlbCRE  conditional knock-out mice. Liver were isolated from mice after 3 months of feeding a choline deficient high fat diet to analyze the effect of miR-33 deficiency.

overall_design: Analyze changes in gene expression occuring in the liver in NAFLD and the regulation mediated by miR-33.

first: Pablo

last: Fernández-Tussy

first: Carlos

last: Fernandez-Hernando


title: Both host and parasite non-coding RNAs co-ordinate the regulation of macrophage gene expression to reduce pro-inflammatory immune responses and promote tissue repair pathways during infection with fasciola hepatica

city: Ultimo

first: Dayna

last: Sais

state: New South Wales

address: 15 Broadway

institute: University of Technology Sydney

summary: Parasitic worms (helminths) ensure their survival to establish chronic infection within mammalian hosts by strategically regulating their host   s immune responses. Deciphering the mechanisms behind this immune modulation will inform the development of novel strategies for infection control. It is now understood that the co-ordinated control of gene expression by non-coding RNAs (ncRNA) underpins the activation and regulation of immune cells. However, it is also clear that pathogens (including helminths) secrete their own ncRNAs to manipulate host gene expression and influence immune outcomes to infection. To discriminate the contribution of host and helminth derived ncRNAs to the activation and/or regulation of innate immune responses during infection, we examined ncRNA expression in the peritoneal macrophages from mice infected with Fasciola hepatica. This revealed an enrichment of several parasitic-derived miRNAs (fhe-miR-277b-3p, fhe-miR-71a-5p, fhe-miR-125b-5p, fhe-miR-125a-5p) within macrophages at 6hr and 18hr after infection which is coincident with the parasite   s migration through the peritoneal cavity. Target prediction analysis indicated that these Fasciola miRNAs regulated host genes associated with the activation of host pro-inflammatory macrophages (Hif1   , Nod1, Nlrp6 and P2rx7). Concomitantly, there was a distinct shift in host ncRNA expression in response to infection, which was most significant at 5 days post-infection. Although, analysis suggested that these host ncRNAs target a different cohort of genes (Adar1, Igf1 and Plec) to the parasite miRNAs, the functional outcome was predicted to be the same, with a reduced pro-inflammatory response and the promotion of a reparative/tolerant phenotype. Combined, these observations uncover the interplay between host and parasitic ncRNAs and reveals a complementary regulation of the immune response that allows the parasite to evade immune detection and promotes tissue repair for the host. This level of characterisation of the ncRNA landscape during helminth infection is highly novel and provides a new understanding of the molecular impact that these parasites have on host immune cells.

overall_design: Performed RNAseq and miRNA-seq on total RNA isolated from peritoneal macrophages harvested from mice infected with Fasciola hepatica at different timepoints including 6hr, 18hr and 5 days post infection and uninfected mice. Mice miRNAs, lncRNAs and mRNAs were assessed and Fasciola hepatica miRNAs were identified.

first: Nham

last: Tran

first: Sheila

last: Donnelley


title: Cell of origin defines epigenetic mechanisms of transformation

city: Boston

first: Grant

last: Rowe

state: MA

address: 1 Blackfan Circle

institute: Boston Children's Hospital

summary: Acute myeloid leukemias (AMLs) show variable clinical outcomes.  The differentiation state of the normal hematopoietic cell of origin impacts the behavior of AML, with AML from hematopoietic stem cells (HSCs) prone to chemotherapy resistance in model systems.  However, the mechanisms by which HSC programs are transmitted to AML are not known.  Here, we introduce a leukemogenic translocation into defined human hematopoietic populations, finding that AMLs from HSCs show the highest stem cell content.  By epigenetic profiling, we identify a putative program from the normal HSC that collaborates with oncogene-driven programs to confer exceptional aggressiveness.  We confirm that components of this program are required for HSC-AML growth and survival and identify RNA polymerase (RNAP) II-mediated transcription as a therapeutic vulnerability.  Overall, we propose a mechanism as to how epigenetic programs from the leukemic cell of origin are inherited through transformation to impact heterogeneity in AML biology.

overall_design:
CUT&RUN and RNA-seq of engineered MLL-AF9 AMLs of defined human hematopoietic stem and progenitor cell origin

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Submitter states that missing raw data are being made available for controlled access in dbGaP.
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title: RNA sequencing of sperm from healthy cattle and horses reveals the presence of a large bacterial population

city: Madrid

first: Alfonso

last: Gutiérrez-Adán

address: Av. Puerta de Hierro 28

department: Animal Reproduction

country: Spain

institute: INIA

summary: RNA molecules within ejaculated sperm can be characterized through whole transcriptome sequencing, enabling the identification of pivotal transcripts that may influence reproductive success. However, the profiling of sperm transcriptomes through next-generation sequencing has several limitations impairing the identification of functional transcripts. In this study, we explored the nature of the RNA sequences present in the sperm transcriptome of two livestock species, cattle and horses using RNA-Sequencing (RNA-Seq) technology. Low mapping rates observed during data processing were mainly attributed to the presence of ribosomal RNA and bacteria in sperm samples which led to a reduced sequencing depth or library size. To explore the possibility that unmapped reads could be associated with bacteria, we then identified bacteria-associated transcripts within RNA-Seq data derived from bovine and equine sperm cell preparations. This analysis revealed bacterial species that may closely interact with sperm and potentially influence male fertility. Identifying these potentially pathogenic or beneficial species and understanding how they may affect sperm quality in each species could be paramount to assess the breeding capacity of livestock.

sample_organism:
Equus caballus
Bos taurus

platform_organism:
Equus caballus
Bos taurus

overall_design: Bacterial abundance estimation of transcriptome samples from sperm preparations of fertile bulls and stallions

first: Paula

last: Navarrete-López

first: Victoria

last: Asselstine

first: María

last: Maroto

first: Marta

last: Lombó

first: Ángela

last: Cánovas


title: Prenatal vitamin D deficiency alters immune cell proportions of offspring in young adult age [scRNA-seq]

city: College Station

first: Masako

last: Suzuki

state: TX

address: 498 Olsen Blvd, Norman E. Borlaug Building 202C

department: Nutrition

institute: Texas A&M University

summary: Vitamin D deficiency is a common micronutrient deficiency worldwide, especially among reproductive-age women, and vitamin D deficiency during pregnancy increases the risks of offspring’s immune-related diseases later in life. The mechanisms of how our body remembers the exposure status of an adverse environment during development have not been fully elucidated yet. Here we show that prenatal vitamin D deficiency exposure alters the immune cell proportion of the offspring at the prenatal and adult stage, which is attributed to transcriptional alterations of vitamin D receptor downstream genes. Further, we assessed the association between maternal vitamin D status and cord blood immune cell profiles from 75 healthy mother and their term baby pairs and found that maternal vitamin D deficiency significantly alters immune cell proportion in cord blood. Our findings demonstrate that prenatal vitamin D deficiency alters the immune cell compositions of offspring by changing the transcriptional properties of stem cells and altering long-term stem cell fate decisions.

overall_design: To investigate the effects of maternal vitamin D deficiency on the hematopoietic system of offspring, we performed scRNA-seq analyses on the fetal liver at embryonic day 14.5 of prenatal vitamin D deficiency exposed (VDD) and not exposed (VDS) male fetus. Samples were processed for scRNA-seq analysis on hashed-tagged single channel of 10x genomics


title: Transcriptional stress responses induced by compartment-targeted misfolding-prone proteins in Drosophila

city: Memphis

first: Yong-Dong

last: Wang

state: TN

address: 262 Danny Thomas Pl, MS1135

institute: St. Jude Children's Research Hospital

summary: Loss of proteostasis is an aging hallmark and the culprit of many age-related diseases. Different cell compartments experience distinctive challenges to maintain protein quality control but it remains underexplored how subcellular proteostasis is regulated by aging. Here, by targeting the misfolding_x0002_prone FlucDM luciferase to the cytoplasm, mitochondria, and nucleus, we have established transgenic sensors to examine subcellular proteostasis in Drosophila. Analysis of detergent-insoluble and -soluble levels of compartment-targeted FlucDM variants indicates that thermal stress, cold shock, and endocrine signaling differentially affect subcellular proteostasis during aging. Moreover, aggregation-prone proteins that cause different neurodegenerative diseases induce a diverse range of outcomes on FlucDM insolubility, suggesting that subcellular proteostasis is deranged in a disease-specific manner. Further analyses with FlucDM and mass spectrometry indicate that pathogenic tauV337M regulates in opposite manners the solubility of protein sets located in distinct organelles. Altogether, compartment-targeted FlucDM variants pinpoint a diverse modulation of subcellular proteostasis by aging regulators.

overall_design: RNA-sequencing data from Drosophila melanogaster strains (whole flies, males, 10-days-old) reared at 18C, 25, and 29C, and that express misfolding-prone proteins localized primarily to the cytoplasm (Cyto-FlucDM), the mitochondria (Mito-FlucDM), and the nucleus (NLS-FlucDM) were compared to isogenic control flies (w1118) that do not express FlucDM.

first: Michelle

last: Curley

first: Mamta

last: Rai

first: Chia-Lung

last: Chuang

first: Vishwajeeth

last: Pagala

first: Anna

last: Stephan

first: Zane

last: Coleman

first: Maricela

last: Robles-Murguia

first: Junmin

last: Peng

first: Fabio

last: Demontis


title: Prenatal vitamin D deficiency alters immune cell proportions of offspring in young adult age.

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

overall_design: Refer to individual Series


title: Deletion of microRNA-33 ameliorates amyloid pathology in APP/PS1 mice

city: Indianapolis

first: Jungsu

last: Kim

state: IN

address: 320 W. 15th Street

institute: Indiana University School of Medicine

summary: Background: ABCA1 has recently been identified as a novel genetic risk factor for Alzheimer’s disease. The major known role of ABCA1 in the brain is to transfer lipids onto lipid poor APOE. Given that APOEε4 is the strongest genetic risk factor for developing late onset Alzheimer’s disease, this recent finding implicates the cholesterol homeostatic pathway in the onset/progression of Alzheimer’s disease. microRNAs (miRs) are small RNA species that negatively regulate expression of their target genes. ABCA1 is regulated by miR-33, and loss of this miR significantly increases protein levels of ABCA1 and increases the lipidation of APOE. However, it is unknown if loss of miR-33 and subsequent increase in ABCA1 protein levels ameliorates amyloid pathology. Methods: We generated miR-33+/+;APP/PS1 and miR-33-/-;APP/PS1 mice to determine changes in amyloid-beta (Aβ) peptides and amyloid plaque formation utilizing biochemical and histological analyses. In addition to amyloid pathology, we assessed if deletion of miR-33 altered the activation of glial cells in the brains of these mice. We utilized in vitro methods to determine if miR-33 alters the phagocytosis of Aβ aggregates. We utilized RNA-sequencing and mass spectrometry to identify the transcriptome and proteome regulation by miR-33 in the context of amyloid pathology. Results: Deletion of miR-33 dramatically reduces insoluble Aβ peptide levels and the deposition of amyloid plaques in APP/PS1 mice. In addition, we identified that astrocyte and microglial activation is markedly decreased in miR-33-/-;APP/PS1 mice through histological analyses. Intriguingly, we show that loss of miR-33 results in amyloid plaques that are more compact, potentially implicating enhanced microglial phagocytosis. We confirm in vitro that loss of miR-33 significantly increases microglial phagocytosis of Aβ aggregates. Our multi-omics analyses reveal that deletion of miR-33 regulates immune response in the context of amyloid pathology. Interestingly, we identified that WNT/Beta-catenin signaling is significantly upregulated in miR-33-/-;APP/PS1 mice. Conclusion: We confirm that the deletion of miR-33 increases APOE lipidation and significantly reduces amyloid pathology as well as glial activation in APP/PS1 mice. Our results agree with previous work identifying APOE lipidation as an important modulator of amyloid pathology. We show, for the first time, that loss of miR-33 increases the phagocytosis of Aβ by microglia. In total, we identify miR-33 as a promising target for the amelioration of amyloid pathology.

overall_design: Quant-seq (3' mRNA-seq) analysis of 8-month-old brain cortical tissue of female APPsw/PSEN1Δ9 (APP/PS1) transgenic mice on a mixed B6/C3H background with miR-33 (miR-33 WT) and without miR-33 (miR-33 KO)

first: Mason

last: Tate

first: HR Sagara

last: Wijeratne

first: Byungwook

first: Stéphanie

last: Philtjens

first: Yanwen

last: You

first: Do-Hun

last: Lee

first: Daniela

last: Gutierrez

first: Daniel

last: Sharify

first: Megan

last: Wells

first: Magdalena

last: Perez-Cardelo

first: Emma

last: Doud

first: Carlos

last: Fernandez-Hernando

first: Cristian

last: Lasagna-Reeves

first: Amber

middle: L

last: Mosley


title: Identification of genes showing altered DNA methylation and gene expression in the renal proximal tubular cells of rats treated with ochratoxin A for 13 weeks

city: Fuchu-shi

first: Shunsuke

last: Ozawa

address: 3-5-8 Saiwai-cho

institute: Tokyo University of Agriculture and Technology

summary: The present study investigated comprehensive gene profiles regarding DNA methylation and gene expression in rat renal tubules after 13-week administration of ochratoxin A (OTA), a karyomegaly-inducing renal carcinogen. OTA-specific genes were obtained by excluding those responding to 3-MCPD, a renal carcinogen not inducing karyomegaly.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for total RNA from OSOM tissue samples obtained from untreated controls, OTA (210 µg/kg, dissolved in corn oil), MCPD (400 ppm, dissolved in drinking water) or TCP (125 mg/kg, dissolved in corn oil) treated rats for 13 weeks. The total RNA of each sample was pooled from six animals in each group to prepare one sample (n=1/group).

first: Ryota

last: Ojiro

first: Qian

last: Tang

first: Xinyu

last: Zou

first: Gye-Hyeong

last: Woo

first: Toshinori

last: Yoshida

first: Makoto

last: Shibutani


title: Unmasking of Protein Phosphatase 2 Regulatory Subunit B as a crucial factor in the development and progression of dilated cardiomyopathy

first: Fang

last: Lin

address: 150 Ji Mo Lu, Pu Dong

department: Shanghai East Hospital

institute: Tongji University School of Medicine, Shanghai

summary: The PPP2R5D encodes for a Protein phosphatase 2A (PP2A), one of the four major Ser/Thr phosphatases negatively controlling cell growth and division. PP2A is consisting of a common heteromeric core enzyme with a catalytic subunit and a B regulatory subunit that might control the substrate selectivity and catalytic activity. We investigated the potential role of Ppp2r5d for the cardiomyocyte (cultured mouse cardiomyocytes).

overall_design: The interfering RNA against Ppp2r5d (Case) or the negative control siRNA (Control) were transfected into MCMs（mouse cardiomyocytes） with Lipofectamine™ RNAiMAX transfection reagent. Forty-eight hours after transfection, the medium was changed to glucose-free media. The samples were then collected for a microarray gene expression study after overnight incubation.  One sample for each group.

first: Luying

last: Peng

first: Huimin

last: Fan

first: Li

last: Li


title: Genome-wide CRISPR Knockout Screen in LNCaP Cells Treated with Enzalutamide

city: London

first: Fred

last: Dick

state: Ontario

address: 1151 Richmond St

department: Pathology and Laboratory Medicine

country: Canada

institute: Western University

summary: To categorize gene loss events in enzalutamide-treated LNCaP cells, a genome-wide CRISPR knockout (KO) screen was performed. We quantified sgRNA abundance between initial and final timepoints in DMSO and enzalutamide treated cell populations

overall_design: Comparative sgRNA abundance and enrichment analysis of CRISPR Screen data for LNCaP cells treated with Enzalutamide or DMSO (T0-DMSO, T0-EZ, TF-DMSO, TF-EZ)

first: Michael

last: Roes


title: A mitochondrial unfolded protein response-independent role of DVE-1 in longevity regulation

status: Public on Sep 27 2024

city: Gainesville

first: Yi

last: Sheng

state: FL

address: 1600 SW Archer Road

department: Department of Physiology & Aging

institute: UNIVERSITY OF FLORIDA

summary: The special AT-rich sequence-binding (SATB) protein DVE-1 is widely recognized for its pivotal involvement in orchestrating the retrograde mitochondrial unfolded protein response (mitoUPR) in C. elegans. In our study of downstream factors contributing to lifespan extension in sensory ciliary mutants, we find that DVE-1 is crucial for this longevity effect independent of its canonical mitoUPR function. Additionally, DVE-1 also influences lifespan under conditions of dietary restriction and germline loss, again distinct from its role in mitoUPR. Mechanistically, while mitochondrial stress typically prompts nuclear accumulation of DVE-1 to initiate the transcriptional mitoUPR program, these long-lived mutants reduce DVE-1 nuclear accumulation, likely by enhancing its cytosolic translocation. This observation suggests a cytosolic role for DVE-1 in lifespan extension. Overall, our study implies that, in contrast to the more narrowly defined role of the mitoUPR-related transcription factor ATFS-1, DVE-1 may possess broader functions than previously recognized in modulating longevity and defending against stress.

overall_design: To compare the transcriptomic changes dependent on transcription factors DVE-1 and ATFS-1 in the daf-10(p821) and eat-2(ad465) mutant backgrounds, RNA-sequencing experiments were performed.

first: Rui

last: Xiao


title: Effect of D-glucose and L-glucose on gene expression of zebrafish embryos at 72 hpf (hours post fertilization) and 96 hpf.

city: nantong

first: wang

last: xiaoning

state: jiangsu

address: Qixiu Road 19

institute: Nantong University

summary: Artificially sweetened beverages containing noncaloric monosaccharides were suggested as healthier alternatives to sugar-sweetened beverages. Nevertheless, the potential detrimental effects of these noncaloric monosaccharides on blood vessel function remain inadequately understood. Presently, we have established a zebrafish model that exhibits significant excessive angiogenesis induced by D-glucose and L-glucose. Utilizing this model, we observed that glucose and noncaloric monosaccharides could induce excessive formation of blood vessels, especially intersegmental vessels (ISVs). We analyzed and compared the differentially expressed genes of control, high D-glucose-treated and high L-glucose-treated embryos. The results revealed that 1259 and 1074 genes were up-regulated significantly in high D-glucose and high L-glucose treated embryos, respectively, compared with control。

overall_design: Embryos were treated with D-glucose and L-glucose at 24 hpf and then collected for transcriptome sequencing at 72 hpf and 96 hpf.

first: Xiaoning

last: Wang

first: Jinxiang

last: Zhao

first: Jiehuan

last: Xu

first: Bowen

first: Xia

last: Liu

first: Gangcai

last: Xie

first: Xuchu

last: Duan

first: Dong


title: PGLYRP-1 Confers Immune Evasive Properties to Pancreactic Cancer Stem Cells [2014]

first: Susana

last: García-Silva

state: madrid

address: Melchor Fernandez Alamgro

department: Molecular Oncology

institute: Spanish national Cancer Research Centre

summary: The crosstalk between tumor and immune cells has important implications for cancer treatment, in particular for immunotherapies. Pancreatic ductal adenocarcinoma (PDAC) generally displays a chemoresistant phenotype and is refractory to immune-based therapies. Highly tumorigenic and stem-like cells known as cancer stem cells (CSCs) within PDAC tumors have been demonstrated to contribute to its aggressiveness, metastatic capacity and chemoresistance. Here, we show that CSCs could be also relevant to establish an immunosuppresive environment. Using genetically engineered mouse models (GEMMs) of PDAC we isolated a triple positive (EpCAM+, Sca-1+ and CD133+) population of tumor cells, functionally validated these cells as bona fide CSCs and probed their transcriptional profile by microarray analysis. In addition to stem pathways, signatures related to tumor immune evasion, immune modulation, invasiveness, and innate immune response were enriched in this population. Peptidoglycan recognition protein 1 (Pglyrp1), an innate immune response anti-bacterial protein expressed primarily by neutrophils, was highly expressed in this triple-positive population and in CSC-enriched spheres from human cell lines. Interestingly, modulation of Pglyrp1 expression in murine PDAC primary cultures affected their immune evasive properties, specifically their ability to escape macrophage- and T-cell-mediated killing in vitro and to establish tumors in immunocompetent hosts. Pglyrp1 expression in tumor cells seemed to interfere with TNFα-mediated killing by T cells and to promote activated T-cell cytotoxicity. Importantly, these results could be validated in CSCs from human patient-derived xenografts, and PGLYRP1 protein levels were also significantly higher in PDAC patient samples versus healthy controls. Thus, our study demonstrates a hierarchical organization of cancer cells in a murine model of PDAC, validating the CSC concept, and identifies Pglyrp1 as a putative PDAC biomarker that confers immune privilege properties to CSCs which could have important therapeutic implications.

overall_design: Cells from fresh pancreatic tumors from 8-weeks old LSL- KrasG12D/+;LSL-Trp53R172H/+;Pdx-1-Cre mice were isolated and sorted by flow cytometry according to EpCAM, CD133 and Sca-1 markers.

last: Silva

first: Bruno

last: Sainz

first: Christopher

last: Heeschen