title: ICOS-expressing Treg cells influence the composition of anti-tumor CTL population

city: Montreal

first: Woong-Kyung

last: Suh

state: Quebec

address: 110 avenue des Pins

institute: IRCM

summary: The role of ICOS in anti-tumor T cell responses and overall tumor progression has been controversial. Here, we compared tumor progression in mice lacking ICOS only in Treg cells or in all T cells. We found that Treg-specific ICOS knockout reduces the overall tumor burden compared to Cre control mice with increased T effector/Treg ratios in the tumor.  In contrast, there was no difference in the tumor burden in mice lacking ICOS in all the T cell compartments. This suggests a dual role of ICOS costimulation in promoting pro- and anti-tumor T cell responses.  Consistent with reduced tumor burden, we found that Treg-specific deletion of ICOS leads to an increase of CD8+ CTLs that express high levels of granzyme B and perforin. Moreover, single-cell transcriptome analysis revealed an increase of Ly108hiEomeshi CD8+ T cell subset at the cost of Ly108hiT-bethi subset in Treg-specific knockout mice. These results suggest that ICOS-expressing Treg cells suppress CTL maturation process at the level of Eomes upregulation, a critical step known to drive perforin expression and cytotoxicity. Collectively, our data imply that cancer immunotherapies using ICOS agonist antibodies would work better in Treg-low tumors or when they are combined with regimens that deplete tumor-infiltrating Treg cells.

overall_design: Foxp3-YFP Cre ICOS f/f versus Foxp3-YFP Cre +/+ control Treg, CD8 and CD4 T cells were sorted from the lungs 10 days post-tumor injection.

first: Nikoletta

last: Diamantopoulos

first: Joanna

first: Antoine

last: Bouchard

first: Loick

last: Joumier

first: Saba

last: Mohammaei

first: Vincent

last: Panneton

first: Jinsam

last: Chang

first: Mohan

last: Malleshaiah


title: Influence of low-input RNA from FF and FFPE samples on gene expression quantification by NanoString, microarray and RNA-seq: a comparative study [NanoString]

status: Public on Jul 19 2024

city: Paris

first: Jennifer

last: Wong

address: 12 rue lhomond

country: France

institute: Institue Curie

summary:
Purpose: The goals of this study is to determine the best method of gene expression quantification (RNA-seq, Microarray, NanoString) and amplification kits adapted to low-input and/or low-quality RNA samples (FFPE samples)
Methods: Mouse bladder cancer cell line (mouse bladder cancer cell line, BC57) and mouse normal mouse normal urothelium were fixed in formalin and embedded in paraffin (FFPE), andfesh frozen (FF) in liquid nitrogen. The total RNA of these 4 samples were tested by 3 technologies (NanoString, RNA-seq and Microarray) and the results were compared to its reference (high-quality and high-input RNA of mouse bladder cancer cell line and mouse normal mouse normal urothelium). For NanoString with low-input RNA samples,  each sample was tested by NanoString quantification after amplification by SMARTer Stranded Total RNA-Seq Kit - Pico Input mammelian and Ovation SoLo NuGEN RNA-seq System, and NanoString based on PCR approach with three input quantities: 50pg, 250pg and 2ng of total RNA, except for NanoString quantification after amplification by SMARTer Stranded Total RNA-Seq Kit - Pico Input mammelian kit for which the minimum recommended quantity was 250pg of total RNA. NanoString direct quantification was also done for FF and FFPE samples at high amount (50ng of total RNA) and results obtained from FF samples were considered as the reference.  To determine which is the method for NanoString technology,  low-input and  low-quality RNA samples, we performed NanoString control quality metrics, principal component analysis,  and a differential analysis between the mouse bladder cancer cell lines and the mouse normal mouse normal urothelium for each input quantity, amplification method and method of sample preservation (FF or FFPE).
Results:  The NanoString based PCR based approach is recommended for quantification of gene expression of FFPE and FF samples from 250pg of total RNA. However, NanoString quantification after amplification by SMARTer Stranded Total RNA-Seq Kit - Pico Input mammelian and Ovation SoLo NuGEN RNA-seq System is not recommended for FF and FFPE from low-input samples.

overall_design: For NanoString,  the 4 samples were tested in triplicate by 3 amplification methods: NanoString PCR based approach,  SMARTer Stranded Total RNA-Seq Kit - Pico Input mammelian and Ovation SoLo NuGEN RNA-seq System with three input quantities: 50pg, 250pg and 2ng of total RNA, except for NanoString after amplification by SMARTer Stranded Total RNA-Seq Kit - Pico Input mammelian kit for which the minimum recommended quantity was 250pg of total RNA. These 4 samples were also tested by NanoString direct quantification and results obtained from FF samples were considered as the reference.

first: David

last: Gentien

first: François

last: Radvanyi

first: Benoit

last: Albaud

first: Audrey

last: Rapinat


title: Decoding gene expression heterogeneity in Triple Negative Breast Cancer

status: Public on Jul 17 2024

city: Athens

first: Spyros

last: Foutadakis

address: Soranou

country: Greece

institute: Biomedical Research Foundation Academy of Athens

type: Expression profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Cadherins modulate the self-organizing potential of gastruloids (ATAC-seq)

status: Public on Jul 18 2024

city: LAUSANNE

first: ALEXANDRE

last: MAYRAN

state: Waadt

address: Station 19

country: Switzerland

institute: EPFL

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Gastruloids have recently emerged as an efficient four-dimensional model for studying some aspects of post-implantation embryonic patterning. Their ability to undergo gastrulation-like processes leading to the self-organization into highly reproducible biological objects, has opened new avenues to investigate early embryonic patterning. Here, we sought to uncover the molecular and cellular mechanism underlying this remarkable property. We report that self-organization competence is associated with a cell-specific coordination of a Cadherin switch. We find that N-Cadherin hinders gastruloids morphogenetic competence, for its inactivation leads to the formation of trunk-like structures without relying on the otherwise requested extra-cellular matrix analogues such as Matrigel. In contrast, the repression of E-Cadherin by Snai1 is critical for self-organization: Snai1 establishes a cell-specific repressive pace by triggering the repression of a pluripotency-associated transcription program and its chromatin landscape, thus allowing a proper transition from E- to N-Cadherin to occur. Altogether, this work establishes a molecular mechanism that integrates the exit from pluripotency and the pace of cell differentiation, leading to the observed self-organizing potential of gastruloids.

overall_design: ATAC-seq on gastruloids from WT and mutant conditions

first: Alexandre

last: Mayran

first: Rita

last: Amândio

first: Lucille

last: Lopez-Delisle

first: Denis

last: Duboule


title: Co-activation of NF-κB and MYC renders cancer cells addicted to IL6 for survival and phenotypic stability

city: London

first: Dinis

middle: Pedro

last: Calado

address: Midland Road

country: United Kingdom

institute: The Francis Crick Institute

summary: Gene expression profile of Plasmablast without or with MYC, or IKK2 or IKK2 and MYC overexpression

overall_design: B cells from  mice were isolated from splenocyte suspensions using CD43 microbeads (Miltenyi Biotec), and plated at a density of 1x106/mL in B-cell media (DMEM high glucose with Glutamax (Gibco), supplemented with Fetal Bovine Serum (GE Healthcare), non-essential aminoacids (Gibco), HEPES buffer (Gibco), sodium pyruvate (Gibco), Penicillin-Streptomycin (Gibco), and 2-Mercaptoethanol (Sigma-Aldrich)). B cells were stimulated with Lipopolysaccharide (LPS; Sigma-Aldrich) at a concentration of 10ug/mL. For gene expression profiling of in vitro derived activated B cells and plasmablasts, cells were FACS sorted at day 3 of LPS stimulation according to the expression of CD19 and CD138 markers (activated B cells – CD19+ CD138neg; plasmablasts – CD19low CD138+).

last: Barbosa

first: Martin

last: Janz


title: SUMOylation inhibition potentiates CAR T activity against multiple myeloma (RNA-Seq)

city: Duarte

first: Hsun

middle: Teresa

last: Ku

state: CA

address: 1500 E. Duarte Road

department: Translational Research and Cellular Therapeutics

country: USA

institute: City of Hope

summary: Chimeric antigen receptor (CAR)-T cell therapy has shown remarkable clinical efficacy against hematologic malignancies; however, tumor relapse occurs commonly due to T cell dysfunction presenting as exhaustion and loss of effector function. Here, we identified SUMOylation inhibition promoted T cell effector function and prevented T cell exhaustion. Combination of SUMO E1 inhibitor TAK-981, significantly potentiated CAR T cell anti-tumor activity and improved persistence of CAR-presenting T cells in vivo, presenting a potent novel therapeutic approach.

overall_design: CS1-CAR T cells were treated with DMSO (Vehicle, Veh) or 0.1µM TAK-981 (TAK) for 16 h, then CD4+ and CD8+ subsets of CS1 CAR T cells treated were purified by FACS sorting after staining with CD4 and CD8 antibodies. In co-culture experiment, CS1-CAR T cells were treated with vehicle (Veh) or TAK-981 (0.1µM, TAK) for 16 h. CAR T were spin down and washed off compound, then CAR T cells were cultured with MM1S-Luc cells at 1:1 ratio for 24 h. Cell mixtures were harvested then CD4+ and CD8+ CAR T cells were purified by FACS sorting after staining with CD4 and CD8. In both experiments, CS1 CAR T cells generated from two individual donors were used as biological replicates.

first: Li

last: Du

first: Steven

middle: T

last: Rosen


title: CARM1 hypermethylates the NuRD chromatin remodeling complex to promote cell cycle gene expression and breast cancer development [ChIP-Seq]

city: Xiamen

first: Jiancheng

last: Ding

state: Fujian

address: School of Pharmaceutical Sciences, Xiamen University Xiang`an South Road

country: China

institute: Xiamen University

summary: The nucleosome remodeling and deacetylase (NuRD) complex is a large multi-subunit complex that couples ATP-dependent chromatin-remodeling and histone deacetylase activities. Emerging evidence suggested that NuRD are associated with active genes and modulates their expression, but the underlying molecular mechanisms remain ill-defined. Here, we reported that the transcriptional coactivator CARM1 is associated with NuRD through its direct interaction with the GATAD2A/2B subunit, expanding the activities of NuRD to include protein arginine methylation. CARM1 and NuRD co-bind and -activate a large cohort of genes with implications in cell cycle control to facilitate the G1 to S phase transition. This gene activation process requires CARM1 to hypermethylate a key subunit in the NuRD complex, GATAD2A/2B, which is critical for the recruitment of the NuRD complex. The biological significance of this gene activation mechanism is underscored by the high expression of CARM1 and NuRD in breast cancers, and the fact that knockdown CARM1 and NuRD inhibits breast cancer cell growth in vitro and tumorigenesis in vivo. These findings reveal a gene activation program that requires the dual specificity established by CARM1 on chromatin and a key chromatin remodeler.

overall_design: ChIP-seq performed in this study was designed to understand the molecular mechanisms underlying CARM1/NuRD in gene transcriptional regulation.


title: Serial Changes of Circulating Tumor Cells in Patients with Hepatocellular Carcinoma Treated with Atezolizumab Plus Bevacizumab

city: FUKUI

first: Yosuke

last: Murata

address: 23-3 Matsuoka Shimoaizuki, Eiheiji-cho, Yoshida-gun

department: second Department of Internal Medicine

country: Japan

institute: University of Fukui

summary: Background and aims: Immune checkpoint inhibitors have promising outcomes in patients with hepatocellular carcinoma (HCC); however, there is no reliable biomarker for predicting disease progression. Circulating tumor cells (CTCs) derived from peripheral blood have attracted attention in monitoring therapeutic efficacy. In this study, CTCs were serially collected from patients with HCC undergoing atezolizumab plus bevacizumab (Atezo+Bev) treatment, and changes in molecular expression and CTC numbers were analyzed to identify effective biomarkers. Approach and results: The peripheral blood samples were collected serially from 22 patients with HCC treated with Atezo+Bev, and CTCs were enriched using RosetteSep. The CD45(-)PanCK(+) cell counts were measured using flow cytometry. RNA extracted from enriched CTCs underwent targeted RNA sequencing with next-generation sequencing (NGS) and performed unsupervised hierarchical clustering analysis. Changes in CTC numbers during Atezo+Bev treatment reflected the tumor volume. NGS analysis revealed that patients with elevated transforming growth factor (TGF)-β signaling molecules had a poorer response, whereas those with elevated apoptosis signaling molecules had a favorable response (p < 0.05). In addition, compared with changes in CTC counts, changes in TGF-β signaling molecule expression in CTCs accurately and promptly predicted treatment response. Conclusions: NGS analysis of CTC-derived RNA showed that changes in TGF-β signaling molecules predict treatment response earlier than changes in CTC counts. These findings suggest that changes in the expression of TGF-β molecules in CTCs could serve as novel biomarkers for the early prediction of therapeutic response in patients with unresectable HCC undergoing Atezo+Bev therapy.

overall_design: To evaluate the changes in molecular expression of CTCs in patients with HCC treated with Atezo+Bev, we designed an NGS panel comprising 373 genes associated with stem cell potency, epithelial–mesenchymal transition (EMT), HCC progression, and cancer immunotherapy.

first: Takuto

last: Nosaka

first: Yu

last: Akazawa

first: Tomoko

last: Tanaka

first: Kazuto

last: Takahashi

first: Tatsushi

last: Naito

first: Hidetaka

last: Matsuda

first: Masahiro

last: Ohtani

first: Yasunari

last: Nakamoto


title: Alternative polyadenylation contributes to the Resistance of the Jiangxi hybrid rice to blast rice using transcriptomics and metabolomics

city: Nanchang

first: shaochun

last: Liu

address: Jiaoqiao town

institute: Jiangxi Agricultural University

summary: Rice (Oryza sativa) is one of the world's major rations. The widely planted hybrid rice in Jiangxi Province is seriously affected by Magnaporthe oryzae, which seriously restricts the rice yield in Jiangxi Province. In recent years, studies have found that alternative polyadenylation (APA) is an important post-transcriptional regulation in eukaryotes. The genetic law and function of APA in the occurrence of hybrid rice blast in Jiangxi are not clear. In this study, Wufengyou T025 (WFY) and its parents (male parent Changhui T025(CH), and female parent Wufeng B(WFB)) were used as the research objects. Transcriptome and metabolome sequencing, combined with a variety of bioinformatics analysis methods and modern molecular biology experimental techniques, revealed the APA expression profile during the occurrence of Jiangxi hybrid rice blast. To explore the regulatory mechanism of APA core factors during the occurrence of rice blast. This study not only provides a new understanding of the occurrence of Jiangxi hybrid rice blast, but also provides more abundant resources for molecular breeding.

sample_organism:
Oryza sativa Indica Group
Oryza sativa Japonica Group

overall_design: Rice (Oryza sativa L.) varieties were the hybrid Wufengyou T025 (WFY) along with its male line Changhui T025 (CH) and female line Wufeng B (WFB). The transgenic lines of wd-1 were generated by wild type (WT) Nipponbare plants. Appropriate amount of rice leaves was taken at 0 hours, 12 hours, 24 hours, 36 hours, and 48 hours, respectively.

first: Shaochun

first: Dong

last: Han

first: Xinyi

last: Li

first: Xinlei

last: Jiang

first: Shangwei

last: Yu

first: Junying

last: Huang

first: Hao

last: wang

first: Junru

last: Fu

first: Dahu

last: Zhou

first: Xiaorong

last: Chen

first: Jie

last: Xu

first: Haohua

last: He

first: Haihui


title: Control of innate olfactory valence by segregated cortical amygdala circuits

city: La Jolla

first: Cory

middle: Matthew

last: Root

address: 3119 Pacific Hall, 9500 Gilman Drive

department: Biological Sciences

institute: University of California, San Diego

summary: Animals perform innate behaviors that are stereotyped responses to specific evolutionarily relevant stimuli in the absence of prior learning or experience. These behaviors can be reduced to an axis of valence, whereby specific odors evoke approach and avoidance. The cortical amygdala (plCoA) mediates innate attraction and aversion to odor. However, little is known about how this brain area gives rise to behaviors of opposing motivational valence. Here, we sought to define the circuit features of plCoA that give rise to innate olfactory behaviors of valence. We characterized the physiology, gene expression, and projections of this structure, identifying a divergent, topographic organization that selectively controls innate attraction and avoidance to odor. First, we examined odor-evoked responses in these areas and found sparse encoding of odor identity, but not valence. We next considered a topographic organization and found that optogenetic stimulation of the anterior and posterior domains of plCoA elicits attraction and avoidance, respectively, suggesting a functional axis for valence. Using single cell and spatial RNA sequencing, we identified the molecular cell types in plCoA, revealing an anteroposterior gradient in cell types, whereby anterior glutamatergic neurons preferentially express Slc17a6 and posterior neurons express Slc17a7. Activation of these respective cell types recapitulates appetitive and aversive valence behaviors, and chemogenetic inhibition reveals partial necessity for valence responses to innate appetitive or aversive odors. Finally, we identified topographically organized circuits defined by projections, whereby anterior neurons preferentially project to medial amygdala, and posterior neurons preferentially project to nucleus accumbens, which are respectively sufficient and necessary for innate negative and positive olfactory valence. Together, these data advance our understanding of how the olfactory system generates stereotypic, hardwired attraction and avoidance, and supports a model whereby distinct, topographically distributed plCoA populations direct innate olfactory valence responses by signaling to divergent valence-specific targets, linking upstream olfactory identity to downstream valence behaviors, through a population code.  This represents a novel circuit motif in which valence encoding is represented not by the firing properties of individual neurons, but by population level identity encoding that is routed through divergent targets to mediate distinct valence.

overall_design: Comparative single-cell gene expression profiling of pooled anterior and posterior posterolateral cortical amygdala samples using snRNA-seq

first: James

last: Howe


title: Single cell RNA sequencing of nc886, a non-coding RNA transcribed by RNA polymerase III, with a primer spike-in strategy

city: Seoul

first: GyeongJin

last: Shin

state: Seoul

address: 222, Banpo-daero, Seocho-gu

department: Biomedicine and Health Sciences, Microbiology

country: South Korea

institute: The Catholic University of Korea

type: Non-coding RNA profiling by high throughput sequencing

summary: Single cell RNA sequencing (scRNA-seq) has emerged as a versatile tool in biology, enabling comprehensive genomic-level characterization of individual cells. Currently, most scRNA-seq methods generate barcoded cDNAs by capturing polyA tails of mRNAs, which excludes many non-coding RNAs (ncRNAs), especially those transcribed by RNA polymerase III (Pol III). Although previously thought to be expressed constitutively, Pol III-transcribed ncRNAs are expressed variably in healthy and disease states and play important roles therein, necessitating their profiling at the single cell level. In this study, we have developed a measurement protocol for nc886 as a model case, as an initial step for scRNA-seq for Pol III-transcribed ncRNAs. Specifically, we spiked in an oligo-tagged nc886-specific primer during the polyA tail capture process for the 5’-reading in scRNA-seq. We then produced sequencing libraries for standard 5’ gene expression and oligo-tagged nc886 separately, to accommodate different cDNA sizes and ensure undisturbed transcriptome analysis. We applied this protocol in three cell lines which express high, low, and zero levels of nc886, respectively. Our results show that the identification of oligo tags exhibited limited target specificity, and sequencing reads of nc886 enabled the correction of non-specific priming. These findings suggest that gene-specific primers (GSPs) can be employed to capture RNAs lacking a polyA tail, with subsequent sequence verification ensuring accurate gene expression counting. Moreover, we embarked on an analysis of differentially expressed genes in cell line sub-clusters with differential nc886 expression, demonstrating variations in gene expression phenotypes. Collectively, the primer spike-in strategy allows us for a combined analysis of ncRNAs and gene expression phenotype.

overall_design: We developed a method to measure nc886 using scRNA-seq, involving spiking an nc886-specific primer during polyA tail capture for 5’ sequencing. Separate sequencing libraries were prepared for standard 5’ gene expression and nc886 to handle different cDNA sizes and maintain transcriptome analysis integrity. This approach was tested on three cell lines with varying nc886 expression levels.

first: Hae-Ock

last: Lee

first: Gyeong-Jin


title: The endothelin-1-driven tumor-stroma feed-forward loops in high-grade serous ovarian cancer

city: Torino

first: Ivan

last: Molineris

state: TO

address: Via Nizza 52

department: Life Science and System Biology

country: Italy

institute: University of Turin

summary: The high-grade serous ovarian cancer (HG-SOC) tumor microenvironment (TME) is constellated by cellular elements and a network of soluble constituents that contribute to tumor progression. In the multitude of the secreted molecules, the endothelin-1 (ET-1) has emerged to be implicated in the tumor/TME interplay, however the molecular mechanisms induced by the ET-1-driven feed-forward loops (FFL) and associated with the HG-SOC metastatic potential need to be further investigated. The tracking of the patient-derived (PD) HG-SOC cell transcriptome by RNA-seq identified the vascular endothelial growth factor (VEGF) gene and its associated signature among those mostly upregulated by ET-1 and down-modulated by the dual ET-1R antagonist macitentan. Within the ligand-receptor pairs concurrently expressed in PD-HG-SOC cells, endothelial cells and activated fibroblasts, we discovered two intertwined FFL, the ET-1/ET-1R and VEGF/VEGF receptors, concurrently activated by ET-1 and shutting-down by macitentan, or by the anti-VEGF antibody bevacizumab. In parallel, we observed that ET-1 fine-tuned the tumoral and stromal secretome towards a pro-invasive pattern. Into the fray of the HG-SOC/TME double and triple co-cultures, the secretion of ET-1 and VEGF, that share a common co-regulation, was inhibited upon the administration of macitentan. Functionally, macitentan, mimicking the effect of bevacizumab, interfered with the HG-SOC/TME FFL-driven communication that fuel the HG-SOC invasive behaviour. The identification of ET-1 and VEGF FFL as tumor and TME actionable vulnerabilities, reveal how ET-1R blockade, targeting the HG-SOC cells and the TME simultaneously, may represent an effective therapeutic option for HG-SOC patients.

overall_design: In this work we report the application of the RNA-sequencing analysis to explore the contribution of endothelin-1 (ET-1)/ET-1 receptors (ET-1R) axis activation on the fluctuations in the transcriptional traits of high-grade serous ovarian cancer (HG-SOC) cells. We performed a global transcriptional mapping in a preclinical relevant model of patient-derived primary cultures of HG-SOC cells (PMOV10), harboring TP53 mutation, isolated from ascitic fluid. PMOV10 cells were stimulated with endothelin-1 (ET-1, 100 nM), or with the ET-1R antagonist macitentan (MAC, 1µM), alone or in combination with ET-1, or with acetic acid (1% in H20), as vehicle (CTR) for 24 hours, by employing 4 biological replicates for each condition.

first: Piera

last: Tocci

first: Celia

last: Roman

first: Rosanna

last: Sestito

first: Valentina

last: Caprara

first: Valeriana

last: Di Castro

first: Andrea

last: Sacconi

first: Giovanni

last: Tonon

last: Blandino

first: Anna

last: Bagnato


title: PiR-hsa-4447944 serves as an oncogenic mediator in prostate cancer and promotes the development of castration resistance by inhibiting NEFH expression

city: SHA TIN

first: Qiang

last: PENG

state: HONG KONG

address: 30-32 NGAN SHING ST

country: Hong Kong

institute: The Chinese University of HongKong

summary: PiR-hsa-4447944 showed a significantly higher expression level in both CRPC tissues and CRPC cell lines. Functionally, piR-hsa-4447944 overexpression conferred, whereas piR-hsa-4447944 suppression inhibited castration resistance ability in vitro and in vivo. Enforced piR-hsa-4447944 expression in vitro promoted PCa cells migration and invasion, as well as reduced cell apoptosis.  To explore the potential targets of piR-hsa-4447944, two PCa cells 22RV1 and LNCaP were transfected with control or piR-hsa-4447944 mimic, and then the extracted total RNA was used for mRNA sequencing and bioinformatic analysis.

overall_design: We treated PCa cells 22RV1 and LNCaP with control or piR-hsa-4447944 mimic, and then extracted total RNA for mRNA sequencing and bioinformatic analysis.

last: Peng

first: Yu

last: Chen

first: Tingting

last: Xie

first: Dandan

last: Pu

first: Vincy

last: WHo

first: Jingkai

last: Sun

first: Kang

last: Liu

first: Ronald

middle: C

last: Chan

first: Xiaofan

last: Ding

first: Jeremy

middle: Y

last: Teoh

first: Xin

last: Wang

first: Peter

middle: K

last: Chiu

first: Chi-Fai

last: Ng


title: LINC01133 promotes pancreatic ductal adenocarcinoma epithelial-mesenchymal transition mediated by SPP1 through binding to Arp3

city: Nanjing

first: Zhihong

last: Zhang

state: Jiangsu

address: Guangzhou Road 300

institute: Jiangsu Province Hospital

summary: Pancreatic ductal adenocarcinoma (PDAC) is a lethal disease with limited treatment methods. Long non-coding RNAs (lncRNAs) have been found involved in tumorigenic and progression. The present study revealed that LINC01133, a fewly reported lncRNA, was one of 16 hub genes that could predict PDAC patients' prognosis. LINC01133 was over-expressed in PDAC tumors compared to adjacent pancreas, and could promote PDAC proliferation and metastasis in vitro and in vivo, as well as inhibited PDAC apoptosis. LINC01133 expression positively correlated to secreted phosphoprotein 1 (SPP1) expression, leading to an enhanced epithelial-mesenchymal transition (EMT) process. LINC01133 bound with actin-related protein 3 (Arp3), the complex reduced SPP1 mRNA degradation which increased SPP1 mRNA level, ultimately leading to PDAC proliferation. This research revealed a novel mechanism of PDAC development and provided a potential prognosis indicator that may benefit PDAC patients.

overall_design: To investigate the function of LINC01133 in PDAC cell line, we established LINC01133 knockdown BXPC-3 cell line with negative control. RNA sequencing was performed and differential expression was analyzed.

first: Yefan

last: Yang

first: Yuxi

last: Gong

first: Ying

first: Rumeng

last: Bai

first: Shuaishuai

last: Zhuo


title: Effect of depletion of C15ORF48/miR-147 on gene expression in primary colonocytes [HCT116]

city: Arcadia

first: Mark

last: Boldin

state: California

address: 1500 Duarte Road

institute: City of Hope Beckman Research Institute

summary: Chronic inflammation is epidemiologically linked to the pathogenesis of gastrointestinal diseases, including inflammatory bowel disease (IBD) and colorectal cancer (CRC). However, our understanding of the molecular mechanisms controlling gut inflammation remains insufficient, hindering the development of targeted therapies for IBD and CRC. In this study, we uncovered C15ORF48/miR-147 as a novel negative regulator of gut inflammation, operating through the modulation of epithelial cell metabolism. C15ORF48/miR-147 encodes two molecular products, C15ORF48 protein and miR-147-3p microRNA, which are predominantly expressed in intestinal epithelium. C15ORF48/miR-147 ablation leads to gut dysbiosis and exacerbates chemically-induced colitis in mice. C15ORF48 and miR-147-3p work together to suppress colonocyte metabolism and inflammatory responses, and thus bridging mitochondrial metabolism and inflammation.

overall_design: To define the molecular mechanism by which C15ORF48/miR 147 controls gut inflammation, we performed global transcriptome analysis of purified C15ORF48/miR 147-sufficient and  deficient colonocytes from unchallenged and DSS challenged mice using RNA-seq.


title: Clonal Competition Assays Identify Fitness Signatures in Cancer Progression and Resistance in Multiple Myeloma

city: Würzburg

first: Larissa

middle: Anita

last: Haertle

state: Bavaria

address: Josef-Schneider-Str. 2, Haus C11

department: Medizinische Klinik und Poliklinik II

country: Germany

institute: Universitätsklinikum Würzburg (UWK)

summary: Multiple Myeloma is a genetically heterogeneous disease and the management of relapses is one of the biggest clinical challenges. TP53 alterations are established high-risk markers of MM and are included in the current disease staging criteria. KRAS is the most frequently mutated gene affecting around 20% of MM patients. Applying Clonal Competition Assays (CCA) co-culturing color-labeled genetically modified cell lines, we recently showed that both, mono- and biallelic single-point mutations in TP53 transmit a fitness advantage to the cells. Here we report a similar dynamic for two mutations in KRAS (G12A and A146T). The fitness benefit of TP53 and KRAS mutations was treatment-independent, unlike patient-derived drug resistance alterations that only induce an advantage when the drug is present. CUL4B KO and IKZF1 A152T, both previously confirmed to transmit resistance against immunomodulatory agents, as well as PSMB5 A20T, a mutation located in the binding site of proteasome inhibitors do not transfer a fitness advantage to the cells per se, rather a disadvantage in comparison to the wildtype cell line. They only outcompete the culture when the respective drug was applied. Thus, to prevent the selection of clones harboring the potential of inducing a relapse, these results argue in favor of treatment-free breaks or alternatively for a switch of the drug class given as maintenance therapy. Furthermore, our data gives a biological rationale for the high frequency of KRAS and TP53 alterations at MM relapse. CCAs are suitable models for the study of clonal evolution and competitive (dis)advantages conveyed by a specific genetic lesion of interest, in dependence on external factors such as the treatment.

overall_design: Monoallelic KRAS variants (A146T and G12A) were introduced into the OPM2 MM cell line by stable transfection with sleeping beauty vectors. RNA sequencing was conducted from the wildtype OPM2 cell line and the two derivates in triplicates.


title: Gene expression profile of PTPN14 silence with PDGF-BB stimulation in HA-VSMCs

city: Tianjin

first: Qiannan

last: Ma

address: 22 Qiqiangtai Road

institute: Tianjin Medicial University

summary: The moderate response of smooth muscle cells is beneficial to the repair of vascular injury, while the continuous exposure of intravascular growth factors, and other stimulating factors will cause the dysfunction of smooth muscle cells, leading to the pathological remodeling of blood vessels, which is called neointimal hyperplasia. The aim of this study is to investigate the biological function of PTPN14 in vascular smooth muscle cells (VSMCs) and the mechanism of PTPN14 in regulating neointimal hyperplasia.

overall_design: HA-VSMCs were transfected with PTPN14 or control siRNA followed by treatment with or without PDGF-BB for 24 h.Then we performed whole transcriptome analysis using RNA-sequencing.

first: Yi

last: Zhu

first: Jinlong

last: He


title: LncRNA SLC7A11-AS1 suppresses ferroptosis in hepatocellular carcinoma to promote tumorigenesis

city: Chengdu

first: Yida

address: No.24, South Section of First Ring Road, Wuhou District

institute: Sichuan University

summary: LncRNAs are playing essential roles in epigenetic regulation, mRNA translation, and protein modification. However,  the function of SLC7A11-AS1, an antisense lncRNA derived from the solute carrier family 7 member 11 (SLC7A11) gene, remains incompletely known. In this study, we utilized shRNA technology to knock down SLC7A11-AS1 in HepG2 cells, aiming to investigate the role of SLC7A11-AS1 in hepatocellular carcinoma. RNA-seq results revealed that there were 2536 differentially expressed genes upon SLC7A11-AS1 knockdown.

overall_design: In order to investigate the role of SLC7A11-AS1 in hepatocellular carcinoma, we stably knocked down SLC7A11-AS1 in the hepatocellular carcinoma cell line HepG2 using shRNA technology. RNA-seq sequencing was performed with three replicates for each group, including the control group.

first: Xiao

last: Yuan


title: Diverse gene regulatory mechanisms alter rattlesnake venom gene expression at fine evolutionary scales

city: Arlington

first: Siddharth

last: Gopalan

state: TX

address: 501 S. Nedderman Dr, Life Sciences Building RM 337

department: Biology

institute: University of Texas at Arlington

summary: Understanding and predicting the relationships between genotype and phenotype is often challenging, largely due to the complex nature of eukaryotic gene regulation. A step towards this goal is to map how phenotypic variation evolves through genomic changes that modify gene regulatory interactions. Using the Prairie Rattlesnake (Crotalus viridis) and related species, we integrate mRNA-seq, proteomic, ATAC-seq and whole genome resequencing data to understand how specific evolutionary modifications to gene regulatory network components produce variation in venom gene expression. Through comparisons within and between species, we find a remarkably high degree of gene expression and regulatory network variation across even a shallow level of evolutionary divergence. We use these data to test hypotheses about the roles of specific trans-factors and cis-regulatory elements, how these roles may vary across venom genes and gene families, and how variation in regulatory systems drive variation in venom phenotypes. Our results illustrate that variation in chromatin and genotype at regulatory elements plays major roles in modulating expression. However, we also find that enhancer deletions, variation in transcription-factor expression, and variation in activity of the insulator protein CTCF also impact downstream venom phenotypes. Our findings provide insight into the diversity and gene-specificity of gene regulatory features and highlight the value of comparative studies to link gene regulatory network variation to phenotypic variation.

sample_organism:
Crotalus viridis
Crotalus concolor
Crotalus lutosus

overall_design: Venom glands from 12 snakes were dissected, snap frozen, and sent for ATAC-seq to Active Motif (Carlsbad, California, USA). The resulting reads were processed following methods decribed in the manuscript. The processed files are bigwig format (.bw), which are used for several visualizations and peak magnitude quantifications in the paper.

first: Gopalan

middle: S

last: Siddharth

first: Perry

middle: W

last: Blair


title: Modulating Mesenchymal Stromal Cell Microenvironment Alters Exosome RNA Content and Ligament Healing Capacity

city: Cleveland

first: Peng

last: Jiang

state: OH

address: 2121 Euclid Ave

institute: Cleveland State University

summary: Mesenchymal stromal cells (MSCs) hold great promise in regenerative medicine due to their potential to promote tissue repair and regeneration. However, applying MSC-based cell therapy in actual clinical settings remains challenging due to issues such as immunocompatibility and cell stability. Recent shifts in therapeutic strategies have highlighted MSC-derived exosomes, small vesicles carrying various bioactive molecules, as a promising cell-free therapy to promote tissue regeneration. However, it remains largely unknown regarding the ability to customize the content of MSC-derived exosomes, how alterations in the MSC microenvironment influence exosome content, and the effects of such alterations on healing efficiency and mechanical properties in tissue repair when utilized as a therapy. In this study, we used an in vitro system of human MSC-derived exosomes and an in vivo rat ligament injury model to address these questions. We found a context-dependent correlation between exosomal and parent cell RNA content. Under native conditions, the correlation was moderate but heightened with microenvironmental changes. In vivo rat ligament injury model showed that MSC-derived exosomes increased ligament max load and stiffness. We also found that changes in the MSCs' microenvironment significantly influence the mechanical properties driven by exosome treatment. Additionally, a link was identified between altered exosomal microRNA levels and expression changes in microRNA targets in ligaments. These findings elucidate the nuanced interplay between MSCs, their exosomes, and tissue regeneration.

sample_organism:
Homo sapiens
Rattus norvegicus

platform_organism:
Homo sapiens
Rattus norvegicus

overall_design: In this study, we utilized a human BM MSC-derived exosomes in vitro system and a rat ligament injury in vivo model to address three fundamental questions: (a) whether the exosomal RNA content is determined by their parent cells; (b) whether the exosomal RNA content is customizable via perturbation of their parent cells’ microenvironment; (c) and how the alternation of RNA content in MSCs-derived exosomes affect the healing outcome in a ligament injury animal model.

first: Connie

last: Chamberlain

first: Archana

last: Prabahar

first: John

middle: A

last: Kink

first: Erika

last: Mueller

first: Yiyao

last: Li

first: Stephanie

last: Yopp

first: Christian

middle: M

last: Capitini

first: Peiman

last: Hematti

first: William

middle: L

last: Murphy

first: Ray

last: Vanderby


title: Decoding gene expression heterogeneity in Triple Negative Breast Cancer [scRNA-seq]

city: Athens

first: Spyros

last: Foutadakis

address: Soranou

institute: Biomedical Research Foundation Academy of Athens

summary: In this study, we have employed both bulk RNA- and sc-RNA-seq to investigate the transcriptional status of TNBC cells, grown as 2D or 3D cultures, prior and after development of resistance to two widely used chemotherapeutic drugs, paclitaxel and doxorubicin. Our aim was to uncover the gene expression programs that support drug tolerance in treatment-naïve cells and drug resistance in heterogeneous chemoresistant populations. Analysis of the data from the two techniques yielded similar results to a large degree, yet several low abundance gene expression changes in the chemoresistant cells were detected only by scRNA-seq.

overall_design: Targeted single cell RNA-seq experiments using the BD Rhapsody Onco-BC Panel  and SUM159 attached or speroid cells untreated or chemoresistant to paclitaxel or doxorubicin, for a total of six populations. No replicates are provided. The BD Single-Cell multiplexing Ki SampleTags 1,2,3  are assigned to SUM159 attached untreated, paclitaxel or doxorubicin resistant respectively. The BD Single-Cell multiplexing Ki SampleTags 4,6,8  are assigned to SUM159 spheroid untreated, paclitaxel or doxorubicin resistant respectively.

first: Angeliki

last: Magklara


title: Global gene expression profile of colon biopsy samples from healthy patients and colorectal cancer.

city: Logrono

first: María

last: de Toro

state: La Rioja

address: C/Piqueras 98

department: Genomics & Bioinformatics Core Facility

country: Spain

institute: Centro de Investigación Biomédica de La Rioja

summary: Mutations in Integrator complex subunit 6 (INTS6) correlate with different types of tumors. Lack of Integrator complex function, measured by an increased level of unprocessed snRNA, is a prognostic biomarker and correlates with a poorer prognosis in colorectal patients. The transcriptomic profile of all analyzed colorectal tumors shows a strong alteration of the metabolic state of tumor cells compromising standard energy production by mitochondrial respiration, known as the Warburg effect. In addition, there is a significant upregulation of genes involved in extracellular matrix organization and collagen rearrangement. This is consistent with tissue reorganization in a growing tumor forming a polyp. Crossing the molecular data generated in this study with the follow-up of patients from population screening indicates that population screening combined with early typing of tumors appear to be the most efficient way to increase patient survival.

overall_design:
To investigate if unprocessing snRNAs serves as a prognostic biomarker in colorectal cancer, a cohort of 90 patients showing different degrees of illness and 10 healthy individuals were selected from the San Pedro Hospital's Digestive System Department (La Rioja, Spain) based on the appearance of a lesion suspected to be of tumor origin during a diagnostic colonoscopy
Colorectal tumors were classificated based on INTS6 levels and snRNA processing
Transcriptomic analysis was performer from samples from different groups

first: Juan

last: Cabello


title: Clinical and molecular risk factors in extracranial malignanat rhabdoid tumors - towards an integrated model of high-risk tumors

city: Augsburg

first: Victoria

middle: Elisabeth

last: Fincke

address: Stenglinstraße 2

institute: Childens Cancer Center - University hospital Augsburg

type: Methylation profiling by genome tiling array

summary:
We characterize relapse patterns in eMRT and analyzed DNA methylation of eMRT primary and relapse tissues. Using NMF-based clustering, we identify 3 subgroups of which ne subgroup displayed significantly improved survival rates.
Based on the subgroups, we provide a random forest-based model to prognosticate survival.

overall_design: The DNA methylation of 80 eMRT tumor samples was analyzed.

middle: E

first: Mona

last: Steinbügl

first: Hye-Jung

last: Chun

first: Karolina

last: Nemes

first: Marlena

last: Mucha

first: Felix

last: Dorn

first: Katharina

last: Gastberger

first: Thomas

last: Kröncke

first: Reiner

last: Siebert

first: Patrick

last: Melchior

first: Rhoikos

last: Furtwängler

first: Matthias

last: Schlesner

last: Vokuhl

first: Christoph

last: Röcken

first: Sebastian

last: Bühner

first: Maurice

last: Loßner

first: Pascal

middle: D

last: Johann

first: Michael

last: Frühwald


title: PRDM6 promotes medulloblastoma by repressing chromatin accessibility and altering gene expression

city: San Francisco

first: Bjoern

last: Schwer

institute: University of California, San Francisco

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

overall_design: Refer to individual Series


title: PRDM6 promotes medulloblastoma by repressing chromatin accessibility and altering gene expression [RNA-Seq]

summary: SNCAIP duplication may promote Group 4 medulloblastoma via induction of PRDM6, a poorly characterized member of the PRDF1 and RIZ1 homology domain-containing (PRDM) family of transcription factors. Here, we investigated the function of PRDM6 in human hindbrain neuroepithelial stem cells and tested PRDM6 as a driver of Group 4 medulloblastoma. We report that human PRDM6 localizes predominantly to the nucleus, where it causes widespread repression of chromatin accessibility and complex alterations of gene expression patterns. Genome-wide mapping of PRDM6 binding reveals that PRDM6 binds to chromatin regions marked by histone H3 lysine 27 trimethylation that are located within, or proximal to, genes. Moreover, we show that PRDM6 expression in neuroepithelial stem cells promotes medulloblastoma. Surprisingly, medulloblastomas derived from PRDM6-expressing neuroepithelial stem cells match human Group 3, but not Group 4, medulloblastoma. We conclude that PRDM6 expression has oncogenic potential but is insufficient to drive Group 4 medulloblastoma from neuroepithelial stem cells. We propose that both PRDM6 and additional factors, such as specific cell-of-origin features, are required for Group 4 medulloblastoma. Given the lack of PRDM6 expression in normal tissues and its oncogenic potential shown here, we suggest that PRDM6 inhibition may have therapeutic value in PRDM6-expressing medulloblastomas.

overall_design: To elucidate the function of PRDM6, we established human neuroepithelial stem (NES) cells expressing human PRDM6 (PRDM6 NES) and matching control cells (EV NES). Moreover, we collected tumors derived from PRDM6 NES cells.

first: Christin

last: Schmidt

first: Sarah

last: Cohen

first: Brian

last: Gudenas

last: Husain

first: Annika

last: Carlson

first: Samantha

last: Westelman

first: Linyu

last: Wang

first: Joanna

middle: J

last: Phillips

first: Paul

last: Northcott

first: William

last: Weiss


title: Fgf9 promotes adipogenesis and reduces osteogenesis by regulating mesenchymal stromal cells differentiation in adult bone marrow

city: Shanghai

first: Mingmei

last: Chen

address: 197 Ruijin Road II, Building #17

institute: Shanghai Jiao Tong University

summary: In this study, we found that Fgf9 regulates the bone-fat balance by modulating the cell fate determination of BMSCs. Histology and micro-CT analysis demonstrate that Fgf9 S99N mutation (loss-of-function) significantly inhibited the formation of bone marrow adipose tissue (BMAT) in adult mice and alleviated the ovariectomized (OVX) induced bone loss and BMAT accumulation. In vitro cytodifferentiation assays unveiled that the Fgf9 S99N mutation hindered adipogenesis while promoting osteogenesis in BMSCs. Furthermore, recombinant FGF9 stimulation and Fgf9 overexpression in BMSCs demonstrated that Fgf9 significantly promoted adipocyte formation and inhibited osteogenesis in vitro and in vivo. Cytodifferentiation assays at various stages of BMSC differentiation indicated that FGF9 altered the osteogenic and adipogenic potential of BMSCs, particularly during the early stages of differentiation. Transcriptomic and gene expression analyses demonstrated that FGF9 significantly upregulated the expression of adipogenic genes while downregulating osteogenic gene expression at both mRNA and protein levels. KEEG analysis revealed and in vitro differentiation assays with specific inhibitors confirmed that FGF9 modulated bone-fat balance by inhibiting osteogenesis via the MAPK/ERK pathway and promoting adipogenesis by activating the PI3K/AKT and Hippo pathways.

overall_design: To investigate the pivotal mechanism, we performed RNA-seq on 6 groups of BMSCs, which were cultured separately with or without 20 ng/mL FGF9 in culture medium (CM, CM_F9), osteogenic induction medium (OI, OI_F9), and adipogenic induction medium (AI, AI_F9). There are the triplicate samples within every group.

first: Zhugang

first: Lingyun

last: Tang


title: Exercise accelerated the degeneration of lumbar IVDs from surgical lumbar instability, similar to the clinical degeneration process

city: Wuhan

first: Cao

last: Yang

state: Hubei

address: Jiefang average

institute: Wuhan Union Hospital

summary: Given the leading cause of disability worldwide, low back pain (LBP) is recognized as a pivotal socio-economic challenge to the aging population, which is importantly attributed to intervertebral disc degeneration (IVDD), a highly prevalent affliction of aging. Elastic nucleus pulposus (NP) tissue is essential for maintenance of IVD structural and functional integrity. Native NP cells exhibit crucial functions for regulating extracellular matrix homeostasis, constructing an accommodating biomechanical environment and maintaining the gelatinous property of NP tissue. Mechanical stresses, including compulsion position and aberrant mechanical loading, are regarded as etiological factors of IVDD, and to further investigate the effect of mechanical exercise during the degeneration of IVDs, we surgically resected the lumbar 4th-lumbar 5th (L4-L5) spinous processes of the rat spine along with the supraspinous and interspinous ligaments to induce lumbar surgical instability (LSI). Additionally, we applied RNA sequencing technology to describe the degeneration-associated molecular atlas of the LSI model during exercise, and found that exercise accelerated the degenerative process of IVDs from LSI, which is involved in cytosolic DNA sensing-mediated inflammatory activation, similar to the degenerative patterns of the clinical IVDD process.

overall_design: The transcriptional profiles of nucleus pulposus (NP) cells from three degenerated and three no-degenerated human NP tissues. The transcriptional profiles of NP cells from rat lumbar IVDs in the sham operation, LSI and LSI-E groups.

first: Weifeng

last: Zhang

first: Gaocai

last: Li

first: Xingyu

last: Zhou


title: Decoding gene expression heterogeneity in Triple Negative Breast Cancer [bulk RNA-seq]

first: Spyros

last: Foutadakis

overall_design: RNA-seq experiments were performed in duplicates using SUM159 attached cells chemoresistant to  doxorubicin

first: Angeliki

last: Magklara


title: Glioneuronal tumor with ATRX alteration, kinase fusion and anaplastic features (GTAKA) with leptomeningeal dissemination and ZMIZ1::RET fusion [RNA-seq]

city: Rome

first: Evelina

last: Miele

address: Piazza di Sant'Onofrio 4

department: Oncoematologia

institute: Ospedale Pediatrico Bambino Gesù

summary: Herein we describe a case with histological, immunohistochemical and molecular features of GTAKA showing widespread leptomeningeal dissemination.

overall_design: Tumor case report


title: Effect of depletion of C15ORF48/miR-147 on gene expression in primary colonocytes [colonocytes]

first: Mark

last: Boldin


title: Genome-wide identification of beta-catenin related genes in CD34 + Hematopoietic Stem and Progenitor Cells of patients with Acute Myeloid Leukemia

city: ankara

first: nevin

last: belder

address: gumusdere

country: Turkey

institute: ankara university

summary:
Background: Acute myeloid leukaemia is a disease characterised by the accumulation of large number of aberrant, immature myeloid cells in the bone marrow and peripheral blood as a result of a variety of genetic alterations in early haematopoietic stem cells. Normal stem cells, which have the ability to renew themselves, can undergo neoplastic transformation as a result of mutations in signalling pathway genes, changes in epigenetics or gene expression levels. The gene expression levels of beta-catenin, a key element of the Wnt signalling pathway, which is particularly active during embryogenesis and in various cancers, have been widely studied in the literature. In these studies, which were consistent with each other, serious differences in beta-catenin gene expression levels were found in AML patients.
On this basis, our aim of this study was to determine beta-catenin gene expression levels in AML patients. In the next part of the study, it is planned to compare the genes between AML patient samples grouped according to beta-catenin gene expression levels by DNA microarray analysis. When the gene group identified in this way is combined with the genes in the healthy control group, the aim is to determine the genes and pathways that are associated with beta-catenin in AML patients.
Material and Method: In this study, beta-catenin gene expression levels were determined in bone marrow/blood CD34+ cells of 19 AML patients and 3 healthy controls by qRT-PCR. Transcriptome analysis was performed on AML patient samples grouped according to beta-catenin expression levels. After transcriptome analysis, differentially expressed genes (DEGs) were identified using a 1.5-fold change threshold. DEGs were further investigated using the online analysis tools DAVID, GO, KEGG and STRING.
Results: In this study, the mRNA analysis showed that beta-catenin levels varied between AML samples. Based on these results, the AML samples were divided into 2 groups: high and low beta catenin. The transcriptome profiles of the AML samples showed different molecular signature profiles according on their beta-catenin levels (high-low) when compared to the healthy control group. In our study, it was found that hub genes related to cell cycle, ribosome biogenesis and transcription factor pathways were beta-catenin-related genes and were prominent in the group of AML patients with high beta-catenin levels.
Conclusion: It is suggested that the identification of beta-catenin-related gene profiles in AML may help to select new molecular therapeutic targets for the treatment of AML.

overall_design:
AML patients (newly diagnosed) which were categorized into 2 groups based on the expression levels of the beta-catenin gene were compared with healthy control samples by human genome microarray expression profiling. Gene expression profiles were compared between the group of AML patients (n=19) with high beta-catenin levels (n=8) and healthy donor controls and the group of AML patients with low beta-catenin levels (n=7) and healthy controls (n=3).  CD34+ cells were isolated from the bone marrow or blood of AML patients and controls. RNAs were isolated from CD34+ cells by Trizol (Invitrogen, ABD). 500 ng RNAs were used to generate amplified and biotinylated cRNA with the GeneChip® 3′ IVT Express Kit (Affymetrix, Santa Clara, CA). 15 µg of fragmented biotin-labeled cRNA was hybridized with Human Genome U133 Plus 2.0 Affymetrix GeneChips (Affymetrix, Santa Clara, CA, USA). Arrays were washed, stained and finally scanned using the GeneChip® Scanner 3000.
We identified dysregulated genes and pathways associated with beta-catenin in patients with AML.

first: B

last: Altinok Gunes

first: T

last: Ozkan

first: A

last: Karadag

first: S

last: Dalkilic

first: N

last: Belder

first: Z

last: Ozkeserli

first: H

last: Ozdag

first: M

last: Beksac

last: Sayinalp

last: Yagci

last: Sunguroglu


title: New Drosophila promoter-associated architectural protein Mzfp1 interacts with CP190 and is required for housekeeping gene expression and insulator activity [ChIP-seq]

city: Moscow

first: Natalia

last: Klimenko

address: 34/5 Vavilova Street

country: Russia

institute: Institute of Gene Biology (IGB) of the Russian Academy of Sciences

summary: In Drosophila, a group of zinc finger architectural proteins recruits the CP190 protein to the chromatin, an interaction that is essential for the functional activity of promoters and insulators. In this study, we describe a new architectural C2H2 protein called Madf and Zinc-Finger Protein 1 (Mzfp1) that interacts with CP190. Mzfp1 has an unusual structure that includes six C2H2 domains organized in a C-terminal cluster and two tandem MADF domains. Mzfp1 predominantly binds to housekeeping gene promoters located in both euchromatin and heterochromatin genome regions. In vivo mutagenesis studies showed that Mzfp1 is an essential protein, and both MADF domains and the CP190 interaction region are required for its functional activity. The C2H2 cluster is sufficient for the specific binding of Mzfp1 to regulatory elements, while the second MADF domain is required for Mzfp1 recruitment to heterochromatin. Mzfp1 binds to the proximal part of the Fub boundary that separates regulatory domains of the Ubx and abd-A genes in the Bithorax complex. Mzfp1 participates in Fub functions in cooperation with the architectural proteins Pita and Su(Hw). Thus, Mzfp1 is a new architectural C2H2 protein involved in the organization of active promoters and insulators in Drosophila.

overall_design: ChIP-seq signal of the Mzfp1 protein occupancy in wt lines for adult flies and embryos and in deltaM2, deltaZf and delta42 lines for adult flies.

first: O

last: Maksimenko


title: A novel gain-of-function phosphorylation site  modulates PTPN22 inhibition of TCR signaling

city: Los Angeles

first: Richard

last: Ainsworth

address: 8700 Beverly Blvd

institute: Cedars-Sinai Medical Center

summary: Protein Tyrosine Phosphatase Non-receptor type 22 (PTPN22) is encoded by a major autoimmunity gene and is a known inhibitor of T cell receptor (TCR) signaling and drug target for cancer immunotherapy. However, little is known about PTPN22 post-translational regulation. Here we characterize a phosphorylation site at Ser325 situated C-terminal to the catalytic domain of PTPN22, and its roles in altering protein function. Signaling through the major TCR-dependent pathway under PTPN22 control was enhanced by CRISPR/Cas9 mediated suppression of Ser325 phosphorylation and inhibited by mimicking it via glutamic acid substitution. Next-generation sequencing (NGS) revealed it differentially regulates the expression of chemokines and T cell activation pathways. In conclusion, this study explores the function of a novel phosphorylation site of PTPN22 that is involved in complex regulation of TCR signaling .

overall_design:
We generated the CRISPR/Cas9 mediated mutagenesis of Ser325 to glutamic acid and Alanine to explore the roles of  Ser325 phosphorylation in activated Jurkat T cells
The cells were starved and stimulated by antibodies against human CD3/CD28 antibodies for 16h, and cells were collected, washed and used for bulk RNA sequencing.

first: Bottini

last: Nunzio

first: Yang

last: Shen

first: Ainsworth

last: Richard


title: Protein Phosphatase PP1 Regulation of Pol II Phosphorylation is Linked to Transcription Termination and Allelic Exclusion of VSG Genes and TERRA in Trypanosomes.

first: Haidong

last: Yan

state: Georgia

address: 220 Mark Twain Cir Apt D

institute: University of Georgia

summary: Base J is a modified DNA base that is enriched at RNA polymerase II termination sites. We previously found that base J functions to prevent readthrough transcription within gene clusters via the PJW/PP1 complex. Analysis of the complex in T. brucei faild to identify the catalytic PP1 component. We now show the RNAi ablation of PP1-1 in T. brucei leads to readthrough transcription and expression of downstream genes.

overall_design: The role of PP1-1 in regulating transcription termination was investigated using RNAi ablation in T. brucei cell lines. We used 6 RNA seq libraries to determine gene expression changes following the loss of PP1-1. As a control we used 6 RNA seq libraries to determine changes following the loss of PP1-7.

first: Robert

last: Sabatini

first: Rudo

last: Kieft

last: Zhang

last: Schmitz


title: TAF7L REGULATES EARLY STAGES OF MALE GERM CELL DEVELOPMENT

city: Kansas City

first: Ayelen

last: Moreno-Irusta

state: Kansas

address: 3901 Rainbow Blvd., 3050

institute: University of Kansas Medical Center

summary: Male germ cell development is dependent on the orchestrated regulation of gene networks. TAF7 like (Taf7l) is situated on the X chromosome and has been implicated in testis development. We examined the biology of TAF7L in testis development using the rat. Taf7l disruption resulted in male infertility due to compromised testis development and failed sperm production. An arrest in the progression of meiosis was observed.

overall_design: RNA-seq was performed in testis from Taf7l WT and mutant rat at postnatal day 60.

last: Moreno Irusta

first: Esteban

last: Dominguez

first: Khursheed

last: Iqbal

first: Michael

last: Soares


title: Trematode DIPLOSTOMUM PSEUDOSPATHACEUM INDUCING DIFFERENTIAL GENE EXPRESSION IN SEXUAL AND GYNOGENETIC GIBEL CARP (Carassius gibelio): PARASITES FACILITATING THE COEXISTENCE OF TWO REPRODUCTIVE FORMS of the invasive species

city: Liběchov

first: Tomáš

last: Tichopád

address: Rumburská 89

country: Czech Republic

institute: ÚŽFG

summary: Parasite-mediated selection is considered one of the potential mechanisms contributing to the coexistence of asexual-sexual complexes. Gibel carp (Carassius gibelio), an invasive fish species in Europe, often forms populations composed of gynogenetic and sexual specimens. In the present study, experimental infection was induced in gynogenetic and sexual gibel carp using eye-fluke Diplostomum pseudospathaceum (Trematoda), and the transcriptome profile of the spleen as a major immune organ in fish was analyzed to reveal the differentially expressed immunity-associated genes related to D. pseudospathaceum infection differing between gynogenetic and sexual gibel carp. High parasite infection was found in gynogenetic fish when compared to genetically diverse sexuals. Although metacercariae of D. pseudospathaceum are situated in an immune-privileged organ, our results show that eye trematodes may induce a host immune response. We found differential gene expression induced by eye-fluke infection, with various impacts on gynogenetic and sexual hosts, documenting for the majority of DEGs upregulation in sexuals, and downregulation in asexuals. Differences in gene regulation between gynogenetic and sexual gibel carp were evidenced in many immunity-associated genes. GO analyses revealed the importance of genes assigned to the GO terms: immune function, the Notch signaling pathway, MAP kinase tyrosine/threonine/phosphatase activity, and chemokine receptor activity. KEGG analyses revealed the importance of the genes involved in 12 immunity-associated pathways – specifically, FoxO signaling, adipocytokine signaling, TGF-beta signaling, apoptosis, Notch signaling, C-type lectin receptor signaling, efferocytosis, intestinal immune network for IgA production, insulin signaling, virion - human immunodeficiency virus, Toll-like receptor signaling, and phosphatidylinositol signaling system. Our study indicates the limited potential of asexual fish to cope with higher parasite infection (likely a loss of capacity to induce an effective immune response) and highlights the important role of molecular mechanisms associated with immunity for the coexistence of gynogenetic and sexual gibel carp, potentially contributing to its invasiveness.

overall_design: A total of 9 sexual and 9 gynogenetic immunologically naïve specimens of Carassius gibelio obtained by artificial breeding were selected for experimental infection by Diplostomum pseudospathaceum, and 6 sexual and 6 gynogenetic non-infected fish were used as a control. Four samples from the gynogenetic and 5 from sexual groups of infected fish were selected along with the control groups (4 uninfected gynogenetic and 4 uninfected sexual gibel carp) for RNAseq.

first: Md

last: Mehedi Hasan Fuad

first: Markéta

last: Ondračková

first: Kristína

last: Civáňová Křížová

first: Mária

last: Seifertová

first: Kristýna

last: Voříšková

first: Martin

last: Demko

first: Lukáš

last: Vetešník

first: Andrea

last: Šimková


title: Impact of benzoapyrene and ionizing radiation on gene expression of MCF7 cells

city: Mainz

first: Christian

last: Schwarzenbach

address: Obere Zahlbacher Str. 67

department: Institute of Toxicology

institute: University medical center Mainz

summary: Transcriptomic gene expression analysis of MCF7 cells stimulated for 120 h with benzoapyrene, ionizing radiation or nothing

overall_design: To investigate the gene expression profile of MCF7 cells upon exposure to benzoapyrene and ionizing radiation, MCF7 cells were exposed or unexposed for 120 h to 1 µM benzoapyrene, 5 Gy ionizing radiation or nothing. We then performed comparative gene expression profiling analysis using RNA-seq data obtained from 3 independent experiments.

first: Sebastian

last: Allmann

first: Ariane

last: Schmidt

first: Christmann

last: Markus

first: Sergi

last: Sayols Puig


title: New Drosophila promoter-associated architectural protein Mzfp1 interacts with CP190 and is required for housekeeping gene expression and insulator activity

first: Natalia

last: Klimenko


title: Bulk RNA sequencing of CD8a+ and CD8a- CD56bright and CD56dim human NK cells

city: St. Louis

first: Todd

last: Fehniger

state: MO

address: 660 S Euclid Ave, Campus Box 8007

department: Oncology

institute: Washington University School of Medicine

summary: In patients treated with memory-like NK cellular therapy with AML, a negative association with CD8a expression on donor NK cells and treatment response was found. The goal of this project was to determine how this finding extended to conventional NK cells, and to characterize the expression and functional role of CD8a. Peripheral blood NK cells were sorted on CD8 expression and analyzed by bulk RNA sequencing within CD56bright and CD56dim NK cell subsets.

overall_design: Freshly isolated peripheral blood NK cells were rested overnight in 1 ng/mL IL-15, then gated based on expression of CD56 and CD16 to distinguish CD56bright and CD56dim NK cells, then sorted into CD56bright CD8+, CD56bright CD8-, CD56dim CD8+, or CD56dim CD8- populations. Cells were placed in trizol immediately after sorting. NK cells were sorted from 6 unique healthy donors. A dump gate was used to exclude cells expressing CD3, CD19, or CD14. Comparative gene analysis was performed on CD8+ vs CD8- CD56bright and CD56dim NK cells.


title: Exercise rescues aberrantly expressed genes in diet-induced obese rats: a potential role of miR-211 modulation in the hypothalamic arcuate nucleus

city: Rishon LeZiyyon

first: Noam

last: Meiri

address: 68 HaMakkabbim Road

country: Israel

institute: Agricultural Research Organization, The Volcani Center

summary: Obesity is a major public health concern that is associated with negative health outcomes. Exercise and dietary restriction are commonly recommended to prevent, or combat obesity. The purpose of this study was to examine the mechanism by which aberrantly expressed genes in the hypothalamic arcuate nucleus (ARC) of diet-induced obese (DIO) rats is attenuated through voluntary exercise. Methods: A transcriptomic approach assessed novel genes in the ARC that affect DIO by voluntary wheel running and a combined approach of physiology, pharmacology, transcriptomic and bioinformatics analysis were used to evaluate the role of miR in the reversal of obesity. Results: Exercise attenuated body weight gain, decreased fat mass, and restored gene expression in the ARC. As high-fat diet (HFD) consumption can cause dysregulation of satiety/hunger regulation mechanisms in the ARC, we outlined transcriptional clusters which depicted alterations in patterns of gene expression through running. Among them were genes involved with inflammation and cellular structure. To uncover regulatory mechanisms governing gene expression in DIO attenuation, we explored the role of miR-211, as it has been implicated in systemic inflammation. The DIO overexpression of miR-211 was ameliorated by exercise, demonstrating its pivotal role in the regulation of inflammation in the ARC. Further, in vivo central administration of miR-211-mimic affected the expression of immunity and cell cycle related genes. By comparing genes attenuated by running and genes downregulated by miR-211, we produced a list of candidate genes that might be involved in the modulation by miR-211 in attenuating obesity by exercise. Conclusion: This research suggests that exercise may have a rescue effect on obesity through changes in gene expression that are mediated partially though miR-211.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for the arcuate nucleus of Wisat rats that were either i) chow fed/sedentary, ii) diet-induced obesity (HF fed)/sedentary, iii) diet-induced obese/volunray wheel running, iv) injected with MiRIDIAN hsa-miR-211-mimic, v) injected with MiRIDIAN hsa-miR-211-hairpin inhibitor

first: Rapps

last: Kayla

first: Marco

last: Asaf

first: Pe'er

last: Hilla

first: Kisoulik

last: Tatiana

first: Stemp

last: Gabrielle

first: Yadid

last: Gal

first: Weller

last: Aron

first: Meiri

last: Noam


title: Glioneuronal tumor with ATRX alteration, kinase fusion and anaplastic features (GTAKA) with leptomeningeal dissemination and ZMIZ1::RET fusion [methylation array]

first: Evelina

last: Miele


title: Combination of dual JAK/HDAC inhibitor with regorafenib  reduces tumor growth, metastasis, and regorafenib-induced toxicity in colorectal cancer

city: Birmingham

first: Darshan

last: Shimoga Chandrashekar

state: Alabama

address: 619 19th Street South, WP P220D

department: Pathology

institute: University of Alabama at Birmingham

summary: To evaluate the differential  gene expression contributing to the efficacy of the combination treatment of JAK/HDAC inhibitor with regorafenib, compared to single drug treatment,  we performed the RNA-sequencing

overall_design: SW480 cells were treated at 500nM concentration of JAK/HDACi and regorafenib as single drugs, and their combination. Dmso was used as control.

first: Upender

last: Manne

first: Prachi

last: Bajpai


title: PRDM6 promotes medulloblastoma by repressing chromatin accessibility and altering gene expression [ATAC-Seq]

first: Bjoern

last: Schwer

first: Christin

last: Schmidt

first: Sarah

last: Cohen

first: Brian

last: Gudenas

last: Husain

first: Annika

last: Carlson

first: Samantha

last: Westelman

first: Linyu

last: Wang

first: Joanna

last: Phillips

first: Paul

last: Northcott

first: William

last: Weiss


title: ROS1 regulates blueberry fruit ripening in a negatively ABA manner (RNA-Seq)

city: Beijing

first: Zejia

address: Yanyuan Street

institute: Peking University

summary: Characterization of WGBS and RNA-seq in  blueberry fruits

overall_design: This dataset contains 15 WGBS data and 15 RNA-seq of cultivated blueberries.

first: Yangyan

last: Zhou

first: Qikun

last: Liu


title: Title: An IL-23-STAT4 Axis Regulates Classical Dendritic Cell Expansion and Function in Experimental Autoimmune Encephalomyelitis

city: INDIANAPOLIS

first: Nada

last: Alakhras

state: Indiana

address: 635 Barnhill Dr. Bldg MS218 VanNuys Med Sci

department: Immunology & Microbiology

institute: Indiana university school of medicine

summary: The signal transducer and activator of transcription 4 (STAT4) promotes protective immunity and autoimmunity downstream of pro-inflammatory cytokines including IL-12 and IL-23. In experimental autoimmune encephalomyelitis (EAE), an animal model of multiple sclerosis (MS), Stat4-/- mice are resistant to the development of inflammation and paralysis. Here, we examined cell-type requirements and found that in addition to T cells, STAT4 is required in dendritic cells for development of EAE. Deficiency of STAT4 in CD11c-expressing cells resulted in decreased T cell priming and inflammation in the CNS. EAE susceptibility was recovered following adoptive transfer of wild type bone marrow-derived DC to mice with STAT4-deficient DCs, but not adoptive transfer of STAT4- or IL-23R-deficient DCs. Single cell RNA-seq identified STAT4-dependent genes in DC subsets that paralleled a signature in MS patient DCs. Together, these data define a novel IL-23/DC/STAT4 pathway in DCs that could be a key to novel therapeutic targets in MS.

overall_design: Mice from the two strains WT and Stat4fl/flCD11cCre were immunized for EAE. On day 15 post-immunization, mice were euthanized and mononuclear cells were recovered from the CNS of EAE mice. Cells were pooled from each group and stained with viability stain for 15 minutes,  preincubated with FC block for 10 minutes at 4ºC, followed by staining with fluorescent conjugated-antibodies for 30 minutes at 4ºC, and then washed with 1% BSA in PBS.  Cells were FACS sorted for all MHCII+ CD11c+ populations. Sorted cells suspension were partitioned into an emulsion of nanoliter-sized droplets using 10x Genomics Chromium Single Cell Controller

first: Mark

last: Kaplan


title: m3C HAC-Seq analysis in HEK293T WT cells, METTL2A/2B knockout cells, METTL6 knockout cells, METTL2A/2B/6 knockout cells.

city: Boston

first: Qi

state: MA

address: 1 Blackfan Circle

institute: Boston Children's Hospital

summary: The ‘epitranscriptome’ includes a diversity of RNA modifications that influence gene expression. N3-methylcytidine (m3C) mainly occurs in the anticodon loop (position C32) of certain tRNAs yet its role is poorly understood. Here, using HAC-Seq, we report comprehensive METTL2A/B-, METTL6-, and METTL2A/B/6-dependent m3C profiles in human cells. METTL2A/B modifies most tRNA-Arginine and tRNA-Threonine members, whereas METTL6 modifies the tRNA-Serine family. However, decreased m3C32 on tRNA-Ser-GCT isodecoders was only observed with combined METTL2A/B/6 deletion.  Ribo-Seq revealed altered translation of genes related to cell cycle and DNA repair pathways in METTL2A/2B/6-deficient cells, and these mRNAs are enriched in AGU codons that require tRNA-Ser-GCT for translation. These results, supported by reporter assays, help explain the observed slowed proliferation, altered cell cycle, and increased Cisplatin-sensitivity phenotypes of METTL2A/B/6-deficient cells. Thus, we define METTL2A/B/6-dependent methylomes and uncover a particular requirement of m3C tRNA modification for Serine codon-biased mRNA translation of cell cycle, and DNA repair genes.

overall_design: Examination of  m3C modification in  HEK293T WT cells, METTL2A/2B knockout cells, METTL6 knockout cells, METTL2A/2B/6 knockout cells.

first: Jia

last: Cui

first: Richard

middle: I

last: Gregory


title: New Drosophila promoter-associated architectural protein Mzfp1 interacts with CP190 and is required for housekeeping gene expression and insulator activity [RNA-seq]

first: Natalia

last: Klimenko

overall_design: RNA-seq in wt and in Mzfp1_attP lines.

first: O

last: Maksimenko

first: N


title: CARM1 interacts and hypermethylates the NuRD chromatin remodeling complex to promote gene transcriptional activation and cell cycle progression

city: Xiamen

first: Jiancheng

last: Ding

state: Fujian

address: School of Pharmaceutical Sciences, Xiamen University Xiang`an South Road

institute: Xiamen University

summary: Protein arginine methyltransferase CARM1 has been shown to methylate a large number of non-histone proteins, and play important roles in gene transcriptional activation, cell cycle progress, and tumorigenesis. However, the critical substrates through which CARM1 exerts its functions remain to be fully characterized. Here, we reported that CARM1 directly interacts with the GATAD2A/2B subunit in the nucleosome remodeling and deacetylase (NuRD) complex, expanding the activities of NuRD to include protein arginine methylation. CARM1 and NuRD bind and activate a large cohort of genes with implications in cell cycle control to facilitate the G1 to S phase transition. This gene activation process requires CARM1 to hypermethylate GATAD2A/2B at a cluster of arginines, which is critical for the recruitment of the NuRD complex. The clinical significance of this gene activation mechanism is underscored by the high expression of CARM1 and NuRD in breast cancers, and the fact that knockdown CARM1 and NuRD inhibits breast cancer cell growth in vitro and tumorigenesis in vivo. These findings reveal a gene activation program that requires the dual specificity established by CARM1 on chromatin and a key chromatin remodeler.

overall_design: Refer to individual Series


overall_design: ChIP-seq performed in this study was designed to understand the molecular mechanisms underlying CARM1/NuRD in gene transcriptional regulation.

first: Wen

first: Xue

last: Chen

first: Yaohui

last: He

first: Wenjuan

last: Zhang

first: Mingfeng

last: Huang


title: Effect of depletion of C15ORF48/miR-147 on gene expression in primary colonocytes

city: Arcadia

last: Boldin

address: 1500 Duarte Road

institute: City of Hope Beckman Research Institute

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: ARL11 Stable Expression in NHU-hTERT cells

city: Houston

first: Bogdan

last: Czerniak

address: 1515 Holcombe

institute: UT MD Anderson Cancer Center

summary: Analyses of the whole genome mRNA gene expression profiling performed on the normal urothelium cells with stably expressed ARL11 following serum starvation. The results revealed that TP53, RB1 and CDKN2A pathways were activated and the E2F1 and MYC pathways wer inhibitedin cells expressing ARL11. Cells expressing ARL11 also inhibited RAS pathway activation.

overall_design: Total RNA was extracted from NHU-hTERT cells transducted with ARL11 and empty vector

first: Sangkyou

last: Lee

first: Tadeusz

last: Majewski


title: DDX24 Promotes Lymphangiogenesis and Lymph Node Metastasis via AGRN Production in Cervical Squamous Cell Carcinoma

city: Zhuhai

first: Baibin

last: Wang

address: The Fifth Affiliated Hospital of Sun Yat-sen University

summary:
To investigate the factor produced by CSCC cells to facilitate lymphangiogenesis, we analyzed the transcriptomics of CSCC cells upon DDX24 has been knocked down by siRNA.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 2 different cell lines.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Cervical Squamous Cell Carcinoma cell lines (MS751 and SiHa) and their DDX24 KD derivatives .

first: Huanhuan

first: Yanhui

last: Jiang


title: Prolyl hydroxylase domain enzyme PHD2 inhibits proliferation and metabolism in non–small cell lung cancer cells in HIF-dependent and HIF-independent manner

city: Wuhan

first: Hongyan

last: Deng

address: No. 7 Donghu South Road, Wuchang District

institute: Institute of Hydrobiology, Chinese Academy of Sciences

summary: Prolyl hydroxylase domain protein 2 (PHD2) is one of the intracellular oxygen sensors that mediates proteasomal degradation of hypoxia-inducible factor (HIF)-α via hydroxylation under normoxia. Because of its canonical function in the hypoxia signaling pathway, PHD2 is generally regarded as a tumor suppressor. However, the effects of PHD2 in tumorigenesis are not entirely dependent on HIF-α. Based on the data obtained from The Cancer Genome Atlas (TCGA) database, we found that the expression of PHD2 is upregulated in non-small cell lung cancer (NSCLC), which accounts for approximately 80-85% of lung cancers, suggesting that PHD2 may play an important role in NSCLC. However, the function of PHD2 in NSCLC remains largely unknown. In this study, we established PHD2-deficient H1299 cells to investigate the function of PHD2 in NSCLC, and found that PHD2 suppressed cell proliferation and metabolism, but induced ROS levels in human NSCLC cells. Further results indicated that the function of PHD2 in NSCLC is dependent on its enzymatic activity and partially independent of HIF. Moreover, we performed RNA-seq and transcriptomics analysis to explore the underlying mechanisms, and identified some potential targets and pathways regulated by PHD2, apart from the canonical HIF-mediated hypoxia signaling pathway. These results provide some clues to uncover novel roles of PHD2 in lung cancer progression.

overall_design: Since the function of PHD2 in NSCLC cells is partially independent of its canonical function in the hypoxia signaling pathway, we performed gene expression profiling analysis using RNA-seq data of PHD2-deficient and wildtype H1299 cells to explore the possible mechanisms of PHD2 functions in lung cancer.

first: Zixuan

first: Chunchun

last: Zhu

first: Zhu


title: PRDM6 promotes medulloblastoma by repressing chromatin accessibility and altering gene expression [CUT&Run]

city: San Francisco

first: Bjoern

last: Schwer

state: CA

institute: University of California, San Francisco

summary: SNCAIP duplication may promote Group 4 medulloblastoma via induction of PRDM6, a poorly characterized member of the PRDF1 and RIZ1 homology domain-containing (PRDM) family of transcription factors. Here, we investigated the function of PRDM6 in human hindbrain neuroepithelial stem cells and tested PRDM6 as a driver of Group 4 medulloblastoma. We report that human PRDM6 localizes predominantly to the nucleus, where it causes widespread repression of chromatin accessibility and complex alterations of gene expression patterns. Genome-wide mapping of PRDM6 binding reveals that PRDM6 binds to chromatin regions marked by histone H3 lysine 27 trimethylation that are located within, or proximal to, genes. Moreover, we show that PRDM6 expression in neuroepithelial stem cells promotes medulloblastoma. Surprisingly, medulloblastomas derived from PRDM6-expressing neuroepithelial stem cells match human Group 3, but not Group 4, medulloblastoma. We conclude that PRDM6 expression has oncogenic potential but is insufficient to drive Group 4 medulloblastoma from neuroepithelial stem cells. We propose that both PRDM6 and additional factors, such as specific cell-of-origin features, are required for Group 4 medulloblastoma. Given the lack of PRDM6 expression in normal tissues and its oncogenic potential shown here, we suggest that PRDM6 inhibition may have therapeutic value in PRDM6-expressing medulloblastomas.

overall_design: To elucidate the function of PRDM6, we established human neuroepithelial stem (NES) cells expressing human PRDM6 (PRDM6 NES) and matching control cells (EV NES). Moreover, we collected tumors derived from PRDM6 NES cells.

first: Christin

last: Schmidt

first: Sarah

last: Cohen

first: Brian

last: Gudenas

last: Husain

first: Annika

last: Carlson

first: Samantha

last: Westelman

first: Linyu

first: Joanna

last: Phillips

first: Paul

last: Northcott

first: William

last: Weiss


title: Enhanced meningeal lymphangiogenesis and glymphatic drainage ameliorates neuroinflammation and white matter demyelination

city: Hangzhou

first: Rui

last: Xue

address: 88# Jiefang Road

department: Department of Neurology

institute: the Second Affiliated Hospital of Zhejiang University, School of Medicine

summary: White matter hyperintensity (WMH) is a pressing global medical issue linked to cognitive decline and stroke risk. Despite its significance, the underlying mechanisms remain unclear. Here, we directly demonstrated in humans that high WMH burden correlated with delayed glymphatic pathway drainage. Additionally, a longitudinal cohort study revealed that glymphatic dysfunction predicted WMH progression. Next, in a rat model of WMH, we confirmed the presence of impaired lymphangiogenesis and glymphatic drainage, followed by elevated microglial activation and white matter demyelination. Notably, enhancing meningeal lymphangiogenesis and glymphatic drainage through adenoviral delivery of Vascular Endothelial Growth Factor-C (VEGF-C) mitigated microglial gliosis and white matter demyelination. Conversely, blocking the growth of meningeal lymphatics with a VEGF-C trap strategy exacerbated these changes. Our findings highlight the role of meningeal lymphatics and glymphatic pathway dysfunction in aggravating brain white matter injury and advancing WMH, providing a potential novel strategy for WMH prevention and treatment.

overall_design: RNA-sequencing data of corpus callosum from Spontaneously hypertensive rats (SHR), Wistar Kyoto rats (WKY), AAV2/9-CMV-rVEGF-C treated SHR and AAV2/9-CMV-mNeonGreen (as control)treated SHR.

first: Ying

last: Zhou

first: Yifei

last: Li

first: Jiaping

first: Wang

last: Ran

first: Yuping

last: Chen

first: Zhongyu

last: Luo

first: Kemeng

last: Zhang

first: Ruoxia

first: Junjun

first: Mengmeng

last: Fang

first: Cong

first: Min

last: Lou


title: BET bromodomain inhibition potentiates ocular melanoma therapy by inducing cell cycle arrest

city: Shanghai

first: Nestor

address: Dongchuan Road

institute: Shanghai Jiao Tong University

summary: Ocular melanoma is a common primary malignant ocular tumor in adults with limited effective treatments, so novel therapeutic approaches are desperately needed. Epigenetic regulation plays an important role in tumor development. The SWI/SNF chromatin remodeling complex and bromodomain and extraterminal domain (BET) family proteins are epigenetic regulators involved in several cancers. We aimed to screen a candidate small molecule inhibitor targeting the SWI/SNF complex or BET proteins and investigate its effect and mechanism in ocular melanoma. Colony formation assays were applied to select the most effective candidate inhibitor (JQ-1). We observed phenotypes caused by knockdown of the corresponding gene and synergistic effects with BRD inhibitor (BRDi) treatment and SWI/SNF complex knockdown. We further validated the efficacy of JQ-1 in 10 ocular melanoma cell lines and a mouse xenograft model. The effect of JQ-1 on ocular melanoma cell cycle and apoptosis was analyzed with flow cytometry. We performed RNA sequencing in 2 pairs of ocular melanoma cell lines treated with JQ-1 and control cells treated with DMSO. Gene set enrichment analysis (GSEA) was performed for pathway analysis of the differentially expressed genes (DEGs). We also validated the correlations of DEGs with BRD4 and patient outcomes. Overall, JQ-1 may act downstream of BRD4 and suppress ocular melanoma growth by inducing G1 cell cycle arrest.

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of cells (MEL270 and MEL290) treated with JQ-1 (0.04 μM) or DMSO at two times.

first: Jianfeng

last: Shen

first: Zhe


title: FOXQ1 Regulates Mitochondrial Cristae Formation and Energy Metabolism in Mouse Brain Endothelial Cells [RNA-seq]

status: Public on Jul 16 2024

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:
Purpose: To gain  futher insight into how FOXQ1 regulates the brain endothelial cells ,RNA-seq was used to analyze the genome-wide changes resulting from the cerebral cortical endothelial cells  of E18 FOXQ1 conditional knock out mice and littermate wild-type.
Methods: Total RNA from E18 Flow sorting of endothelial cells of wild-type(WT) and FOXQ1fl/fl;Tie2-Cre mice was extracted. Specifically, Agilent 2100 Bioanalyze was used to quality controlled and quantified. then, total RNA was converted to cDNA and bound the library. RNA-sequencing analysis was used by the Illumina HiSeq 6000 platform in Annoroad Genomics
Approximately  one thousand transcripts showed differential expression between the wild-type(WT) and FOXQ1fl/fl;Tie2-Cre mice cortical endothelial cells, with a fold change ≥1.5 and p value <0.05. These results reflected FOXQ1 plays a role in brain endothelial cells.
Conclusions:  RNA-seq based transcriptome characterization would provide a overall understanding how FOXQ1 works in endothelial cells.

overall_design: Total mRNA profiles of E18 wild-type(WT) and FOXQ1fl/fl;Tie2-Cre mice were generated by deep sequencing, using Illumina HiSeq 6000.

first: Wenzheng

last: Zou


title: FOXQ1 Regulates Mitochondrial Cristae Formation and Energy Metabolism in Mouse Brain Endothelial Cells [CUT&TAG]

summary: To explore FOXQ1’s transcriptional role, we utilized an HA-tagged FOXQ1 plasmid for CUTTag enabling high-resolution mapping of FOXQ1 binding sites on the genome.

overall_design: Examination of gene which FOXQ1 binding within primary brain vessel endothelial cells.


title: Epigenetic activation of SOX11 is associated with recurrence and progression of DCIS to invasive breast cancer

first: Justin

last: Wong

address: 1155 Pressler St

institute: MD Anderson Cancer Center


title: Investigate how Sox9 overexpression influences ATII lineage plasticity by sc-multiome

city: South San Francisco

first: David

last: Garfield

address: 1 DNA Way

department: OMNI Bx

institute: Genentech

summary: Wound healing in response to acute injury is mediated by the coordinated and transient activation of parenchymal, stromal, and immune cells that resolves to homeostasis. Environmental, genetic, and epigenetic factors associated with inflammation and aging can lead to persistent activation of the microenvironment and fibrosis. Here, we identify opposing roles of IL-4 cytokine signaling in interstitial macrophages and type II alveolar epithelial cells (ATIIs). We show that IL4Ra signaling in macrophages promotes regeneration of the alveolar epithelium after bleomycin-induced lung injury. Using organoids and mouse models, we show that IL-4 directly acts on a subset of ATIIs to induce the expression of the transcription factor SOX9 and reprograms them toward a progenitor-like state with both airway and alveolar lineage potential. In the contexts of aging and bleomycin-induced lung injury, this leads to aberrant epithelial cell differentiation and bronchiolization, consistent with cellular and histological changes observed in interstitial lung disease.

overall_design: When culturing mouse alveolarspheres, we will seed mouse ATIIs from young and old mice, and grow them using serum-free and feeder-free system. On day 9, cells were infected with either AAV9_Cre or AAV9_Sox9Cre (to overexpress Sox9 together with Cre recombinase. Then we switched the culture medium to ATII differentiation medium to induce ATI differentiation for 4 days. We collected tdTomato+ cells by FACS and extracted nuclei for sc-multiome analysis.

first: Xiaoyu

last: Cai

first: Minxue

last: Jia

first: Jason

last: Rock


title: Cavβ3 contributes to the maintenance of the blood-brain barrier and alleviates symptoms of experimental autoimmune encephalitis

city: Heidelberg

first: Anouar

last: Belkacemi

address: Im Neuenheimer Feld 366

institute: Heidelberg University

summary: Brain microvascular endothelial cells (BMECs) are part of the blood-brain barrier (BBB). These cells express Cacnb3 transcripts encoding the Cavβ3 protein, which is a subunit of the voltage-gated Ca2+ (Cav) channels. However, potassium depolarization and electrophysiological recordings in BMECs did not reveal a significant Cav channel function, regardless of the presence or absence of Cavβ3. In vivo, the integrity of the BBB was reduced in the absence of Cavβ3. Following induction of experimental autoimmune encephalomyelitis (EAE), Cavβ3-deficient (Cavβ3-/-) mice showed earlier disease onset with exacerbated clinical disability and increased infiltration of T-cells. In vitro, the trans-endothelial resistance of Cavβ3-/- BMEC monolayers was lower than that of wild-type, permeability to albumin and dextran was increased, and the organization of the junctional protein ZO-1 was impaired in the absence and presence of the pro-inflammatory mediator thrombin.  The results suggest that Cavβ3, independent of its function as a subunit of Cav channels, tightly controls cytoplasmic [Ca2+] and Ca2+-dependent MLC phosphorylation and that this role of Cavβ3 in BMECs contributes to the integrity of the BBB and decreases severity of clinical EAE disease.

overall_design: RNA-seq from primary brain microvascular endothelial cells (BMECs) from wild-type and Cavβ3-deficient mice with four independent biological replicates to investigate the role of Cavβ3 in regulating of endothelial function.

first: Veit

last: Flockerzi

first: Damian

last: Martus


title: Ribosome Footprinting (RiboSeq) analysis of mRNA translation in HEK293T WT and METTL2A/2B/6 knockout cells

first: Qi

last: Liu

overall_design: Examination of translatome in HEK29T METTL2A/2B/6 knockout cells compared to HEK293T WT cells, in triplicate, using Ribo-Seq techique.

first: Jia

last: Cui

first: Richard

last: Gregory


title: The murine 900 kb downsteam region from Gata3 interacts to the transciption start site and three enhancers in Th2 cells.

city: Chiba-shi

first: Arifumi

last: Iwata

state: Chiba

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

department: Department of Allergy and Clinical Immunology

institute: Chiba University

summary: Murine counterpart of the region (mG900 region), in which SNPs associated with human asthma are enriched, is located 900 kb downstream from the transcription start site (TSS) of Gata3. Gata3-TSS interacted with mG900 region in only cultured Th2 cells but not in naive CD4 T cells or cultured Th0 cells. The mG900-deficient Th2 cells exhibited reduced interaction between Gata3-TSS and three enhancers.

overall_design: 4C-seq were perfromed for cultured CD4 T cells using two baits of transcription start site of Gata3 and the region located at 932 downstream from Gata3.

first: Atsushi

last: Okabe


title: Dynamic analysis of mononuclear transcription profiles of fat in different parts of mice during aging

city: chengdu

first: yujie

last: wu

address: 211 Huimin Road, Wenjiang District

department: animal science and technology

institute: Sichuan Agricultural University

summary: Adipose tissue shows significant changes during aging. Here, we used single-nucleus RNA-seq to map the single-nucleus transcription profiles of mouse subcutaneous adipose tissue ( SAT ) and visceral adipose tissue ( VAT ) at a single-nucleus resolution, showing the differences in visceral and subcutaneous adipose tissue changes with aging. The mononuclear sequencing method enabled us to restore all major cell types in mouse white adipose tissue, and we characterized adipocytes, immune cells, and preadipocytes. We demonstrated the existence of different adipocyte subsets and showed that aging leads to a decrease in adipogenic subsets. In addition, with aging, both subcutaneous adipose tissue and visceral adipose tissue showed a decrease in immune mechanisms.

overall_design: Subcutaneous mouse adipose tissue depots were dissected from 2 months and 26 months female C57BL/6J mice into ice-cold PBS. diluted in diethyl pyrocarbonate (DEPC) water.White adipose tissue (SAT and VAT) was surgically removed and placed in 1x PBS on ice. Cells were then stained with desired antibodies, and subjected to FACS or snRNA-seq.

first: Yujie

last: Wu

first: Long

last: Chen

first: Xingyan

last: Tong

first: Can

first: Mingzhou

last: Li

last: Jin

first: Ying

last: Sun


title: Epigenetic activation of SOX11 is associated with recurrence and progression of DCIS to invasive breast cancer [Nanostring]

first: Justin

last: Wong

summary: Epigenetic activation of SOX11 is associated with recurrence and progression of DCIS to invasive breast cancer. SOX11 and its epigenetic regulators can be developed as prognostic markers for DCIS patients with recurrence risk independent of traditional clinical and pathologic characteristics.

overall_design: NanoString nCounter analysis system was performed using a custom codeset consisting of 53 genes-of-interest plus 5 housekeeping genes commonly identified from public available DCIS gene expression datasets and correlated with recurrence events using Kessler's breast cancer dataset.

first: Warapen

last: Treekitkarnmongkol

first: Vandna

last: Shah

first: Kazuharu

last: Kai

first: Hiroshi

last: Katayama

first: Farah

last: Ladha

first: Brian

last: Menegaz

first: Sarah

last: Pinder

first: Wei

last: Lu

first: Fei

last: Yang

first: Ximing

last: Tang

first: Savitri

last: Krishnamurthy

first: Ignacio

last: Wistuba

first: Elinor

last: Sawyer

first: Alistair

last: Thompson

first: Subrata

last: Sen


title: Epigenetic activation of SOX11 is associated with recurrence and progression of DCIS to invasive breast cancer [ATAC-seq]

overall_design: ATAC-seq was performed to assess chromatin accessibility in the genome of SUM225 cell line without and with MK2206 treatment


title: Single-cell transcriptomic profiling of mouse enteric neurons and enteric mesenchymal cells in enteric neurosphere cultures.

first: Rhian

last: Stavely

address: 185 Cambridge Street, CPZN, 6100

department: Pediatric Surgery

institute: Massachusetts General Hospital

summary: This study was undertaken to define the molecular subtypes of cells within enteric neurospheres. Methods: We performed single-cell RNA sequencing on 3-dimensional neurosphere cultures derived from the small intestines of Plp1::GFP mice. These data show profiling results from the PLP1::GFP negative cell fraction ancillary to the positive fraction in series GSE184981. Results: We identify populations of enteric neurons and fibroblasts in the PLP1::GFP negative cell fraction of enteric neurospheres.

overall_design: Use of 10X Genomics technology to analyze single-cell transcriptomics in 3-dimensional neurosphere cultures derived from the small intestine after performing FACS to purify the PLP1::GFP negative cell fraction.

first: Richard

last: Guyer

first: Allan

last: Goldstein