title: PRMT1 methylation of WTAP promotes multiple myeloma tumorigenesis by activating oxidative phosphorylation via m6A modification of NDUFS6

city: Xi'an

first: Yachun

last: Jia

state: None Selected

address: No. 157#, The West 5th Road

institute: xian jiaotong university

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

overall_design: Refer to individual Series


title: Clock-driven waves of Tbx6 expression prefigure somite boundaries

status: Public on Nov 09 2023

city: Lausanne

first: Andrew

middle: Charles

last: Oates

address: Station 19

department: SV IBI

country: Switzerland

institute: EPFL

summary: One of the major events of vertebrate embryonic development is the segmentation of the body axis into transient blocks of tissue, called somites, that ultimately give rise to vertebrae, ribs, and skeletal muscles of the adult body. Somites bud off from the presomitic mesoderm (PSM) by the sequential and rhythmic formation of new boundaries. The periodicity of the process is controlled by the segmentation clock, which manifests as spatiotemporal waves of Hes/Her gene expression travelling anteriorly in the PSM and reiterating during the formation of each somite. In zebrafish, the genes her1 and her7 form a the core of this genetic oscillator. We discovered that the protein expression of the gene Tbx6 oscillates, driven by the Her1;Her7 loop. Although Her binding to gene regulatory sequences has been tested in vitro, the binding of Her1 or Her7 to regulatory regions in the embryo remains unknown. To assess whether Her1 and Her7 directly bind to tbx6, we performed CUT&Tag using anti-GFP antibodies to address the genomic binding landscape of the fusion proteins Her1-YFP and Her7-YFP from their respective transgenic lines, as no antibodies against Her1 and Her7 currently exist.

overall_design: We performed Cut&Tag on Tg(her1:her1-YFP) or Tg(her1:nls-mkate2,her7:her7-YFP) zebrafish embryos. Briefly, 120 bud stage embryos per replicate were dechorionated using 1mg/ml Pronase (Roche) and dissociated into single cells by pipetting up and down using a 200 µl pipette. For each transgenic line, we performed two replicates with two different antibodies.

first: Chloé

last: Jollivet

first: Olga

last: Rosspopoff

first: Olivier

last: Venzin

middle: C

first: Clément

last: Helsens


title: Sequencing analysis of CAR T cell products and apheresis cells in DLBCL patients treated with tandemCAR-T cell

city: Beijing

first: Wang

last: Yao

address: No. 28, fuxing street

country: China

institute: Chinese general PLA hospital

type: Expression profiling by high throughput sequencing

summary: In this study, 58 r/r DLBCL patients treated with tandem CD19/CD20 CAR T cells. Twenty-seven patients had durational responses for more than 24 months, and the median PFS was 21.7 months. But 15 patients still did not have an objective response, and 11 patients relapsed within 1 year. The analysis found that CD8+TSCM cells with higher frequency and stronger activation ability in CART products were the key to achieving clinical sustained objective response.   Bulk RNA-Seq and single-cell RNA-Seq then were performed on CAR-T cell products and pre-manufacture T cells of patients with DLBCL. We note that a CD8+ stem cell-like memory T cell population with a higher proportion and stronger activating capacity of the CAR-T cell products was key to achieving durable clinical response. By analyzing autologously-derived, pre-manufacture T cells, our data suggest that heterogeneity in the cellular and molecular features of pre-manufacture T cells contribute to the variation in efficacy after CAR-T cell therapy in DLBCL.  The differences in anti-tumour efficacy of CAR-T cells among patients with different clinical outcomes appear to be due to the loss of CCR7 gene expression accompanied by increased expression of activation- and inhibitor-related genes in the CD8+ naïve-T cell populations among the apheresis T cells from patients with a poor molecular response. These findings significantly advance our understanding of the underlying molecular determinants of pre-manufacture T cell function.

overall_design: To perform an in-depth characterization of the outcome-associated CAR-T cell populations, we then employed droplet-based 5′ scRNA-seq  sequencing to profile a set of infused CAR-T cells and pre-manufacture T cells from 3 DR and 3 resistant patients.

first: Yao

last: Wang

first: Weidong

last: Han


title: Comparative Transcriptomics Analysis of Shiga Toxin Producing Escherichia coli O157:H7 Grown in Bovine Rectoanal Junction Cells and Human Colonic Epithelial Cells

city: Gainesville

first: Subhashinie

last: Kariyawasam

state: Florida

address: 1945 SW 16th Ave

department: Comparative, Diagnostic, and Population Medicine

country: USA

institute: University of Florida

summary: Shiga toxin-producing Escherichia coli (STEC) O157:H7 is a notorious foodborne pathogen capable of causing severe gastrointestinal infections in humans. The bovine rectoanal junction (RAJ) has been identified as a primary reservoir of STEC O157:H7, playing a critical role in its transmission to humans through contaminated food sources. Despite the relevance of this host-pathogen interaction, the molecular mechanisms behind the adaptation of STEC O157:H7 in the bovine RAJ and its subsequent infection of human colonic epithelial cells remain largely unexplored. This study aimed to unravel the intricate dynamics of STEC O157:H7 in two distinct host environments: bovine RAJ squamous epithelial (RSE) cells and human colonic epithelial cells. Comparative transcriptomics analysis was employed to investigate the differential gene expression profiles of STEC O157:H7 during its interaction with these cell types. The bacterial cells were cultured under controlled conditions to simulate the microenvironments of both bovine RAJ and human colonic epithelial cells. Using high-throughput RNA sequencing, we identified key bacterial genes and regulatory pathways that are significantly modulated in response to each specific host environment. Our findings reveal distinct expression patterns of virulence factors, adhesion proteins, and stress response genes in STEC O157:H7 grown in bovine RAJ cells as opposed to human colonic epithelial cells. Additionally, the comparative analysis highlights the potential role of certain genes in host adaptation and tissue-specific pathogenicity. Furthermore, this study sheds light on the potential factors contributing to the survival and persistence of STEC O157:H7 in the bovine reservoir and its ability to colonize and cause disease in humans.

overall_design: To investigate the differential gene expression in E. coli O157:H7, we infected CCD841 and RSE cells with E. coli O157:H7.

first: Lekshmi

middle: K

last: Edison

first: Indira

middle: T

last: Kudva


title: Characteristics of premanufacture CD8+T cells determine CAR-T efficacy in patients with diffuse large B-cell lymphoma

summary: In this study, 58 r/r DLBCL patients treated with tandem CD19/CD20 CAR T cells. Twenty-seven patients had durational responses for more than 24 months, and the median PFS was 21.7 months. But 15 patients still did not have an objective response, and 11 patients relapsed within 1 year. The analysis found that CD8+TSCM cells with higher frequency and stronger activation ability in CART products were the key to achieving clinical sustained objective response.   Bulk-RNA-seq results confirmed that CD8+CART cells in CR group had higher expression of memory-related genes and transcription factors and lower expression of activation/depletion related genes than those in PD patients.   Naive CD8 cells also showed similar differential expression in apheresis.   The use of Naive cells as the source cell population for CART preparation could partially improve CART function, but could not completely reverse it.  It is suggested that the resistance of DLBCL to tandem CD19/CD20 CAR T cell therapy may be caused by the decreased function and the loss of expression of memory genes of the source Naive T cells.

overall_design:
Sequencing samples were collected from 5-6 PD patients with significantly reduced killing efficacy in previous efficacy experiments, and CR patients with disease characteristics similar to Resistant patients.  CAR T cell products of these patients were divided into CD8 positive and CD4 positive，apheresis cells from the same patients were divided into Naive CD8 positive T cells, Naive CD4 positive T cells, non-naive CD4 positive T cells, and non-CD8 positive T cells for performed bulk RNA-seq.

CR patient: patient who achieved complete remission after TanCAR7 T cell therapy
PD patient: patient who had progressive disease after TanCAR7 T cell therapy

first: Chuan

last: Tong

first: Zhiqiang

last: Wu

first: Yuting

last: Lu

first: Yelei

last: Guo

first: Yang

last: Liu

first: Chunmeng

first: Jianshu

last: Wei

first: Qingming

last: Yang


title: Circulating exosomal circRNAs as diagnostic biomarkers for chronic coronary syndrome

first: Xiaoyan

address: 8 Gongren Tiyuchang Nanlu, Chaoyang District

institute: Beijing Chao-Yang Hospital

type: Non-coding RNA profiling by high throughput sequencing

summary:
Background: Circular RNA (circRNA) has been reported to be involved in the pathogenesis of cardiovascular disease (CVD), however, it is unclear whether circRNA carried by exosomes (exos) can be used as biomarkers for chronic coronary syndrome (CCS). This study aimed to investigate the expression pattern of exosomal circRNAs in the plasma of CCS patients, and to screen exo-circRNAs that can act as biomarkers for the diagnosis of CCS.
Methods: High-throughput sequencing technology was carried out in the plasma exosomal RNA of 15 CCS patients and 15 non-cardiac chest pain patients (NCCP, control group) (sequencing cohort) to screen for differentially expressed circRNAs. Selected differentially expressed exo-circRNAs were further verified by real time polymerase chain reaction (RT-PCR) in a small-sample cohort (derivation cohort) and a large-sample cohort (validation cohort). Receiver operating characteristic (ROC) curve analysis was performed to evaluate the diagnostic value of exo-circRNAs for CCS patients.
Results: By high-throughput sequencing of circRNAs in 15 CCS patients and 15 NCCP
patients, 276 circRNAs differentially expressed in plasma exosomes of CCS patients were screened by using |log2(Fold change) |>1 and q-value<0.001, and 103 were up-regulated and 173 were down-regulated. Among the 103 up-regulated circRNAs, 5 circRNAs with high expression levels and significantly increased in plasma exosomes of CCS patients were selected for validation. Twice RT-PCR validation demonstrated that exo-hsa_circ_0075269 and exo-hsa_circ_0000284 were significantly up-regulated in patients with CCS (P<0.001). Circulating exo-hsa_circ_0075269 and exo-hsa_circ_0000284 yielded the area under the curve (AUC) values of 0.761 (P<0.001, 95%CI=0.669, 0.852) and 0.623 (P=0.015, 95%CI=0.522, 0.724) for CCS, respectively by ROC curve analysis. Moreover, AUC of hsa_circ_0075269 combined with hsa_circ_0000284 for diagnosing CCS was 0.741 (P<0.001, 95%CI=0.667, 0.850).
Conclusion: The expression profile of circRNA in plasma exosomes of patients with CCS was significantly different from that of the control group. Plasma exo-hsa_circ_0075269 and exo-hsa_circ_0000284 have the potential to be new biomarkers for CCS diagnosis.

overall_design: To screen for differentially expressed circulating exosomal circRNAs in CCS patients, high-throughput sequencing technology was carried out in the plasma exosomal of 15 CCS patients and 15 non-cardiac chest pain patients. The blood samples of every five subjects were pooled into one collective sample, and thus “3 CCS” and “3 control” samples were profiled.

first: Meili

last: Zheng

first: Ruinjuan

first: Ziyang

last: Yu

first: Wen

last: Yuan

first: Boqiao

last: Xie

first: Yeping

last: Zhang

first: Jiuchang

last: Zhong

first: Lefeng

first: Lixia

first: Xinming


title: EphrinA5 regulates cell motility by modulating the targeting of DNMT1 to the Ncam1 promoter via lncRNA/DNA triplex formation

city: Aachen

first: Geraldine

middle: Marion

last: Zimmer-Bensch

state: NRW

address: Worringer Weg 3

department: Neuroepigenetic

country: Germany

institute: RWTH Aachen

type: Methylation profiling by genome tiling array

summary:
Cell-cell communication is mediated by membrane receptors and their cognate ligands, such as the Eph/ephrin system, and dictate sphysiological processes, including cell proliferation and migration. However, whether and how Eph/ephrin signaling culminates in transcriptional regulation is largely unknown. Epigenetic mechanisms are key for integrating external “signals”, e.g., from neighboring cells, into the transcriptome. We have previously reported that ephrinA5 stimulation of immortalized cerebellar granule (CB) cells elicits transcriptional changes of lncRNAs and protein-coding genes. LncRNAs represent important adaptors for epigenetic writers through which they regulate gene expression.
We found that Snhg15, a cancer-related lncRNA, forms a triplex structure with the Ncam1 promoter and interacts with DNMT1. EphrinA5 stimulation leads to reduced Snhg15 expression, diminished Snhg15/DNMT1 interaction and decreased DNMT1 association with the Ncam1 promoter. These findings can explain the attenuated Ncam1 promoter methylation and elevated Ncam1 expression that in turn elicits decreased cell motility of CB cells. Hence, we propose that ephrinA5 influences gene transcription via lncRNA-targeted DNA methylation underlying the regulation of cellular motility.

overall_design: 6 control samples (CB cells treated with FC prtotein for control) and 6 treatment samples (CB cells treated with recombinant EphrinA5-Fc), bisulphite converted samples were hybridised to the Illumina Mouse Methylation Bead Chip

first: Julia

last: Gehrmann

first: Daniel

last: Pensold

first: Mira

last: Jakovcevski


title: PRMT1 methylation of WTAP promotes multiple myeloma tumorigenesis by activating oxidative phosphorylation via m6A modification of NDUFS6 [RNA-seq]

first: Yachun

last: Jia

summary: Epigenetic modifications play important roles during the pathogenesis of multiple myeloma (MM). Here, we found that protein arginine methyltransferase 1 (PRMT1) was highly expressed in MM patients and its expression level was positively correlated with MM stages. High PRMT1 expression were notably related to adverse prognosis in MM patients. We further showed that silencing PRMT1 inhibited MM proliferation and tumorigenesis in vitro and in vivo. Mechanistically, we revealed that knockdown of PRMT1 reduced the oxidative phosphorylation (OXPHOS) of MM cells through downregulation of NDUFS6. Meanwhile, we identified that WTAP, a key component of the m6A methyltransferase complex, was methylated by PRMT1 and NDUFS6 was identified as a bona fide m6A target of WTAP. Finally, we found that PRMT1 inhibitor and bortezomib combination synergistically inhibited MM progression. Collectively, our results demonstrate that PRMT1 plays a crucial role during MM tumorigenesis and suggest that PRMT1 could be a potential therapeutic target in MM.

overall_design: To identify the functional downstream target genes responsible for the observed phenotype, MM.1S cells knocked down for PRMT1 were used for RNA-Seq.

first: Guangyao

last: Kong


title: Next Generation Sequencing (RNA-Sequencing) for the analysis of RUNX3 and YAP1 targets in TGFb-stimulated HEK 293 cells

city: Cheongju

first: Jung-Won

last: Lee

address: 1, Chungdae-ro

department: Department of Biochemistry, School of Medicine

country: South Korea

institute: Institute for Tumor Research

summary: Comparision of the gene expression profiles of the TGFb-stimulated and si-Con, si-RUNX3 and si-YAP1 treated cells.

overall_design: Methods: HEK293 cells were treated with control siRNA (si-con), RUNX3-specific siRNA (si-RUNX3), or YAP1-specific siRNA (si-YAP1), and then stimulated with TGFβ1. RNA was extracted from the cells at the indicated time points, and gene expression patterns were analyzed by mRNA sequencing (n=3; biological replicates). Total RNA was isolated using Trizol reagent (Invitrogen). RNA quality was assessed using an Agilent 2100 bioanalyzer (Agilent Technologies, Amstelveen, The Netherlands) and RNA quantification was performed using a ND-2000 Spectrophotometer (Thermo Inc., DE, USA). Libraries were prepared from total RNA using the NEBNext Ultra II Directional RNA-Seq Kit (NEW ENGLAND BioLabs, Inc., UK). Isolation of mRNA was performed using the Poly(A) RNA Selection Kit (LEXOGEN, Inc., Austria). The isolated mRNAs were used for cDNA synthesis and shearing in accordance with the manufacturer’s instructions. Indexing was performed using the Illumina indexes 1–12. The enrichment step was carried out using PCR. Subsequently, libraries were checked using the TapeStation HS D1000 Screen Tape (Agilent Technologies, Amstelveen, The Netherlands) to evaluate the mean fragment size. Quantification was performed using the library quantification kit and a StepOne Real-Time PCR System (Life Technologies, Inc., USA). High-throughput sequencing was performed as paired-end 100 sequencing using NovaSeq 6000 (Illumina, Inc., USA). Quality control of raw sequencing data was performed using FastQC. Adapters and low-quality reads (<Q20) were removed using FASTX_Trimmer and BBMap. Then, the trimmed reads were mapped to the reference genome using TopHat. The Read Count data were processed based on a FPKM + Geometric normalization method using EdgeR within R. FPKM (Fragments Per kb per Million reads) values were estimated using Cufflinks. Data mining and graphic visualization were performed using ExDEGA (Ebiogen Inc., Seoul, Korea).

first: Min-Kyu

last: Kim

first: Sang-Hyun

last: Han

first: Suk-Chul

last: Bae


title: The influence on Muc2 positive cells and Gli1 positive cells after the knockout of Smad4 or Alk3 in Gli1 positive cell and the effect of IL1 or IL17 on colonic organoids

first: Ye-guang

last: Chen

address: Tsinghua Road, Medical Building

department: School of life science

institute: Tsinghua University

summary:
To investigate the influecne of BMP signaling on Gli1+ cells, RNA-seq were performed after Smad4 or Alk3 knockout. Next, RNA-seq of Muc2-mCherry cells were performed to reveal the regulation of Gli1+ cell on intestinal epithelium. Finally,  RNA-seq of colonic organoids were performed to reveal the regulation of IL-1 or IL-17 on epithelium.
To investigate the influecne of BMP signaling on Gli1+ cells, RNA-seq were performed after Smad4 or Alk3 knockout. Next, RNA-seq of Muc2-mCherry cells were performed to reveal the regulation of Gli1+ cell on intestinal epithelium. Finally,  RNA-seq of colonic organoids were performed to reveal the regulation of IL-1 or IL-17 on epithelium.

overall_design: One monthe after tamoxifen administration, FACS was performed to sort Muc2-mCherry or Gli1-tdTomato cells and then performed  RNA sequencing. Alao, RNA-seq were performed in colonic organoids at 12 or 72 hours after IL-1 or IL-17 treatments.

first: Yalong

last: Wang

first: Zhe

first: Ruoyu

last: Lou


title: single cell multiome for MSCs

city: Indianapolis

first: Yunlong

last: Liu

state: IN

address: 410 West 10th Street

department: Medical and Molecular Genetics

institute: Indiana University School of Medicine

type: Genome binding/occupancy profiling by high throughput sequencing

summary: we used single-cell multiome analysis to profile the transcriptome and epigenome of MSCs from four healthy donors.

first: Yue

first: Xiaona

last: Chu

first: Hongyu

last: Gao


title: Transcriptome analysis of renal cortex from mice subjected to cecal ligation and puncture compared to control mice [RNA-seq]

city: Zhanjiang

first: Tongtong

last: Ma

state: Guangdong

address: No. 57 South Renmin Avenue

department: Affiliated hospital of Guangdong Medical University

institute: Guangdong Medical University

summary: Sepsis is a complex syndrome characterized by organ dysfunction triggered by dysregulated host response to infection, and the kidney is the most commonly injured organ. To model septic-induced AKI in animal, a well-established mouse model induced by caecal ligation and puncture (CLP) was established.

overall_design:
To reveal the dysregulated mRNAs in renal cortex from Sham and CLP mice, we carried out global gene expression profiling by using RNA sequencing technology. We collected the renal cortex fom mice subjected to CLP treatment (n=3) and control mice (n=3).
Comparative gene expression profiling analysis of RNA-seq data for CLP mice and control mice.


title: Transcriptomic analysis of podocytes exposed to high glucose in co-culture with glomerular endothelial cells

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

summary: In diabetic nephropathy (DN), glomerular endothelial cells (GECs) and podocytes undergo pathological alterations, which are influenced by metabolic changes characteristic of diabetes, including hyperglycaemia (HG) and elevated methylglyoxal (MGO) levels. However, it remains insufficiently understood what effects these metabolic factors have on GEC and podocytes and to what extent the interactions between the two cell types can modulate these effects. To address these questions, we established a co-culture system in which GECs and podocytes were grown together in close proximity, and assessed transcriptional changes in each cell type after exposure to HG and MGO. We found that HG and MGO had distinct effects on gene expression and that the effect of each treatment was markedly different between GECs and podocytes. HG treatment led to upregulation of “immediate early response” genes, particularly those of the EGR family, as well as genes involved in inflammatory responses (in GECs) or DNA replication/cell cycle (in podocytes). Interestingly, both HG and MGO led to downregulation of genes related to extracellular matrix organisation in podocytes. Crucially, the transcriptional responses of GECs and podocytes were dependent on their interaction with each other, as many of the prominently regulated genes in co-culture of the two cell types were not significantly changed when monocultures of the cells were exposed to the same stimuli. Finally, the changes in the expression of selected genes were validated in BTBR ob/ob mice, an established model of DN. This work highlights the molecular alterations in GECs and podocytes in response to the key diabetic metabolic triggers HG and MGO, as well as the central role of GEC-podocyte crosstalk in governing these responses.

overall_design: RNA-seq analysis of human podocytes that were co-cultured with glomerular endothelial cells and exposed to high glucose (HG) for 48 hr or 96 hr

first: Michael

last: Albrecht

first: Jonathan

middle: P

last: Sleeman

first: Boyan

last: Garvalov


title: CircRNA profile of renal cortex from mice subjected to cecal ligation and punture compared to control mice

overall_design: To reveal the dysregulated circRNAs in renal cortex from Sham and CLP mice, we carried out circRNA expression profiling by using circRNA microarray. We collected the renal cortex fom mice subjected to CLP treatment (n=3) and control mice (n=3).


title: Transcriptomic analysis of glomerular endothelial cells and podocytes exposed to methylglyoxal in co-culture

overall_design: RNA-seq analysis of human glomerular endothelial cells and podocytes that were co-cultured together in a transwell system and exposed to 200 µM methylglyoxal (MGO) for 96 hr


title: Transcriptomic analysis of glomerular endothelial cells exposed to high glucose in co-culture with podocytes

overall_design: RNA-seq analysis of human glomerular endothelial cells that were co-cultured wih podocytes and exposed to high glucose (HG) for 48 hr or 96 hr


title: Gene expression profile of lung tissues comparing between ISM1-/- and wildtype mice.

city: Singapore

first: Jong

middle: Huat

last: Tee

state: Singapore

address: 14 Science Drive 4

department: Department of Biological Sciences

country: Singapore

institute: National University of Singapore

summary: Isthmin 1 (ISM1) is a secreted 60 kDa protein that exhibits pro-apoptotic and anti-angiogenic functions in experimental settings. We generated ISM1 knockout mice (ISM1-/- ) in C57BL/6J background through CRISPR gene editing technology to understand the physiological function of endogenous ISM1. The ISM1-/- mice presented spontaneous pulmonary emphysema and immune infiltration under the ambient environment. These findings suggest that ISM1 might be an anti-inflammatory protein important for maintaining lung homeostasis. To investigate the role of ISM1 in the lung under steady state, we compare the gene expression in the ISM1 knockout lungs with that of the wild type. Lungs of young adult mice (2 months old) from wild type and ISM1-/- mice were harvested and bulk RNASeq was performed.

overall_design: Total RNA extracted from whole lung tissue of ISM1-/- and WT mice at 2 months old in triplicates

first: Tee

middle: J

last: Huat

first: Udhaya

last: Vijayakumar

first: Ruowen

last: Ge


title: Molecular alterations in GECs and podocytes in response to the key diabetic metabolic triggers HG and MG


title: CRISPR screen identified CLEC16A suppresses astrocyte inflammasome-involved pathology via mitophagy: EAE study

city: Boston

first: Zhaorong

last: Li

address: 60 Fenwood Road

institute: Dana Farber Cancer Institute

summary: CLEC16A conditional knockout using GFAP-Cre

overall_design: 12 samples of astrocytes and 12 samples of microglia sorted from EAE mice (day 30)

first: Atsushi

last: Kadowaki

first: Francisco

last: Quintana


title: DNA methylation profiles of mouse leukocyte

city: Shinagawa-ku

first: Hideyuki

last: Takeshima

state: Tokyo

department: Institute for Advanced Life Sciences

country: Japan

institute: Hoshi University

summary: DNA methylation profiles were compared between individual types of mouse leukocytes.

overall_design: Genome-wide DNA methylation analysis was conducted by an Infinium Mouse Methylation BeadChip.

first: Kazuhiro

last: Nishiyama

first: Hitomi

last: Nishinakamura

first: Liu

last: Yuyu

first: Naoko

last: Hattori

first: Satoshi

last: Yamashita

first: Toshikazu

last: Ushijima


title: ATF1 regulating signaling pathways between nasopharyngeal carcinoma cells and immortalized epithelial cells

city: Dongguan

first: Guoliang

last: Huang

address: No.1 Xincheng Avenue, Songshan Lake High-tech Park (Guangdong Medical University)

institute: Graduate School of Guangdong Medical University

summary: The aim of this study is to provide a comprehensive pathways regulated by ATF1 and to screen the differences between cancer and normal cells. Genome-wide mRNA expression microarrays were performed using RNA isolated from ATF1 over-expressing CNE1 and NP69 cells. The ATF1 regulating expression pattern and pathways were analyzed by KEGG pathway, GO annotation and PPI networks. A total of 1651 genes were differentially expressed between CNE1-ATF1 and CNE1-control cells, among which 799 genes were up-regulated and 852 genes were down-regulated. A total of 4304 genes were differentially expressed between NP69-ATF1 and NP69-control cells, among which 2071 genes were up-regulated and 2233 genes were down-regulated.

overall_design: CNE1-ATF1 was designated as the CNE1 cells stably expressing ATF1, and CNE1-control as the negative control. NP69-ATF1 was the NP69 cells stably expressing ATF1, while NP69-control as the negative control. Cells (5×105) were inoculated in a 60 mm culture dish for 2 days, and then RNA was isolated and measure changes in gene expression.

first: Fangfang

last: Wang


title: Potentiating NaV1.1 in Dravet Syndrome patient iPSC-derived GABAergic neurons increases neuronal firing frequency and decreases network synchrony

status: Public on Nov 10 2023

city: Cambridge

first: Laura

last: Chipman

state: MA

address: 1 Portland St

institute: Pfizer

summary: Dravet syndrome is a developmental and epileptic encephalopathy characterized by seizures, behavioral abnormalities, developmental deficits, and elevated risk of sudden unexpected death in epilepsy (SUDEP). Most patient cases are caused by de novo loss-of-function mutations in the gene SCN1A, causing a haploinsufficiency of the alpha subunit of the voltage-gated sodium channel NaV1.1. Within the brain, NaV1.1 is primarily localized to the axons of inhibitory neurons, and decreased NaV1.1 function is hypothesized to reduce GABAergic inhibitory neurotransmission within the brain, driving neuronal network hyperexcitability and subsequent pathology. We have developed a human in vitro model of Dravet syndrome using differentiated neurons derived from patient iPSC and enriched for GABA expressing neurons. Neurons were plated on high definition multielectrode arrays (HD-MEAs), permitting recordings from the same cultures over the 7-weeks duration of study at the network, single cell, and subcellular resolution. Using this capability, we characterized the features of axonal morphology and physiology. Neurons developed increased spiking activity and synchronous network bursting. Recordings were processed through a spike sorting pipeline for curation of single unit activity and to assess the effects of pharmacological treatments. At 7-weeks, the application of the GABAAR receptor agonist muscimol eliminated network bursting, indicating the presence of GABAergic neurotransmission. To identify the role of NaV1.1 on neuronal and network activity, cultures were treated with a dose-response of the NaV1.1 potentiator δ-theraphotoxin-Hm1a. This resulted in a strong increase in firing rates of putative GABAergic neurons, an increase in the intraburst firing rate, and eliminated network bursting. These results validate that potentiation of NaV1.1 in Dravet patient iPSC-derived neurons results in decreased firing synchrony in neuronal networks through increased GABAergic neuron activity and support the use of human neurons and HD-MEAs as viable high-throughput electrophysiological platform to enable therapeutic discovery.

overall_design: A single cell RNA sequencing experiment was performed to understand the cell identity of Dravet patient induced pluripotent stem cell (iPSC) derived neurons. Neurons were thawed following the manufacturer’s protocol and plated in 24-well plate format at 300,000 live cells/well. Base media contained DMEM/F-12 media (0.5x, Gibco), Neurobasal media (0.5x, Gibco), B-27 supplement (1x, Gibco), N-2 supplement (1x, Gibco), GlutaMax (0.5 mM, Gibco), brain-derived neurotrophic factor (BDNF, 10 ng/mL, PeproTech), glial-derived neurotrophic factor (GDNF, 10 ng/mL, PeproTech), and TGF-β1 (1 ng/mL, PeproTech), for a total of 500 mL/well. For seeding media at DIV 0, GABA neuron seeding supplement (1x, BrainXell) was added. At DIV 4, base media plus Day 4 Supplement (1x, BrainXell) and Supplement K (1x, BrainXell) were added at 500 mL/well. Starting at DIV 7, a 50% media change 2x per week was performed using base media. Cells were disassociated at DIV 21 following protocol for mature neuronal culture outlined (Julie Jerber, 2020). Cells in suspension were 89% viable (Countess II) following disassociation. Initial steps of sample QC and cDNA synthesis were conducted at GENEWIZ, LLC./Azenta US, Inc (Waltham, MA, USA). Library preparations, sequencing reactions, and data analysis were conducted at GENEWIZ, LLC./Azenta US, Inc (South Plainfield, NJ, USA).

first: Matt

middle: R

last: Kelley

middle: B

first: Shoh

last: Asano

first: Matthew

last: Knott

first: Samantha

last: Howard

first: Allison

last: Berg


title: Bypass of an epigenetic S-phase transcriptional module by convergent nutrient stress signals

city: Geneva 4

first: Patrick

middle: H.

last: Viollier

address: Rue Michel Servet 1

department: Dept.  Microbiology and Molecular Medicine

institute: University of Geneva, Faculty of Medicine / CMU

summary: The signals feeding into bacterial S-phase transcription are poorly understood. Cellular cycling in the alpha-proteobacterium Caulobacter crescentus is driven by a complex circuit of at least three transcriptional modules that direct sequential promoter firing during the G1, early and late S cell cycle phases. In alpha-proteobacteria, the transcriptional regulator GcrA and the CcrM methyltransferase epigenetically activate promoters of cell division and polarity genes that fire in S-phase. By evolving Caulobacter crescentus cells to cycle and differentiate in the absence of the GcrA/CcrM module, we discovered that phosphate deprivation and (p)ppGpp alarmone stress signals converge on S-phase transcriptional activation. The cell cycle oscillations of the CtrA protein, the transcriptional regulator CtrA that implements G1 and late S-phase transcription, are essential in our evolved mutants, but not in wild-type cells, showing that the periodicity in CtrA abundance alone can sustain cellular cycling without GcrA/CcrM. While similar nutritional sensing occurs in other alpha-proteobacteria, GcrA and CcrM are not encoded in the reduced genomes of obligate intracellular relatives. We thus propose that the nutritional stress response induced during intracellular growth obviated the need for an S-phase transcriptional regulator.

overall_design: Examination of PhoB whole genome binding/occupancy (ChIP-Seq) in WT Caulobacter crescentus and ΔpstS mutant

first: Marie

last: Delaby

first: Gaël

last: Panis

first: Coralie

last: Fumeaux

first: Laurence

last: Degeorges

middle: H


title: Time course of respiratory syncytial virus (RSV) infection in healthy and cystic fibrosis (CF) human airway epithelial cell cultures

status: Public on Nov 08 2023

city: Iowa City

first: Alejandro

middle: A.

last: Pezzulo

state: Iowa

address: 6316 Pappajohn Biomedical Discovery Building

department: Department of Internal Medicine

institute: Universty of Iowa

summary: The goal of this study was to examine changes in gene expression over time in healthy and cystic fibrosis (CF) human airway epithelia infected with RSV.

overall_design: CF and Non-CF primary human airway epithelia were infected with RSV, prepared for RNA sequencing, and sequenced on Illumina HiSeq 4000 system using 2x150bp paired end SBS chemistry.

first: Jennifer

middle: A

last: Bartlett

first: Sateesh

last: Krishnamurthy

first: Brajesh

last: Singh

first: Andrew

middle: L

last: Thurman

last: Sinn


title: CRIPSR screen identified CLEC16A suppresses astrocyte inflammasome-involved pathology via mitophagy: human in vitro study

first: Zhaorong

last: Li

summary: CLEC16A knocked down human embryonic stem cell (hESC) derived astrocytes

overall_design: 23 samples of hESC astrocytes collected after  CLEC16A shRNA knockdown and TNFα/IL-1β stimulation.

first: Atsushi

last: Kadowaki

first: Francisco

last: Quintana


title: Ikaros and Aiolos directly regulate AP-1 transcriptional complexes and are essential for natural killer cell development [CUT&Run]

city: Monash University

first: Harrison

last: Sudholz

state: VIC

address: 15 Innovation walk

department: Biochemistry and Molecular Biology

country: Australia

institute: Monash University

summary: Ikaros family transcription factors regulate lymphocyte biology and are targets of the immunomodulatory imide drugs (IMiDs) for hematological malignancies. Ikaros (Ikzf1/IKZF1) is the most broadly expressed family member in lymphocytes, yet its role in innate lymphopoiesis is unknown. Here we used gene inactivation to reveal that NK cell-expression of Ikaros is essential for normal NK lymphopoiesis. Mechanistically, IKZF1 directly repressed Cish and Socs2, known negative regulators of IL-15R resulting in impaired IL-15 signaling in Ikzf1-null NK cells. Bcl2l11/BIM levels and apoptosis were increased in Ikzf1-null NK cells which in part accounted for the NK lymphopenia since both apoptosis and NK cell frequency were restored to normal levels when Ikzf1 and Bcl2l11 were co-deleted. Ikzf1-null NK cells presented extensive transcriptional alterations with a striking reduction in expression of genes encoding AP-1 transcriptional complexes (Fos/Jun members) and a compensatory increase in Ikzf2 and Ikzf3. Both IKZF1 and IKZF3 directly bound AP-1 family members and deletion of both Ikzf1 and Ikzf3 in NK cells resulted in a further reduction in Jun/Fos expression and a complete loss of peripheral NK cells in mice. Consistently, IKZF1 bound Jun/Fos genes at the same locations in activated B cells identifying a novel and conserved role for IKZF1 in Jun/Fos regulation. Collectively we show the Ikaros-family are novel regulators of apoptosis, cytokine responsiveness and AP-1 transcriptional activity required for NK cell development and function.

overall_design: 500,000 freshly isolated cells from cultured, splenic NK cells. Mnase-pA was provided by Bo Sun.


title: Ikaros and Aiolos directly regulate AP-1 transcriptional complexes and are essential for natural killer cell development [RNA-seq]

overall_design: We generated NK cell conditional knockout mice for Ikzf1, Ikzf3, or Ikzf1/Ikzf3 and compared these to Cre only control mice. Splenic NK cells were either directly sorted from mice or cultured prior to RNA isolation and sequencing.


title: Ikaros and Aiolos directly regulate AP-1 transcriptional complexes and are essential for natural killer cell development [ChIP-seq]

overall_design: Chromatin immunoprecipitation (ChIP) DNA sequencing of ex vivo expanded, splenic NK cells for Ikzf1 in WT and NKp46-conditional Ikzf1 knockout NK cells.


title: Ikaros and Aiolos directly regulate AP-1 transcriptional complexes and are essential for natural killer cell development [ATAC-seq]

overall_design: We generated NK cell conditional knockout mice for Ikzf1 and compared these to Cre negative, floxed control mice. Viable splenic NK (NK1.1+ NKp46+ CD3- TCRβ- 7AAD-) cells were directly sorted from the spleens of mice prior to processing for ATAC-seq.


title: Ikaros and Aiolos directly regulate AP-1 transcriptional complexes and are essential for natural killer cell development

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

overall_design: Refer to individual Series


title: RNA sequencing analysis of gene expression profiles in WT and Etv5-deficient TFH cells

city: Pohang

first: Jiho

last: Park

address: 77, Cheongam-ro

institute: POSTECH

summary:
Purpose: The aim of this study is compare the gene expression profiles between wild-type (WT) and Etv5-deficient follicular helper T (TFH) cells to identify the molecular mechanism of how ETV5 promotes the TFH cell differentiation.
Methods: TFH cells (CD4+CD44+CXCR5+PD-1+) from the spleen of WT and Etv5f/f;Cd4-Cre mice immunized with OVA in alum for 7 days were sorted by a MoFlo-XDP (Beckman Coulter). Total RNA was extracted using TRIzol (GeneAll) according to the manufacturer’s instruction. The library for RNA sequencing was generated using the Truseq stranded mRNA library prep kit (Illumina), and sequencing was performed with Novaseq 6000 (Illumina).
Results: Reads were mapped to the mouse reference genome (mm10) with Tophat (v2.0.13), and the aligned results were analyzed with Cuffdiff (v2.2.0) for differentially expressed genes (DEGs). A total of 92 genes were differentially expressed in Etv5-deficient TFH cells (46 genes upregulated and 46 genes downregulated) when compare with WT TFH cells (fold change > 2 and P-value < 0.05).
Conclusions: Our study presents the first comparative gene expression analysis of TFH cells from control and T cell-specific Etv5-deficient mice. Since ETV5 usually acts as a transcription activator, we focused on the downregulated genes in Etv5-deficient TFH cells. Through this study, we identified the candidate genes that are targeted by ETV5 for TFH cell differentiation.

overall_design: mRNA profiles of TFH cells from the spleen of wild type (WT, Etv5f/f) and Etv5f/f;Cd4-Cre mice immunized with OVA in alum for 7 days. Two replicates for each genotypes were anaylzed.

first: Yoontae

last: Lee


title: RNA-seq of MC903 model with SB328437  treatment

city: Henan

first: Wenhao

last: Zhang

address: 开封

institute: Henan University

summary: Differential gene expression of SB328437  treatment in MC903  model

overall_design: RNA sequencing of 6  samples was performed. They are 3 samples of SB328437  treatment, and 3 samples from control

first: Jianghui

last: Meng


title: HOXA11 promotes lymphatic metastasis of gastric cancer via transcriptional activation of TGFβ1

city: Guangzhou

first: Zhenyuan

address: 1838th North Guangzhou Avenue, Southern Medical University

institute: Southern Medical University

summary: Most gastric cancer (GC) patients with early stage often have no lymph node (LN) metastases, while LN metastases appear in the advanced stage. However, there are some patients who present with early stage LN metastases and no LN metastases in the advanced stage. To explore the deeper molecular mechanisms involved, we collected clinical samples from early and advanced stage GC with and without LN metastases, as well as metastatic lymph nodes. Herein, we identified a keytarget, HOXA11, that was upregulated in GC tissues and closely associated with lymphatic metastases. HOXA11 transcriptionally regulates TGFβ1 expression and activates the TGFβ1/Smad2 pathway, which in turn promotes the development of EMT. In addition, enhanced Smad2 expression promotes the secretion of VEGF-C, which in turn induces lymphangiogenesis. These findings provide a plausible mechanism forHOXA11-modulated tumor in lymphatic metastasis and suggest thatHOXA11 may represent a potential therapeutic target for clinical intervention in LN-metastatic gastric cancer.

overall_design:
To identify critical genes that promote lymph node metastasis in gastric cancer, next-generation sequencing (NGS) was performed in 16 pairs gastric cancer tissues (GCs) and normal adjacent tissues (NATs), as well as 8 cases of metastatic lymph nodes (LNMs). These clinical samples included 4 pairs of T1 and T2 early LN-negative GCs and NATs, 4 pairs of T1 and T2 early LN-positive GCs and NATs, and the corresponding LNMs, 4 pairs of T3 and T4 advanced LN-negative GCs and NATs, 4 pairs of T3 and T4 advanced LN-positive GCs and NATs, and the corresponding LNMs.
Genes (a) are those that are highly expressed in differential analysis of gastric cancer with LN metastasis and its adjacent normal gastric tissue. It represent the portion of genes that are associated with gastric carcinogenesis and also with lymph node metastasis. Genes (b) are those that are highly expressed in differential analysis of gastric cancer without LN metastasis and its adjacent normal gastric tissue. It represent this fraction of genes that are associated with gastric carcinogenesis, but less associated with lymph node metastasis. Therefore, the genes we obtained by (a-b) are those that are not only associated with the development of gastric cancer, but also have a higher correlation with gastric cancer lymph node metastasis. Subsequently, Genes (c) are those obtained from differential analysis of metastatic lymph nodes versus normal gastric tissue. It represent those that are highly expressed in metastatic lymph nodes. Finally, the genes obtained from the Genes (a-b) and Genes (c) intersection analysis were those with the highest correlation with lymph node metastasis in gastric cancer.

first: Tailiang

last: Lu

first: Yanfeng

last: Hu


title: Muscle epigenomic changes with once-weekly prednisone at 4- vs 24-months of age

city: Cincinnati

first: Mattia

last: Quattrocelli

state: OH

address: 240 Sabin Way

institute: Cincinnati Children's Hospital Medical Center

summary: this dataset encompasses the muscle GR epigenomic changes elicited in quadriceps muscles of 4- vs 24-month-old mice (males + females) with a 12-week-long regimen of once-weekly ZT0 prednisone (1mg/kg i.p.)

overall_design: Aged (24 months-old at treatment start) and young control (4 months-old at treatment start) male and female cohorts were obtained from the NIA Aged Rodent Colony, C57BL/6JN background. Weekly prednisone treatment consisted of once-weekly i.p. injection of 1mg/kg prednisone (#P6254; Sigma-Aldrich; St. Louis, MO) 31. The injectable solution was diluted from a 5mg/ml stock in DMSO (#D2650; Sigma-Aldrich; St. Louis, MO) in 50ml volume. Injections were conducted at the beginning of the light-phase (ZT0; lights-on). Muscles were collected 4 hours after last injection.


title: muscle transcriptional changes with once-weekly prednisone at 4- vs 24-months of age

summary: this dataset encompasses the muscle transcriptomic changes elicited in quadriceps muscles of 4- vs 24-month-old mice (males + females) with a 12-week-long regimen of once-weekly ZT0 prednisone (1mg/kg i.p.)


title: RNA-seq of MC903 model with basophils VAMP7 knockout mouse

summary: Differential gene expression of basophil VAMP7 knockout in MC903 induced acute pruritus model

overall_design: RNA sequencing of 6  samples was performed. They are 5 samples of basophils VAMP7 knockout mouse, and 5 samples from wide type


title: Next Generation Sequencing of WT, ORP4L KI, Wild-type, LCK/R26Tax, ORP4Lcko;LCK/R26Tax T-cells Transcriptomes.

status: Public on Nov 11 2023

first: Wenbin

last: Zhong

address: No.601, West Huangpu Avenue

institute: Jinan University

summary:
Purpose: The goals of this study is to uncover the cellular pathways that are essential for T-cell malignant transformation driven by ORP4L and HTLV-1 oncogene Tax.
Methods: T-cell mRNA profiles of WT, ORP4L KI, Wild-type, LCK/R26Tax, ORP4Lcko;LCK/R26Tax mice were generated by deep sequencing, using Illumina NovaSeq 6000 sequencer for 318 cycles.Reads that passed the Illumina quality filters were kept for the subsequent analyses. Adapters were trimmed from the reads, and reads shorter than 17 nt were discarded. The reads were mapped to the Mouse mRNA reference database using FANSe3 algorithm on Chi-Cloud NGS Analysis Platform (Chi-Biotech Co. Ltd., Shenzhen, China).
Results: We use edgeR to analysis ORP4kI-vs-WT, LCK/R26Tax-vs-Wild-type，ORP4Lcko;LCK/R26Tax-vs-Wild-type，with a |log2 (FoldChange)| > 1 and p value <0.01. Hierarchical clustering of differentially expressed genes uncovered several as yet uncharacterized genes that may contribute to promote T-cell malignant.
Conclusions: Our study represents the first detailed analysis of transcriptomes that promote T-cell malignant transformation driven by HTVL-1 oncogene Tax.

overall_design: Examination of transcriptomes in T-cells from WT, ORP4L KI, Wild-type, LCK/R26Tax, ORP4Lcko;LCK/R26Tax mice.


title: Characterization of the Limbal Epithelial Stem Cell Niche

city: Houston

first: Isabel

middle: Yi

last: Moreno

state: Texas

address: 4901 Calhoun Rd., Room 2195

department: College of Optometry

institute: University of Houston

summary: Limbal epithelial stem cells (LESCs) reside within the LSC niche (LSCN), located at the annular transition zone between the cornea and conjunctiva. LESCs are important for the long-term maintenance of the corneal epithelium and critical for repopulating the corneal epithelium after injury. We have recently identified that a hyaluronan (HA)-rich extracellular matrix (ECM) exists within the LSCN, and that this HA matrix is necessary for maintaining LESCs in the “stem cell” state. Herein we further characterized the composition of the LSCN, identifying key components of the HA-rich matrix. We identified that the hyaladherins IαI, TSG-6 and versican are highly expressed in the limbus when compared to the cornea. For IαI, Heavy chain 5 (HC5) was found to be the most highly expressed HC in the mouse and human cornea, and associates with HA forming HA/HC5 specific matrices. CD44 is the most likely receptor that mediates the interaction between LESCs and the HA-specific matrix. The LSCN is composed of a rich HA matrix that contains HA/HC5. HA/HC5 complexes could be used as an improved substrate for culturing LESCs during ex vivo expansion for limbal stem cell transplantation.

overall_design:
To understand the composition of the LSCN we extracted mRNA from dissected corneal buttons and limbal rims of mouse corneas and sequenced them using a NextSeq 500 (Illumina).
We then performed gene expression analysis using data obtained from RNA-seq of the two different regions of the cornea.
We then performed gene expression analysis of the RNA-seq data of limbus and cornea buttons. The differential expression between cornea and limbus for the identified genes of interest were confirmed by qPCR, Western blotting, and immunohistochemistry.

middle: Y

first: Arian

last: Parsaie

first: Tarsis

middle: F

last: Gesterira

first: Vivien

last: Caoulson-Thomas


title: Bacterial lipopolysaccharide-induced inflammation promotes iron accumulation in human adipocytes

city: Salt

first: Núria

last: Oliveras Cañellas

address: Dr Castany s/n

country: Spain

institute: IdiBGi

summary:
In vitro experiments were performed during human adipocyte differentiation and in adipocytes
We then performed gene expression profiling analysis using data obtained from RNA-seq of adipocytes treat with/without LPS

overall_design: Comparative gene expression profiling analysis of RNA-seq data for subcutaneous adipocytes cells treat with/without LPS

last: Oliveras-Cañellas

first: José

middle: M

last: Fernández-Real

last: Moreno-Navarrete


title: RNA-seq of MC903-OVA model with basophils VAMP7 knockout mouse

summary: Differential gene expression of basophil VAMP7 knockout in MC903-OVA induced acute pruritus model

overall_design: RNA sequencing of 6  samples was performed. They are 3 samples of basophils VAMP7 knockout mouse, and 3 samples from wild type


title: Homodimer-mediated phosphorylation of C/EBPα-p42 S16 modulates acute myeloid leukaemia differentiation through liquid-liquid phase separation [ChIP-seq]

city: Jinan

first: Chunyan

last: Ji

address: Wenhua West Road

institute: Qilu Hospital

summary: CCAAT/enhancer binding protein α (C/EBPα) regulates myeloid differentiation, and its dysregulation contributes to acute myeloid leukaemia (AML) progress. Clarifying its functional implementation mechanism is of great significance for its further clinical application. Here, we show that C/EBPα regulates AML cell differentiation through liquid-liquid phase separation (LLPS), which can be disrupted by C/EBPα-p30. Considering that C/EBPα-p30 inhibits the functions of C/EBPα through the LZ region, a small peptide TAT-LZ that could instantaneously interfere with the homodimerization of C/EBPα-p42 was constructed, and dynamic inhibition of C/EBPα phase separation was observed, demonstrating the importance of C/EBPα-p42 homodimers for its LLPS. Mechanistically, homodimerization of C/EBPα-p42 mediated its phosphorylation at the novel phosphorylation site S16, which promoted LLPS and subsequent AML cell differentiation. Finally, decreasing the endogenous C/EBPα-p30/C/EBPα-p42 ratio rescued the phase separation of C/EBPα in AML cells, which provided a new insight for the treatment of the AML.

overall_design: Here, we show that C/EBPα promotes AML cell differentiation through LLPS, which can be disrupted by its dominant negative mutant C/EBPα-p30. Mechanistically, homodimer-mediated phosphorylation of C/EBPα S16 modulates the LLPS and thus governs AML differentiation. At last, we decreased the endogenous C/EBPα-p30/C/EBPα ratio to rescue the phase separation of C/EBPα in AML cells and significantly enhance drug efficacy. Our study clearly depicts a model in which LLPS is dependent on homodimers-mediated phosphorylation, which lays a theoretical foundation for understanding the regulatory mechanism of LLPS by an endogenous dominant negative mutant.

first: Dongmei

last: Wang

first: Tao

last: Sun

first: Fei


title: Homodimer-mediated phosphorylation of C/EBPα-p42 S16 modulates acute myeloid leukaemia differentiation through liquid-liquid phase separation [RNA-seq]


title: c-MYC-dependent transcriptional inhibition of autophagy is implicated in Cisplatin sensitivity in HPV-positive Head and Neck Cancer

city: Milano

first: Susanna

last: Chiocca

address: Via Adamello 16

country: Italy

institute: European Institute of Oncology, IEO

summary: Autophagy is important for removal, degradation and recycling of damaged organelles, proteins, and lipids through the degradative action of lysosomes. In addition to its catabolic function, autophagy is important in cancer and viral-mediated tumorigenesis, including Human Papillomavirus (HPV) positive cancers. HPV infection is a major risk factor in a subset of Head and Neck Cancer (HNC), for which no targeted therapies are currently available. Herein, we assessed autophagy function in HPV-positive HNC. We showed that HPV-positive HNC cells presented a transcriptional and functional impairment of autophagic process compared to HPV-negative cells, which was reactivated by knocking-down HPV E6/E7 oncoproteins, the drivers of cellular transformation. We found that the oncoprotein c-MYC was stabilized and triggered in HPV-positive cell lines. This resulted in the reduced binding of the MiT/TFE transcription factors to their autophagy targets due to c-MYC competition. Thus, knock-down of c-MYC induced the upregulation of autophagic and lysosomal genes in HPV-positive HNC cells, as well as the increase of autophagic markers at the protein level. Moreover, HPV oncoprotein E7 upregulated the expression of the phosphatase inhibitor CIP2A, accounting for c-MYC upregulation and stability in HPV+ HNC cells. CIP2A mRNA expression negatively correlated with autophagy gene expression in tumor tissues from HNC patients, showing, for the first time, its implication in a transcriptional autophagic context. Both CIP2A and c-MYC knock-down, as well as pharmacological downregulation of c-MYC, resulted in increased resistance to Cisplatin treatment. Our results not only show a novel way by which HPV oncoproteins manipulate the host machinery, but also provide more insights on the role of autophagy in chemoresistance, with possible implications for targeted HPV-positive HNC therapy.

overall_design: 4 biological replicates of Primary human keratinocytes were transduced with the retroviral vector pLXN Empt, HPV16 E6, HPV16 E7, or HPV16 E6/E7. After 5 days of selection with G-418 at the appropriate concentration cells were harvested and RNA extracted.RNA was used to generate the library using Truseq kit from Illumina.

first: Alessandro

last: Medda

first: Ottavio

last: Croci


title: ChIp-Seq on Normal Human Cholangiocytes

city: Rochester

first: Alexander

middle: Quinn

last: Wixom

state: MN

address: 200 1st St SW

department: Quantitative Health Sciences

institute: Mayo Clinic

summary: Epithelial cells subjected to low levels of irradiation can induce DNA damage response and senescence through variety of mechanisms.  We perfomed ChIP-seq for H3K27ac to investigate the gene pathways activated to induce senescence in cholangiocytes.

overall_design: We subjected normal human cholangiocytes. NHC, to 10GY irradiation, incubated them for 5 days at 37C . Cells were then crosslinked with formaldehyde for 10 mins at room temperature. The cells were then utilized for ChIP with H3K27ac antibody and subjected to sequencing

first: Nidhi

last: Jalan-Sakrikar

first: Robert

middle: C

last: Huebert


title: Enhancing sensitivity and versatility of Tn5-based single cell omics VI

city: Heidelberg

first: Isabelle

last: Seufert

address: Im Neuenheimer Feld 280

institute: DKFZ

summary: The analysis of chromatin features in single cells centers around the use of Tn5 transposase and exploits its activity to simultaneously fragment target DNA and integrate adapter sequences of choice. This reaction provides a direct readout in the transposase-accessible chromatin in single cells (scATAC-seq) assay to map open chromatin regions. Furthermore, by targeting Tn5 to antibody-bound chromatin epitopes, features like histone modifications can be mapped in single cells. Thus, enhancing Tn5 activity to improve genomic coverage for scATAC-seq or facilitating multi-omics readout of chromatin features via Tn5 together with the transcriptome is of great interest. Here, we address these issues by optimizing scATAC-seq for an increased number of integrations per cell. In addition, we provide a protocol that combines mapping of histone modification with scRNA-seq from the same cell. Our experimental workflows improve the results obtained from the downstream data analysis and serve to better resolve epigenetic heterogeneity and transcription regulation in single cells.

overall_design:
TF1-IDH2 wildtype and mutant cells were analyzed by Multiome scRNA-seq.
-------------------------------------
Authors state:
For human data, we are in the process of uploading the raw data to EGA. We will provide the EGA accession numbers to you as soon as we obtain them.

first: Karsten

last: Rippe

first: Jan-Philipp

last: Mallm


title: Homodimer-mediated phosphorylation of C/EBPα-p42 S16 modulates acute myeloid leukaemia differentiation through liquid-liquid phase separation


title: Enhancing sensitivity and versatility of Tn5-based single cell omics IV

overall_design:
Human PBMCs were analyzed by scATAC-seq using 10xTn5 or Tn5hc.
-------------------------------------
Authors state:
For human data, we are in the process of uploading the raw data to EGA. We will provide the EGA accession numbers to you as soon as we obtain them.


title: Enhancing sensitivity and versatility of Tn5-based single cell omics II

overall_design:
Human PBMCs were analyzed by Multiome scATAC-seq using 10xTn5 or Tn5hc.
-------------------------------------
Authors state:
For human data, we are in the process of uploading the raw data to EGA. We will provide the EGA accession numbers to you as soon as we obtain them.


title: Enhancing sensitivity and versatility of Tn5-based single cell omics I

overall_design: MEFs treated with interferon beta for 6 hours were analyzed by scATAC-seq using 10xTn5 or Tn5hc.


title: Enhancing sensitivity and versatility of Tn5-based single cell omics III

overall_design:
Human PBMCs were analyzed by Multiome scRNA-seq using 10xTn5 or Tn5hc for corresponding ATAC.
-------------------------------------
Authors state:
For human data, we are in the process of uploading the raw data to EGA. We will provide the EGA accession numbers to you as soon as we obtain them.


title: Irisin deficiency exacerbates diet-induced insulin resistance and cardiac dysfunction and promotes ischemia and reperfusion injury

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

summary: The myokine irisin is involved in the regulation of a variety of physiological conditions, metabolism, and survival. We and others have demonstrated that recombinant irisin contributes critically to modulation of insulin resistance and cardiac function. However, the molecular mechanisms by which irisin exerts its physiological effects on cardiac function and insulin sensitivity remain unclear.  We utilized the CRISPR/Cas9 genome editing system to delete irisin. Irisin deficiency did not result in abnormalities in development, growth, or cardiac function; however, gene expression profiling showed that several key signaling pathways related to growth, insulin signaling, and integrin signaling were coordinately downregulated. However, loss of irisin resulted in more severe insulin resistance and metabolic derangement when mice were exposed to a high fat diet, which was associated with profound cardiac dysfunction and hypertrophic remodeling. In addition, the loss of irisin also exacerbated myocardial ischemia-reperfusion injury, as indicated by a reduction of post-ischemic ventricular function and an increase in infarct size. Taken together, our results indicate that loss of irisin exacerbates insulin resistance and cardiac depression in response to high fat diet and promotes myocardial ischemia-reperfusion injury. This evidence suggests a role for irisin in modulating insulin resistance, cardiac function and ischemic injury.

overall_design: Cardiomyocytes were obtained from wild type and irisin knockout animals and gene expression was profiled using Affymetrix microarrays.

first: Ting

last: Zhao


title: N6-methyladenosine RNA modification drives a rapid shift to cisplatin resistance in bladder cancer by regulating SLC7A11 expression via YTHDF3 [RNA-seq]

city: Los Angeles

first: Emmanuelle

last: Hodara

state: CA

address: 1450 Biggy Street

institute: Keck School of Medicine of USC

summary: Our study examines the role of m6A RNA modification in regulating gene expression of transcripts promoting cisplatin resistance in bladder cancer.

overall_design: RNA-seq of T24 vs T24R2 BC cell lines in 5 replicatesg rown to 3 days confluence

first: Aubree

last: Mades

first: Tong

last: Xu

first: Daniel

last: Bsteh

first: Lisa

last: Swartz

first: Maheen

last: Iqbal

first: Peggy

last: Farnham

first: Suhn

middle: K

last: Rhie

first: Amir

last: Goldkorn


title: Endothelial to Mesenchymal Transition in Neonatal Hyperoxic Lung Injury: Role of sex as a biological variable

city: Philadelphia

first: Abiud

last: Cantu

state: Pennsylvania

address: 3615 Civic Center Blvd

department: Neonatology

institute: Children's Hospital of Philadelphia

summary: Bronchopulmonary dysplasia (BPD) is characterized by an arrest in alveolarization, abnormal vascular development and variable interstitial fibroproliferation in the premature lung. Endothelial to mesenchymal transition (Endo-MT) may be a source of pathologic fibrosis in many organ systems.  Whether Endo-MT contributes to the pathogenesis of BPD is not known. We tested the hypothesis that pulmonary endothelial cells will show increased expression of Endo-MT markers upon exposure to hyperoxia and that sex as a biological variable will modulate differences in expression.  WT and Cdh5-PAC CreERT2 (endothelial reporter) neonatal male and female mice (C57BL6) were exposed to hyperoxia (0.95 FiO2) either during the saccular stage of lung development (95% FiO2; PND1-5)  or through the saccular and early alveolar stages of lung development (75% FiO2; PND1-14). Expression of Endo-MT markers were measured in whole lung and endothelial cell mRNA. Sorted lung endothelial cells were subjected to bulk RNA-Seq. We show that exposure of the neonatal lung to hyperoxia leads to upregulation of key markers of EndoMT Neonatal male mice show higher expression of genes related to EndoMT. Furthermore, using lung sc-RNAseq data from neonatal lung we were able to show that xxx. Markers related to Endo-MT are upregulated in the neonatal lung upon exposure to hyperoxia and show sex-specific differences. Mechanisms mediating EndoMT in the injured neonatal lung can modulate the response of the neonatal lung to hyperoxic injury and need further investigation.

overall_design: Cdh5-PAC Cre Td tomato mice on a (C57BL6/J background) male and female neonatal mice were exposed to room air or hyperoxia (75% FiO2 from PND1-14). Mice were given one dose of tamoxifen 20ug/20ul on PND1 to label the endothelium. On PND14, lungs from Cre+ mice in room air or hyperoxia were subjected to flow cytometry. Viable, CD45-, TdTom/CD31+ cells were sorted and subjected to bulk-RNA seq.

first: Manuel

last: Cantu Gutierrez

first: Yuhao

last: Zhang

first: Xiaoyu

last: Dong

first: Gabriel

last: Batzil

first: Krithika

last: Lingappan


title: Host transcriptome profiling analysis induced byMd5BAC, Md5BAC △LORF9, Md5BAC △UL23,Md5BAC △LORF9-Re, Md5BAC △UL23-Re reconbinant viruses.

city: Zhengzhou

first: ZHU Xiaojing

middle: Xiaojing

last: ZHU

state: Henan

address: 15 Longzihu University Park, Zhengdong New District

institute: Henan Agricultural University

summary: Marek's disease virus (MDV) causes immunosuppression and tumor diseases in chickens. MDV encodes more than 100 genes, most of which are homologous to HSV-1 genes, and are mainly involved in viral genome DNA replication, virus particle assembly and morphogenesis. Although the functions of some genes have been analyzed, many genes are unknown because of the huge genome of MDV. In order to explore the pathogenesis of LORF9 and UL23 in vivo, LORF9 and UL23 gene deletion strains were constructed. Gene expression profiles of recombinant virus and Md5BAC wild strains were analyzed by RNA-seq data. To clarify the gene expression level of recombinant virus in the early stage of cytolytic infection.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Md5BAC and 4 recombinant viruses ( Md5BAC△LORF9, Md5BAC△ UL23, Md5BAC△LORF9-Re, Md5BAC△ UL23-Re).

first: Guoqing

last: Zhuang

first: Aijun

last: Sun


title: Thapsigargin inhibition of coronavirus PHEV replication by Ca2+ mediated metabolic reprogramming

city: changchun

first: junchao

last: Shi

state: jilin

address: xi'an road

department: College of Veterinary Medicine

institute: Jilin University

summary: The coronaviruses (CoVs) represent a large family of human and animal pathogens that cause significant health and economic burdens worldwide. Porcine hemagglutinating encephalomyelitis virus (PHEV), belonging to the genus Betacoronavirus, is one of the six coronaviruses that infect pigs, for which no effective drug or vaccine is commercially available. Here, we found that thapsigargin (Tg), an ER stress inducer, potently blocks PHEV replication in non-cytotoxic levels and the antiviral effect is long-lasting at least 60 h post-Tg exposure in different cells. Time-of-addition assay demonstrated that Tg significantly inhibit PHEV replication in N2a cells when treated immediately before, during, or after virus infection. Tg does not directly interact with PHEV particles and transcriptome analysis reveals a unique antiviral mechanism of Tg through Ca2+ mediated metabolic reprogramming. Crucially, oral administration of Tg prolong the survival time and reduced virus titres in the brains of treated mice. Besides, Tg also exerts a profound antiviral effect on alphacoronavirus, deltacoronavirus, rhabdoviruses, parapoxvirus and picornavirus. Taken together, Tg exerts antiviral effects by targeting host factors shared by different viruses, suggesting that this compound (or derivatives thereof) may be developed into broad-spectrum antiviral drugs without considering the drug resistance caused by virus mutation.

overall_design:
To investigate the antiviral potential and target of Thapsigargin, mock or PHEV-infected N2a cells were treated with Thapsigargin or DMSO.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 4 different treatment groups at 24 h.
Comparative gene expression profiling analysis of RNA-seq data for DMSO-treated (M), Thapsigargin-treated (T), PHEV-infected (P) , PHEV-infected and Thapsigargin-treated (PT) N2a cells.

first: Junchao

first: Qianhan

last: Jia

first: Zi

last: Li

first: Wenqi

last: He


title: Defective RNA helicase genes underlie predisposition to colorectal and hematological malignancies

city: Helsinki

first: Alisa

last: Olkinuora

address: Haartmaninkatu 8

country: Finland

institute: University of Helsinki

summary: Background: Causative genes are mostly unknown for the mismatch repair-proficient category of familial colorectal cancers designated as FCCTX. Recent evidence suggests shared susceptibility factors between colorectal and hematological malignancies. Study design: We investigated 28 FCCTX families by exome sequencing, supplemented with whole genome sequencing, RNA-sequencing, and tumor studies to identify the predisposing genes. Guided by the findings, germline and somatic exomes of ~400 patients with acute leukemia, myelodysplastic syndrome, and myeloma were subsequently examined. Results: A family with hematological and solid malignancies revealed a truncating variant in the DEAH-box RNA helicase gene DHX40 co-segregating with disease in seven family members. Neoplastic tissues revealed no apparent “second hit”, implying a haploinsufficiency model of tumorigenesis. DHX40 siRNA-treated cell lines exhibited a 13% increase in aberrantly spliced transcripts vs. GAPDH-siRNA or non-target siRNA-treated cells. Two additional families showed truncating germline variants in the TDRD9 and TDRD5 genes encoding Tudor domain-containing RNA-binding proteins. In the hospital-based hematological series, 18% of germline and 28% of somatic exomes revealed possibly pathogenic DEAD/H box gene variants, including somatic variants of DHX40 in four. Conclusions: This study identifies DHX40, TDRD9, and TDRD5 as novel candidate genes for FCCTX predisposition. In the family segregating the truncating DHX40 variant, two carriers had hematological neoplasia, suggesting possible analogy to DDX41, a DEAD-box RNA helicase gene previously linked to myeloid malignancies. Our findings emphasize aberrant RNA metabolism behind FCCTX and hematological neoplasia.

overall_design: Whole transcriptome RNA-seq data from siRNA treated (DHX40, GAPDH, Non-Target, and Untreated) cell lines (HEK293, CCD841 CoN, K562) in triplicate.

first: Juho

last: Väänänen


title: N6-methyladenosine RNA modification drives a rapid shift to cisplatin resistance in bladder cancer by regulating SLC7A11 expression via YTHDF3

first: Emmanuelle

last: Hodara

type: Methylation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Effect of RANKL on gene expression during osteoclast differentiation

city: Shimotsuke

first: Yasuhiro

last: Omata

state: Tochigi

address: 3311-1 Yakushiji

department: Department of Medicine

institute: Jichi Medical University

summary: To investigate effect of RANKL on osteoclast differentiation, bone marrow cells were cultured with M-CSF and RANKL.

overall_design: We performed gene expression analysis using the data of RNA-seq from cultured bone marrow cells.

first: Hideyuki

last: Tachibana

first: Yoshimi

last: Aizaki

first: Toshihide

last: Mimura

first: Kojiro

last: Sato


title: Gene expression profile at single cell level of BT-549 TNBC Spheroid cultures with inducible expression of CTL or MUC1 targeting knockdown

city: Buffalo

first: Mark

middle: D

last: Long

state: NY

address: Elm & Carlton Streets

department: Bioinformatics & Biostatistics

institute: Roswell Park Comprehensive Cancer Center

summary: The MUC1-C protein evolved in mammals for adaptation of barrier tissues to loss of homeostasis. Prolonged activation of MUC1-C in settings of chronic inflammation promotes lineage plasticity, epigenetic reprogramming and the cancer stem cell (CSC) state. The effects of MUC1-C on the metabolism of CSCs remain unexplored. We used single cell RNA sequencing (scRNA-seq) to analyze the diversity of BT-549 spheroid cultures with and without knockdown of MUC1 to examine the effects of MUC1 on CSC renewal and metbolic states.

overall_design: Pelleted single-cell suspensions of BT-549 spheroid cultures were washed in 1,000 ul of PBS plus 0.4% BSA, transferred to low-retention microcentrifuge tubes (Fisher Scientific, Hampton, NH, USA), and then centrifuged for 10 minutes at 300g at 4C. Pellets were resuspended in 800 ul of PBS plus 0.4% BSA, and cells were counted by eye using INCYTO C-Chip Neubauer Improved Disposable Hemacytometers (VWR International Ltd., Radnor, PA, USA). A total of > 10,000 cells per sample were loaded per channel of the Chromium Next GEM Chip K for processing on the 10x Chromium Controller (10x Genomics, Pleasanton, CA, USA) followed by cDNA generation and library construction, as per manufacturer’s instructions (Chromium Next GEM Single Cell 5ʹ Reagent Kits v2 User Guide, Rev E). Libraries were normalized and pooled for sequencing on an Illumina NextSeq 500 system using a 150 cycle Mid-Output flow cell (Illumina, Inc., San Diego, CA, USA) with run parameters 26, 10, 10, 90. Sequenced libraries were demultiplexed using cellranger mkfastq (Cell Ranger v6.1.1). As part of the cellranger count pipeline, demultiplexed libraries were aligned to the human transcriptome (excluding introns) based on the 10X Genomics pre-computed human reference, GRCh38-2020-A. Both raw and cell-associated gene expression feature matrices (cell barcodes x gene counts) were output for use in downstream analyses.

first: Donald

last: Kufe


title: Enhancing sensitivity and versatility of Tn5-based single cell omics V

first: Isabelle

last: Seufert

overall_design:
TF1-IDH2 wildtype and mutant cells were analyzed by Multiome scChIP-seq H3K27me3.
-------------------------------------
Authors state:
For human data, we are in the process of uploading the raw data to EGA. We will provide the EGA accession numbers to you as soon as we obtain them.

first: Karsten

last: Rippe

first: Jan-Philipp

last: Mallm


title: Chromosomal instability and deregulated cell cycle pathways are associated with increased metastatic capacity in treatment naïve, localized, high-risk gastrointestinal stromal tumours

city: Oslo

first: Leonardo

last: Meza-Zepeda

address: Ullernchausseen 70

department: Department of Tumor Biology

country: Norway

institute: Oslo University Hospital

summary: The aim of the GIST Risk study was to identify genomic and transcriptomic profiles that could be associated with disease relapse and thus a more aggressive tumour phenotype. The cohort consisted of 21 patients with primary, untreated, resectable, high-risk GIST divided into two groups; patients who developed metastatic disease within three years and patients without disease relapse for more than five years follow-up after adjuvant imatinib treatment.

overall_design: We performed miRNA transcriptome profiling of 21 untreated,  resectable, high-risk GIST with different capacity to metastasize. Data was egnerated using the nanoString Human V3 miRNA assay and normalisation and differentially expressed gene analysis were performed using NanostringDiff R package.

first: Heidi

last: Namløs

first: Ksenia

last: Khelik


title: Single cell RNA sequencing on chronic deletion of hepatic O-GlcNAc Transferase in mice

city: Kansas City

first: Dakota

last: Robarts

state: KS

address: 3901 Rainbow Blvd

institute: University of Kansas Medical Center

summary: Single cell RNA sequencing, 5 week deletion of  O-GlcNAc transferase (OGT) in hepatocytes

overall_design: Hepatocytes and nonparenchymal cells (NPC) were isolated from either control or OGT knockout mice and underwent 10x Chromium 3' single cell RNA sequencing

first: Udayan

last: Apte


title: The Essential Role of O-GlcNAcylation in Hepatic Differentiation


title: The profound effects of solid tumour-induced B cell dysregulation

first: Xiang

last: Zhang

address: One Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

summary: Solid tumours evade immunosurveillance through a plethora of mechanisms. It remains elusive how the development and functions of B cells vary in different tumour contexts. Here, we observed distinct patterns of B cell abnormality in triple-negative breast cancer and termed these patterns “tumour-induced B cell abnormality” type (TiBA). TiBA results from disrupted early B cell development in the bone marrow, which is associated with abnormal myelopoiesis.  This study highlights the heterogeneity of tumour-induced systemic changes on B cells and lays foundation for the precision treatment of patients with different B cell abnormalities.

overall_design: To study the B cells changes in response to tumour burden at single-cell level, we collected the peripheral blood (PB) or bone marrow (BM) cells from sham (naive) mice or mice-bearing orthotopic triple-negative breast cancer tumours including, PyMT-N, T11, T12, 2208L) and  performed scRNA-seq.


title: Itaconate-producing neutrophils regulate local and systemic inflammation following trauma

city: Dallas

first: Robert

middle: J

last: Tower

address: 5323 Harry Hines Blvd

institute: UTSW

overall_design:
10-week old mice were subjected to burn to the back in combination with a full tenotomy of the Achille's tendon. Bone marrow, mononucleated cells from the blood and the tendon injury site (single cell suspension generated with enzymatic digetsion) were isolated
Unsorted cells isolated from the bone marrow, blood and HO injury site 3 days post burn/tenotomy surgery

first: Ben

last: Levi


title: Factor inhibiting HIF (FIH) promotes lung cancer progression

city: Derio

first: Ana

middle: Maria

last: Aransay

state: BIZKAIA

address: Parque tecnologico de Bizkaia, Building 801-A

department: Genome Analysis Platform

institute: CIC bioGUNE

summary: Factor-inhibiting HIF (FIH) is an asparagine hydroxylase that acts on hypoxia-inducible factors (HIFs) to control cellular adaptation to hypoxia. FIH is expressed in several tumor types, but its impact in tumor progression remains largely unexplored. We observed that FIH was expressed on human lung cancer tissue. Deletion of FIH in mouse and human lung cancer cells resulted in an increased glycolytic metabolism, consistent with increased HIF activity. FIH-deficient lung cancer cells exhibited decreased proliferation. Analysis of RNA-Seq data confirmed changes in the cell cycle and survival and revealed molecular pathways that were dysregulated in the absence of FIH, including the upregulation of angiomotin (Amot), a key component of the Hippo tumor suppressor pathway. We show that FIH-deficient tumors were characterized by higher immune infiltration of NK and T cells compared with FIH competent tumor cells. In vivo studies demonstrate that FIH deletion resulted in reduced tumor growth and metastatic capacity. Moreover, high FIH expression correlated with poor overall survival in non-small cell lung cancer (NSCLC). Our data unravel FIH as a therapeutic target for the treatment of lung cancer.

overall_design: Eight samples are analyzed. There are duplicates per each condition as followed: WTNOR, KONOR, WTHYP, WTHYP.

last: Garcia-del Rio

first: Leire

last: Egia-Mendituke

first: Endika

last: Prieto-Fernandez

first: Asier

last: Antoñana-Vildosola

first: Borja

last: Jimenez-Lasheras

first: So

last: Lee

first: Adrián

last: Barreira-Manrique

first: Samanta

last: Romina-Zanetti

first: Ander

last: de Blas

first: Paloma

last: Beltran-Velasco

first: Alexandre

last: Bosch

first: Asis

last: Palazon


title: Bi-steric mTORC1 inhibitors induce apoptotic cell death in tumor models with hyperactivated mTORC1

first: Heng

last: Du

address: 45 Francis St

institute: Brigham and Women's Hospital

summary: The PI3K-AKT-mTOR pathway is commonly dysregulated in cancer. Rapalogs exhibit modest clinical benefit likely due to their lack of effects on 4E-BP1. We hypothesized that bi-steric mTORC1-selective inhibitors would have greater potential for clinical benefit than rapalogs in tumors with mTORC1 dysfunction.  We assessed this hypothesis in tumor models with high mTORC1 activity both in vitro and in vivo.  Bi-steric inhibitors had strong growth inhibition, eliminated phosphorylated 4EBP1, and induced more apoptosis than rapamycin or MLN0128. Multi-omic analysis showed extensive effects of the bi-steric inhibitors in comparison to rapamycin. De novo purine synthesis was markedly and selectively inhibited by bi-sterics through reduction in JUN and its downstream target PRPS1 and appeared to be the cause of apoptosis. Hence, bi-steric mTORC1-selective inhibitors are a novel therapeutic strategy to treat tumors driven by mTORC1 hyperactivation.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: To gain a detailed view of how bi-steric mTORC1-selective inhibition contrasted with the effects of rapamycin, RNA-seq was performed on two representative cell lines (HCV29 TSC1-null and 705 Tsc2-null) treated with RMC-6272 (3 nM, 24h), rapamycin (10 nM, 24h), or DMSO as the negative control.


title: Deciphering the regulatory network of the NAC transcription factor FvRIF, a master regulator in controlling strawberry fruit ripening [DAP-seq]

city: Beijing

first: Xiaojing

last: Li

state: Beijing

address: No.20 Nanxincun, Xiangshan, Beijing

department: Institute of Botany

institute: Chinese Academy of Sciences

summary: To better understand FvRIF-mediated transcriptional regulation of fruit ripening, we performed DNA affinity purification sequencing (DAP-seq) to unravel FvRIF binding sites at the genome level. For DAP-seq analysis, the recombinant FvRIF fusion protein was used to purify the sheared genomic DNA of strawberry fruits. Two independent biological replicates of DAP-seq and DNA ‘input’ negative control libraries were prepared and submitted for deep sequencing.

overall_design: Genomic DNA enrichment profiles in strawberry fruits of 22 DPA wild-type were generated by DAP-seq, in two independent biological replicates of DAP-seq and input, using Illumina Nova S4.

first: Guozheng

last: Qin


title: Deciphering the regulatory network of the NAC transcription factor FvRIF, a master regulator in controlling strawberry fruit ripening [RNA-seq]

summary: To identify genes that are transcriptionally regulated by FvRIF during fruit ripening, we performed comparative transcriptome analysis through RNA sequencing (RNA-seq) using fruits of the wild type and the mutant lines (FvRIF-cr-6 and FvRIF-cr-13) at 28 DPA. Three independent biological replicates were applied for the RNA-seq analysis.

overall_design: Transcriptome analysis profiles in strawberry fruits of 28 DPA wild-type and 28 DPA FvRIF mutant lines (FvRIF-cr-6 and FvRIF-cr-13) were generated by RNA-seq, in triplicate, using Illumina Nova seq 6000.


title: Analysis of Reproducibility and Robustness of a Renal Proximal Tubule Microphysiological System OrganoPlate® 3-lane 40 for In Vitro Studies of Pharmacokinetics and Toxicodynamics

city: College Station

first: Ivan

last: Rusyn

state: TX

address: VIDI(Veterinary Medicine 2), 2, 402 Raymond Stotzer Pkwy

department: Interdisciplinary Faculty of Toxicology

institute: Texas A&M University

summary:
Microphysiological systems are a promising new experimental tool for drug and chemical safety evaluation. These models are rapidly evolving, and concerns exist about the reproducibility, robustness and relative benefits when compared to traditional in vitro cultures. This study used OrganoPlate® 3-lane 40, a microfluidics-based model of the renal proximal tubule and compared it to multi-well static cultures using a number of human renal proximal tubule epithelial cell (RPTEC) types. We followed previously published protocols but adapted them to the varying cell proliferation rates of different RPTECs; primary cells required up to 7 days in culture before experiments, while some immortalized cell lines could be used in 3 days.
Function of various tubule-specific transporters, permeability of small molecules (cisplatin, tenofovir and perfluorooctanoic acid) and fluorescent dextrans (60-150 kDa), basal and chemical-effected gene expression, and cell viability were tested. Different RPTEC types and culture conditions (OrganoPlate® 3-lane 40 vs multi-well plates) were compared. We found that there are advantages offered by OrganoPlate® 3-lane 40 as compared to multi-well cultures – presence of media flow, albeit intermittent, and fairly high throughput. However, this model appears to offer only limited (e.g., MRP-mediated transport) advantages in terms of either gene expression or transporter function when compared to the multi-well plate culture conditions. It can also be used to study cellular uptake and direct toxic effects of small molecules; still, it may have limited utility for studies of pharmaco-/toxico-kinetics because drug transport between blood and tubule compartments is considerably affected by the gel barrier.

overall_design: Comparative gene expression profiling analysis of TempO-Seq data for RPTEC cells using different platforms, cells that over-expressed certain transporter proteins, and chemical treatment conditions.

first: Courtney

last: Sakolish

first: Haley

last: Moyer

first: Han-Hsuan

last: Tsai

first: Lucie

last: Ford

first: Allison

middle: N

last: Dickey

first: Fred

last: Wright


title: Mediator Subunit 30 Directs Myc Oncogenesis

city: La Jolla

first: Guofeng

last: Zhao

address: 9500 Gilman Dr.

department: Medicine

institute: UCSD


title: Longitudinal dynamics  of circulating miRNAs  in a swine model of familial  hypercholesterolemia during early  atherosclerosis

city: MADISON

first: Hadjer

last: Namous

state: WI

address: 1675 Observatory Dr

department: Animal and Dairy Sciences

institute: University of Wisconsin Madison

summary: Atherosclerosis is a chronic disease involving multiple biological mechanisms. A study aimed to identify changes in miRNA expression at early stages using a large swine model. 18 female pigs were studied, 9 with familial hypercholesterolemia and 9 normal controls. Plasma was collected at 3, 6, and 9 months of age. In vivo imaging and histopathology were performed to document the presence of coronary atherosclerosis. miRNA sequencing was carried out on plasma cell-free RNA. Results showed that circulating miRNA dynamics change over time during atherosclerosis development and specific DE miRNAs may be promising biomarkers for early detection of coronary atherosclerosis.

overall_design: To investigate the temporal changes of miRNAs in early atherosclerosis,a total of 18 female pigs; 9 familial hypercholesterolemic (WMS-FH) and 9 normal control swine (WMS-N) were studied. Plasma was collected at 3, 6, and 9 months of age.

first: Juan

last: Granada

first: Hasan

last: Khatib

first: Jess

last: Reed


title: Mediator Subunit 30 Directs Myc Oncogenesis [Cut&Tag]

overall_design: to test the influence of MED30 overexpression(OE) on other factors binding, Myc, MED1,MED30 cut&tag was performed in teton MED30 OE Mia PaCa-2 cells. To test the influence of MED30 knockdown on other factors binding, MED1,17,23, H3k4me3, K27ac cut&tag was performed in teton shMED30 Mia PaCa-2 cells

first: Chunyu

last: Jin

first: Guogeng

first: Michael

middle: G

last: Rosenfeld


title: Expression data from mice hematopoietic progenitor cells

first: Yasuhiro

last: Omata

summary:
Nfatc1 short isoform-specific KO mice are embryonic lethal. This isoform is essential for osteoclast differentiation and is responsible for the gene expression of various osteoclast markers, including the isoform itself.
We used clariom s assay to explore genes showing altered expresssion during osteoclast differentiation in cultured hematopoietic progenitor cells from KO mice.

overall_design: To investigate the effect of RANKL and the Nfatc1 short isoform on gene expression profiles, probes for genomewide genes were hybridized with total RNA isolated from cultured cells. Four samples including hematopoetic prognitor cells from WT and KO mice treated with or without RANKL were used.

first: Hideyuki

last: Tachibana

first: Yoshimi

last: Aizaki

first: Toshihide

last: Mimura

first: Kojiro

last: Sato


title: RNA-Seq study of small follicles and large follicles in Indian Ghoongroo pigs

city: Guwahati

first: Jaya

last: Bharati

state: ASSAM

address: ICAR-NRC on Pig, Rani

department: Animal Physiology

country: India

institute: ICAR-National Research Centre on Pig, Guwahati, Assam

summary: To gain insight into the differentially expressed genes (DEGs) and signalling pathways regulating development of small follicles (SF diameter ≥3 mm to <6 mm) into large follicles (LF diameter ≥6 mm) in Ghoongroo pigs, a comprehensive transcriptome profiling of porcine follicles was conducted using NovaSeq600 sequencing platform. The DEGs were identified using DESeq2 with threshold of padj <0.05 and log2 Fold Change cut off 0.58. Functional annotations and bioinformatics analysis of the DEGs were performed to find out biological functions, signalling pathways and hub genes regulating follicular development and function.

overall_design: Differential  gene expression profiling analysis of RNA-seq data for Large follicle (3) and Small follicle (2)

first: Satish

last: Kumar

first: N

middle: H

last: Mohan

first: Bikash

last: Das

first: Vivek

last: Gupta


title: Functional Involvement of Septal miR-132 in Extinction and Oxytocin-mediated Reversal of Social Fear

city: Regensburg

first: Uwe

last: Schwartz

address: Universitätstraße 32

department: NGS Analysis Center

institute: University of Regensburg

summary: Social interactions are critical components for the survival of mammalian biology and evolution. Dysregulation of social behavior often leads to psychopathologies such as social anxiety disorder, which is characterized by an intense fear and avoidance of social situations. Using the social fear conditioning (SFC) paradigm, we analyzed expression levels of miR-132-3p and miR-124-3p within the septum, a brain region essential for social behavior and fear, after acquisition and extinction of social fear. Functional in vivo approaches using pharmacology, functional inhibition of miR-132-3p, viral miR-132 overexpression and shRNA-mediated knockdown of miR-132-3p within oxytocin receptor positive neurons confirmed septal miR-132-3p to be involved in social fear extinction and the oxytocin-mediated reversal of social fear. Moreover, Argonaute-RNA-co-immunoprecipitation-microarray analysis and further target mRNA quantification, depicted growth differentiation factor-5 (GDF-5) to be involved in miR-132-3p-mediated regulation of social fear extinction. Local application of GDF-5 resulted in impaired social fear extinction, an effect which seems to be mediated by miR-132-3p. In summary, we show that septal miR-132-3p is functionally involved in social fear extinction learning and oxytocin-mediated reversal of social fear.

overall_design: Septal Ago2 was pulled down by means of Argonaute-co-immunoprecipitation (6F4). To determine a target of miR-132-3p, miR-132-3p inhibitor (Inh) or scrambled LNA (Scr) was infused into the septum of male mice and tissue was punched 2 days thereafter. IPs were performed in duplicates and for each condition one Input sample was analysed.

first: Anna

last: Bludau

first: Daniela

last: Zeitler

first: Gunter

last: Meister

first: Inga

last: Neumann


title: Gene expression analysis of the skeletal muscles of a mouse model of spinal and bulbar muscular atrophy (SBMA) with or without exercise

city: Nagoya

first: Tomoki

last: Hirunagi

state: Aichi

address: 65 Tsurumai-cho, Showa-ku

department: Neurology

institute: Nagoya University GraduateSchool of Medicine

summary: To investigate the molecular pathway underlying the effect of exercise, we performed microarray gene expression analysis of the quadriceps of transgenic mice carrying full-length human androgen receptor (AR) with 97 CAGs (AR97Q) at 9 weeks of age with or without exercise. Exercise was started from 5 weeks of age and maintained for 4 weeks.

overall_design: Male AR97Q mice were examined at 9 weeks of age for each group (sedentary or exercise). Total RNA was isolated from the quadriceps of three mice in each group.

first: Hideaki

last: Nakatsuji

first: Masahisa

last: Katsuno


title: Distinct disease mutations in DNMT3A result in a spectrum of behavioral, epigenetic, and transcriptional disruptions

city: St. Louis

first: Diana

middle: Christian

last: Beard

state: Missouri

address: 660 S. Euclid Ave.

department: Neuroscience

institute: Washington University in St. Louis

summary: Phenotypic heterogeneity in monogenic neurodevelopmental disorders can arise from differential severity of variants underlying disease, but how distinct alleles drive variable disease presentation is not well understood. Here, we investigate missense mutations in DNMT3A, a DNA methyltransferase associated with overgrowth, intellectual disability, and autism, to uncover molecular correlates of phenotypic heterogeneity. We generate a DNMT3A P900L/+ mouse mimicking a mutation with mild-to-moderate severity, and compare phenotypic and epigenomic effects with a severe R878H mutation. P900L mutants exhibit core growth and behavioral phenotypes shared across models but show subtle epigenomic changes, while R878H mutants display extensive disruptions. We identify mutation-specific dysregulated genes which may contribute to variable disease severity. Shared transcriptomic disruption identified across mutations overlaps dysregulation observed in other developmental disorder models and likely drives common phenotypes. Together, our findings define central drivers of DNMT3A disorders and illustrate how variable epigenomic disruption contributes to phenotypic heterogeneity in neurodevelopmental disease.

overall_design:
Low and Hi-depth whole genome bisulfite sequencing (WGBS) of mouse cerebral cortex from 8-week WT and DNMT3A mutant mice

Low-depth whole genome bisulfite sequencing (WGBS) of mouse brain region tissue from 8-week WT and DNMT3A mutant mice

Chromatin immunoprecipitation DNA sequencing (ChIP-seq) for histone modification H3K27ac in 8-week wildtype and DNMT3A mutant mouse cerebral cortex

Comparative gene expression profiling analysis of total RNA-seq data from 8-week WT and DNMT3A mutant mouse cerebral cortex

Chromatin immunoprecipitation DNA sequencing (ChIP-seq) for MeCP2 in 8-week wildtype and DNMT3A mutant mouse cerebral cortex

first: Dennis

last: Wu

first: Nicole

last: Hamagami

first: Alyssa

last: Erickson

first: Harrison

middle: W

last: Gabel


title: Protection of mouse by blockade to TNF-α signaling is due to inhibition against IL-17A

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

summary: We have previously reported that the dengue virus (DENV) type 3 P12/08 strain caused a lethal systemic infection, severe vascular leakage at terminal stage in IFN-α/β and γ receptors knockout mice (IFN-α/β/γRKO mice), and blockade of TNF-α signaling drastically protected mice. However, the detailed pathological mechanism remains unknown. Therefore, we performed transcriptome analysis of liver and intestinal specimens, which showed most clearly exhibited vascular leakage, chronologically collected from infected- IFN-α/β/γRKO mice with/without anti-TNF-α Ab treatment.

overall_design: We applied mouse microarray to profile global gene expression of liver and small intestine of four mouse groups, DENV-3 P12/08 infected mouse Day 3 and 4 p.i. with or without anti-TNF-α Ab treatment, and mock-infected mice.

first: Takeshi

last: Kurosu


title: Deciphering the regulatory network of the NAC transcription factor FvRIF, a master regulator in controlling strawberry fruit ripening

first: Xiaojing

last: Li

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

overall_design: Refer to individual Series


title: Transcriptomic profiling of mouse amygdala during opioid dependence and withdrawal by single-cell RNA sequencing

city: Miami

first: Sabita

last: Roy

state: Florida

address: 1501 NW 10th Ave

department: Surgery

institute: University of Miami

summary: The development of substance use disorder (SUD) is a complex process involving multiple neurocircuitries and brain regions. The amygdala is a region that mediates the withdrawal effect as well as anxiety and depression-like behaviors. However, the transcriptional changes in each cell type during SUD is largely unknown. Here we performed single-cell RNA sequencing and classified all cell types in the mouse amygdala under opioid dependence and withdrawal states. Our data revealed distinct changes in key biological processes, such as immune response, inflammation, synaptic transmission, and mitochondrial respiration in different cell populations. Dramatic differences were unraveled in the transcriptional profiles between dependence and withdrawal states. This report is the first single-cell RNA sequencing dataset from the amygdala under opioid dependence and withdrawal conditions, providing unique insights in understanding brain alterations during SUD, especially at the molecular and cellular levels.

overall_design: Amygdala was dissected from naïve mice, opioid dependent and withdrawal mice. Total of 9 samples were analyzed with scRNA sequencing.

first: Yan

last: Yan

first: Bridget

last: Herlihy

first: Sean

last: Boyles

first: Junyi

last: Tao

first: William

last: Hulme


title: Features and protective efficacy of human monoclonal antibodies targeting M. tuberculosis arabinomannan

city: Bronx

first: Jacqueline

middle: M.

last: Achkar

address: 1300 Morris Park Avenue

institute: Albert Einstein College of Medicine

summary:
Human antibody responses to AM/LAM are heterogenous and knowledge of reactivity to specific glycan epitopes at the monoclonal level is limited.
Using novel glycan arrays, we characterized a very high affinity monoclonal antibody P1AM25 to AM/LAM, determined this mAb recognized distinct glycan epitopes from other anti-AM/LAM mAbs reported.

overall_design: Monoclonal antibodies at 5 ug/ml were tested for direct binding to 61 synthetic oligosaccharides

first: Yanyan

last: Liu

first: Tingting

last: Chen

first: Todd

middle: L

last: Lowary


title: Mediator Subunit 30 Directs Myc Oncogenesis [PRO-seq]

first: Guofeng

last: Zhao

overall_design: To investage the effect of med30 overespression on transcription, PRO-seq was performed in teton MED30 overexpression Mia PaCa-2 cells. Dox-induced MED30 expression Mia PaCa-2 stable cell line were treated or untreated with 0.5μg/ml doxycycline for 2 days before nuclei isolation. 1/50 number of drosophila S2 cells were spike-in for overall input control.

first: Chunyu

last: Jin

first: Soohwan

last: Oh

first: Wei

last: Yuan

first: Michael

last: Rosenfeld


title: EMT-associated network collapse induced by YWHAG deficiency leads to oxidative cell death and prevents metastasis.

city: Singapore

first: Nguan Soon

last: Tan

address: 11 Mandalay Rd

institute: Lee Kong Chian School of Medicine

summary: Transcriptomics of MKN74 and MKN74YWHAG cells undergoing EMT.

overall_design: Inducing EMT with DMOG and TGFβ in MKN74 and MKN74YWHAG cells

first: Jeannie

middle: X

last: LEE

first: Nguan

middle: S


title: The Enterotoxigenic Bacteroides fragilis (ETBF) in intestinal inflammation and colorectal carcinogenesis [whole cell RNA]

city: Shanghai

first: Haoyan

state: Shanghai

address: 145 Shandong Road

institute: Renji Hospital

summary: To elucidate whether  Enterotoxigenic Bacteroides fragilis (ETBF) plays a role in  intestinal inflammation and colorectal carcinogenesis, a RNA-seq analysis was performed to compare the microRNA profiles of  ETBF treated HCT116 colorectal cancer cell lines.

overall_design: miRNA-seq was performed in HCT116 colorectal cancer cells after ETBF treatment.

first: Yingying

last: Cao