title: C-terminal Mutations in RUNX1 Induce Differentiation Block and Alter Transcription through Changes in Enhancer-Promoter Interactions [GRID-Seq]

city: La Jolla

first: Dong-Er

state: California

address: 3855 Health Sciences Dr

department: Pathology

institute: University of California, San Diego

summary: The hematopoietic master regulator RUNX1 is frequently mutated in myeloid and lymphoid malignancies. Analyses of RUNX1 mutations across hematopoietic tissues revealed frequent mutations outside of the N-terminal DNA binding domain. The vast majority of these C-terminal mutations were found to be nonsense and frameshifts resulting in truncated protein products predicted to escape nonsense mediated decay pathways. We modeled this class of truncation mutation using the pathogenic RUNX1 R320* mutation found in both germline and sporadic hematological disease. Homozygous knock-in of RUNX1 R320* in K562 leukemia cells resulted in a megakaryocytic differentiation block and DNA damage sensitivity phenotypes. Gene expression analysis demonstrated that RUNX1 R320* dysregulated unique gene sets when compared to RUNX1 knockdown in addition to shared genes related to megakaryocyte and platelet function. DNA binding across the genome was examined between RUNX1 wild-type and RUNX1 R320* through ChIP-seq, revealing that RUNX1 R320* differential binding was most enriched at enhancer regions. To detect RUNX1 R320* dysregulated enhancer-promoter (E-P) connections we performed GRID-seq and uncovered extensive remodeling of E-P interactions genome-wide in RUNX1 R320* cells. Furthermore, we uncovered a novel role for FOXK2 at RUNX1 regulated enhancers. Analysis of the well-studied MYC enhancer region demonstrated cooperation between RUNX1 R320* and FOXK2 at hematopoietic MYC enhancers NDME and BENC resulting in the significant upregulation of the MYC oncogene. In conclusion, the truncation of RUNX1 results in impaired megakaryocytic differentiation, unique transcriptional alterations, and remodeling of enhancer-promoter connections in cooperation with FOXK2, together contributing to leukemogenesis.

overall_design: To investigate the changes in enhancer-promoter connections (GRID-seq) between RUNX1 wild-type and RUNX1 R320* K562 cells.


title: UPF1 ATPase autoinhibition and activation modulate RNA binding kinetics and NMD efficiency 2

status: Public on May 29 2024

city: Bethesda

first: J. Robert

last: Hogg

state: MD

address: 50 South Drive, Room 2341

department: Biochemistry and Biophysics Center

country: USA

institute: National Heart, Lung, and Blood Institute

type: Expression profiling by high throughput sequencing

summary: The RNA helicase UPF1 interacts with mRNAs, mRNA decay machinery, and the terminating ribosome to promote nonsense-mediated mRNA decay (NMD). Structural and biochemical data have revealed that UPF1 exists in an enzymatically autoinhibited “closed” state. Upon binding the NMD protein UPF2, UPF1 undergoes an extensive conformational change into a more enzymatically active “open” state, which exhibits enhanced ATPase and helicase activity. However, mechanically deficient UPF1 mutants can support efficient NMD, bringing into question the roles of UPF1 enzymatic autoinhibition and activation in NMD. Here, we identify two additional important features of the activated open state: slower nucleic acid binding kinetics and enhanced ATP-stimulated nucleic acid dissociation kinetics. Computational modeling based on empirical measurements of UPF1, UPF2, and RNA interaction kinetics predicts that the majority of UPF1-RNA binding and dissociation events in cells occur independently of UPF2 binding. We find that UPF1 mutants with either reduced or accelerated dissociation from RNA have NMD defects, whereas UPF1 mutants that are more dependent on UPF2 for catalytic activity remain active on well-established NMD targets. These findings support a model in which the kinetics of UPF1-mRNA interactions are important determinants of cellular NMD efficiency.

overall_design: Paired-end high-throughput RNA sequencing of rRNA depleted RNA from triplicate biological replicates of Flp-In 293 T-REx  cell lines stably expressing a CLIP-tagged UPF1 mutant transfected with non-targeting control siRNA or siRNA against endogenous UPF1. Cells were reverse-transfected with the indicated siRNAs and harvested 72 hrs post-transfection.

first: Joseph

middle: H

last: Chapman

first: J

middle: R


title: Respiratory Syncytial virus (RSV) directly binds host microRNAs and de-regulates host gene targets [miRNA-seq]

city: Edinburgh

first: José

middle: Roberto

last: Bermúdez-Barrientos

state: Lothian

address: Charlotte Auerbach Rd

department: Institute of Immunology & Infection

country: United Kingdom

institute: The University of Edinburgh

type: Non-coding RNA profiling by high throughput sequencing

summary:
To investigate how RSV affects miRNA expression, we performed small RNA-seq at of 48 hrs of viral infection
We also compared polyphosphatase-treated samples to non-polyphosphatase-treated samples to identify tri-phosphorylated small RNAs

overall_design: small RNA-seq data of A549 cells infected with RSV or mock-treated after 48 of infection

first: Sarah

last: Ressel

first: Sujai

last: Kumar

first: Jose

last: Bermudez-Barrientos

first: Katrina

last: Gordon

first: Julia

last: Lane

first: Jin

last: Wu

first: Cei

last: Abreu-Goodger

first: Amy

last: Buck


title: Nuclear Acly protects liver from ischemia-reperfusion injury

city: Ann Arbor

first: Wenbin

last: Gao

state: MI

address: NCRC 2800 Plymouth

institute: University of Michigan

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We examine the RNA profile of WT and Alb-cre:Aclyf/f liver in both Sham and IR condition. We also analyze the changes of Acly, H3K27ac, and H3K9ac level in primary hepatocytes in normoxia and HR condition.

overall_design: For RNA seq, mouse liver from WT and Alb-cre:Aclyf/f mice were subjected to Sham or IR surgery. After 24 hours, liver tissue from broader zone were collected for RNA-seq analysis. For Cut-Run seq, primary hepatocytes were isolated from WT and Alb-cre:Aclyf/f mice, after 24 hours, primary hepatocytes were then cultured in normaixa and hypoxia-reperfusion condition. The hepatocytes were then collected for Cut&run assay using CST cut&run assay kit.

first: Wei-zhen

last: Zhang


title: C-terminal Mutations in RUNX1 Induce Differentiation Block and Alter Transcription through Changes in Enhancer-Promoter Interactions [ChIP-Seq]

overall_design: To investigate the differential binding (ChIP-seq) between RUNX1 wild-type and RUNX1 R320* K562 cells.


title: Effect of BMN/PAZA combination therapy on lung cancer cells

city: Pittsburgh

first: Zhangyi

last: Luo

state: PA

address: 4041 Bigelow Blvd, Apt 112

institute: University of Pittsburgh

summary: To investigate the BMN/PAZA combination in DNA repair and epigenetic regulation. Dose effect is considered.

overall_design: Comparative gene expression profiling analysis of RNA-seq data LLC cell with various treatment based on BMN/PAZA

first: Song

last: Li

first: Jingjing

last: Sun


title: LINE-associated cryptic splicing induces dsRNA-mediated interferon response and tumor immunity

city: Houston

first: Chonghui

last: Cheng

state: TX

address: 1 Baylor Plaza

department: Breast Center

institute: Baylor College of Medicine

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

overall_design: Refer to individual Series


title: LINE-associated cryptic splicing induces dsRNA-mediated interferon response and tumor immunity [iCLIP]

summary: RNA splicing plays a critical role in post-transcriptional gene regulation. Exponential expansion of intron length poses a challenge for accurate splicing. Little is known about how cells prevent inadvertent and often deleterious expression of intronic elements due to cryptic splicing. In this study, we identify hnRNPM as an essential RNA binding protein that suppresses cryptic splicing through binding to deep introns, preserving transcriptome integrity. Long interspersed nuclear elements (LINEs) harbor large amounts of pseudo splice sites in introns. hnRNPM preferentially binds at intronic LINEs and represses LINE-containing pseudo splice site usage for cryptic splicing. Remarkably, a subgroup of the cryptic exons can form long dsRNAs through base-pairing of inverted Alu transposable elements scattered in between LINEs and trigger interferon immune response, a well-known antiviral defense mechanism. Notably, these interferon-associated pathways are found to be upregulated in hnRNPM-deficient tumors, which also exhibit elevated immune cell infiltration. These findings unveil hnRNPM as a guardian of transcriptome integrity. Targeting hnRNPM in tumors may be used to trigger an inflammatory immune response thereby boosting cancer surveillance.

overall_design: Extraction and calling of significant peaks representing hnRNPM binding across human genome in HMLE cells

first: Ryan

middle: A

last: Flynn

first: Samuel

middle: E

last: Harvey


title: Identification of LC3B's binding mRNAs through a n-RIP-seq

city: Suwon-si

first: Ho Chul

last: Kang

state: Gyeonggi-do

address: World cup-ro, Yeongtong-gu

department: Physiology

country: South Korea

institute: Ajou university school of medicine

summary: To identify RNAs that bind to LC3B, we employed n-RIP-seq. After obtaining the nRIP-seq data and applying a rigorous threshold for peak calling, we detected 5,285 significant peaks associated with LC3B. The coverage analysis revealed a mean coverage of 99% for LC3B-associated peaks, suggesting widespread binding throughout the transcriptome

overall_design: U2OS cells were subjected in to n-RIP seq sing a LC3 Ab. Ig-G was used as negative control.

first: Yiseul

last: Hwang

first: Junghyun

last: Yoon

first: Hansol

last: Yun

first: Ho

middle: C


title: BMI1 dynamic balance destroy blunts immunotherapy efficacy in HCC

city: Hang Zhou

last: Xu

address: Huansha Roud

country: China

institute: Zhejiang University

summary:
m6A-binding RNAs were analyzed by imprinting RNA-sequencing of anti-m6A antibody-retrieved complexes from primary T cells.
We then performed gene expression profiling analysis using data obtained from RIP-seq of primary T cells treated with PTC

overall_design: Examination of m6A-binding RNA from primary T cells

first: Shuai

last: Wang


title: mRNA Location and Translation Rate Determine Protein Targeting to Dual Destinations

first: Nicholas

last: Guydosh

address: 8 Center Dr, Bldg 8, 220

department: NIDDK

institute: National Institutes of Health

summary: Numerous proteins are targeted to two or multiple subcellular destinations where they exert distinct functional consequences. The balance between such differential targeting is thought to be determined post-translationally, relying on protein sorting mechanisms. Here, we show that protein targeting can additionally be determined by mRNA location and translation rate. Our model, the NET1 protein, distributes between the nucleus and cytosol and functions in cell motility. N-terminal NLSs and an internal PH domain competitively determine NET1 distribution. Peripheral localization of the NET1 mRNA and fast translation lead to higher cytosolic retention through the PH domain. By contrast, perinuclear mRNA location and/or slower translation rate favor nuclear targeting through importin β1. NET1 mRNA location is modulated by physiological stimuli and profoundly impacts NET1 function in cell motility. Indeed, perinuclear NET1 mRNA localization causes reduced RhoA activity, impedes focal adhesion maturation and results in slower cell migration to an extent similar as that observed upon knockdown of NET1 expression. Overall, these results reveal that the location of protein synthesis and the rate of translation elongation act in coordination to influence the ability of competing domains within a polypeptide to determine protein distribution and function.

overall_design: Ribosome and disome profiling were performed to identify sites of ribosome stalling and collisions on the NET1 mRNA.

first: Sezen

last: Meydan


title: Follicular lymphoma regulatory T cell origin and function

city: Rennes

first: Stephane

last: Rodriguez

state: France

address: 2, Av Pr. Leon Bernard

country: France

institute: INSERM

summary: GeneChip Human Transcriptome Array 2.0 of sorted T cells from human tonsils or follicular lymphoma

overall_design: We analyzed sorted Naive CD4, Memory CD4, Tfh, Treg from 3 human tonsils and Naive CD4, Memory CD4, Tfh, Tfr from 3 human follicular lymphoma. CDNA were hybridized on GeneChip Human Transcriptome Array 2.0. CEL files were processed with Affymetrix Expression Console software 1.3.1 using RMA and default settings.

first: Stéphane

first: Mehdi

last: Alizadeh

first: Claire

last: Lamaison

first: Alexis

last: Saintamand

first: Céline

last: Monvoisin

first: Rachel

last: Jean

first: Laurent

last: Deleurme

first: Inaki

last: Martin-Subero

last: Pangault

first: Karin

last: Tarte

first: Patricia

last: Amé-Thomas


title: Epigenetic checkpoint regulates anti-tumor immunity of CD4 T cell in Hepatocellular carcinoma II

summary:
To investigated how CD4 T cells change in the development of hepatocelluar carcinoma
We then performed gene expression profiling analysis using data obtained from RNA-seq of CD4 T cells

overall_design: Comparative gene expression profiling analysis of RNA-seq data for CD4 T cells sorted from tumor of mice hepatocellular carcinoma orthotopic transplantation model.


title: Expression data from wild type and Pten mutant mammary fibroblasts

city: Charleston

first: Michael

last: Ostrowski

state: SC

address: 86 Jonathan Lucas street

department: Biochemistry and Molecular Biology

institute: Medical University of South Carolina

summary:
The PtenF341V allele, which fails to suppress the PI3K-AKT pathway was used to dissect the PTEN activity required for mammary development as well as, to suppress mammary tumorigenesis from the stromal fibroblast compartment.
Genes differentially expressed in  PtenF341V   MMFs exhibit a expression pattern similar to wild type MMFs than Pten null MMFs and are not enriched in human breast cancer stroma.

overall_design: Mammary fibroblasts from PtenF341V, wild type and Pten null mice were used to extract total RNA and the gene expression analysis performed using microarray

first: Sudarshana

middle: M

last: Sharma


title: LINE-associated cryptic splicing induces dsRNA-mediated interferon response and tumor immunity [RNA-seq]

first: Chonghui

last: Cheng

overall_design: Comparative gene expression profiling and splicing landscape analyses from RNA-seq data for control vs. hnRNPM knockdown in multiple cell lines

first: Rong

last: Zheng

first: Samuel

last: Harvey


title: Effect of depletion of IDE on gene expression in adult pancreatic islets during a metabolic stress

city: Paris

first: François-Xavier

last: MAUVAIS

address: 160 rue de Vaugirard

summary: To investigate the role of IDE in the regulation of stress response in the pancreatic islets, we fed Ide-/- and Ide+/+  C57BL/6 adult mice with a high-fat diet.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for pancreatic islets from Ide-/- and Ide+/+ C57BL/6J female fed for 2 weeks with a high-fat diet starting from 10 weeks of age

first: Emmanuelle

last: Waeckel-Enée

last: Mauvais

first: Peter

last: van Endert


title: Genome-wide enrichment of YAP and TEAD1 stimulated by lactate

city: shanghai

first: junyi

last: ju

address: 301 middle yanchang road

institute: Shanghai Tenth People’s Hospital

summary: The goal of this study is to find out the genome-wide occupancy of YAP and TEAD1 under lactate stimulation.

overall_design: 293FT cells were transfected with HA-YAP and Flag-TEAD1 and cultured in glucose-free DMEM supplemented with 25mM lactate. 24h after lactate treatment, cells were collected for ChIP-seq analysis using HA and Flag antibodies.

first: Junyi

last: Ju

first: Shi

last: Jiao

first: Liwei

last: An


title: Transcriptomes analyses of AARS1 knockdown HGC-27 cells treated with lactate

summary: To investigat the role of AARS1 in HGC27 cells treated with lactate, we transfected HGC27 cells with AARS1 siRNA and then treated the cells with 25mM lactate for 24h

overall_design: Total RNA was extracted from control and AARS1 knockdown HGC27 cells cultured in glucose-free medium with exogenous 25mM lactate in duplicate and then sent for transcriptomes analysis.

first: Yang

last: Tang


title: Transcriptomes analyses of gastric cancer HGC-27 cell line treated with lactate

summary: Lactate is a major metabolite of tumor cell as a result of Warburg effect. Yet it remains elusive whether and how intracellular lactate may ever drive tumor cell proliferation. To investigat the role of lactate in proliferating cancer cells, we treated HGC27 cells with lactate and then sent for RNA-sequencing analysis.

overall_design: Total RNA was extracted from HGC27 cells cultured in glucose-free medium with or without exogenous 25mM lactate in duplicate and then sent for transcriptomes analysis.


title: Epstein-Barr virus protein EBNA-LP engages YY1 through leucine-rich motifs to promote naïve B cell transformation

status: Public on May 28 2024

city: Durham

first: Jana

last: Cable

state: NC

address: 213 Research Dr.

department: Molecular Genetics and Microbiology

institute: Duke University

summary: Epstein-Barr Virus (EBV) is associated with numerous cancers including B cell lymphomas. In vitro, EBV transforms primary B cells into immortalized Lymphoblastoid Cell Lines (LCLs) which serves as a model to study the role of viral proteins in EBV malignancies. EBV induced cellular transformation is driven by viral proteins including EBV-Nuclear Antigens (EBNAs). EBNA-LP is important for the transformation of naïve but not memory B cells. While EBNA-LP was thought to promote gene activation by EBNA2, EBNA-LP Knock Out (LPKO) virus-infected cells express EBNA2-activated cellular genes efficiently. Therefore, a gap in knowledge exists as to what roles EBNA-LP plays in naïve B cell transformation. We developed a trans-complementation assay wherein transfection with wild-type EBNA-LP rescues the transformation of peripheral blood- and cord blood-derived naïve B cells by LPKO virus. Despite EBNA-LP phosphorylation sites being important in EBNA2 co-activation; neither phospho-mutant nor phospho-mimetic EBNA-LP was defective in rescuing naïve B cell outgrowth. However, we identified conserved leucine-rich motifs in EBNA-LP that were required for transformation of adult naïve and cord blood B cells. Because cellular PPAR-g coactivator (PGC) proteins use leucine-rich motifs to engage transcription factors including YY1, a key regulator of DNA looping and metabolism, we examined the role of EBNA-LP in engaging cellular transcription factors. We found a significant overlap between EBNA-LP and YY1 in ChIP-Seq data. By Cut&Run, YY1 peaks unique to WT compared to LPKO LCLs occur at more highly expressed genes.  Moreover, Cas9 knockout of YY1 in primary B cells prior to EBV infection indicted YY1 to be essential for EBV-mediated transformation. We confirmed EBNA-LP and YY1and confirmed their biochemical association in LCLs by endogenous co-immunoprecipitation and. Moreover, we found that the EBNA-LP leucine-rich motifs were required for YY1 interaction in LCLs. Finally, we used Cas9 to knockout YY1 in primary total B cells and naïve B cells prior to EBV infection and found YY1 to be essential for EBV-mediated transformation. We propose that EBNA-LP engages YY1 through conserved leucine-rich motifs to promote EBV transformation of naïve B cells.

overall_design: To investigate the role of EBNA-LP in modulating the association of YY1 with chromatin in LCLs, Cut&Run was performed in WT and LPKO LCLs

first: Nicolas

last: Reinoso-Vizcaino

first: Robert

last: White

first: Micah

last: Luftig


title: C-terminal Mutations in RUNX1 Induce Differentiation Block and Alter Transcription through Changes in Enhancer-Promoter Interactions [RNA-Seq]

first: Dong-Er

last: Zhang

summary: The hematopoietic master regulator RUNX1 is frequently mutated in myeloid and lymphoid malignancies. Analyses of RUNX1 mutations across hematopoietic tissues revealed frequent mutations outside of the N-terminal DNA binding domain. The vast majority of these C-terminal mutations were found to be nonsense and frameshifts resulting in truncated protein products predicted to escape nonsense mediated decay pathways. We modeled this class of truncation mutation using the pathogenic RUNX1 R320* mutation found in both germline and sporadic hematological disease. Homozygous knock-in of RUNX1 R320* in K562 leukemia cells resulted in a megakaryocytic differentiation block and DNA damage sensitivity phenotypes. Gene expression analysis demonstrated that RUNX1 R320* dysregulated unique gene sets when compared to RUNX1 knockdown in addition to shared genes related to megakaryocyte and platelet function. DNA binding across the genome was examined between RUNX1 wild-type and RUNX1 R320* through ChIP-seq, revealing that RUNX1 R320* differential binding was most enriched at enhancer regions. To detect RUNX1 R320* dysregulated enhancer-promoter (E-P) connections we performed GRID-seq and uncovered extensive remodeling of E-P interactions genome-wide in RUNX1 R320* cells. Furthermore, we uncovered a novel role for FOXK2 at RUNX1 regulated enhancers. Analysis of the well-studied MYC enhancer region demonstrated cooperation between RUNX1 R320* and FOXK2 at hematopoietic MYC enhancers NDME and BENC resulting in the significant upregulation of the MYC oncogene. In conclusion, the truncation of RUNX1 results in impaired megakaryocytic differentiation, unique transcriptional alterations, and remodeling of enhancer-promoter connections in cooperation with FOXK2, together contributing to leukemogenesis.

overall_design: To investigate the transcriptional differences between RUNX1 wild-type and RUNX1 R320* K562 cells.


title: RNA sequencing for the toyocamycin- or vehicle-treated ILC2s in vitro

city: Jinan

first: Jing

last: Shen

address: Wenhua West Road 44

institute: Shandong University

summary: RNA sequencing was performed for the toyocamycin- or vehicle-treated ILC2s sorted from the large intestine of C57BL/6 mice (n = 3 per group).

overall_design: Sorted large intestinal ILC2s from C57BL/6 mice were cultured in complete IMDM media containing IL-2 (10 ng/mL), IL-7 (10 ng/mL), IL-25 (10 ng/mL), and IL-33 (10 ng/mL) for 5 days, followed by treatment with toyocamycin for 16 hours. The toyocamycin- or vehicle-treated ILC2s were harvested by centrifugation and lysed for RNA extraction.

first: Yanyan

last: Cui

first: Yatai

last: Chen

first: Detian

last: Yuan

first: Shiyang

last: Li


title: Modified CLEAR-CLIP reveals sequestration of miRNAs by Respiratory syncytial virus and functional nuclear targets of miR-27

first: José

last: Bermúdez-Barrientos

summary: To investigate miRNA-target networks in RSV infection we generated CLEAR-CLIP libraries in Mock and RSV-infected A549 cells

overall_design: CLEAR-CLIP data of A549 cells infected with RSV or mock-treated

first: Sarah

last: Ressel

first: Sujai

last: Kumar

first: Jose

last: Roberto Bermudez-Barrientos

first: Katrina

last: Gordon

first: Julia

last: Lane

first: Jin

last: Wu

first: Cei

last: Abreu-Goodger

first: Amy

last: Buck


title: Respiratory Syncytial virus (RSV)

overall_design: Refer to individual Series


title: Respiratory Syncytial virus (RSV) directly binds host microRNAs to de-regulate host gene targets [RNA-seq miR-27 over-expression]

summary:
To validate miR-27 mRNA targets, we generated miR-27 overexpressing cell lines using the shMIMIC lentiviral transduction system (Dharmacon)
In addition, we transfected miR-27 miRNA mimics and inhibitors to overexpress and inhibit the miRNA and performed total RNAseq

overall_design: RNA-seq data of A549 cells, WT and miR-27 overexpressing (shMIMIC) lines, as well as mimic and inhibitor transfected cells

last: Bermudez-Barrientos


title: FACT orchestrates the interplay between chromatin structure and transcription

status: Public on May 30 2024

city: Goettingen

first: Abrar

last: Aljahani

address: Am Fassberg 11

country: Germany

institute: Max Planck Institute for Multidisciplinary Sciences

summary: FACT has been identified as a histone chaperone that enables transcription through chromatin in vitro, but its role in regulating chromatin structure and transcription in vivo remains unclear. In this study, we have investigated the function and molecular mechanism of FACT in unprecedented detail, by using a rapid depletion system in combination with high-resolution genomic analyses. We show that acute depletion of FACT leads to changes in 3D chromatin structure and a concomitant multilayered transcriptional defect, including loss of promoter-proximal pausing, deregulated elongation and increased drop-off of RNA Pol II. Integration of in vitro transcription assays shows that FACT stimulates RNA Pol II pausing by stabilizing nucleosomal architecture, while simultaneously promoting transcription through the +1 nucleosome. In addition to providing detailed mechanistic insight into the seemingly contradictory functions of FACT and the regulation of promoter-proximal pausing, our study indicates a direct coupling of chromatin structure and transcription.

overall_design: Tiled-Micro-Capture-C (Tiled-MCC). Details are described in the Methods section of the paper.

first: A

last: Oudelaar


title: Identification of hypoxia-induced isoforms and novel genes with nanopore long reads sequencing

city: guangzhou

first: shengqi

last: shen

address: zhongshan road #104

institute: GDPH

summary: Long-read nanopore sequencing is capable of continuously reading thousands of base pairs. Here, we report the application of nanopore sequencing technology for analysing hypoxia-specific transcriptomes in normal liver and liver cancer cell lines, which help us to better understand the mechanism of cell survival and metastasis under hypoxia. We conducted transcriptomic sequencing of normal liver and liver cancer cell lines under normoxia or hypoxia, founding that long-read sequencing could detect thousands of hypoxia-specific isoforms and unannotated novel genes. At the cellular level, we have verified that the novel gene 644 is most up-regulated novel gene under hypoxic conditions. We observed that the novel gene 644 possesses classical mRNA characteristics, with its CDS region encoding 91 amino acids. Through protein structure predictions, we discovered that the novel gene 644 contains a transmembrane domain. Experimental validation confirmed that the novel gene 644 is a membrane protein, and knockdown of the novel gene 644 significantly suppresses the proliferative capacity of liver cancer cells under hypoxic conditions. Furthermore, we revealed the protein structure alteration of hypoxia specific isoforms with molecular dynamics simulation. The results indicate that our hypoxic dataset can serve as a foundation for the structural simulation of hypoxic-specific proteins. In summary, we have presented a hypoxic-specific third-generation sequencing dataset for further analysis, which provides sufficient details on cellular transcriptomes and is particularly valuable for understanding the survival and metastasis of tumor under hypoxic conditions. From this dataset, we have validated the importance of novel gene 644 for tumor survival under hypoxia and identified alterations in hypoxic-specific protein structures. These discoveries can bring us new knowledge about hypoxia, leading to the identification of potential tumor treatment targets and biomarkers.

overall_design: To figure out the influence of hypoxia on liver cancer cell with nanopore sequencing, we treated THLE-3 and Hep3B cell lines in 48 hours under normoxia or hypoxia and extracted mRNA for furthur nanopore sequencing.

first: Li

last: Gao

first: Shengqi

last: Shen


title: Glioblastoma disrupts cortical network activity at multiple spatial and temporal scales

first: Kwanha

last: Yu

address: One Baylor Plaza, BCM505

department: CAGT

summary: The emergence of glioblastoma in cortical tissue initiates early and persistent neural hyperexcitability with signs ranging from mild cognitive impairment to convulsive seizures. The influence of peritumoral synaptic density, expansion dynamics, and spatial contours of excess glutamate upon higher order neuronal network modularity is unknown. We combined cellular and widefield imaging of calcium and glutamate fluorescent reporters in two glioblastoma mouse models with distinct synaptic microenvironments and infiltration profiles. Functional metrics of neural ensembles are dysregulated during tumor invasion depending on the stage of malignant progression and tumor cell proximity. Neural activity is differentially modulated during periods of accelerated and inhibited tumor expansion. Abnormal glutamate accumulation precedes and outpaces the spatial extent of baseline neuronal calcium signaling, indicating these processes are uncoupled in tumor cortex. Distinctive excitability homeostasis patterns and functional connectivity of local and remote neuronal populations support the promise of precision genetic diagnosis and management of this devastating brain disease.

overall_design: Exam the contributions of GPC6 on gliomagenesis through a native mouse model of GBM

first: Jochen

last: Meyer

first: Benjamin

last: Deneen

first: Jeffrey

last: Noebels

first: Estefania

last: Luna-Figueroa


title: Treehouse compendium of ribosomal-depletion RNA-Seq gene expression data from 296 tumors

city: Santa Cruz

first: Olena

middle: Morozova

last: Vaske

state: CA

address: MCDB, Sinsheimer Labs, 1156 High Street

institute: UCSC

summary: We uniformly analyze sequence data to generate a resource for comparative gene expression studies. Specifically, we obtained access to primary RNA sequence data from repositories and clinical partners, consistently processed the data, harmonized metadata, and released the expression values and metadata without access restrictions

overall_design:
The data contains 296 consistently processed gene expression datasets from 7 studies.. Gene expression in each sample is uniformly quantified using the dockerized TOIL RNA-Seq pipeline versions from 3.2 to 3.4.1 (Vivian et al., 2017); all of these versions produce bitwise identical RSEM gene expression outputs. The pipeline uses RSEM Version 1.2.25 (Li and Dewey, 2011) for quantification after aligning reads with STAR v 2.3.2a (Dobin et al., 2013) using indices generated from the human reference genome GRCh38 and the human gene models GENCODE 23 as described at https://github.com/UCSC-Treehouse/pipelines. Quality is assessed with the MEND pipeline https://github.com/UCSC-Treehouse/mend_qc (Beale et al., 2021).
Data pocessing steps were as follows:

Adapters are removed with CutAdapt v1.9 (Martin, 2011)
Reads are  aligned by STAR v 2.4.2a using indices generated from the human reference genome GRCh38 and the human gene models Gencode 23 (Dobin et al., 2013)
RSEM 1.2.25 is used to quantify gene expression (Li and Dewey, 2011).
Gene level expression in TPM is log transformed: log2(TPM+1)
genome build: GRCh38
processed data files format and content: Gene level expression in TPM is log transformed: log2(TPM+1)

first: Holly

last: Beale

last: Learned

first: Ellen

last: Kephart

first: Sneha

last: Jariwala

first: Reyna

last: Antilla

first: Allison

last: Cheney

first: Alfred

middle: G

last: Lyle

first: Yvonne

last: Vasquez

first: Lauren

last: Sanders

first: David

last: Haussler

first: Sofie

last: Salama


title: Respiratory Syncytial virus (RSV) directly binds host microRNAs and de-regulates host gene targets [RNA-seq]

first: José

last: Bermúdez-Barrientos

address: Charlotte Auerbach Rd

summary:
To investigate RNA expression changes in RSV infection, we performed total RNA-seq from Mock and RSV-infected A549 cells
In addition, we investigated the association of RNAs with AGO2 by performing AGO2 immunoprecipitation and total RNA-seq of AGO2-bound RNAs in Mock and RSV-infected A549 cells

overall_design: RNA-seq data of A549 cells infected with RSV or mock-treated

first: Sarah

last: Ressel

first: Sujai

last: Kumar

first: Jose

last: Bermudez-Barrientos

first: Katrina

last: Gordon

first: Julia

last: Lane

first: Jin

last: Wu

first: Cei

last: Abreu-Goodger

first: Amy

last: Buck


title: Effects of chronic ingestion of soy peptide supplementation on gut microbial composition during juvenile social isolation

city: Shinagawa-ku

first: Hideki

last: Tamura

state: Tokyo

country: Japan

institute: Hoshi University

summary:
To investigate the effect of soy peptides on gut microial composition during juvenile social isolation, group-house (GH) and social isolation (SI) mice were fed a diet consisting of soy peptides or a control diet for 4 weeks post-weaning.
We then performed microbial community analysis using data obtained from bacterial 16S rRNA gene sequencing in the fecal samples of 4 mice groups (control diet-fed GH, soy peptide-diet fed GH, control diet-fed SI, and soy peptide-diet fed SI mice).

overall_design: Microbial composition profiling analysis of 16S rRNA-seq data for control diet-fed GH (GC), soy peptide-diet fed GH (GP), control diet-fed SI (SC), and soy peptide-diet fed SI (SP) mice.

first: Minoru

last: Narita


title: A NAD + Metabolic Checkpoint Regulates Hematopoietic Stem Cell Activation and Aging

city: Berkeley

first: Danica

last: Chen

address: 130 Hilgard Way,

department: NST

institute: UC Berkeley

summary: How hematopoietic stem cells (HSCs) maintain metabolic homeostasis to support tissue repair and regeneration throughout the lifespan is elusive. Here we show that CD38, a NAD+ metabolic enzyme, promotes HSC proliferation by inducing mitochondrial Ca2+ influx and mitochondrial metabolism at young age. Conversely, aberrant CD38 upregulation during aging is a driver of HSC deterioration due to compromised mitochondrial stress management. Pharmacological inactivation of CD38 reverses HSC aging and the pathophysiological changes of the aging hematopoietic system. Blocking mitochondrial Ca2+ influx inhibits HSC proliferation at young age yet prevents HSC aging. Our study highlights a NAD+ metabolic checkpoint that balances mitochondrial activation to support HSC proliferation and mitochondrial stress to enhance HSC self-renewal throughout the lifespan, and links aberrant Ca2+ signaling to HSC aging.

overall_design: To investigate the function of CD38 in regulating HSC fate decisions under homeostasis, ex vivo cytokine stimulation, and chronological aging, freshly isolated HSCs (Lin-ckit+scal1+) from 2-month-old or 24-month-old WT or CD38 KO mice were subjected to 3' Tag RNA sequencing directly or after ex vivo stimulation for 24 hours.


title: The roles of nuclear orphan receptor NR2F6 in anti-viral innate immunity

city: Wuhan

first: Chen-Yu

last: Wang

state: Hubei

address: 299 Bayi Road, Wuchang District

institute: Wuhan University

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


title: C-terminal Mutations in RUNX1 Induce Differentiation Block and Alter Transcription through Changes in Enhancer-Promoter Interactions

city: La Jolla

first: Dong-Er

last: Zhang

address: 3855 Health Sciences Dr

institute: University of California, San Diego


title: Effect of pituitary stalk electrical lesion (PEL) and growth hormone (GH) treatment on hypothalamic and hippocampal gene expression

first: guangsen

last: wu

address: 广东省广州市广州大道北1838号南方医科大学南方医院

institute: Southern Medical University Nanfang Hospital

summary: To investigate the effects of PEL and GH treatment on hypothalamic and hippocampal gene expression, we established a PEL model and administered GH treatment, and then we performed gene expression profiling using data obtained from RNA-seq of 12 different tissues at two time points

overall_design: Comparative gene expression profiling of RNA-seq data from sham mice, PEL mice and GH-treated mice.

first: Mingfeng

last: Zhou

first: Guangsen

first: Kai

last: Li


title: Differentially expressed genes affected by CSRNP1 overexpression in human-derived vaginal fibroblasts

status: Public on May 27 2024

city: Shenyang

first: Zhijun

last: Xia

address: 36 Sanhao Street

institute: Shengjing Hospital of China Medical University

summary: Pelvic organ prolapse (POP) is a group of diseases caused by extracellular matrix (ECM) degradation in the pelvic supportive tissues. Cysteine and serine rich nuclear protein 1 (CSRNP1) is involved in cell proliferation and survival regulation, and reportedly facilitates collagen breakdown in human chondrocytes. We here uncovered CSRNP1 as a key driver on collagen degradation in human-derived vaginal fibroblasts. Apoptosis of POP patient-derived vaginal fibroblasts was suppressed after knocking down CSRNP1. Silencing of CSRNP1 inhibited hydrogen peroxide (H2O2)-triggered apoptosis, ROS generation and collagen loss in normal vaginal fibroblasts. In line with this, CSRNP1 overexpression led to proliferation inhibition, apoptosis and collagen degradation in normal subject-derived vaginal fibroblasts. Silencing of CSRNP1 also reduced the expression of cell senescence markers p21 and γ-H2Ax (the histone H2Ax phosphorylated at Ser139), as well as curbed collagen breakdown in normal vaginal fibroblasts caused by a DNA damage agent etoposide. Transcriptomic analysis showed that differentially expressed genes affected by CSRNP1 overexpression in normal vaginal fibroblasts were mainly enriched in the Wnt signaling pathway, which was crucial for the onset and progression of POP. Silencing of CSRNP1 upregulated the expression of nuclear β-catenin and induced nuclear translocation of β-catenin in H2O2-induced normal vaginal fibroblast. Furthermore, collagen deposition caused by CSRNP1 knockdown was curbed after treatment with a Wnt pathway inhibitor DKK1. Our study indicates that the CSRNP1 may be involved in POP progression through the Wnt signaling, which provides a potential therapeutic strategy for POP.

overall_design: To investigate the effect and underlying mechanisms of CSRNP1 on collagen degradation in human-derived vaginal fibroblasts, we isolated vaginal fibroblasts from normal-derived anterior vaginal wall tissues in which CSRNP1 was highly expressed by lentivirus overexpression system. We then performed gene expression profiling analyses using data from mRNA-seq for vaginal fibroblasts of CSRNP1 overexpression versus controls.

first: Jing

last: Zhu

first: Hainan

last: Xu

first: Te

last: Lin


title: Disruption of BMI1 dynamic balance blunts immunotherapy efficacy in HCC

address: Huansha Roud

summary:
To investigated how BMI1 inhibitor (PTC) affected the function of primary T cells, we treated Tcells with PTC.
We then performed gene expression profiling analysis using data obtained from RNA-seq of peritoneal macrophages with PTC 209.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for treated with PTC or not.

first: Shuai


title: YAP1 and WWTR1 are required for murine pregnancy initiation

city: Grand Rapids

first: Genna

last: Moldovan

address: 400 Monroe Ave NW

department: Obstetrics, Gynecology and Reproductive Biology

institute: Michigan State University

summary: Endometrial stromal cell decidualization is required for pregnancy success. Although this process is integral to fertility, many of the intricate molecular mechanisms contributing to decidualization remain undefined. One pathway that has been implicated in endometrial stromal cell decidualization in humans in vitro, is the Hippo signaling pathway. Two previously conducted studies showed that the effectors of the Hippo signaling pathway, YAP1 and WWTR1, were required for decidualization of primary stromal cells in culture. To investigate the in vivo role of YAP1 and WWTR1 in decidualization and pregnancy initiation, we generated a Progesterone Cre mediated partial double knockout (pdKO) of Yap1 and Wwtr1. Female pdKOs exhibited subfertility, a compromised decidualization response, partial interruption in embryo transport, blunted endometrial receptivity, delayed implantation and subsequent embryonic development, and a unique transcriptional profile. Bulk mRNA sequencing revealed aberrant maternal remodeling evidenced by significant alterations in extracellular matrix proteins at 7.5 days post coitus in pdKO dams, and enrichment for terms associated with fertility compromising diseases like pre-eclampsia and endometriosis. Our results indicate a required role for YAP1 and WWTR1 for successful mammalian uterine function and pregnancy success.

overall_design:
To investigate the role of Yap1 and Wwtr1 in the murine female reproductive tract, we generated Progesterone Cre mediated knockout of one allele of Yap and two alleles of Wwtr1 (Pgr Cre/+ Yap +/f Wwtr1 f/f).
Pregnant female uterine cross sections from floxed controls (Pgr +/+ Yap f/f Wwtr1 f/f) (n=4) and knockouts (Pgr Cre/+ Yap +/f Wwtr1 f/f) (n=3) at 7.5 days post coitus were sent for bulk mRNA sequencing to determine the transcriptional consequences of Yap and Wwtr1 loss in the murine uterus during pregnancy.

first: Noura

last: Massri

first: Erin

middle: L

last: Vegter

first: Ivonne

last: Pauneto-Delgado

first: Gregory

middle: W

last: Burns

first: Niraj

last: Joshi

first: Bin

last: Gu

first: Ripla

last: Arora

first: Asgerally

middle: T

last: Fazleabas


title: Single-cell analysis identifies PLK1 as a driver of immunosuppressive tumor microenvironment in LUAD

city: Houston

first: Chaohao

address: 1881 East Rd

institute: MD Anderson Cancer Center

summary: PLK1 (Polo-like kinase 1) plays a critical role in the progression of lung adenocarcinoma (LUAD). Recent studies have unveiled that targeting PLK1 improves the efficacy of immunotherapy, highlighting its important role in the regulation of tumor immunity. Nevertheless, our understanding of the intricate interplay between PLK1 and the tumor microenvironment (TME) remains incomplete. Here, using genetically engineered mouse model and single-cell RNA-seq analysis, we report that PLK1 promotes an immunosuppressive TME in LUAD, characterized with enhanced M2 polarization of tumor associated macrophages (TAM) and dampened antigen presentation process. Mechanistically, elevated PLK1 coincides with increased secretion of CXCL2 cytokine, which promotes M2 polarization of TAM and diminishes expression of class II major histocompatibility complex (MHC-II) in professional antigen-presenting cells. Furthermore, PLK1 negatively regulates MHC-II expression in cancer cells, which has been shown to be associated with compromised tumor immunity and unfavorable patient outcomes. Taken together, our results reveal PLK1 as a novel modulator of TME in LUAD and provide possible therapeutic interventions.

overall_design: 8-week-old LSL-KrasG12D/Trp53fl/fl (KP) and LSL-KrasG12D/Trp53fl/fl/ Rosa26LSL-Plk1 (KPP) mice (n = 3 each group) were intratracheally instilled with adenovirus-expressing Cre recombinase at a viral titer of 2.5 × 10^7PFU per mouse to induce lung cancer. Mice were sacrificed after 12 weeks of adenovirus delivery. Single cell suspensions of tumor tissues were prepared following 10x Genomics Cell Preparation Guide.

first: Xiaoqi

last: Liu

first: Yifan

last: Kong

first: Jinpeng

first: Sai

last: Wu


title: Treehouse compendium of polyA selected RNA-Seq gene expression data from 33 PDX

first: Olena

last: Vaske

overall_design:
The data contains 33 consistently processed gene expression datasets from 3 studies. Gene expression in each sample is uniformly quantified using the dockerized TOIL RNA-Seq pipeline versions from 3.2 to 3.4.1 (Vivian et al., 2017); all of these versions produce bitwise identical RSEM gene expression outputs. The pipeline uses RSEM Version 1.2.25 (Li and Dewey, 2011) for quantification after aligning reads with STAR v 2.3.2a (Dobin et al., 2013) using indices generated from the human reference genome GRCh38 and the human gene models GENCODE 23 as described at https://github.com/UCSC-Treehouse/pipelines. Quality is assessed with the MEND pipeline https://github.com/UCSC-Treehouse/mend_qc (Beale et al., 2021).

Data pocessing steps were as follows:

Adapters are removed with CutAdapt v1.9 ?(Martin, 2011)?
Reads are  aligned by STAR v 2.4.2a using indices generated from the human reference genome GRCh38 and the human gene models Gencode 23 ?(Dobin et al., 2013)
RSEM 1.2.25 is used to quantify gene expression ?(Li and Dewey, 2011)?.
Gene level expression in TPM is log transformed: log2(TPM+1)

genome build/assembly: GRCh38
processed data files format and content: Gene level expression in TPM is log transformed: log2(TPM+1)

first: Holly

last: Beale

first: Katrina

last: Learned

first: Ellen

last: Kephart

first: Sneha

last: Jariwala

first: Reyna

last: Antilla

first: Allison

last: Cheney

first: Alfred

last: Lyle

first: Yvonne

last: Vasquez

first: Lauren

last: Sanders

first: David

last: Haussler

first: Sofie

last: Salama


title: Targeting SUMOylation sensitizes Acute myeloid leukemia to Venetoclax treatment

city: Duarte

first: Hsun

middle: Teresa

last: Ku

address: 1500 E. Duarte Road

department: Translational Research and Cellular Therapeutics

institute: City of Hope

summary: Acute myeloid leukemia (AML) is a hematopoietic cancer characterized by the proliferation and accumulation of aberrant immature myeloid progenitor blasts in bone marrow and peripheral blood. Venetoclax (VEN), a selective B-cell lymphoma 2 (BCL-2) inhibitor, has received FDA approval for AML treatment in combination with hypomethylating agents (HMA). However, treatment failure and therapy resistance present an urgent need for new therapies to overcome VEN resistance and enhance VEN efficacy. We propose inhibition of SUMOylation as a novel therapy with the potential to address this need. SUMOylation regulates protein function by covalently attaching Small Ubiquitin-like MOdifier (SUMO) proteins to target proteins via an enzymatic cascade. Our study aims to evaluate the effects of SUMOylation inhibition on anti-AML activity of VEN and dissert the underlying mechanism.

overall_design: Here, we use TAK-981, a selective SUMO-activating enzyme (SAE) inhibitor, to inhibit global SUMOylation. AML cell line KG1a cells were treated with TAK-981(5µM), VEN(1µM), or both for 48h. DMSO was used as vehicle control (ctrl). Total RNA was purified using miRNeasy RNA isolation kit (Qiagen) then Ribo-Zero RNA-seq was performed.

first: Li

last: Du

first: Steven

last: Rosen


title: HIFα-regulated genes in small intestine epithelial cells from  naïve mice

city: Erlangen

first: Pang

last: Lyu

address: Glückstr. 6

department: Department of Internal Medicine 3

institute: University Hospital Erlangen

summary: HIFα works as an important transcription factor to induce target genes mediating cell proliferation, metabolism and inflammation. To gain new insights into  HIFα modulated genes, we used high-throughput sequencing to analyze potential HIFa regulated genes in  small intestine epithelial cells from naive mice at steady state.

overall_design: RNA-seq was used to define differentially expressed genes in small intestine epithelial cells from naïve mice of HIF1α∆IEC, HIF2α∆IEC mice and littermate control mice.

first: Jinming

last: Wen

first: Aline

last: Bozec


title: Single cell sequencing to investigate the alteration of urea cycle in DFMO treated mouse

city: Shanghai

first: Haoyan

last: Chen

state: Shanghai

address: 145 Shandong Road

institute: Renji Hospital

overall_design: We incubated 2*10^5 MC38 cells into the back of C57BL/6 mouse. And 7 days after incubation, we started gavage of DFMO or water(NC) daily for 14 days. Xenograft tumors were collected and digested into single cells, followed by Ficoll seperation to obtain immune cells. We mix cells from xenografts of 4 mice per group  for single cell sequence.

first: Shi-Yuan

last: Lu

first: Tianying

last: Tong


title: DPYSL2/CRMP2 isoform B knockout in human iPSC-derived glutamatergic neurons confirms its role in mTOR signaling and neurodevelopmental disorders

city: Baltimore

first: Dimitrios

last: Avramopoulos

state: Maryland

address: 733 North Broadway

department: Genetic Medicine

institute: Johns Hopkins University

summary: The DPYSL2/CRMP2 gene encodes a microtubule-stabilizing protein crucial for neurogenesis and is associated with numerous psychiatric and neurodegenerative disorders including schizophrenia, bipolar disorder, and Alzheimer's disease. DPYSL2 generates multiple RNA and protein isoforms, but few studies have differentiated between them. We previously reported an association of a functional variant in the DPYSL2-B isoform with schizophrenia (SCZ) and demonstrated in HEK293 cells that this variant reduced the length of cellular projections and created transcriptomic changes that captured schizophrenia etiology by disrupting mTOR signaling-mediated regulation. In the present study, we follow up on these results by creating, to our knowledge, the first models of endogenous DPYSL2-B knockout in human induced pluripotent stem cells (iPSCs) and neurons. CRISPR/Cas9-faciliated knockout of DPYSL2-B in iPSCs followed by Ngn2-induced differentiation to glutamatergic neurons showed a reduction in DPYSL2-B/CRMP2-B RNA and protein with no observable impact on DPYSL2-A/CRMP2-A. The average length of dendrites in knockout neurons was reduced up to 58% compared to controls. Transcriptome analysis revealed disruptions in pathways highly relevant to psychiatric disease including mTOR signaling, cytoskeletal dynamics, immune function, calcium signaling, and cholesterol biosynthesis. We also observed a significant enrichment of the differentially expressed genes in SCZ-associated loci from genome-wide association studies (GWAS). Our findings expand our previous results to neuronal cells, clarify the functions of the human DPYSL2-B isoform and confirm its involvement in molecular pathologies shared between many psychiatric diseases.

overall_design: iPS cells from a healthy donor were edited to knock out one DPYSL2 transcript and 6 edited and 6 unedited clones  differentiated to excitatory neurons. RNA was extracted and subjected to RNA sequencing, after which the transcriptomes of edited and unedited cells were compared. Details in our publication Mol Psychiatry. 2023 Oct;28(10):4353-4362. doi: 10.1038/s41380-023-02186-w. Epub 2023 Jul 21. PMID: 37479784

first: K

last: Feuer

first: D


title: Treehouse compendium of ribosomal-depletion RNA-Seq gene expression data from 43 PDX

first: Olena

last: Vaske

overall_design:
The data contains 43 consistently processed gene expression datasets from 1 study. Gene expression in each sample is uniformly quantified using the dockerized TOIL RNA-Seq pipeline versions from 3.2 to 3.4.1 (Vivian et al., 2017); all of these versions produce bitwise identical RSEM gene expression outputs. The pipeline uses RSEM Version 1.2.25 (Li and Dewey, 2011) for quantification after aligning reads with STAR v 2.3.2a (Dobin et al., 2013) using indices generated from the human reference genome GRCh38 and the human gene models GENCODE 23 as described at https://github.com/UCSC-Treehouse/pipelines. Quality is assessed with the MEND pipeline https://github.com/UCSC-Treehouse/mend_qc (Beale et al., 2021).
Data pocessing steps were as follows:

Adapters are removed with CutAdapt v1.9 (Martin, 2011)
Reads are  aligned by STAR v 2.4.2a using indices generated from the human reference genome GRCh38 and the human gene models Gencode 23 (Dobin et al., 2013)
RSEM 1.2.25 is used to quantify gene expression (Li and Dewey, 2011).
Gene level expression in TPM is log transformed: log2(TPM+1)
genome build: GRCh38
processed data files format and content: Gene level expression in TPM is log transformed: log2(TPM+1)

first: Holly

last: Beale

first: Katrina

last: Learned

first: Ellen

last: Kephart

first: Sneha

last: Jariwala

first: Reyna

last: Antilla

first: Allison

last: Cheney

first: Alfred


title: A Bidirectional Non-Coding RNA Promoter Mediates Long-Range Gene Expression Regulation [4C-seq]

status: Public on May 26 2024

city: Mexico City

first: Carlos

middle: Alberto

last: Peralta-Alvarez

state: Ciudad de México

address: Circuito Exterior s/n Ciudad Universitaria, Coyoacán

department: Genética Molecular

country: Mexico

institute: Universidad Nacional Autónoma de México

summary: Recent evidence suggests that human gene promoters display gene expression regulatory mechanisms beyond the typical single gene local transcription modulation. In mammalian genomes, genes with an associated bidirectional promoter are abundant; bidirectional promoter architecture serves as a regulatory hub for a gene pair expression. However, it has been suggested that its contribution to transcriptional regulation might exceed local transcription initiation modulation. Despite their abundance, the functional consequences of bidirectional promoter architecture remain largely unexplored. This work studies the long-range gene expression regulatory role of a long-non-coding RNA gene promoter using chromosome conformation capture methods. We found that this particular bidirectional promoter contributes to distal gene expression regulation in a target-specific manner by establishing promoter-promoter interactions. In particular, we validated that bidirectional promoter is contacting multiple gene promoter elements, including BBX promoter, upon loss-of-function assays reduced bidirectional-promoter interactions associated with increased BBX promoter-enhancer and augmented gene expression. Moreover, long-range regulatory functionality is not directly dependent on its associated non-coding gene pair expression levels.

overall_design: To investigate transcriptome-wide changes upon removal of a long-non-coding-RNA bidirectional promoter associated to DUBR and LINC00882 transcription start sites (BBQ element), we created a CRISPR-Cas9 model on K562 cells

first: Angel

middle: J

last: Cerecedo-Castillo

first: Hober

middle: N

last: Nuñez-Martinez

first: Felix

last: Recillas-Targa


title: Treehouse compendium of polyA selected RNA-Seq gene expression data from 12,747 tumors

overall_design:
The data contains 12747 consistently processed gene expression datasets from 34 studies. Gene expression in each sample is uniformly quantified using the dockerized TOIL RNA-Seq pipeline versions from 3.2 to 3.4.1 (Vivian et al., 2017); all of these versions produce bitwise identical RSEM gene expression outputs. The pipeline uses RSEM Version 1.2.25 (Li and Dewey, 2011) for quantification after aligning reads with STAR v 2.3.2a (Dobin et al., 2013) using indices generated from the human reference genome GRCh38 and the human gene models GENCODE 23 as described at https://github.com/UCSC-Treehouse/pipelines. Quality is assessed with the MEND pipeline https://github.com/UCSC-Treehouse/mend_qc (Beale et al., 2021).
Data pocessing steps were as follows:

Adapters are removed with CutAdapt v1.9 (Martin, 2011)
Reads are  aligned by STAR v 2.4.2a using indices generated from the human reference genome GRCh38 and the human gene models Gencode 23 (Dobin et al., 2013)
RSEM 1.2.25 is used to quantify gene expression (Li and Dewey, 2011).
Gene level expression in TPM is log transformed: log2(TPM+1)

genome build: GRCh38
processed data files format and content: Gene level expression in TPM is log transformed: log2(TPM+1)

last: Lyle

first: Yvonne

last: Vasquez

first: Lauren

last: Sanders

first: David

last: Haussler

first: Sofie

last: Salama


title: Transcriptome Analysis Reveals Potential Protective Effects and Biomarkers of Pien Tze Huang on CCl4-induced Liver Cancer (miRNA)

first: Yongzhi

last: Wang

address: Huashan Road 1954

institute: Shanghai Jiao Tong University

summary:
Pien Tze Huang (PZH) is a traditional Chinese medicinal formula that has been extensively used in Asia for the treatment of liver diseases. We created two groups of liver cancer mouse models induced by carbon tetrachloride (CCl4): one group received treatment with PZH and the other did not receive any treatment. In the non-PZH treated group, we observed a significant increase in liver function indices including albumin (ALB), alanine aminotransferase (ALT), and aspartate aminotransferase (AST). Histological examination using hematoxylin and eosin (HE) staining revealed inflammation around the hepatic vein in the non-PZH treated group. Furthermore, Masson's trichrome staining demonstrated the presence of blue-stained collagen fibers around the hepatic vein in the non-PZH treated group. These findings suggest that PZH may have therapeutic effects on liver inflammation and cancer.

To further explore the molecular mechanisms of PZH's action, we conducted mRNA, long non-coding RNA (lncRNA), circular RNA (circRNA), and microRNA (miRNA) sequencing to identify potential drug targets at the transcriptome level. We identified 478 differentially expressed protein-coding transcripts and 68 differentially expressed lncRNA transcripts. Our study provides insights into potential transcriptional therapeutic targets for the clinical use of PZH in treating liver diseases.

overall_design: We construct two groups liver cancer mice model using CCl4, one group using PZH treatment, and the other did not receive any treatment. We also did a blank experiment with normal mice using water.In the 22nd week, we selected six mice from each group for miRNA sequencing.

first: Hao

last: Wu

first: Shengying

last: Qin


title: A Bidirectional Non-Coding RNA Promoter Mediates Long-Range Gene Expression Regulation

first: Gustavo

last: Tapia-Urzua


title: Knockdown CPT1 in NCI-H460 lung cancer cell line

city: shanghai

first: Xiaolan

middle: Phenome

last: Zhou

state: State

address: Songhu road

institute: fudan

summary: CRISPRi-mediated transcriptional inhibition of CPT1 with two distinct sgRNAs in NCI-H460 lung cancer cells, to investigate the dynamics of gene expression regulation upon CPT1 knockdown.

overall_design: inhibiting the expression of CPT1 in NCI-H460 lung cancer cells by two distinct sgRNAs.

first: Zhaozhao

last: Zhao

first: Limin

last: Lin


title: CircJPH1 promote the malignant progression of esophageal squamous cell carcinoma

city: Shijiazhuang

first: Jingjing

last: Liu

state: Hebei

address: Research Center, the Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, 050017, People's Republic of China

institute: Hebei Medical University

summary: The gene-level signaling theory of circJPH1 downstream target was searched by Ailgent expression microarray technology, and the differentially expressed genes in KYSE150 cells before and after overexpression of circJPH1 were analyzed by gene microarray, and they were deleted and analyzed by GO and KEGG.

overall_design: Comparative gene expression profiling analysis using data for KYSE150 and its overexpression derivatives (OE-circJPH1)

first: Zishuan

last: Wei


title: Presenilin deficiency results in cellular cholesterol accumulation by impairment of protein glycosylation and NPC1 function.

city: Bonn

first: Ulrich

last: Schweizer

state: NRW

address: Nussallee 11

department: Institut für Biochemie und Molekularbiologie

institute: Universitätsklinikum Bonn

summary:
Presenilin (PS) proteins represent the catalytic subunits of γ-secretase, and play a critical role in the generation of the Amyloid β (Aβ) peptide and the pathogenesis of Alzheimer’s disease (AD). Indeed, mutations in presenilin 1 (PS1) or PS2 are a major cause of early onset familial Alzheimer’s disease (FAD). However, PS proteins also exert multiple functions beyond Aβ generation. In this study, we examine the individual roles of PS1 and PS2 in cellular cholesterol metabolism. Deletion of PS1 or PS2 in mouse models led to cholesterol accumulation in cerebral neurons. Cholesterol accumulation was also observed in lysosomes of embryonic fibroblasts from PS1-KO and PS2-KO mice, and associated with decreased expression of the Niemann-Pick type C1 (NPC1) protein involved in intracellular cholesterol transport at late endosome/lysosome. Mass spectrometry and complementary biochemical methods also revealed abnormal N-glycosylation of NPC1 and several other membrane proteins in PS1-KO and PS2-KO cells. Interestingly, pharmacological inhibition of N-glycosylation resulted in intracellular cholesterol accumulation prominently in lysosomes as well as decrease of NPC1 expression in wild-type MEFs, thereby resembling the changes in PS1-KO and PS2-KO MEFs. In turn, treatment of PS1-KO and PS2-KO MEFs with a chaperone inducer, Arimoclomol, attenuated decrease of NPC1 and rescued the lysosomal cholesterol accumulation. Additionally, the intracellular cholesterol accumulation in PS1-KO and PS2-KO MEFs was prevented by NPC1 overexpression. Collectively, these data indicate that PS/γ-secretase dysfunction results in an impairment of protein N-glycosylation, which eventually causes NPC1 decrease and intracellular cholesterol accumulation.
3'RNASeq of mouse embryonic fibroblasts with PS1- or PS2-deficiency compared with controls. Biological replicates

overall_design: Comparative gene expression profiling analysis of RNA-seq data for mouse embryonic fibroblasts derived from WT, Psen1-, Psen2-KO mice

first: Marietta

last: Fabiano

first: Jochen

last: Walter

first: Naoto

last: Oikawa


title: Single cell gene expression from the hippocampus of 5xFAD mice subjected to stroke

city: Miami

first: Anthony

last: Griswold

state: FL

address: 1501 NW 10th Ave, BRB 318

institute: University of Miami

summary: Neurogenesis after stroke compounded with amyloid beta plaques around the cerebral vasculature has implications in delaying tissue recovery. We used single cell RNA sequencing (scRNA-seq) to understand the cellular interactions in the hippocampus during post-stroke recovery with CAA.

overall_design: The hippocampus of 5xFAD or WT mice was isolated 7 days post-stroke. The contralateral and ipsilateral side were collected on ice in Hibernate A medium and homogenized into a single cell suspension for analysis using scRNA-seq.

first: Olivia

last: Osborne


title: Cell atlas of colon tissue from DSS-induced colitis mouse

city: Jinan

first: Jing

last: Shen

address: Wenhua West Road 44

institute: Shandong University

summary: Inflammation markedly alters the microenvironment of intestinal tissue. To explore alterations in the cell composition and transcription of intestinal tissue during colitis, we conducted single-cell RNA sequencing analysis of the colonic tissues obtained from the mice treated with 3% DSS for 6 days.

overall_design: 7-week-old SPF mice received 3% DSS for 6 days, and the mid-colon tissues were harvested for single-cell RNA sequencing.

first: Yanyan

last: Cui

first: Yatai

last: Chen

first: Detian

last: Yuan

first: Shiyang

last: Li


title: Treehouse compendium of polyA selected RNA-Seq gene expression data from 932 cell lines

city: Santa Cruz

first: Olena

last: Vaske

address: MCDB, Sinsheimer Labs, 1156 High Street

institute: UCSC

summary: We uniformly analyze sequence data to generate a resource for comparative gene expression studies. Specifically, we obtained access to primary RNA sequence data from repositories and clinical partners, consistently processed the data, harmonized metadata, and released the expression values and metadata without access restrictions

overall_design:
The data contains 43 consistently processed gene expression datasets from 1 study. Gene expression in each sample is uniformly quantified using the dockerized TOIL RNA-Seq pipeline versions from 3.2 to 3.4.1 (Vivian et al., 2017); all of these versions produce bitwise identical RSEM gene expression outputs. The pipeline uses RSEM Version 1.2.25 (Li and Dewey, 2011) for quantification after aligning reads with STAR v 2.3.2a (Dobin et al., 2013) using indices generated from the human reference genome GRCh38 and the human gene models GENCODE 23 as described at https://github.com/UCSC-Treehouse/pipelines. Quality is assessed with the MEND pipeline https://github.com/UCSC-Treehouse/mend_qc (Beale et al., 2021).
Data pocessing steps were as follows:
Adapters are removed with CutAdapt v1.9 (Martin, 2011)
Reads are  aligned by STAR v 2.4.2a using indices generated from the human reference genome GRCh38 and the human gene models Gencode 23 (Dobin et al., 2013)
RSEM 1.2.25 is used to quantify gene expression (Li and Dewey, 2011).
Gene level expression in TPM is log transformed: log2(TPM+1)

genome build: GRCh38
processed data files format and content: Gene level expression in TPM is log transformed: log2(TPM+1)

first: Holly

last: Beale

first: Katrina

last: Learned

first: Ellen

last: Kephart

first: Sneha

last: Jariwala

first: Reyna

last: Antilla

first: Allison

last: Cheney

first: Alfred

last: Lyle

first: Yvonne

last: Vasquez

first: Lauren

last: Sanders

first: David

last: Haussler

first: Sofie

last: Salama


title: Plant parasitic nematodes single embryo RNA sequencing

status: Public on May 25 2024

first: Dadong

last: Dai

address: 1st street Shizishan

department: Department of Life science and technology

institute: Huazhong Agricultural University

summary: In order to study the similarities and differences in embryonic development between plant-parasitic nematodes and free-living nematodes, we performed RNA-seq on embryos of three plant-parasitic nematodes at a total of 11 stages from the single-cell stage to the J1 stage

sample_organism:
Meloidogyne incognita
Heterodera glycines
Ditylenchus destructor

overall_design: We recorded the embryonic development process of Meloidogyne incognita, Heterodera glycines, and Ditylenchus destructor species, and constructed transcriptome datasets of single embryos of these three species utilized low-input smart-seq2 RNA-seq technology. The datasets encompassed 11 complete embryonic development stages, which are Zygote, 2-cell, 4-cell, 8-cell, 24-44 cell, 64-78 cell, Comma, 1.5-fold, 2-fold, Moving, L1, which each stage generated four to five replicates. a total of 162 high-resolution transcriptome libraries were obtained.


title: Kinomic analysis of excitotoxicity in primary neuronal cultures

city: Toledo

first: Isaac

last: Schiefer

state: OH

address: 3000 Arlington Ave

institute: University of Toledo

summary: Glutamate excitotoxicity plays a critical role in neurodegeneration by triggering NMDA receptorhyperactivation, leading to elevated synaptic calcium levels and subsequent neuronal cell death. Tobetter understand how glutamateaffects neurons in neurological diseases, we conducted acomprehensive analysis of molecular changes at the transcriptome and kinome levels.Our research used primary cortical cultures from rat embryos to study glutamate excitotoxicity. Non-neuronal cells,like astrocytes, typically enhance neuron tolerance to glutamate excitotoxicity. We useda neuron-rich cultured system and observed that the effects of glutamate on neurons are concentration-dependent. Intermediate doses of glutamate had significant neurotoxic effects, while high and lowdoses resulted in less cell mortality, aligning with previous findings related to calcium influx.Glutamate is known to inhibit protein synthesis in neurons and leads to a rise in cytosolic calcium, a keystep in synapticplasticity and delayed neuronal cell death. Kinome profiling indicated activation of PKAand PKG phosphorylation, essential for synaptic plasticity-related gene expression.

overall_design: Rat neuron cells (5 x 104cells per mL, 3 mLtotal volume)were plated on a 6-well poly-D-lysine coated plate. Incubated the plate at 37°C and 5% CO2 for 8 dayswith half of the growth medium (1.5 mL) replaced every other day. Prior to treatment, plates werescanned in the IncuCyte S3 (25 scans perwell, 20 X magnification). After scanning, the growth mediumwas aspirated and replaced with a glutamate-based medium (2 mL, 250 μM final concentration) or freshgrowth medium and scanned in IncuCyte S3 at the same specification for 4 h

first: Nguyen

last: Jennifer

first: Zhang

last: Xiaolu

first: Madhavaram

last: Anvitha

first: Eby

last: Hunter

first: Bretz

last: James

first: Tackie-Yarboi

last: Ethel

first: Alganem

last: Khaled

first: Ryan

last: William

first: Zajac

last: Kelsee

first: Imami

last: Ali

first: Lundh

last: Anna

first: Schiefer

last: Isaac

first: McCullumsmith

last: Robert


title: Multiple responses contribute to the enhanced drought tolerance of the autotetraploid Ziziphus jujuba Mill. var. spinosa

city: Beijing

first: Yingyue

last: Li

address: Haidian District, Beijing

institute: Beijing Forestry University

summary:
Purpose: Mechanism of gene expression changes in autotetraploid drought resistance variation
Methods: Leaves under control and drought treatment of 6h, 12h and 48h were sampled from diploid and the autotetraploid for RNA-seq. Total RNA was extracted from 100mg sample with RNeasy plant mini kit (Omega Biotech, China) and purified with RNase-Free DNase set. Following, cDNA library was constructed and the library concentration and insert size was respectively assessed on the Qubit2.0 (Invitrogen, USA) and Agilent Bioanalyzer 2100 system, and then the effective concentration of the library was accurately quantified through Q-PCR. Prepared high quality libraries were sequenced on Illumina HiSeq X-ten platform to generate paired-end raw reads. qRT–PCR validation was performed using SYBR Green assays.
Results: The study findings showed that the autotetraploid sour jujube exhibited a superior drought tolerance and enhanced regrowth potential after dehydration in comparison with the diploid counterpart. The physiological responses gradually triggered important functions in the autotetraploid sour jujube under extreme drought conditions. Furthermore, a comparative transcriptome analysis showed that more differentially expressed genes (DEGs) were detected in autotetraploid after drought stress. Through GO enrichment analysis, many DEGs between the diploid and autotetraploid sour jujube after drought-stress exposure were respectively annotated to the oxidation–reduction process, photosystem, DNA binding transcription factor activity, oxidoreductase activity. Consistently, six reactive oxygen species scavenging-related genes were specifically differentially expressed, positive changes of the genes involved in glutathione metabolism pathways were greater and the lower O2− level and malonaldehyde (MDA) content and higher antioxidant enzymes activity were detected in the autotetraploid under drought-stress conditions. The higher chlorophyll content and differentially enriched genes during photosynthesis suggest that the photosynthetic system in the autotetraploid, having variations in stomatal and cellular characteristics, was enhanced during drought stress. In addition, DEGs in the autotetraploid after stress exposure were significantly enriched in DNA-replication and plant hormone, including auxin, abscisic acid and gibberellin signal-transduction pathways. Under osmotic stress conditions, genes associated with the synthesis and transport of osmotic regulatory substances including anthocyanin biosynthesis were differentially expressed, and the soluble sugar, soluble protein and proline contents were significantly higher in the autotetraploid. Moreover, several genes encoding transcription factors (TFs) including GRAS, Bhlh, MYB, WRKY and NAC were induced specifically or to higher levels in the autotetraploid under drought-stress conditions, and hub genes, LOC107403632, LOC107422279, LOC107434947, LOC107412673 and LOC107432609, related to up-regulated transcription factors in the autotetraploid compared with the diploid were identified.
Conclusions: Owing to the whole-genome doubling, many functional genes in the autotetraploid plants were differentially expressed compared with in the diploid during drought stress, resulting in resistance difference.

overall_design: Transcriptomes Analysis of diploid and the autotetraploid sour jujube under 6h, 12h and 48h of drought stress

first: Meng


title: Transcriptional profile at single cell level of Schistosoma mansoni following knocking down Krüppel-like factor 4 (klf4) [scRNA-Seq]

city: DALLAS

first: Lu

last: Zhao

address: 6001 Forest Park Road, ND7.300

department: Pharmacology

institute: The University of Texas Southwestern Medical Center

summary: klf4 is enriched in a putative tegument associated lineage of S. mansoni. To characterize cellular and molecular changes associated with klf4 loss of function, we performed single-cell RNAseq on control (RNAi) and  klf4 (RNAi) worms

overall_design: Adult male parasites were treated with either klf4-targeting dsRNA or control dsRNA for 17 days before dissociation, then live, single isolated cells were sorted by Fluorescence-activated cell sorting (FACS) and analyzed using scRNAseq.Further data processing was carried out in Seurat (v4.3)

first: George

last: Wendt

first: James

last: Collins


title: Transcriptional profiling of Schistosoma mansoni following knocking down Krüppel-like factor 4 (klf4) [RNA-Seq]

summary: klf4 is enriched in a putative tegument associated lineage of S. mansoni. To investigate the function of klf4, we compared transcriptional profiles of klf4 (RNAi) worms to those of control (RNAi) worms.

overall_design: Adult male parasites were treated with either klf4-targeting dsRNA or control dsRNA for 17 days, then subjected to RNAseq.


title: hESC- and hiPSC-derived Schwann cells are Molecularly and Functionally Equivalent

city: Los Angeles

first: Riki

last: Kawaguchi

address: 760 Westwood Plaza, Room 37-420

department: Department of Psychiatry and Neurology Department of Psychiatry

institute: University of California, Los Angeles

summary: Establishing robust models of human myelinating Schwann cells is critical for studying peripheral nerve injury and disease. Stem cell differentiation has emerged as a key model of human cells and disease motivating development of Schwann cell differentiation protocols. Human embryonic stem cells (hESCs) are considered the ideal pluripotent cell but ethical concerns regarding their use have propelled the popularity of human induced pluripotent stem cells (hiPSCs). Given that the equivalence of hESCs and hiPSCs remains controversial, we sought to compare the molecular and functional equivalence of hESC- and hiPSC-derived Schwann cells generated with our previously reported protocol. We identified only modest transcriptome differences by RNA sequencing and insignificant proteome differences by antibody array. Additionally, both cell types comparably improved nerve regeneration and function in a chronic denervation and regeneration animal model. Our findings demonstrate that Schwann cells derived from hESCs and hiPSCs with our protocol are molecularly comparable and functionally equivalent.

overall_design: RNA sequencing was performed on ɑ4-integrin CD49d-positive Schwann cells differentiated from three hESC lines (H1, H7 and H9) and three hiPSC lines (GM01582, GM02623 and GM08398). One biological replicate was used for each cell type.

first: Kathryn

last: Moss

first: Ruifa

last: Mi

first: Ahmet

last: Höke


title: Genome-wide DNA methylation analysis of driver gene-negative and EGFR-mutation lung adenocarcinoma and ajacent normal tissue

city: Guangzhou

first: Man

last: Shu

state: Guangdong

address: No.58 Zhongshan Er Road

institute: the First Affiliated Hospital of Sun Yat-sen University

type: Methylation profiling by genome tiling array

summary: Genome-wide DNA methylation profiling of normal and lung adenocarcinoma fresh tissue samples. The Illumina Infinium MethylationEPIC BeadChip (850K) was used to obtain DNA methylation profiles across 860,000 CpGs in fresh tissue of lung adenocarcinoma and adjacent histological normal lung tissue samples. Samples included 30 paired tumor-normal driver gene-negative lung adenocarcinoma tissues and 35 paired tumor-normal EGFR-mutation positive lung adenocarcinoma tissues.

overall_design: Bisulphite converted DNA from the 130 samples were hybridized to the Illumina Infinium MethylationEPIC BeadChip

first: Ke

last: Zunfu

first: Shu

last: Man

first: Huang

last: Leilei

first: Chen

last: Yu

first: Wang

last: Yanxia

first: Xie

last: Zhongpeng


title: sRNA-seq of Aspergillus fumigatus RNAi double knockouts

city: Jena

first: Matthew

middle: George

last: Blango

address: Adolf-Reichwein-Str. 23

department: Junior Resaerch Group RNA Biology of Fungal Infections

institute: Leibniz Institute for Natural Product Research and Infection Biology

summary: The RNA interference (RNAi) pathway has evolved numerous functionalities in eukaryotes, with many on display in Kingdom Fungi. RNAi can regulate gene expression, facilitate drug resistance, or even be altogether lost to improve virulence potential in some fungal pathogens. In the WHO fungal priority pathogen, Aspergillus fumigatus, the RNAi system is known to be intact and functional. To extend our limited understanding of A. fumigatus RNAi, we performed a multi-condition sRNA-seq analysis comparing expression of several RNAi double knockout mutants with the wild-type strain in conidia and mycelium grown for 24 or 48 hours.

overall_design: Small RNA profiling analysis of RNAi double knockouts (𝚫dclA/B, 𝚫ppdA/B, 𝚫rrpA/B) in the RNAi pathway of Aspergillus fumigatus conidia, 24-h-mycelium, and 48-h-mycelium.

first: Abdulrahman

last: Kelani

first: Xiaoqing

last: Pan


title: Inflammatory stress-mediated chromatin changes underlie dysfunction in endothelial cells. [ATAC-Seq]

city: Unionville

first: Haibo

last: Liu

state: CT

address: 164 Plantation St

department: MCCB

institute: UMass Chan

summary: Inflammatory stresses underlie endothelial dysfunction and contribute to the development of chronic cardiovascular disorders such as atherosclerosis and vascular fibrosis. The initial transcriptional response of endothelial cells to pro-inflammatory cytokines such as TNF-alpha is well established. However, very few studies uncover the effects of inflammatory stresses on chromatin architecture. We used integrative analysis of ATAC-seq and RNA-seq data to investigate chromatin alterations in human endothelial cells in response to TNF-alpha and febrile-range heat stress exposure. Multi-omics data analysis suggests a correlation between the transcription of stress-related genes and endothelial dysfunction drivers with chromatin regions exhibiting differential accessibility.

overall_design: To investigate genome-wide changes in chromatin accessibility, we performed ATAC-seq on EC cells, exposed to either 2hr of 39ºC febrile-like heat stress or 6hr of 10 ng/ml TNF-alpha.

first: Amada

middle: D

last: Caliz

first: Heather

last: Learnard

first: Milka

last: Koupenova

first: John

middle: F

last: Keaney

first: Shashi

last: Kant

first: Lihua

last: Zhu

first: Anastassiia

last: Vertii


title: tRF & tiRNA sequencing of Aspergillus fumigatus

summary: Aspergillus fumigatus is an important human pathogen and a leading fungal killer. This study aimed to determine the tRNA fragment and tRNA half repertoire of A. fumigatus in wild-type conidia and mycelium grown for 24 or 48 hours in liquid culture.

overall_design: tRF & tiRNA sequencing (performed by CD Genomics) on wild-type Aspergillus fumigatus CEA10 conidia, 24-h-mycelium, and 48-h-mycelium.

middle: A


title: microRNA and the Posttranscriptional Response to Oxidative Stress During Neuronal Differentiation

city: Newcastle

first: Behnaz

last: Khavari

address: University Dr

country: Australia

institute: University of Newcastle

summary: Oxidative stress is an important environmental exposure associated with psychiatric disorders, but the underlying molecular mechanisms remain elusive. We recently observed enrichment of neurodevelopmental processes and diseases among a large number of differentially expressed genes during or after exposure to oxidative stress in an in vitro model of neuronal differentiation. To further explore the regulatory mechanisms that might account for a coordinated response to this exposure, we investigated changes in the expression of small non-coding miRNA in this system and estimated their interaction with differentially expressed mRNA. These molecules are thought to play a crucial role in brain development and its response to stress. Here we observed more than a hundred differentially expressed miRNAs, including 72 previously reported to be dysregulated in psychiatric disorders. The 7 most influential miRNAs associated with pre-treatment exposure were miR-138-5p, miR-96-5p, miR-34c-5p, miR-1287-5p, miR-497-5p, miR-195-5p, and miR-16-5p. These were sup-ported by at least 10 negatively correlated mRNA connections, and formed hubs in interaction network with 134 genes enriched with neurobiological function. Whereas in the co-treatment con-dition, miRNA-mRNA interaction pairs were enriched not only in neuronal processes, but also in cardiovascular and immunity-related disease ontologies. Interestingly, 12 differentially expressed miRNAs originated from the same genomic location, DLK1-DIO3, which encodes a schizophre-nia-associated miRNA signature. Collectively, these findings suggest that early exposure to oxida-tive stress, before and during prenatal neuronal differentiation, might increase the risk of mental illnesses in adulthood by disturbing the expression of miRNAs that regulate neurodevelopmental-ly significant genes and networks.

overall_design: Hydrogen peroxide (H2O2) at a final concentration of 10 µM was applied through two different protocols to induce chronic oxidative stress in neuroblasts. In the co-treatment approach, the cell culture medium was simultaneously supplemented with all-trans retinoic acid (ATRA) and H2O2 for a 7-day period, while in the pre-treatment regimen, cells were first exposed to H2O2 for 72 hours, and upon its removal were treated with ATRA for 7 days. All experiments were performed in biological triplicates, such that for each approach, there existed 3 replicates for peroxide-treated and 3 replicates for untreated samples. One of the samples was known as an outlier and removed from analysis.

first: Michelle

last: Barnett

first: Ebrahim

last: Mahmoudi

first: Michael

middle: P

last: Geaghan

first: Adam

last: Graham

first: Murray

last: Cairns


title: LKB1-SIK2 loss drives uveal melanoma proliferation and hypersensitivity to SLC8A1 and ROS inhibition

city: Nice

first: Corine

last: Bertolotto

address: 151 route Saint-Antoine de Ginestière

institute: C3M - U1065 INSERM - CENTRE MEDITERRANEEN DE MEDECINE MOLECULAIRE

summary: Metastatic uveal melanomas are highly resistant to all existing treatments. To address this critical issue, we performed a genome-wide CRISPR-Cas9 knockout screen, which revealed the LKB1-SIK2 module in restraining uveal melanoma tumorigenesis. Functionally, LKB1 loss enhances proliferation and survival through SIK2 inhibition and up-regulation of the sodium/calcium (Na+/Ca2+) exchanger SLC8A1. This signalling cascade promotes increased level of intracellular calcium and mitochondrial reactive oxygen species, two hallmarks of cancer. We further demonstrate that combination of an SLC8A1 inhibitor and a mitochondria-targeted antioxidant promotes enhanced cell death efficacy in LKB1- and SIK2-negative uveal melanoma cells compared to control cells. We also designed an LKB1-deficient prognostic gene signature of patient survival that may be predictive of response to this combination. Our data thus identify not only metabolic vulnerabilities, but also new prognostic markers, thereby providing a therapeutic strategy for particular subtypes of metastatic uveal melanoma.

overall_design:
To gain insights into the mechanisms by which LKB1 restricts metastatic uveal melanoma cell growth, we profiled the transcriptomes of Ctl and LKB1-KO cells in biological replicates.
6 samples of total RNA with 3 cell lines control, 3 KO cell lines for LKB1

first: Thomas

last: Strub


title: Effect of ARL11 overexpression on gene expression of MDA-MB-231 cells during olaparib treatment

first: Hanqiu

last: Zheng

address: Haidian District

institute: Tsinghua university

summary: To investigate the function ARL11  in the regulation of PARPi resistance, we established MDA-MB-231 cells overexpressing ARL11. We then performed gene expression profiling analysis using data obtained from RNA-seq of ARL11 overexpression or vector control MDA-MB-231 cells treated with or without Olaparib.

overall_design: 5×10^5 ARL11 overexpression or vector control MDA-MB-231 cells were plated on 10 cm dishes and cultured for 24 hours. Cells were then treated with either 40 μM DMSO or Olaparib for 3 days. Cells were lysed for RNA extraction and cDNA library construction and RNA-seq analysis;

first: T

last: Zhang

first: H


title: RNA-seq of TM3 Leydig and TM4 Sertoli cells under MEHP exposure

first: LI

middle: Yong

last: Ning

address: 7 Panjiayuan Nanli

institute: China National Center for Food Safety Risk Assessment

summary: This study was designed to investigate the toxicological effects of MEHP on TM3 Leydig and TM4 Sertoli cells.

overall_design: For experiments, TM3 Leydig and TM4 Sertoli cells were seeded at 1.5 × 105 cells/ml in 2 ml/well in 6-well plates. After 24 hours, cells were exposed to 100 uM mono-(2-ethylhexyl) ester (MEHP; AccuStandard, ALR-138N), a major metabolite of DEHP in vivo, for another 72 hours. MEHP was dissolved in dimethyl sulfoxide (DMSO; Sigma-Aldrich, D2438), with 0.1% DMSO treatment used as a control.

first: Yongning

last: Li

first: Hui

last: Yang


title: Intratumoral antigen-signalling traps CD8+ T cells to confine exhaustion to the tumour site (scRNA-Seq)

city: Cambridge

first: James

last: Thaventhiran

address: Tennis Court Road

institute: MRC Toxicology Unit

summary: Immunotherapy advances have been hindered by difficulties tracking the behaviours of lymphocytes following antigen-signalling. Here we present the antigen-receptor signalling reporter (AgRSR) mouse to fate-map lymphocytes responding to antigen at specific times and locations, to determine the behaviour of T cells involved in the tumour immune response. Contrary to reports of ready egress of T cells out of the tumour, we find that intratumoral antigen-signalling traps CD8+ T cells in the tumour. These clonal populations expand and become increasingly exhausted over time. In contrast, antigen- signalled regulatory T cell (Treg) clonal populations readily recirculate out of the tumour. Consequently, intratumoral antigen-signalling acts as a gatekeeper to compartmentalize CD8+ T cell responses – even within the same clonotype, enabling immunity to confine exhaustion to a specific tissue site.

overall_design: YUMMER1.7 bearing AgRSR mice were injected with tamoxifen (intraperitoneally or intratumorally).  8 or 18 days after injection, EYFP+ cells were sorted from the secondary lymphoid tissues and tumour, and processed through scRNA/TCR-seq.

first: Munetomo

last: Takahashi

first: Tsz

middle: Y

last: So


title: Effect of KHSRP acetylation on gene expression in LNCaP cells

city: Shanghai

first: Renjie

last: Cai

address: 280 Mohe Road, Baoshan District

department: Department of Oncology

institute: Shanghai 9th People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China

summary:
We established LNCaP cells in wihch KHSRP was knocked down along with LNCaP cells with silenced KHSRP and re-introduced HA-tagged KHSRP-WT/K205R.RNA-seq was carried out in the stable LNCaP cell lines  to determine the underlying mechanism of KHSRP acetylation in PCa tumorigenesis.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 4 different cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for LNCaP control cells and LNCaP KD cells(shKHSRP) and comparative gene expression profiling analysis of RNA-seq data for LNCaP WT cells (sh-KHSRP-re-introduced-KHSRP-WT) and LNCaP K205R cells (sh-KHSRP-re-introduced-KHSRP-K205R)

first: Haihua

last: Yuan

first: Ming

last: Xu


title: The disruption of CtBP regulates DUX-dependent and -independent genetic program for the 2-cell-like state in murine embryonic stem cells [RNA-seq and RRBS]

city: Sanda

first: Yoshiyuki

last: Seki

state: hyogo

address: 1, Gakuen Uegahara

department: School of Biological and Environmental Sciences

institute: Kwansei Gakuin University

type: Methylation profiling by high throughput sequencing

summary: After fertilization, maternally deposited mRNA is cleared, and de novo mRNA is transcribed from the zygotic genome through zygotic genome activation (ZGA), which is called maternal-to-zygotic transition (MZT) occurring in the mouse at 2-cell (2C) stage. 2C-like cells (2CLCs) marked by MERVL expression and transcriptionally similar to 2C embryos spontaneously emerge from mouse embryonic stem cells (mESCs). Although the emergence of 2CLCs completely depends on DUX function, a recent knockout study clearly showed that DUX is dispensable for mouse embryos, suggesting that DUX-independent molecular pathways are not recapitulated in 2CLCs.  We present here that the disruption of C-terminal binding protein 1/2 (Ctbp1/2) activates DUX-dependent and -independent molecular pathway associated with the development of early mouse embryos mediated by the upregulation of Preferentially expressed antigen of melanoma family-like 7 (PRAMEL7). Furthermore, the abnormality of the gene expression profile caused by Dux KO is partially rescued by the overexpression of PRAMEL7 in mESCs. Our study provides new insights into the DUX-independent molecular pathway for developing early mouse embryos.

overall_design: RNA-seq experiments of WT, Dux KO, Ctbp1/2 KO, Pramel7 KO, Dppa2 KO and Pramel7-overexpressing embryonic stem cells and RRBS experiements of WT, Ctbp1/2 DKO, Dppa2 KO and TKO embryonic stem cells.


title: Genetic drivers of pancreatic islet function [pancreatic islet]

status: Public on May 24 2024

city: Bar Harbor

first: Gary

last: Churchill

state: Maine

address: 600 Main St

institute: The Jackson Laboratory

summary: Study to map diabetes-related traits in the Diversity Outbred (DO) mouse cohort. The DO is an outbred mouse population derived from 8 inbred mouse strains, including 3 wild-derived strains. The DO captures a broad range of genetic variation comparable to that found in human populations (SVENSON et al. 2012), and presents a similarly broad range of individual susceptibility to T2D. We metabolically challenged 500 DO mice with a high-fat/high-sucrose diet, measured a host of diabetes-related physiological phenotypes (e.g., plasma glucose and insulin), and isolated their pancreatic islets for functional and molecular characterization. We performed RNA-seq to determine the genetic architecture of gene expression in islets

overall_design: transcription profiling by high-throughput sequencing design

first: Mark

last: Keller

first: Candice

last: Baker


title: Transcriptome profiling of non-islet metabolic tissues in ~500 DO mouse liver, adipose, heart, and skeletal muscle tissue from mice fed high-fat, high-sugar diet [heart]

summary: Perform RNAseq with existing frozen mouse DO tissues from ~500 DO mice were sensitized on a HFHS diet (Keller, Gatti et al. 2018). The same mice have been extensively characterized for T2D-relevant clinical phenotypes, ex-vivo islet function, and other features including microbiome profiling.  Gene expression and proteomic profiling has already been completed in islets. We will collect and analyze the genetic architecture of gene expression in liver, adipose, heart, skeletal muscle. Tissues will be sent to JAX Bar Harbor from Alan Attie’s lab. These tissues were from the same mice used for transcriptome analysis of islets (Genetics May 1, 2018 vol. 209 no. 1 335-356)


title: A transcriptional enhancer regulates cardiac maturation [RNA-seq]

city: Baltimore

first: Emmanouil

last: Tampakakis

address: 720 Rutland Ave, Ross 1033

department: Division of Cardiology

institute: Johns Hopkins School of Medicine

summary: Cardiomyocyte maturation is crucial for generating adult cardiomyocytes and the application of human pluripotent stem cell derived-cardiomyocytes (hPSC-CMs). However, regulation at the cis-regulatory element level, and its role in heart disease remain unclear. Alpha-actinin 2 (ACTN2) levels increase during CM maturation. Here, we investigate a clinically relevant, conserved ACTN2 enhancer’s effects on CM maturation using hPSC and mouse models. Heterozygous ACTN2 enhancer deletion led to abnormal CM morphology, reduced function, and mitochondrial respiration. Transcriptomic analyses in vitro and in vivo showed disrupted CM maturation and upregulated anabolic mammalian target for rapamycin (mTOR) signaling promoting senescence and hindering maturation. As confirmation, ACTN2 enhancer deletion induced heat shock protein 90A expression, a chaperone mediating mTOR activation. Conversely, targeting the ACTN2 enhancer via enhancer CRISPR activation (enCRISPRa) promoted hPSC-CM maturation. Our studies reveal the transcriptional enhancer’s role in cardiac maturation and disease, offering insights into potentially fine-tuning gene expression to modulate cardiomyocyte physiology.

overall_design:
To investigate the role of a conserved ACTN2 enhancer in vivo, we used CRISPR/Cas9 and generated heterozygotes and homozygotes mice with enhancer deletion. We then performed bulk RNA-Seq analysis in adult P40 mouse hearts.
Submitter states that we are unable to provide the FASTQ files for WT1 and WT2 samples. The FASTQ files were corrupted during file transfer and can not be recovered. However, the raw counts file (raw_counts_ACTN2.csv) does include all the samples in our bulk RNA-seq experiment.

first: Elaine

middle: Z

last: Chen


title: A transcriptional enhancer regulates cardiac maturation [scRNA-seq]

overall_design: To investigate the role of a conserved ACTN2 enhancer in vitro, we used CRISPR/Cas9 and deleted this enhancer genomic region in human pluripotent stem cells (hPSCs) (H9). We then differentiated the cells to cardiomyoaytes (hPSC-CMs) and perfomed single cell RNA-Seq at differentiated day 20 CMs.


title: Enhanced Phase Separation Mediated Oncogenicity [HiC IMR-90]

city: hangzhou

first: kuang

last: junqi

address: No.18 Shilongshan Road

institute: westlake University

summary: Chromosome translocation is known to generate oncogenes such as SS18-SSX1, but the underlying mechanism remains unknown. Here we show that enhanced phase separation acquired by translocation mediates oncogenic transformation. SSX fusion dramatically enhances the phase separation property of SS18 protein through H2AK119ub. Super condensates generated by SS18-SSX recruit acetyltransferases CBP/P300 as wild type SS18, but exclude HDACs such that H3K27ac accumulates abnormally at loci from those normally occupied by SS18, resulting aberrant silencing and activation of target genes. Consistently, we show that inhibition of H3K27ac can attenuate the tumorigenicity of the fusion oncoprotein. These results provide the first case for phase separation as a transforming event  to generate oncogene and super phase separation can be targeted for cancer therapy.

overall_design: We analyzed the chromatin interaction by  HiC experiment in IMR-90 cells with expression of physiological SS18, SS18(YA)-SSX mutant and pathological SS18-SSX onco-fusion, respectively

first: Junqi

last: Kuang

first: Duanqing

last: Pei


title: Up-regulation of cholesterol synthesis by lysosomal defects requires a functional mitochondrial respiratory chain

city: Hershey

first: Nuno

last: Raimundo

state: PA

address: 500 University Dr, College Of Medicine, Room C4769

department: Cellular and Molecular Physiology

institute: Penn State College of Medicine

summary: To understand the common and opposite effects of mitochondrial and lysosomal perturbations on cellular signaling, we performed RNAseq in HeLa cells stably silenced for the mitochondrial respiratory chain subunit UQCRC1 (as a model of chronic mitochondrial respiratory chain deficiency), for lysosomal hydrolase acid alpla-glucosidase (GAA), or for lysosomal cathepsin B (CTSB). The controls were HeLa cells with scrambled shRNA.

overall_design: Two lines of HeLa-scrambled, two lines of UQCRC1-kd (each with a different shRNA), two lines of GAA-kd (each a different shRNA) and two lines of CTSB-kd (each with a different shRNA).

first: King

last: Yambire


title: HB21 induction in Arabidopsis inflorescence apexes

city: Valencia

first: Vicente

last: Balanzà

state: Valencia

address: Av de los Naranjos s/n

department: Development and hormonal action

country: Spain

institute: IBMCP (CSIC-UPV)

summary: HB21 is a homeodomain leucine zipper transcription factor involved in the establishment of bud axillary dormancy. In this work we have characterized the role of HB21 in the control of the inflorescence arrest at the end of flowering. HB21, together with HB40 and HB53, are upregulated in the inflorescence apex at the end of the flowering phase promoting the floral bud arrest associated with the process. We also show that ABA accumulation occurs in the inflorescence apex at the end of flowering in physiological conditions, and that this accumulation depends on HB genes. Our work has allowed us to propose a physiological role of ABA in the control of floral bud arrest at the end of flowering

overall_design: To obtain more clues on the mechanism and the regulatory networks acting downstream the HB genes in the control of inflorescence arrest we analyzed the transcriptomic response to changes in HB activity in this context. An HB21 dexamethasone inducible line (HB21ind) was used to overcome the redundancy with HB53 and HB40. We treated inflorescence apexes of 2 wab HB21ind lines (active meristems with low endogenous expression of HB21) with Dex or mock. Then, 6 hours post-treatment, we collected inflorescence apexes. 3 independent biological replicates for each treatment were used for RNA sequencing. Transcripts with a log2 fold change (FC) >1 and <-1, and a p-adjusted value < 0.05 were considered as differentially expressed genes (DEG) and selected for further analysis. We obtained 1143 DEGs, 471 activated and 672 repressed by HB21 induction

first: Verónica

last: Sánchez-Gerschon

first: Cristina

last: Ferrándiz