title: DNA methylation insulates exons from CTCF loops with nuclear speckles  (HiChIP)

overall_design: CTCF HiChIP for K562 and HCT116 cells treated with a DNA methylation inhibitor (DNMT1i) and DMSO control. Also, CTCF HiChIP  for speckle dTAG knockin K562 cells treated with dTAG-13 for speckle depletion and DMSO control. All experiments were performed in biolocial duplicate.


title: Transcriptome analysis of multiple myeloma cells (HB, KB) and cells (HA, KA) that were not sorted by microfluidic chip

status: Public on Nov 11 2024

city: 南京

first: yang

last: shu

state: 江苏

address: xianlin road

country: China

institute: Nanjin university of Chinese medicin

type: Expression profiling by high throughput sequencing

summary: Transcriptome sequencing was used to analyze changes in related signaling pathways and gene expression in colon cancer cells when SRD5A1 was knocked down.

overall_design: Two strains and two cell types were examined

first: Shu

last: Yang

first: Mengjie

last: Guo


title: DNA methylation insulates exons from CTCF loops with nuclear speckles (RNA-Seq)

city: Cambridge

first: Brian

last: Liau

state: MA

address: 12 Oxford St.

department: Department of Chemistry and Chemical Biology

country: USA

institute: Harvard University

summary: CTCF is necessary for the formation and maintenance of many DNA loops and Topologically Associating Domains, but the genomic features that influence CTCF looping are incompletely understood. We characterized the downstream effects of treating cells with a DNMT1 inhibitor and acute depletion of nuclear speckles to study the factors that influence CTCF looping.

overall_design: Comparative gene expression profiling analysis of full-length RNA-seq data for K562 and HCT116 cells treated with a DNA methylation inhibitor (DNMT1i) and DMSO control. Also, comparative gene expression profiling analysis of full-length RNA-seq data for speckle dTAG knockin K562 cells treated with dTAG-13 for speckle depletion and DMSO control. All experiments were performed in biolocial triplicate.

middle: B

first: Shelby

middle: A

last: Roseman

first: Allison

middle: P

last: Siegenfeld

first: Ceejay

last: Lee

first: Nicholas

middle: Z

last: Lue


title: Research of lncRNA expression signatures for four molecular subtype of breast cancer

city: Guangdong,Guangzhou

first: He

middle: Yong

last: yin

address: No. 111, Liuhua Road, Yuexiu district, Guangzhou, Guangdong Province, China

department: Department of Laboratory Medicine

institute: Theatre Command of PLA

type:
Expression profiling by array
Non-coding RNA profiling by array

summary: To screen promising serum-based lncRNA biomarkers for different molecular subtype of breast cancer,we uesed a genome-wide lncRNA microarray to identify differentially expressed lncRNAs from serum samples of patients with four different molecular subtype of BC and healthy controls.

overall_design: We selected 15 serum samples—three from luminal A BC patients, three from luminal B BC patients, three from Her-2+ BC patients, three from TNBC patients and three from healthy controls—to perform a genome-wide lncRNA microarray.

first: Yongyin

last: He


title: DNA methylation insulates exons from CTCF loops with nuclear speckles (ChiP-Seq)

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: CTCF ChIP-seq for K562 and HCT116 cells treated with a DNA methylation inhibitor (DNMT1i) and DMSO control. Also, CTCF ChIP_seq data for speckle dTAG knockin K562 cells treated with dTAG-13 for speckle depletion and DMSO control. All experiments were performed in biolocial duplicate.


title: Comparison of bronchial epithelial cells obtained by bronchoscopy from severe asthma patients before and after thermoplasty treatment

city: Leiden

first: Abilash

last: Ravi

address: Albinusdreef 2

department: Department of Pulmonology

country: Netherlands

institute: Leiden University Medical Center

summary: In this study we explore the underlying differences in bronchial epithelial cells from severe asthma patients obtained before and after thermlasty treatment. The effect of the treatment on bronchial epithelial cells will be revealed based on the genes differentialy expressed post treatment.

overall_design: Bronchoscopy was performed in severe asthma patients  before (n=23) and after (n=23) thermoplasty treatment to obtain bronhial epithelial cells. These bronchial brushes were directly subjected to RNA sequencing

first: René

last: Lutter


title: Mutant IDH impairs chromatin binding by PDGFB to promote chromosome instability

status: Public on Nov 10 2024

city: Houston

first: Akdes

last: Serin Harmanci

state: TX

address: One Baylor Plaza

institute: Baylor College of Medicine

summary: Non-canonical roles for growth factors in the nucleus have been previously described, but their mechanism of action and biological roles remain enigmatic. Platelet-derived growth factor B (PDGFB) can drive formation of low-grade glioma and here we show that it localizes to the nucleus of human glioma cells where it binds chromatin to preserve genome stability and cell lineage. Failure of PDGFB to localize to the nucleus leads to chromosomal abnormalities, aberrant heterochromatin architecture and accelerated tumorigenesis. Furthermore, nuclear localization of PDGFB is reliant upon the expression levels and mutation status of isocitrate dehydrogenase (IDH). Unexpectedly, we identified macrophages as the predominant source of PDGFB in human, finding that immune-derived PDGFB can localize to the nucleus of glioma cells. Collectively, these studies show that immune derived PDGFB enters the nucleus of glioma cells to maintain genomic stability, while identifying a new mechanism by which IDH mutations promote gliomagenesis.

overall_design: Single-celll RNA-sequencing of piggyBac in utero electroporation tumors

first: Rachel

middle: N

last: Curry

first: Benjamin

last: Deneen

first: Ganesh

last: Rao


title: ADSC-Exos can improve acute lung injury by regulating alveolar macrophage polarization through IRF7/NLRP3

city: Harbin

first: JingYi

last: Ren

address: No. 148, BaoJian Road, Nangang District, Harbin City, Heilongjiang Province

institute: Second Affiliated Hospital of Harbin Medical University

summary: Alveolar macrophages (AMs) are crucial for pulmonary defense and immune regulation. Exosomes from adipose-derived mesenchymal stem cells (ADSC-Exos) have emerged as a promising therapy for inflammatory lung diseases by modulating immune responses. This study investigates the ability of ADSC-Exos to alleviate inflammation in acute lunag injury (ALI), a condition often triggered by sepsis and characterized by lung permeability and respiratory failure.

overall_design: After treatment with ADSC-Exos, macrophages were subjected to RNA sequencing to identify differentially expressed genes (DEGs) that could reveal the molecular mechanisms underlying the immunomodulatory effects of ADSC-Exos on macrophage polarization.

first: Jingyi

first: Guanhong

last: Lei

first: Ajing

last: Dong

first: Shuyan

last: Cao


title: Deep mutagenesis of PDGF-B reveals sequence constraints for homodimerization and high affinity receptor interactions

city: Urbana

first: Erik

last: Procko

state: IL

address: 601 S Goodwin Ave

department: Biochemistry

institute: University of Illinois

summary: Platelet-derived growth factors (PDGF) are disulfide-bonded dimers that act on PDGF receptors (PDGFR) to stimulate cell proliferation, differentiation, migration, and/or function.  There are multiple isoforms of both the ligand and receptor, which combined with the potential for heterodimerization, gives the system great complexity.  Different ligands may be promiscuous or specific for receptor partners.  To better understand how ligand sequence relates to receptor recognition, the mutational landscape of PDGF-B for binding to the high affinity receptor PDGFRbeta was experimentally determined by deep mutational scanning.  A PDGF-B library containing all possible single amino acid substitutions was displayed on the surface of yeast and sorted for binding to the PDGFRbeta ectodomain.  Following deep sequencing, the enrichment or depletion of all mutations was calculated as a proxy for relative activity.  All PDGF-B cysteines forming three intra- and two interchain disulfides are highly conserved, indicating that PDGF-B is correctly folding into disulfide-linked dimers on the yeast surface.  Indeed, several mutations at the ligand dimer interface are enriched and may enhance dimerization through increased hydrophobic packing or reduced electrostatic repulsion.  Residues from the protruding PDGF-B subunit in contact with the receptor are tightly conserved, whereas interfacial residues from the receding subunit are mutationally tolerant.  There are multiple enriched mutations at the receptor interface that the scan predicts increase PDGF-BB–PDGFRbeta affinity.  The data may prove insightful for engineering PDGF ligands biased towards forming homodimers with increased receptor affinity.

overall_design: The mature protein sequence of PDGF-B (S1 to A104; synthetic codon-optimized sequence) was expressed on the yeast surface fused downstream of Aga2p, with a C-terminal c-myc epitope tag.  A single site-saturation mutagenesis (SSM) library was generated by overlap extension PCR, encoding all possible PDGF-B single amino acid substitutions.  Yeast cultures expressing the library were incubated with a soluble extracellular fragment of PDGFRbeta fused to IgG Fc.  Surface expressed ligand and bound receptor were detected with fluorescent antibodies targeting the c-myc tag and IgG Fc moiety.  Yeast positive for expressed PDGF-B and showing either high or low bound PDGFRbeta were collected by fluorescence-activated cell sorting (FACS).  Plasmid DNA was extracted from the cultures before and after sorting, from which the enrichment or depletion of all PDGF-B sequence variants was determined following Illumina sequencing.

first: Heather

middle: J

last: Young


title: Targeted degradation of host messenger RNA by a bacterial pathogen [CLIP-seq]

city: Clayton

first: Kathleen

last: McCaffrey

state: VIC

address: 25-31 Wright Street

country: Australia

institute: Hudson Institute of Medical Research

summary: Post-transcriptional processing and modification of messenger RNA (mRNA) regulates gene expression in eukaryotes by dictating the stability, localisation and translation of newly synthesised transcripts 1. These epitranscriptomic events are coordinated by an extensive network of RNA-binding proteins 2,3. Here we observed that the bacterial pathogen, Legionella pneumophila, caused the selective degradation of host cellular mRNAs encoding factors involved in glycolysis and related metabolic pathways. Screening of a library of L. pneumophila deletion mutant strains revealed a single effector protein, LegC4, that mediated the post-transcriptional degradation of host mRNAs encoding key glycolytic enzymes, thereby suppressing host glycolysis during infection. Using CLIP-seq and complementary methods, we observed that LegC4 bound to mature processed host mRNA recognising a guanine (G)-rich motif that was overrepresented within mRNAs targeted for degradation. In vitro activity assays showed that LegC4 harboured intrinsic RNase activity and structural determination of a catalytically inactive mutant of LegC4 in complex with single-stranded RNA revealed a unique RNA-binding domain 4. The selective binding and degradation of host mRNA by LegC4 reveals a previously undescribed mechanism of bacterial effector protein activity targeting the host epitranscriptome.

overall_design: To isolate the host RNA-binding targets of Legionella effector protein LegC4, THP-1 macrophages were infected with a Legionella pneumophila 130b strain (deltalegC4) carrying a p4HALegC4-protein expression plasmid or p4HA control plasmid. We then performed cross-linking immunoprecipitation (CLIP) using an anti-HA antibody and RNA-seq of samples isolated by LegC4 (LegC4 IP) versus the control (Control IP) across four independent experiments.

first: Elizabeth

middle: L

last: Hartland


title: Gene expression divergence between locally adapted inland annual and coastal perennial ecotypes of Mimulus guttatus across developmental stages

city: EAST LANSING

first: David

middle: Bryant

last: Lowry

state: MI

address: 612 WILSON RD RM 166

department: Plant Biology

institute: Michigan State University

summary: The action of natural selection across heterogeneous natural landscapes drives local adaptation and the formation of plant ecotypes, the precursors to new species. Plant ecotypes typically differ greatly in morphology, physiology, and development, yet we have a poor understanding of the underlying genetic basis of this divergence. Despite their importance, studies of the molecular underpinnings of ecotypic divergence through developmental stages are rare. In this study, we compared gene expression at different developmental time points between two locally adapted populations derived from the coastal perennial and inland annual ecotypes of the yellow monkeyflower, Mimulus guttatus. We conducted gene co-expression network analyses to identify putative genetic and molecular mechanisms driving ecotypic divergence and evaluated gene ontology enrichment. Overall, we found significant global expression differences between the ecotypes and among developmental stages. We also found evidence to support the hypothesis that interacting hormone pathways, especially the gibberellin and jasmonic acid pathways, may play a key role in annual versus perennial ecotype divergence. Further, genes within known chromosomal inversions were more likely to be differentially expressed than genes in colinear regions, but only in leaves and not for floral buds. Collectively, our results reinforce our existing hypotheses about how ecotype formation has occurred in this system through shifts in hormone biosynthesis/signaling and help advance our understanding of the evolution of annuality versus perenniality in plants.

overall_design: To identify patterns of gene expression divergence between the ecotypes, we compared gene expression for leaves and floral buds collected from one coastal perennial (SWB-4) and one inland annual (LMC-17) accession. Developmentally equivalent leaf pairs and floral buds were collected in a time series manner. Only one tissue was collected per plant to avoid induced responses and repeated measures. For the inland annual plants, we sampled at the two-leaf, four-leaf, and floral bud stages because plants often flowered after producing four true leaves. Because the coastal perennial plants flowered at a later developmental stage, we sampled at the two-leaf, four-leaf, six-leaf, eight-leaf, and floral bud stages. All tissue samples were collected before anthesis. Overall, we collected 10 biological replicates for each developmental stage x ecotype combination (N = 80 total tissue samples).

first: Jason

middle: D

last: Olsen

first: Billie

last: Gould

first: Yani

last: Chen


title: Ketosis Induced Impairment of Fetal Kidney Development

city: Jerusalem

first: Inbar

last: Plaschkes

address: The Hebrew University of Jerusalem - Ein Kerem

department: The Faculty of Medicine - Ein Kerem

country: Israel

institute: HUJI

summary: Maternal ketosis during pregnancy can impact fetal development, yet its effects on kidney development are not well understood. This study investigates the impact of maternal ketosis on offspring nephrogenesis using two mouse models: a ketogenic diet and β-hydroxybutyrate supplementation. Pregnant mice were subjected to either intervention from conception until birth. Offspring kidneys were analyzed at birth and in adulthood for nephron number, glomerular density, and renal function. Nephron progenitor cells (NPCs) were isolated from embryonic kidneys and analyzed using RNA sequencing, immunostaining, and quantitative PCR. Both ketosis models resulted in significantly reduced glomerular density at birth and a 25% decrease in nephron number in adult offspring,  accompanied by impaired renal function. RNA sequencing revealed over 1,000 differentially expressed genes in the ketogenic diet group and 164 in the β-hydroxybutyrate group, with 67 overlapping genes. Pathway analysis showed downregulation of cell cycle and Myc target pathways, and upregulation of inflammatory pathways in both models. Immunostaining confirmed a 40% reduction in NPC proliferation and decreased c-Myc expression under ketotic conditions. Additionally, ketosis increased TNFα expression and activated the NFκB pathway in NPCs. These findings provide the first evidence linking maternal ketosis to impaired nephrogenesis, demonstrating a negative impact on offspring kidney development by altering NPC proliferation, Myc signaling, and inflammatory responses. This study highlights potential risks associated with ketogenic diets or other ketosis-inducing conditions during pregnancy.

overall_design: 12 Pregnant female mice were randomly assigned to one of three regimens from conception until embryonic day E17.5: 4 were assigned a control diet, 4 were assigned a control diet with supplementation of β-hydroxybutyrate, and 4 were assigned the ketogenic diet. On embryonic day E17.5, the embryonic kidneys from the entire litter were extracted, and the nephron progenitor cells were sorted and pooled. The RNA was extracted from the cells and sequenced. Each sample represents one litter.

first: Yaniv

last: Makayes

first: Athar

last: Amleh

first: Morris

last: Nechama

first: Oded

last: Volovelsky


title: Single-cell and spatial transcriptomics identify COL6A3 as a prognostic biomarker in undifferentiated pleomorphic sarcoma

city: Dallas

middle: C

last: Klein

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

summary: Undifferentiated pleomorphic sarcoma (UPS) and related tumors are the most common type of soft tissue sarcoma. However, this spectrum of tumors has different etiologies with varying rates of metastasis and survival. Two dermal-based neoplasms in this class of pleomorphic sarcomas, atypical fibroxanthoma (AFX) and pleomorphic dermal sarcoma (PDS), are challenging to differentiate at initial biopsy but vary significantly in prognosis. We performed single-cell transcriptomics on five AFX and PDS biopsy specimens as well as both single-cell and spatial transcriptomics on one PDS excision specimen to better characterize these tumors. The top differential genes between AFX and PDS were predictive of overall survival in 17 other cancers included in the Human Protein Atlas. Of these genes, COL6A3 and BGN predicted overall survival and metastasis-free survival in independent cohorts of 46 and 38 UPS tumors, respectively. COL6A3 was most predictive of overall survival in UPS patients and outperformed an established sarcoma prognostic gene panel at predicting metastasis in UPS.

overall_design: 10X Visium spatial transcriptomics was performed on a PDS excision specimen by CD Genomics

first: Lei

last: Wang

first: Douglas

last: Strand

first: Chewlan

last: Lastufka

first: Gregory

last: Hosler

first: Gary

last: Hon


title: RNA-seq analysis after MYB (L)/(S) overexpression in Jurkat cells with dTAG-mediated MYB depletion.

city: Singapore

first: Rui

last: Yokomori

address: 14 Medical Drive

country: Singapore

institute: Cancer Science Institute of Singapore, National University of Singapore

summary: RNA-seq analysis was performed in a T-ALL cell line (Jurkat) with FKBP tag knock-in at the MYB locus to analyze gene expression changes after MYB (L)/(S) overexpression in dTAG-mediated MYB-depleted cells.

overall_design: Lentiviral transduction was carried out in FKBP-MYB Jurkat cells to overexpress MYB (L)/(S). Total RNA was harvested after MYB overexpression and dTAG treatment and RNA-seq analysis was performed.

first: Xiaoman

last: Shao

first: Takaomi

last: Sanda


title: ISO-seq analysis of MYB isoforms in T-ALL cell lines and patient-derived xenografts

summary: ISO-seq analysis was performed for two T-ALL cell lines (Jurkat and MOLT-4) and patient-derived xenografts (DFCI09 and DFCI15) after pulldown with MYB-specific probes to identify MYB isoforms

overall_design: Total RNA was harvested from Jurkat, MOLT-4, DFCI09, and DFCI15, pulldown was performed with MYB-specific probes to enrich for MYB transcripts and subject to ISO-seq.


title: Comparison of bronchial epithelial cells obtained by bronchoscopy from mild asthma patients, moderate asthma patients, severe asthma patients and healthy controls

first: Abilash

last: Ravi

summary: In this study we explore the underlying differences in bronchial epithelial cells from asthma patinets compared to healthy controls. In addition we also explore the differential gene expression of severe asthma patients compared to mild and moderate asthma patients to determine if there are genes that lead to severity of the disease

overall_design: Bronchoscopy was performed in healthy controls (n=16), mild asthma patients (n=17), moderate asthma patients (n=5) and severe asthma patients (n=17) to obtain bronhial epithelial cells and were directly subjected to RNA sequencing

first: René

last: Lutter


title: RNA-seq analysis with spike-in RNA after dTAG-mediated MYB depletion in Jurkat cells

type: Expression profiling by genome tiling array

summary: RNA-seq analysis with spike-in was performed in a T-ALL cell line (Jurkat) with FKBP tag knock-in at the MYB locus to analyze gene expression changes after dTAG-mediated MYB depletion.

overall_design: Total RNA was harvested from FKBP-MYB knock-in Jurkat cells after DMSO or dTAG treatment and RNA-seq analysis was performed.


title: ATAC-seq analysis after dTAG-mediated MYB depletion in Jurkat cells

summary: ATAC-seq analysis was performed in a T-ALL cell line (Jurkat) with FKBP knock-in at MYB locus to analyze chromatin accessibility after dTAG-mediated depletion.

overall_design: The cells are incubated with Tn5 transposase. Tagmented DNA fragments are purified with Zymo DNA purification kit. ATAC libraries are purified and sequenced on Illumina NovaSeq at GENEWIZ Azenta Life Sciences Co. Ltd.


title: TNF-α inhibits the chemotherapy resistance caused by upregulation of the PERK-ATF4 pathway in colorectal cancer cells

city: Hangzhou

first: Yifan

last: Zhao

address: Banshan

institute: Zhejiang Cancer Hospital

summary: The unfolded protein response (UPR) is a set of important pathways important for maintaining endoplasmic reticulum homeostasis. Recent evidence suggests that the UPR plays an important role in chemo-resistance. However, the underlying mechanisms are not well understood. We previously found that the PERK pathway, one of three branches of the UPR pathway, is crucial for the resistance of colorectal cancer (CRC) cells to 5-fluorouracil. In this study, we demonstrated that activating transcription factor 4 (ATF4), the key downstream factor of the PERK pathway, is overexpressed in human CRCs and associated with a poor prognosis. Loss of ATF4 sensitized CRC cells to multiple chemotherapy drugs. RNA-seq analysis revealed that the TNF-α signaling pathway was significantly induced upon chemotherapy drug treatment while repressed by ATF4-knockdown. Addition of TNF-α can further potentiate the cytotoxic effects of chemotherapy drugs to ATF4-knockdown cells, highlighting a potential role of the TNF-α signaling pathway in regulating the ATF4-mediated drug sensitivity modulation. In summary, our findings provide a promising approach to overcoming chemotherapy resistance in colon cancer.

overall_design: To explore the role of ATF4 in the development of chemotherapy resistance in CRC cells, mRNA-sequencing analysis was performed on the negative control shScramble SW620 cells and ATF4 knockdown SW620 cell. Additionally, we treated both groups of cells with 5μM 5-FU for 24 hours or 48 hours to observe the changes in mRNA expression following drug treatment.

first: Xiaofu

last: Yu

first: Zhong

last: Shi


title: RNA-seq analysis after dTAG-mediated MYB depletion in Jurkat cells

summary: RNA-seq analysis was performed in a T-ALL cell line (Jurkat) with FKBP tag knock-in at the MYB locus to analyze gene expression changes after dTAG-mediated MYB depletion.


title: CUT&RUN analysis for phospho-MYB and active histone marks in FKBP-MYB Jurkat cells.

summary: CUT&RUN analysis was performed in Jurkat cells with FKBP knock-in at the MYB locus to analyze DNA bindings of phospho-MYB, H3K27ac, H3K4me3 after dTAG-mediated depletion.

overall_design: Jurkat cells were incubated with CUTANA pA/G-Mnase. Chromtin fragments were purified utilizing a Cutana DNA purification kit. Libraries were generated using a NEBNext Ultra II DNA library prep kit and analyzed on Illumina NovaSeq at GENEWIZ Azenta Life Sciences Co. Ltd.


title: Novel Pharmacologic Inhibition of Lysine-specific Demethylase 1 as a Potential Therapeutic for Glioblastoma [RNA-seq]

city: Nagoya

first: Keiko

last: Shinjo

state: Aichi

address: 65 Tsurumai, Showa-ku

department: Cancer Biology

country: Japan

institute: Nagoya Univ. Graduate School of Medicine

summary: Lysine-specific demethylase 1 (LSD1/KDM1A) is a pivotal epigenetic enzyme that contributes to several malignancies including malignant glioma. LSD1 is a flavin adenine dinucleotide dependent histone demethylase that specifically targets histone H3 lysine (K) 4 mono- (me1) and di-methylation (me2) and H3K9me1/2 for demethylation. Herein we report the development of an LSD inhibitor, S2172, which efficiently penetrates the blood-brain barrier. S2172 effectively suppresses LSD1 enzymatic activity, resulting in the depletion of cell growth both in vitro in glioma stem cells (GSCs) (mean half-maximal inhibitory concentration (IC50) of 13.8 μM) and in vivo in a GSC orthotopic xenograft mouse model. Treatment with S2172 robustly reduced the expression of the stemness-related genes MYC and Nestin in GSC cells. Consistent with this, chromatin immunoprecipitation-sequencing revealed a significant S2172-dependent alteration in H3K4me2/H3K4me3 status. Furthermore, we identified 284 newly acquired H3K4me2 peak regions after S2172 treatment, which were encompassed within super-enhancer regions. The altered H3K4me2/H3K4me3 status induced by S2172 treatment affected the expression of genes related to tumorigenesis. Our data suggest that targeting LSD1 with S2172 could provide a promising treatment option for glioblastomas, particularly due to targeting of GSC populations.

overall_design: we performed RNA-seq analysis in GSC1228 cells treated with either DMSO or S2172.

first: Yutaka

last: Kondo

first: Takashi

last: Umehara


title: Transcription factor EB affects the thrombospondin-1 /focal adhesion pathway and inhibits cardiac fibroblast transformation following early acute myocardial infarction

city: Shenzhen

first: cong

last: liu

address: 628 Zhenyuan Road, Guangming District, Shenzhen City

institute: Seventh Affiliated Hospital, Sun Yat-sen University

summary: Acute myocardial infarction (AMI) is currently the most common cause of fibrosis in the heart and has been reported to be closely associated with heart failure (HF). The transformation of cardiac fibroblasts (CFs) into myofibroblasts is key to the process of cardiac fibrosis, where CFs serve as the main effector cells. Accumulating evidence suggests that focal adhesions (FAs) regulate the transformation of CFs. Furthermore, transcription factor EB (TFEB) upregulates the transcriptional expression of genes involved in lysosome and autophagosome biogenesis following AMI. This study investigated whether TFEB directly targets and inhibits the activation of CFs and elucidated the underlying pathomechanisms. We performed a transcriptome analysis employing RNA sequencing in R26-LSL-TFEB [+/+]; Acta2-cre mice. Our study presents the first detailed RNA expression profile of CFs following AMI, demonstrating that TFEB regulates the expression of several RNAs involved in the transformation of CFs, including those associated with extracellular matrix (ECM) receptor pathways and FAs. Thrombospondin-1 (Thbs1) mRNA and protein were markedly upregulated in CFs. Bioinformatic prediction and chromatin immunoprecipitation identified that TFEB binds to the Thbs1 promoter. Experimental validation at both RNA and protein levels demonstrated that TFEB affects the binding of Thbs1 to its receptors and the activation of FAs. Concurrently, TFEB downregulates the expression of α-smooth muscle actin (α-SMA). Taken together, our results highlight that targeting the regulation of Thbs1/FA signaling in CFs via TFEB may be a promising therapeutic approach for cardiac fibrosis.

first: Cong

last: Liu

first: Qiang

last: Zhang

first: Hongyan

last: Wei

first: Dawang

last: Zhou

first: Bo

last: Li

first: Jingge

last: Cheng

first: Xiaoxing

last: Liao

first: Chunlin

last: Hu

first: Yuanzheng

last: Lu


title: Novel Pharmacologic Inhibition of Lysine-specific Demethylase 1 as a Potential Therapeutic for Glioblastoma [ChIP-seq]

overall_design: To precisely evaluate the effects of S2172 on histone modifications at a genome-wide scale, we performed ChIP-seq analysis in GSC1228 cells treated with either DMSO or S2172.


title: Explore the gene regulation mechanism under high temperature and low dissolved oxygen stress in the sea cucumber Apostichopus japonicus by high-throughput RNA-seq technology

city: Qingdao

first: Dongxue

last: Xu

address: Changcheng road No.700

institute: Qingdao Agricultural University

summary: High-throughput RNA-seq technology was used to explore the gene regulation mechanism under high temperature and low dissolved oxygen stress.

overall_design: In the control group, the temperature was maintained at 18°C and the dissolved oxygen was maintained at 3mg/L. In the high temperature group, heating rods were used to raise the temperature to 26°C. In the low oxygen group, nitrogen was injected into the water to make the dissolved oxygen reach 3mg/L. In the combined stress group, the temperature was 26°C and the dissolved oxygen was 3mg/L. After 6h of treatment, the intestines of Apostichopus japonicus were removed, frozen in liquid nitrogen, and then placed at -80°C until the end of analysis.

first: Wenqi

last: Song


title: TE-Seq: A Transposable Element Annotation and RNA-Seq Pipeline

city: Providence

first: Maxfield

last: Kelsey

address: 225 Dyer St.

institute: Brown University

summary: The TE-Seq pipeline conducts an end-to-end analysis of RNA sequencing data, examining both genes and TEs. It implements the most current computational methods tailor-made for TEs, and produces a comprehensive analysis of TE expression at both the level of the individual element and at the TE clade level. Furthermore, if supplied with long-read DNA sequencing data, it is able to assess TE expression from non-reference (polymorphic) loci. As a demonstration, we analyzed proliferating, early senescent, and late senescent lung fibroblast RNA-Seq data, and created a custom reference genome and annotations for this cell strain using Nanopore sequencing data. We found that several retrotransposable element (RTE) clades were upregulated in senescence, which included non-reference, intact, and potentially active elements.

overall_design: We applied our pipeline to RNA-Seq data from our laboratory on LF1 cells spanning three biological conditions: LF1 cells were passaged to replicative senescence, and were harvested 4 and 16 weeks later, yielding early senescence (ESEN) and late senescence (LSEN) conditions. Early passage proliferating LF1 cells (PRO) were used as a control. Poly-A selected, stranded, 150bp paired-end libraries were sequenced in quadruplicate.

middle: M

first: Radha

last: Kalekar

first: John

last: Sedivy


title: Mutant IDH impairs chromatin binding by PDGFB to promote chromosome instability [scATAC-Seq]

first: Akdes

last: Serin Harmanci

summary: Non-canonical roles for growth factors in the nucleus have been previously described, but their mechanism of action and biological roles remain enigmatic. Platelet-derived growth factor B (PDGFB) can drive formation of low-grade glioma and here we show that it localizes to the nucleus of human glioma cells where it binds chromatin to preserve genome stability and cell lineage. Failure of PDGFB to localize to the nucleus leads to chromosomal abnormalities, aberrant heterochromatin architecture and accelerated tumorigenesis. Furthermore, nuclear localization of PDGFB is reliant upon the expression levels and mutation status of isocitrate dehydrogenase (IDH). Unexpectedly, we identified macrophages as the predominant source of PDGFB in human, finding that immune-derived PDGFB can localize to the nucleus of glioma cells. Collectively, these studies show that immune derived PDGFB enters the nucleus of glioma cells to maintain genomic stability, while identifying a new mechanism by which IDH mutations promote gliomagenesis.

overall_design: Single-celll ATAC-sequencing of piggyBac in utero electroporation tumors

first: Curry

last: Rachel Naomi

first: Deneen

last: Benjamin

first: Rao

last: Ganesh


title: Mechanism of enhancing chemotherapy efficacy in pancreatic ductal adenocarcinoma with paricalcitol and hydroxychloroquine

status: Public on Nov 09 2024

city: Indianapolis

first: Ashiq

last: Masood

state: IN

address: Melvin and Bren Simon Comprehensive Cancer Center, Indiana University School of Medicine

department: Hematology & Oncology

institute: IU School Of Medicine

summary: Pancreatic ductal adenocarcinoma (PDAC) has a minimal (<15%) five-year existence, in part due to resistance to chemoradiotherapy. Previous research reveals the impact of paricalcitol (P) and hydroxychloroquine (H) on altering the lysosomal fusion, decreasing stromal burden, and triggering PDAC to chemotherapies. This investigation aims to elucidate the molecular properties of the H and P combination and its potential in sensitizing PDAC to gemcitabine (G). PH potentiates the effects of G in in vitro, orthotopic mouse models, and a patient-derived xenograft model of PDAC. Proteomic and single-cell RNAseq analyses reveal that GPH treatment upregulates autophagy and ER stress-related transcripts. GPH treatment decreases the number of Ki67, FAP, and alpha-SMA-expressing fibroblasts with a decrease in autophagy-related transcripts. The GPH treatment increases M1 polarization, CD4+, and CD8+ T-cells and reduces the CD4+ and CD8+ Tregs. These effects of GPH were confirmed in paired biopsies obtained from patients treated in a clinical trial (NCT04524702).

overall_design: This investigation aims to elucidate the molecular properties of the hydroxychloroquine (H) and paricalcitol (P) combination and its potential in sensitizing pancreatic ductal adenocarcinoma (PDAC) to gemcitabine (G). Proteomic and single-cell RNAseq analyses will reveal that GPH treatment upregulates autophagy and ER stress-related transcripts.

first: Purnachandra Nagaraju

last: Ganji

first: Madhu Sudhana

last: Saddala

first: Jeremy

last: Foote

first: Ateeq

last: Khaliq

first: Bassel

middle: F

last: El-Rayes


title: TTC22 increasing total m6A RNA level and colon cancer metastasis via RPL4-WTAP-YTHDF1 axis

city: Xiamen

first: you

middle: a

last: bin

state: Fujian

address: 55 Zhenhai Road, Siming District, Xiamen

institute: the First Affiliated Hospital of Xiamen University

summary: WTAP is an essential component of the RNA N-6-methyladenosine (m6A) modification complexes that guides METLL3-METLL14 heteroduplexes to target RNAs in the nucleus of mammalian cells. Through mining the genotype-tissue expression (GTEx) datasets, we initially found that TTC22 expression was highly correlated with WTAP and FTO in many normal human tissues. Our experimental results indicate that TTC22 could directly capture RNA binding protein RPL4, induce the binding between RPL4 and WTAP mRNA in the cytoplasm, which increased the m6A level, induced alterative splicing, enhanced the stability and translation efficiency of WTAP mRNA, and consequently upregulated the level of total m6A RNA. These results indicate that WTAP mRNA is a m6A target and there is a positive feedback loop between total m6A and WTAP expression. YTHDF1 was found to be an essential m6A WTAP mRNA binding protein. Downregulation of RPL4, WTAP, or YTHDF1 expression could reverse TTC22-enhanced total m6A RNA level. m6A-specific antibody immunoprecipitated RNA-sequencing (meRIP-seq) demonstrated that TTC22 caused dramatic expression changes of genes related to metabolic pathways, ribosome biogenesis, and RNA spliceosome. Furthermore, we also found that TTC22 upregulated the expression of epithelial-mesenchymal transition (EMT)-related gene SNAI1 via m6A, and promoted metastasis of colon cancer in vitro and in mice. In conclusion, our study illustrates that WTAP mRNA is a m6A target using YTHDF1 as the binding protein. TTC22 could upregulate the levels of WTAP expression and total m6A RNA through the PRL4 binding. The m6A-mediated upregulation of SNAI1 expression may contribute to TTC22-enhanced colon cancer metastasis.

overall_design: meRIP-seq performed in this study was designed to reveal the gene expression regulated by TTC22

first: Dajun

last: Deng

first: Abin

last: You

first: Wei

last: Tian


title: Decoding the chemical language of RiPPs from the untapped Archaea domain

city: Hong Kong

first: GAO

last: Ying

state: China

address: Hong Kong

department: Chemistry

institute: The university of Hong Kong

summary: Chemical communication is crucial in ecosystems with complex microbial assemblages. However, due to archaeal cultivation challenges, our understanding of the structure diversity and function of secondary metabolites (SMs) within archaeal communities is limited compared to the extensively studied and well-documented bacterial counterparts. Our comprehensive investigation into the biosynthetic potential of archaea, combined with metabolic analyses and the first report of heterologous expression in archaea, has unveiled the previously unexplored biosynthetic capabilities and chemical diversity of archaeal ribosomally synthesized and post-translationally modified peptide (RiPP). We have identified twenty-four new lanthipeptides of RiPPs exhibiting unique chemical characteristics, including a novel subfamily featuring an unexplored type with diamino-dicarboxylic (DADC) termini, largely expanding the chemical landscape of archaeal SMs. This sheds light on the chemical novelty of archaeal metabolites and emphasizes their potential as an untapped resource for natural product discovery. Additionally, archaeal lanthipeptides demonstrate specific antagonistic activity against haloarchaea, mediating the unique biotic interaction in the halophilic niche. Furthermore, they showcased a unique ecological role in enhancing the host's motility by inducing the rod-shaped cell morphology and upregulating the archaellum gene flgA1, facilitating the archaeal interaction with abiotic environments. These discoveries broaden our understanding of archaeal chemical language and provide promising prospects for future exploration of SM-mediated interaction.

overall_design: To investigate the function of lanthipeptide biosynthetic gene clusters (BGCs) in the motility activation assay, we collected the cell cultures of the corresponding heterologous expression strains with empty plasmid, BGC cib2 or BGC pel.

first: Zhiman

last: Song

first: Ying

last: Gao

first: Yongxin

last: Li


title: Targeted degradation of host messenger RNA by a bacterial pathogen

first: Kathleen

last: McCaffrey

summary: Post-transcriptional processing and modification of messenger RNA (mRNA) regulates gene expression in eukaryotes by dictating the stability, localisation and translation of newly synthesised transcripts 1. These epitranscriptomic events are coordinated by an extensive network of RNA-binding proteins 2,3. Here we observed that the bacterial pathogen, Legionella pneumophila, caused the selective degradation of host cellular mRNAs encoding factors involved in glycolysis and related metabolic pathways. Screening of a library of L. pneumophila deletion mutant strains revealed a single effector protein, LegC4, that mediated the post-transcriptional degradation of host mRNAs encoding key glycolytic enzymes, thereby suppressing host glycolysis during infection. Using CLIP-seq and complementary methods, we observed that LegC4 bound to mature processed host mRNA recognising a guanine (G)-rich motif that was overrepresented within mRNAs targeted for degradation. In vitro activity assays showed that LegC4 harboured intrinsic RNase activity and structural determination of a catalytically inactive mutant of LegC4 in complex with single-stranded RNA revealed a unique RNA-binding domain 4. The selective binding and degradation of host mRNA by LegC4 reveals a previously undescribed mechanism of bacterial effector protein activity targeting the host epitranscriptome.

overall_design: To investigate the role of Legionella effector protein LegC4 on host mRNA expression, THP-1 macrophages were infected with the Legionella pneumophila 130b strain (WT) or a mutant strain lacking the legC4 gene (deltalegC4). We then performed comparitive gene expression profiling of RNA-seq data from WT versus deltalegC4 infected cells from three independent experiments.

first: Elizabeth

last: Hartland


title: Differential gene expression in paired H146-iPAX5 vs. H146

city: Tianjin

first: Yujie

last: Hao

address: 22 Qixiangtai Road

institute: Tianjin Medical University

summary: RNAseq of SCLC cell line H146 with PAX5 knocked down. The goals of this study are to identify the function of PAX5 in SCLC.

overall_design: Examination of 6 samples of H146 cells, including 3 vector lines and 3 PAX5 knockdown lines.

first: Zhe

last: Liu


title: Apelin promotes Vascular Endothelial Growth Factor-C (VEGF-C)-induced lymphangiogenesis and metastasis in prostate cancer

city: Taichung

first: Chih-Hsin

last: Tang

address: 91 Xueshi

country: Taiwan

institute: China Medical University

summary: Prostate cancer is the most common cancer in men and is often associated with distant metastasis in its later stages. Lymphangiogenesis has been identified as a critical factor in cancer metastasis, and the adipokine apelin has been implicated in cancer progression and metastasis. However, researchers have yet to elucidate the mechanisms by which apelin regulates the key lymphangiogenic factor, Vascular Endothelial Growth Factor-C (VEGF-C), to promote distant metastasis in prostate cancer. This study identified a strong positive correlation between apelin levels and prostate cancer metastasis. Apelin stimulation was shown to upregulate VEGF-C expression, promoting the formation of new lymphatic vessels. Apelin treatment was also shown to downregulate miR-196a-5p expression via the proto-oncogene tyrosine kinase c-Src (c-Src) and Signal transducer and activator of transcription 3 (STAT3) signaling pathways, which regulates VEGF-C expression and lymphangiogenesis in prostate cancer cell lines. In an orthotopic mouse model, apelin inhibition prevented lymphangiogenesis and distant metastasis. These findings suggest that targeting apelin could be a promising therapeutic approach to preventing prostate cancer metastasis and lymphangiogenesis

overall_design: To explore the differentially expressed miRNAs under apelin treatment, PC-3 cells were treated with apelin (10 μg/mL) for 24 h in the culture medium, followed by miRNA sequencing.

first: Shan-Chi


title: Licochalcone B alleviates Crohn’s Disease injury by targeting FTO [meRIP-seq]

city: hefei

first: duo

last: ma

address: No.81 Meishan Road, Shushan District

institute: Anhui Medical University

summary: To investigate the mechanism of demethylase FTO in Crohn's disease，We used m6A MeRIP-seq data from three normal colon samples and three TNBS-induced IBD colon samples of C57 mice for gene expression profiling.

overall_design: Comparative gene expression profiling analysis of m6A MeRIP-seq data from three normal colon samples and three TNBS-induced IBD colon samples of C57 mice

first: Duo

last: Ma

first: Xinhua

first: Yaling

last: Hong

first: Xingxing

last: Zhang


title: Comparative evaluation of the biological characteristics of a novel retinoid X receptor agonist and bexarotene

first: Makoto

last: Inoue

address: 1-100 Kusumoto-cho, Chikusa-ku, Nagoya

department: School of Pharmacy

institute: Aichi Gakuin University

summary: Retinoid X receptor (RXR) is a crucial and distinctive member of the nuclear receptor superfamily, which is involved in regulating various physiological processes. RXR agonists have the potential to treat Alzheimer’s disease (AD). In this study, we identified a novel RXR agonist superior to existing drugs after extensively exploring the biological properties of 6-hydroxy-3’-propyl-[1,1’-biphenyl]-3-propanoic acid (6OHA), a compound synthesized in our laboratory based on the structure of magnaldehyde B. 6OHA exhibited higher selectivity for RXRα over retinoic acid receptor (RARα) and lower transcriptional activity for RXRg compared to the existing RXR agonist bexarotene (Bex). RNA-sequencing analysis, Gene Ontology, and Kyoto Encyclopedia of Genes and Genomes pathway analyses suggest that 6OHA and Bex exhibit similar gene expression patterns but have distinct transcriptional effects; 6OHA was more closely associated with chemotaxis and response to stimuli compared to Bex. Pharmacokinetic studies revealed that 6OHA exhibited faster intestinal absorption, reached higher concentrations in the brain and liver shortly after oral dministration, and was cleared from the body more rapidly than Bex, subsequently inducing target gene transcription in the brain. Bex increased serum triglyceride and decreased serum thyrotropin and free thyroxine levels, whereas 6OHA did not induce these adverse effects, attributable to the distinct properties of 6OHA as an RXR agonist compared to Bex. Our results highlight 6OHA as a promising RXR agonist for treating AD without any adverse effects.

overall_design:
Mouse microglial MG5 cells were treated with 6OHA or Bex at a concentration of 10 µM for 6 h, followed by extraction of total RNA. We then performed gene expression profiling using RNA-seq data from cells treated with 6OHA or Bex or untreated control (n=3).
Bexarotene (Bex), an established retinoid X receptor (RXR) agonist, has demonstrated neuroprotective and anti-neuroinflammatory effects, suggesting its potential for Alzheimer's disease (AD) treatment. However, concerns remain regarding the serious adverse effects associated with Bex, including hypertriglyceridemia, hypothyroidism, and hepatomegaly. In this study, we investigated the differences in agonist activity between 6OHA, a newly synthesized RXR agonist in our laboratory, and Bex, with the goal of identifying alternative RXR agonists that may be suitable for the treatment or prevention of AD.
Comparative gene expression profiling analysis of RNA-seq data for MG5 cells treated with 6OHA or BEX, or untreated cells.

first: Koji

last: Tomita

first: Ken-ichi

last: Nakashima

first: Eiji

last: Yamaguchi

first: Akichika

last: Itoh

first: Kaname

last: Tsutsumiuchi


title: The effect of 70% hepatectomy on G-MDSCs transcription profile at different time points

city: Ramat Gan

first: Niv

last: Pencovich

address: 2 Derech Sheba

department: Surgery and transplantation

institute: Sheba medical center

summary: Liver regeneration depends on sequential activation of pathways and cells involving the remaining organ in recovery of mass. Proliferation of parenchyma is dependent on angiogenesis. Understanding liver regeneration-associated neovascularization may be useful for development of clinical interventions. Myeloid-derived suppressor cells (MDSCs) promote tumor angiogenesis and play a role in developmental processes that necessitate rapid vascularization. We therefore hypothesized that the MDSCs could play a role in liver regeneration. Following partial hepatectomy, MDSCs were enriched within regenerating livers, and their depletion led to increased liver injury and postoperative mortality, reduced liver weights, decreased hepatic vascularization, reduced hepatocyte hypertrophy and proliferation, and aberrant liver function. Gene expression profiling of regenerating liver-derived MDSCs demonstrated a large-scale transcriptional response involving key pathways related to angiogenesis. Functionally, enhanced reactive oxygen species production and angiogenic capacities of regenerating liver-derived MDSCs were confirmed. A comparative analysis revealed that the transcriptional response of MDSCs during liver regeneration resembled that of peripheral blood MDSCs during progression of abdominal tumors, suggesting a common MDSC gene expression profile promoting angiogenesis. In summary, our study shows that MDSCs contribute to early stages of liver regeneration possibly by exerting proangiogenic functions using a unique transcriptional program.

overall_design: To investigate the effect of hepatectomy on the transcriptional profile of G-MDSCs, we performed RNA-seq on liver G-MDSCs at post-operative day (POD) 1, 2, 3 or 4 following 70% hepatectomy compared to a sham operation. 3 replicates per group were used.

first: Ido

last: Nachmany

first: Yoel

last: Bogoch

first: Ayelet

last: Sivan


title: Treatment-associated gene expression in hematopoietic stem/progenitor cells from patients with polycythemia vera (PV) [6 hour treatment]

city: Zurich

first: Ge

last: Tan

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich

country: Switzerland

institute: University of Zurich

summary: The objective of the study was to assess gene expression changes in CD34+ hematopoietic stem/progenitor cells from PV patients upon ex vivo treatment with clusterin (CLU), IKK-16, their combination, with hydroxyurea (HU) or with solvent control.

overall_design: CD34+ hematopoietic stem/progenitor cells from five different PV patients were treated with CLU, IKK-16, their combination, HU or solvent control, resulting in a total of 23 samples.

first: Fabienne

last: Meier-Abt


title: Corpus callosum bulk RNA sequencing of a cuprizone mouse model of demyelination

status: Public on Nov 08 2024

city: Cambridge

first: Timothy

middle: R

last: Hammond

address: 350 Water Street

institute: Sanofi

summary: We used the cuprizone mouse model of multiple sclerosis to determine whether Bruton's tyrosine kinase (BTK) inhibition could attenuate disease-relevant changes to central nervous system gene expression.

overall_design: The corpus callosum was dissected from the brains of a cuprizone mouse model of demyelination. Bulk RNA sequencing was then performed. A subset of mice had been treated with an inhibitor of Bruton’s tyrosine kinase (BTK) after disease induction.


title: H3K27me3 regulates macrophage cytokine transcription and impacts on Collagen Induced Arthritis [ChIP-Seq]

first: zhao

last: zhan

state: Shandong

address: No.23 HongKong East Road,Laoshan District

department: School of Medicine and Pharmacy

institute: Ocean University of China

summary: The role of epigenetic regulation has been introduced in the process of macrophage polarization and the pathogenesis of inflammatory diseases. As a repressive epigenetic marker, tri-methylation of lysine 27 on histone H3 (H3K27me3) was shown to be important for transcriptional gene expression regulation. Here, we comprehensively analysed H3K27me3 binding promoter sequences by ChIP-seq and corresponding genes function by RNA sequencing in two differentially polarized macrophage populations. The results revealed that H3K27me3 binds on the promoter regions of multiple critical cytokine genes and suppressed their transcription, especially in M-CSF derived macrophages but not GM-CSF derived counterparts. The in vivo study results suggested that symptoms of collagen induced arthritis (CIA) mice can be relieved by reversing the loss of H3K27me3 and reducing IL6 parasecretion of macrophages, suggesting that H3K27me3 might act as a switch in the pathological processes of rheumatoid arthritis (RA). Our results may provide a new approach for the treatment of inflammatory and autoimmune disorders.

overall_design: Examination of 2 different histone modifications in BMDM

first: Zhan

last: Zhao


title: Bulk RNA sequencing of human iPSC-derived microglia

summary: We used human induced pluripotent stem cell (iPSC)-derived microglia to determine whether Bruton's tyrosine kinase (BTK) inhibition could attenuate differential gene expression induced by Fc receptor stimulation.

overall_design: Bulk RNA sequencing was performed with human iPSC-derived microglia, treated with an IgG stimulus and/or an inhibitor of Bruton’s tyrosine kinase (BTK).


title: H3K27me3 regulates macrophage cytokine transcription and impacts on Collagen Induced Arthritis [ATAC-Seq]

overall_design: Examination of 2 different ATAC sample: GM-CSF and M-CSF induced BMDM.

first: Zhao

last: Zhan


title: Bulk RNA sequencing of a human iPSC-derived tri-culture

summary: We used a human induced pluripotent stem cell (iPSC)-derived tri-cultures, comprised of neurons, astrocytes, and microglia, to determine whether Bruton's tyrosine kinase (BTK) inhibition could attenuate differential gene expression induced by Fc receptor stimulation.

overall_design: Bulk RNA sequencing was performed with a human iPSC-derived tri-culture, consisting of neurons, microglia, and astrocytes. Tri-cultures had been treated with an IgG stimulus and/or an inhibitor of Bruton’s tyrosine kinase (BTK).


title: Effect of hyperoside on gene expression in K562 cells

city: hangzhou

first: junyi

last: wei

state: zhejiang

address: Yuhangtang Road

institute: zhejiang university

summary: To investigate the role of hyperoside in the regulation of gene expression in K562 cells, we treated K562 cells with hyperoside（2 mM) for 24h, RNA-seq data were obtained in control group and hyperoside group for gene expression profile analysis.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for human chronic myeloid cell lines with or without hyperoside intervention.

first: Junyi

last: Wei

first: Quanyou

last: Chai

first: Yuqiao

last: Qin

first: Long

last: Li

first: Chunling

last: Guo

first: Zhaoyang

last: Lu

first: Huimin

last: Liu


title: Signal recovery in single cell batch integration

city: Philadelphia

first: Andy

last: Minn

address: 421 Curie Blvd

institute: University of Pennsylvania

summary: Data integration to align cells across batches has become a cornerstone of single cell data analysis, critically affecting downstream results. Yet, how much biological signal is erased during integration? Currently, there are no guidelines for when the biological differences between samples are separable from batch effects, and thus, data integration involves a lot of guesswork: Cells across batches should be aligned to be “appropriately” mixed, while preserving “main cell type clusters”. We show evidence that current paradigms for single cell data integration are unnecessarily aggressive, removing biologically meaningful variation and introducing distortion. To remedy this, we present a novel statistical model and computationally scalable algorithm, CellANOVA, that harnesses experimental design to explicitly recover biological signals that are erased during single cell data integration. CellANOVA utilizes a “pool-of-controls” design concept, applicable across diverse settings, to separate unwanted variation from biological variation of interest. When applied with existing integration methods, CellANOVA allows the recovery of subtle biological signals and corrects, to a large extent, the data distortion introduced by integration. Further, CellANOVA explicitly estimates cell- and gene-specific batch effect terms which can be used to identify the cell types and pathways exhibiting the largest batch variations, providing clarity as to which biological signals can be recovered. These concepts are illustrated on studies of diverse designs, where the biological signals that are recovered by CellANOVA are validated by orthogonal assays. In particular, we show that CellANOVA is effective in the challenging case of single-cell and single-nuclei data integration, where it recovered subtle biological signals are can be validated and replicated by external data.

overall_design: To determine the effects of standard radiation on small intestine injury and regeneration, we performed time-course scRNA-sequencing. Wildtype C57BL/6 mice were treated with sham or 14Gy single-fraction whole-abdomen standard irradiation. Small intestines were harvested at various timepoints post-treatment, separated into the epithelial and lamina propria fractions, and subsequently sequenced.

first: Tristan

last: Lim

first: Clara

last: Morral Martinez


title: EOMES establishes mesoderm and endoderm differentiation potential through SWI/SNF-mediated global enhancer remodeling [ChIP-Seq]

city: Freiburg im Breisgau

first: Sebastian

last: Arnold

address: Albertstraße 25

department: Institute of Experimental and Clinical Pharmacology and Toxicology

country: Germany

institute: University Freiburg

summary: In this study we analysed the dynamic changes in the epigenetic landscape during first embryonic lineage decision following pluripotency exit. Here, mouse pluripotent epiblast cells segregate towards mesoderm and endoderm (ME) or neuroectoderm (NE). The analysis of chromatin accessibility, histone modifications and accompanied gene expression confirmed a bias of the epigenetic landscape towards NE fate while ME cis regulatory elements (CREs) are becoming accessible and active during lineage specification. We show that the default state of NE differentiation is actively overcome by the activity of the Tbx transcription factor (TF) EOMES binding to closed ME CREs. We found the ATP-dependent chromatin remodelling complex SWI/SNF is recruited by EOMES to target ME enhancers. The recruitment of the complex by EOMES leads to the remodelling of the enhancer landscape at ME genes. The ME enhancer landscape is remodelled by the activity of EOMES independent on gene expression genome wide.

overall_design: This study involves mouse embryonic stem cells (mESCs) of the following genotypes: wild type (WT), cells deficient for both Tbx TFs Eomes and Tbxt (dKO) and cells expressing Eomes:GFP, Eomes:ER or Tbxt:GFP fusion protein under doxycycline treatment in dKO background (dKOEoGFP, dKOEoER, dKOTbxtGFP). mESCs were differentiated for up to 4 days as embryoid bodies under Activin A treatment. Samples for ATAC-seq, histone modification (H3K4me3, H3K4me1, H3K27ac) ChIP-seq, EOMES ChIP-seq and SWI/SNF subunit SMARCA4 (BRG1) ChIP-seq were collected at different time points during differentiation. ATAC-seq and ChIP-seq experiments were done in biological duplicates. Total RNA was isolated from embryoid bodies at different time points for RNA-seq experiments in 3-4 biological replicates.

first: Chiara

last: Schröder

first: Lea

last: Zissel

first: Mehmet

last: Tekman

first: Arnold

last: Sebastian


title: Obesity escalates Alzheimer’s disease and cancer via excess phosphatidylethanolamine-driven membrane remodeling

city: Houston

first: Li

last: Yang

address: 6565 Fannin Street

department: Department of System Medicine and Bioengineering (SMAB)

institute: METHODIST HOSPITAL RESEARCH INSTITUTE

summary: The paradox of Alzheimer’s disease (AD) and cancer refers to the asynchronism of the two diseases. Understanding the correlation between cancer and AD could enhance research efficiency by consolidating efforts, lead to broader therapeutic impacts through drugs targeting shared mechanisms. Obesity is believed to synchronize this dichotomy by coordinating the onset and progression of both AD and cancer, although the precise mechanism remains unclear. In this study, leveraging integrated multi-modality data, including lipidomics, proteomics, bulk and single-cell RNA transcriptomics, drug repositioning and subcellular visualization, we identified that an overabundance of phosphatidylethanolamine (PEhigh) flux from white adipose tissue in obese individuals underlies this agonist role, driving lipid droplet accumulation and disrupting lipid homeostasis. PEhigh flux escalates both cancer and AD by potentiating immune evasion in tumor models and facilitating amyloidosis and tauopathies in AD models, while restoring PE homeostasis in the brain alleviates cognitive impairment. Mechanistically, our validation demonstrates that PEhigh flux induces autophagic, immunological, and membrane remodeling processes, driving T-cell and microglia dysfunction, spatiotemporal disruption of intracellular signaling, and destabilization of critical membrane structures. The potentially convergent mechanisms and divergent details of PE across AD and cancer highlight its multifaceted implications and the druggability of the associated signaling pathways.

overall_design: Each 7~10-week 5XFAD mouse was intravenously administered with 100 µL phosphate-buffered saline (PBS) or 6.55 X 10^9 exosome-enriched EVs with PE-low or PE-high. Phosphatidylethanolamine (PE).

first: Jianting

last: Sheng

first: Stephen

last: Wong


title: EOMES establishes mesoderm and endoderm differentiation potential through SWI/SNF-mediated global enhancer remodeling [ATAC-Seq]

overall_design: This study involves mouse embryonic stem cells (mESCs) of the following genotypes: wild type (WT), cells deficient for both T-box TFs Eomes and Tbxt (dKO) and cells expressing Eomes:GFP, Eomes:ER or Tbxt:GFP fusion protein under doxycycline treatment in dKO background (dKOEoGFP, dKOEoER, dKOTbxtGFP). mESCs were differentiated for 3.5 days as embryoid bodies under Activin A treatment. Samples for ATAC-seq, histone modification (H3K4me3, H3K4me1, H3K27ac) ChIP-seq, EOMES ChIP-seq and SWI/SNF subunit SMARCA4 (BRG1) ChIP-seq were collected at different time points during differentiation. ATAC-seq and ChIP-seq experiments were done in biological duplicates. Total RNA was isolated from embryoid bodies at different time points for RNA-seq experiments in 3-4 biological replicates.


title: Epigenetic Changes in Cerebrospinal Fluid and Blood of Participants with Neurosyphilis

city: New Haven

first: Sameet

last: Mehta

state: CT

address: 300 Cedar St.

institute: Yale University

summary: Neurosyphilis (NS) is a complication of syphilis that affects the nervous system. Epigenetic changes within immune cells may contribute to neuroinflammation during bacterial infection, but its role in NS has not yet been established. We longitudinally analyzed DNA methylation and RNA expression changes in cerebrospinal fluid (CSF) cells and peripheral blood mononuclear cells (PBMCs) from 11 participants with lab-confirmed NS (CSF VDRL positive) and 11 matched controls with syphilis without NS (non-NS). DNA methylation profiles from CSF and PBMCs of participants with NS significantly differed from those of participants with non-NS. Some genes associated with these differentially methylated sites had corresponding RNA expression changes in the CSF (111/1097, 10.1%), which were enriched in B-cell, cytotoxic-compounds, and insulin-response pathways. Despite antibiotic treatment, approximately 80% of CSF methylation changes persisted; suggesting that epigenetic scars accompanying NS may persistently dysregulate immunity following infection. Future studies must examine whether these sequelae are clinically meaningful.

overall_design: Participants included in this analysis were enrolled in a study at the University of Washington which aimed to define the impact of lumbar puncture with treatment based on CSF findings on outcome of NS treatment. All participants provided written informed consent to participate. The study protocols were approved by the Research Ethics Committee of the University of Washington and Yale University. Study procedures are published . In this analysis, we strictly defined NS as a reactive CSF Venereal Disease Research Laboratory test (VDRL), and non-NS as a participant diagnosed with active syphilis with a nonreactive CSF VDRL and CSF cell count ≤5/uL .  Eleven NS patients and twelve non-NS patients were recruited.  CSF cells and PBMCs were collected and cryopreserved at study entry for all participants. Participants with NS were asked to return for follow-up study visits after undergoing CDC-recommended treatment for NS .  Among the 11 participants with NS, 9 participants returned for lumbar puncture at week 12 post-treatment, 3 participants returned at week 24, and 4 participants returned at week 52.

first: Darius

last: Mostaghimi

first: Priya

last: Kosana

first: Jennifer

last: Yoon

first: Christina

last: Marra

first: Michael

last: Corley

first: Shelli

last: Farhadian


title: Spinal cord single-nuclei RNA sequencing of an EAE mouse model of multiple sclerosis

first: Timothy

last: Hammond

summary: We used the MOG35-55 peptide induction experimental autoimmune encephalomyelitis (EAE) model of multiple sclerosis to determine whether Bruton's tyrosine kinase (BTK) inhibition could attenuate disease-relevant changes to central nervous system gene expression.

overall_design: Lumbar spinal cord was collected from a C57BL/6 experimental autoimmune encephalomyelitis (EAE) mouse model of multiple sclerosis. Single nuclei RNA sequencing was then performed. A subset of mice had been treated with an inhibitor of Bruton’s tyrosine kinase (BTK) after disease induction.


title: Transcriptomic analysis of tissues and embryos from control and triglyceride lipase 2 (TL2)-deficient Anopheles gambiae females.

city: Boston

first: Flaminia

last: Catteruccia

address: 655 huntington ave

institute: Harvard University

summary: We explored the role of triglyceride (TAG) mobilization in the reproductive success of female Anopheles gambiae after a blood meal. Silencing triglyceride lipase 2 (TL2) in An. gambiae reduced egg production and abrogates fertility. Embryos from AgTL2-depleted females develop normally but fail to hatch and are characterized by reduced levels of lipids and key metabolites, including carbohydrates, Tricarboxylic acid (TCA) intermediates, paralleled by increased levels of purine and pyrimidine breakdown products, signifying possible cellular death. To obtain a better understanding of the mechanism underlying embryonic lethality in AgTL2-deficient females, we generated RNA-Seq datasets of tissues and embryos from control and TL2-knockdown females at different time points after blood feeding (for tissues) and oviposition. These analyses revealed that while at earlier time points there is almost no difference, transcriptomic profiles at the later time point of 38 hours after laying were profoundly distinct between both groups. Specifically, pathways involved in neuropeptide signaling, G-protein coupled receptor signaling, and eclosion hormone synthesis were repressed in TL2-knockdown condition while hallmarks of cellular stress were significantly up-regulated. More importantly, pathways involved in de novo lipid synthesis and transport were significantly up-regulated, possibly to compensate for reduced levels of maternally inherited lipids.

overall_design: RNA-Seq datasets of embryos from control and TAG lipase 2-deficient mated Anopheles gambiae females at different time points after egg laying. Samples analyzed include embryos.

first: Itoe

last: Maurice

first: Shaw

last: William Robert

first: Peng

last: Duo


title: Hypothermic oxygenated machine perfusion influences the immunogenicity of donor livers in humans

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

country: Spain

institute: CIBEREHD

summary: Hypothermic oxygenated machine perfusion (HOPE) is an organ preservation strategy shown to reduce ischemia-reperfusion-injury (IRI)-related complications following liver transplantation this remains to be evaluated in humans. Analysis of liver tissue transcriptome at reperfusion revealed an effect of HOPE on the reactive oxygen species pathway. Two weeks post transplantation, HOPE recipients exhibited increased circulating CD4+FOXP3+CD127lo regulatory T cells (Tregs) (p<0.01), which corresponded to a higher frequency of donor specific Tregs (p<0.01) and was followed by reduced alloreactivity index of CD8+ T cells 3 months post-transplant. Our study provides novel mechanistic insight into the capacity of HOPE to influence liver IRI and to modulate effector and regulatory donor-specific Tcell responses post-transplantation. These findings, which confirm observations made in animal models, help explain the decreased rejection rates reported in patients receiving HOPE-treated allografts.

overall_design: Donors after brain death (DBD) Liver biopsies from 9 cryopreserved liver tissue samples [cold] ( before vs after) and 7 Hypothermic oxygenated machine perfusion [machine] (HOPE)

first: J

first: M

last: Elgosbi


title: EOMES establishes mesoderm and endoderm differentiation potential through SWI/SNF-mediated global enhancer remodeling

first: Sebastian

last: Arnold

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

overall_design: Refer to individual Series


title: A paternal cardiac lesion induces cardiac adaptation in the offspring

city: Bern

first: Nadia

last: Mercader

address: Baltzerstrasse 2

institute: University of Bern

summary:
Background: Following cardiac injury, whether the heart is permanently damaged or regenerating, distal organs are subjected to changes in physiological function. It remains largely unknown whether a cardiac lesion can affect gametes and transmit heritable changes to subsequent generations. Here, we report the influence of paternal cardiac injury on the following generation.

Methods: We studied the intergenerational influence of neonatal cardiac injury in the mouse. Neonatal male mice were subjected to ventricular cryoinjury, crossed at adulthood, and their sires were compared with litters derived from uninjured male mice. We used echocardiography, histology, and single nuclei RNA-sequencing to thoroughly characterize cardiac morphology, composition, function, and response to cardiac insult.

Results: We show that paternal cardiac injury affects the heart morphology of offspring under physiological conditions. Furthermore, in response to the same injury, the F1 generation derived from injured fathers shows better systemic and cardiac recovery, with non-pathological left ventricular enlargement and improved cardiac function. This is accompanied by the activation of the immune system healing program at 3 weeks post-injury, together with enhanced transcription of genes associated with physiological hypertrophy.

Conclusions: The memory of a paternal neonatal lesion can be transmitted to offspring and improve their recovery from a cardiac insult.

overall_design: Whole heart processing was performed following the protocol from Cui & Olson with some adaptations. One whole heart per sample was extracted from euthanized male mice 21 days post injury (dpi) with injury performed at 1 day post partum, snap frozen, and stored at -80°C until all samples were available. Two replicates per condition (injured offspring form either uninjured or injured fathers) were used.

first: Coppe

last: Benedetta

first: Galardi-Castlilla

last: Maria

first: Arora

last: Prateek

first: Mercader

last: Nadia


title: Effects of UBXN1 knockdown on gene expression in MHCC97H cell lines

city: Shanghai

first: Kun

last: Jiao

address: No. 800 Dongchuan Road, Shanghai

institute: Shanghai Jiaotong University

summary: To investigate the molecular mechanisms by which UBXN1 promotes tumorigenesis, we performed RNA sequence analysis of the MHCC97H cell line with and without UBXN1.

overall_design: MHCC97H cell  lines were transfected with UBXN1 shRNA. total RNA was isolated and subjected to RNA-seq.

first: Jiao

last: Kun

first: Liu

last: Yongzhong

first: Zhang

last: Li


title: Fibroblast growth factor receptor four inhibitor FGF401 improves the efficacy of trastuzumab in FGFR4-overexpressing breast cancer cells

first: Tzu-Chun

last: Cheng

state: --- Select One ---

address: Address: No. 100, Section 1, Jingmao Road, Beitun District

summary: Breast cancer is the most common cancer among women. Among them, human epidermal growth factor receptor-positive (HER2+) breast cancer is more malignant. Fortunately, many anti-HER2 drugs are currently used in clinical treatments to increase patient survival. However, some HER2+ patients (~15%) still develop drug resistance after receiving trastuzumab treatment, leading to treatment failure. Using CCLE and METABRIC database analyses, we found that fibroblast growth factor receptor 4 (FGFR4) mRNA was highly detected in tumors from HER2+ breast cancer patients (P<0.001) and was associated with poorer survival in breast cancer patients. Through retrospective immunohistochemical staining analysis, we detected higher expression of FGFR4 protein in breast cancer tissues collected from patients who were resistant to trastuzumab therapy compared with breast cancer patients who responded to treatment. An FGFR4 inhibitor (FGF401) effectively inhibits tumor growth in trastuzumab-insensitive patient-derived xenograft (PDX) tumor-bearing mice. For molecular mechanism studies, we demonstrated that HER2/FGFR4 protein complexes were detected on the cell membrane of the tumor tissues in these trastuzumab-insensitive PDX tumor tissues. After trastuzumab treatment in these drug-resistant breast cancer cells, FGFR4 translocates and enters the nucleus. However, trastuzumab-induced nuclear translocation of FGFR4/HER2-intracellular domain protein complex in trastuzumab-resistant cancer cells is blocked by FGF401 treatment. We believe that FGFR4 overexpression and complex formation with HER2 can serve as molecular markers to assist clinicians in identifying trastuzumab-resistant tumors. Our results suggest that FGF401 combined with trastuzumab as adjuvant therapy for patients with trastuzumab-resistant breast cancer may be a potential new treatment strategy.

overall_design: The PDX tumor-bearing mice, specifically J000100674 (PDX-M1) and J000111056 (PDX-M2), were procured from breeding pairs (JAX 4659679) that were acquired from Jackson Laboratories (JAX, 005557, USA). The 4th generation PDX tumor tissues sourced from JAX in our laboratory were transplanted subcutaneously into NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ (NSG) mice for further study. We conducted RNA sequencing analysis to confirm the concordance of the genetic profile between PDX tumors from JAX (2nd generation) and PDX tumors (6th generation) from our laboratory.

first: Yuan-Soon

last: Ho

first: Li-Ching

last: Chen

first: You-Cheng

last: Liao


title: EOMES establishes mesoderm and endoderm differentiation potential through SWI/SNF-mediated global enhancer remodeling [RNA-Seq]

first: Chiara

last: Schröder

first: Lea

last: Zissel

first: Mehmet

last: Tekman

first: Arnold

last: Sebastian


title: LZ and DZ GC B cell throughout lupus

city: Newark

first: Jason

last: Weinstein

state: NJ

address: New Jersey Medical School Cancer Center 205 South Orange Ave

department: Center for Immunity and Inflmmation

institute: Rutgers New Jersey Medical School

summary: DZ (B220+ IgDlo GL-7+ CD95+CXCR4+CD86lo) or LZ (B220+ IgDlo GL-7+ CD95+CXCR4loCD86+) GC B cells were sorted from male Sle1.yaa lupus mice at 2,4,6 months of age. RNA-seq was employed to assess transcriptional changes in the different GC B cell subsets throughout course of disease.

overall_design: Mice were aged to the appropriate age and then GC B cell populations were sorted.

first: Gina

last: Sanchez


title: Interactions of Polychlorinated Biphenyls and Their Metabolites with the Brain and Liver Transcriptome of Female Mice

city: Coralville

first: Amanda

last: Bullert

state: Iowa

address: 2501 Crosspark Rd

department: Occupational and Environmental Health

institute: UNIVERSITY OF IOWA

summary: In this study, we explore the implications of oral exposure to the MARBLES mixture on the brain in adult female mice through two omics approaches, metabolomics and transcriptomics. The individual PCB congeners (PCB 11, 28, 52, 84, 95, 101, 118, 135, 138, 149, 153, and 180) used to make the MARBLES PCB mix. Female C57Bl/6J mice (> 6-week-old) were randomized into exposure groups (N = 4-6) and orally exposed to 0, 0.1, 1, or 6 mg/kg bw/day of the MARBLES mix in organic peanut butter/organic peanut oil for 7 weeks.The striatum and prefrontal cortex were isolated and, together with the liver, prepared for RNA sequencing.

overall_design: To determine the gene expression alterations following MARBLES mixture oral exposure to 0, 0.1, 1, or 6 mg/kg in female mice, striatum, prefrontal cortex and liver regions were processed for RNA sequencing. (N = 4-6 per sex)

first: Bullert

last: Amanda

first: Wang

last: Hui

first: Neier

last: Kari

first: Badley

last: Jessie

first: Valenzuela

middle: E

last: Anthony

first: LaSalle

last: Janine

first: Wilson

last: Rebecca

first: Lein

last: Pamela

first: Hu

last: Xin

first: Lehmler

last: Hans-Joachim


title: Substrate specificity and protein stability drive the divergence of plant-specific DNA methyltransferases

city: St Louis

first: Xuehua

last: Zhong

state: MO

address: One Brookings Drive

department: Biology

institute: Washington University in St. Louis

type: Methylation profiling by high throughput sequencing


title: Substrate specificity and protein stability drive the divergence of plant-specific DNA methyltransferases [RNA-seq]

summary: DNA methylation is an evolutionarily conserved epigenetic mechanism essential for transposon silencing and heterochromatin assembly. In plants, Chromomethylase3 (CMT3) and CMT2 are the major DNA methyltransferases mediating DNA methylation on CHG and CHH (H = A, C or T), respectively, but the underlying mechanisms of how CMT3 and CMT2 methylate different contexts during evolution is poorly known. Here we reveal the mechanisms of CMT3 and CMT2 divergence in flowering plants. CMT2 originates from a duplication of the evolutionarily more ancient CMT3 and change of a key arginine residue recognizing CHG in CMT2 makes it lose CHG methylation activity in most flowering plants. Mutation of the residue to arginine in Arabidopsis (V1200R) greatly increases its methylation activity on CHG DNA. Besides different substrate specificity, CMT2 contains a long and disordered N-terminus compared with a short one in CMT3. The long N-terminus reduces protein stability, especially under high temperature. Moreover, CMT2 N-terminus is plastic to various natural mutations. Together, our study reveals the mechanisms of chromomethylase divergence for methylating different DNA contexts in plants and sheds light on understanding of plant evolution.

overall_design: To investigate transcriptional changes in various CMT2 and CMT3 modifications

first: Jianjun

last: Jiang

first: Sarah

last: Leichter


title: Transcriptomics profiling of the effect of inducible knock-down of the melanocyte inducing transcription factor (MITF) in melanoma cell lines

city: Oxford

first: Pakavarin

last: Louphrasitthiphol

address: Old Road Campus Research Building (off Roosevelt Drive)

department: Nuffield Department of Clinical Medicine

country: United Kingdom

institute: Ludwig Institute for Cancer Research

summary: MITF plays critical role in development and differentiation of melanocytes and in the context of melanoma, as a lineage survival oncogene. Given its crucial role in melanoma biology, it is very difficult to generate complete knock-out (KO) of MITF and in our hands, those that were generated appear to behave differently than the effect observed using siRNA mediated knock-down, possibly indicative of selection. In order to overcome the limitation of the transient effect of siRNA and study the effect of MITF depletion over a longer period of time, we carried out transcriptomic analyses of Doxycycline inducible shMITF knock down after 8 days in 2 melanoma cell lines MeWo (CVCL_0445) and SkMel 28 (CVCL_0526)

overall_design: The cell line was a kind gift from Jiri Vachtenheim DOI: 10.1111/jcmm.13506. MeWo and SkMel28 were seeded on 6 cm dish overnight, the next day, fresh media with 1ug/ml Doxycycline were added. Media with or without Doxycycline were changed every other day. After 8 days, the media was aspirate and the plates snap frozen at -80 °C before total RNA extraction using RNeasy Mini Kit (QIAGEN #74106) as per manufacturer protocol. RNA quality were assessed on Bioanalzyer 2100 (Agilent) using Agilent RNA 6000 Nano Kit (#5067-1511). Only samples with RIN values of over 9.5 were subjected to library prep and sequencing using using the Wellcome Trust genomic service, Oxford. QuantSeq Forward kit (LEXOGEN #0.15.96) was used for library prep, using 500 ng starting material to minimize the PCR amplification step. Samples were sequenced on HiSeq 4000 (Illumina) as paired-end, however, only read 1 contain meaningful data.

first: Colin

last: Goding


title: Substrate specificity and protein stability drive the divergence of plant-specific DNA methyltransferases [Bisulfite-seq]

overall_design: To investigate genome-wide CHG and CHH methylation change in various CMT2 and CMT3 modifications, and to study the effects of DNA methylation change in plants.

first: Dean

last: Sanders


title: Evaluation of gene expression changes upon acquired resistance to anti-EGFR treatment in head and neck squamous cell carcinoma

city: Woluwé

first: Jérôme

last: Ambroise

address: Avenue Hippocrate 54

department: Institut de Recherche Expérimentale et Clinique

country: Belgium

institute: Université catholique de Louvain

summary: We deciphered molecular mechanisms associated with acquired resistance to anti-EGFR targeted therapy in head and neck squamous cell carcinoma (HNSCC) by comparing gene expression profiles in cetuximab-sensitive and -resistant patient-derived xenograft (PDX) models of HNSCC. We generated and validated several HNSCC PDX models. Resistance mechanisms to anti-EGFR therapy were investigated in one of these PDX models (UCLHN04). First, sensitivity to cetuximab treatment was tested. This model showed high sensitivity to this drug. We induced acquired resistance to anti-EGFR therapy in this sensitive model by treating it chronically with anti-EGFR monoclonal antibody (cetuximab, 30 mg/kg/week) until resistance ensues. RNA-seq analysis was performed on samples coming from untreated and cetuximab-resistant PDX, revealing major changes of expression at the mRNA level.

overall_design: We induced acquired resistance to anti- EGFR therapy in the a sensitive model by treating it chronically with anti-EGFR monoclonal antibody (cetuximab, 30 mg/kg/week) until resistance ensues. Resistance was defined as continuous tumor growth under cetuximab and an increase in tumor volume of more than 200% compared with baseline. The resistant models were treated continuously with cetuximab without interruption. Cetuximab-resistant PDX were compared with corresponding non-treated (baseline) PDX, with three biological replicates per condition. The study was approved by the ethics committee from UCLouvain (approval ID UCL/MD/2012/09July/314) in accordance with the principles of the Declaration of Helsinki, and all patients gave their written informed consent.

first: Sandra

last: Schmitz

first: Jean-Pascal

last: Machiels

first: Cyril

last: Corbet


title: BCAT1 regulates glioblastoma cell plasticity and contributes to immunosuppression

city: Saint Louis

first: Pavle

last: Boskovic

address: 4515 McKinley Ave

institute: Washington University in Saint Louis

summary: Glioblastoma is the most common malignant brain tumor in adults. Cellular plasticity and the poorly differentiated features result in a fast relapse of the tumors following treatment. Moreover, the immunosuppressive microenvironment proved to be a major obstacle to immunotherapeutic approaches. Branched-chain amino acid transaminase 1 (BCAT1) is a metabolic enzyme that converts branched-chain amino acids into branched-chain keto acids, depleting cellular α-ketoglutarate and producing glutamate. BCAT1 was shown to drive the growth of glioblastoma and other cancers; however, its oncogenic mechanism remains poorly understood. Here, we show that BCAT1 is crucial for maintaining the poorly differentiated state of glioblastoma cells and that its low expression correlates with a more differentiated glioblastoma phenotype. Furthermore, orthotopic tumor injection into immunocompetent mice demonstrated that the brain microenvironment is sufficient to induce differentiation of Bcat1-KO tumors in vivo. We link the transition to a differentiated cell state to the increased activity of TET demethylases and the hypomethylation and activation of neuronal differentiation genes. In addition, the knockout of Bcat1 attenuated immunosuppression, allowing for an extensive infiltration of CD8 + cytotoxic T-cells and complete abrogation of tumor growth. Further analysis in immunodeficient mice revealed that both tumor cell differentiation and immunomodulation following BCAT1-KO contribute to the long-term suppression of tumor growth. In summary, our study unveils BCAT1's pivotal role in promoting glioblastoma growth by inhibiting tumor cell differentiation and sustaining an immunosuppressive milieu. These findings offer a novel therapeutic avenue for targeting glioblastoma through the inhibition of BCAT1.

overall_design: Total cell RNA was extraced from cultured mGB2 control (NT) and Bcat1-KO (BKO) cells. Prior to RNA extraction, the cells were grown adherentlly on a Ecm marix-coated plate in full glioblastoma stem cell medium (DMEM:F12 containing N2, B27, EGF, FGF). RNA was isolated upon reaching confluency ising the RNeasy kit.

first: Nathalie

last: Wilke

first: Ka-Hou

last: Man

first: Peter

last: Lichter

first: Liliana

last: Francois

first: Bernhard

last: Radlwimmer


title: Effects of 28-day nose-only inhalation of PCB52 (2,2′,5,5′-Tetrachlorobiphenyl) on the brain transcriptome

first: Amanda

last: Bullert

summary: Banned from mass production, polychlorinated biphenyls (PCBs) still pose a neurological health threat decades later. PCB52, a volatile compound, has been found in the indoor air of schools where adolescent students and staff are exposed. The adolescent brain is vulnerable and highly influenced by the environment around it. This study used adolescent Sprague-Dawley rats to determine the neurological effects of a subacute (28-day) PCB52 inhalation exposure. Rats were exposed 4 h a day for 28 consecutive days with neurobehavioral tests conducted during the last 5 days of exposure. Based on the data including brain weights, PCB52 and metabolite levels, gene expression in the striatum and cerebellum, and neurobehavioral tests (Y-maze, HBT, OFT, and EPM); a subacute inhalation of PCB52 results in sex-specific differences in response to exposure. Our results indicate multilevel PCB52 influence that is different in adolescent males and females; from gene expression to downstream innate mechanisms driving behavior.

overall_design: To determine the gene expression alterations following PCB52 inhalation exposure in adolescent rats, male and female striatum and cerebellar regions were processed for RNA sequencing. (N = 6 per sex)

first: Hui

last: Wang

first: Morgan

last: Linahon

first: Michael

middle: S

last: Chimenti

first: Andrea

last: Adamcakova-Dodd

first: Xueshu

last: Li

last: Dailey

first: Aloysius

last: Klingelhutz

first: James

last: Ankrum

first: Hanna

last: Stevens

last: Thorne

first: Hans-Joachim

last: Lehmler


title: The Impact of the CpxA on Regulating Polymyxin B Resistance in Salmonella Typhimurium

status: Public on Nov 07 2024

city: Qinhuangdao

first: Xiaoqing

last: Zhang

address: No. 360 West Section of Hebei Street, Qinhuangdao, Hebei, China. 066004

institute: Hebei Normal University of Science and Technology

summary: Polymyxin B is considered as a last-resort antibiotic for multidrug-resistant or extensively drug-resistant gram-negative bacterial infections. Addressing Salmonella resistance to polymyxin B is crucial for global public health.  In this study, transcriptomic detection and analysis were used to clarify the mechanisms by which CpxA-deleted S.typhimurium is involved in resistance to polymyxin B stress, which may be related to processes such as increased assembly of bacterial flagella.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

overall_design: S.typhimurium and its CpxA-delated strain were inoculated into LB broth containing 0.125 μg/ml polymyxin B, and cultured overnight at 37°C, followed by dilution and subculture. After growing to the logarithmic phase, the bacteria were washed twice with PBS, collected, quickly frozen in liquid nitrogen, and then sent to Beijing Novogene Bioinformatics Technology Co., Ltd. for transcriptome sequencing and analysis.


title: Transcriptomic analysis of a propolis-resistant Saccharomyces cerevisiae strain obtained by evolutionary engineering

city: Istanbul

first: Halil

middle: ibrahim

last: KISAKESEN

state: Istanbul

address: ITU MOBGAM, SARIYER

department: Molecular Biology, Genetics and Biotechnology

country: Turkey

institute: Istanbul Technical University

summary:
A propolis-resistant Saccharomyces cerevisiae mutant strain was obtained using an evolutionary engineering strategy based on successive batch cultivation under gradually increasing propolis levels. The mutant strain FD 11 was selected at a propolis concentration that the reference strain could not grow at all. Whole-genome transcriptomic analysis of FD11 was performed with respect to its reference strain to determine differences in gene expression levels between the two strains.
Saccharomyces cerevisiae

overall_design: Agilent Yeast One-Color DNA microarray systems were used for comparative whole-genome transcriptomic analysis of the selected mutant FD 11 and its reference strain. Prior to gene expression analysis, each culture was grown in triplicate in yeast minimal medium (YMM) at 30°C and 150 rpm. Total RNA isolation was carried out, using RNeasy Mini Kit (Qiagen) at early exponential phase of growth (OD600 ~1.0).

first: Filiz

last: Demir Yilmaz

first: Can

last: Holyavkin

first: Alican

last: Topaloğlu

first: Zeynep

last: Cakar


title: Differential gene expression in breast cancer cell lines treated with a Baicalein at 100 uM concentration

city: Ann Arbor

first: Bioinformatics

last: Core

address: BRCF Bioinformatics Core, 2800 Plymouth Rd

institute: University of Michigan

summary:
To investigate the effect of baicalein on human breast cancer cell lines.
We then performed gene expression profiling analysis using data obtained from RNA-seq of two different breast cancer cell lines, with 3 replicates each of control and treated.

overall_design: RNA libraries for RNA-seq were prepared using  Library Prep Kit following manufacturer's protocols.

first: Besa

last: Xhabija


title: Changes in the transcriptome of the chorioallantois from late gestation to postpartum in normal equine pregnancy

city: Lexington

first: Barry

middle: A.

last: Ball

state: Kentucky

address: 108 Gluck Equine Research Center,

department: Veterinary Scinece

institute: University of Kentucky

summary: The equine chorioallantois (CA) undergoes complex physical and biochemical changes during labor. However, the molecular mechanisms controlling these changes are still unclear. Therefore, the current study aimed to characterize the transcriptome of equine CA during spontaneous labor and compare it to that of normal preterm CA. Placental samples were collected postpartum from mares with normal term labor (TL group, n=4) and from preterm not in labor mares (330 days GA; PTNL group, n=4). Our study identified 4137 differentailly expressed genes (DEGs) (1820 upregulated and 2317 downregulated) in CA during TL as compared to PTNL. TL was associated with the upregulation of several pro-inflammatory mediators (MHC-I, MHC-II, NLRP3, CXCL8, and MIF). Also, TL was associated with the upregulation of matrix metalloproteinase (MMP1, MMP2, MMP3, and MMP9) with subsequent extracellular matrix degradation and apoptosis, as reflected by upregulation of several apoptosis-related genes (ATF3, ATF4, FAS, FOS, and BIRC3). In addition, TL was associated with downregulation of 21 transcripts coding for collagens. The upregulation of proteases, along with the downregulation of collagens, is believed to be implicated in separation and rupture of the CA during TL. Additionally, TL was associated with downregulation of transcripts coding for proteins essential for progestin synthesis (SRD5A1 and AKR1C1) and angiogenesis (VEGFA and RTL1), as well as upregulation of prostaglandin synthesis-related genes (PTGS2 and PTGES), which could reflect the physiological switch in placental endocrinology and function during TL. In conclusion, our findings revealed the equine CA gene expression signature in spontaneous labor at term, which improves our understanding of the molecular mechanisms triggering labor.

overall_design: The transcripts from equine chorioallantois of prepartum and postpartum mares were compared.

first: Hossam

last: El-Sheikh Ali

middle: A


title: Alteration in mRNA expression in hippocampus and next-generation effects due to paternal exposure to the neonicotinoid pesticide clothianidin

city: Toyama

first: Tetsushi

last: Hirano

state: Toyama

address: 2630 sugitani

department: Life Science Research Center

institute: University of Toyama

summary: Accumulating evidence suggests that paternal environmental factors have epigenetic effects on sperm and influence offspring. Neonicotinoid pesticides, which are widely used around the world, are known to affect offspring phenotypes through maternal exposure in mice, but the effect of the paternal exposure remains unknown.The main purpose of this study was to estimate  the neurobehavioral effects on offspring mice resulting from paternal exposure to the neonicotinoid pesticide clothianidin (CLO).Hippocampal RNA sequence data revealed that paternal CLO exposure altered the expression of genes related to the nervous system in male offspring, affecting pathways such as axonal guidance signaling, synaptogenesis signaling pathway, and calcium signaling.

overall_design: To understand the mechanisms of paternal exposure to a neonicotinoid pesticide clothianidin (CLO) to the next generation, male C57BL/6N mice were administered the non-observed-adverse-effect level (NOAEL) of CLO (50 mg/kg/day). The mRNA in hippocampus was purified and analyzed by RNA-seq.

first: Makiko

last: Ito

first: Nobuhiko

last: Hoshi


title: ChIP-seq profile in in vitro produced mouse morula stage embryos treated with siRNA targeting Pcgf5

city: Kyoto

first: Satoshi

last: Mashiko

address: Sakyoku oiwakecho

institute: Kyoto university

summary: We obtained H3K27me3 profiles in mouse morula stage embryos (72 h post-insemination (hpi)) which had been in vitro treated with siRNA targeting Pcgf5 from one-cell stage (3 hpi).

overall_design: In vitro produced mouse morula stage embryos were processed to ChIP-seq. The experiments were duplicated using 40 embryos per group.

first: Naojiro

last: Minami

first: Shuntaro

last: Ikeda

first: Shinnosuke

last: Honda


title: Trans-generational adaptation to maternal climate through hormone transport in plants [scRNA-seq]

city: Norwich

first: William

last: Bezodis

address: Norwich Research Park, Colney Lane

department: Crop Genetics

institute: John Innes Centre

summary: Whether and how organisms can inherit environmental information from their parents is a major question in evolutionary theory. Plants have evolved to link reproductive development to seasonal environmental cues and seed dormancy is highly contingent on the environmental temperature during seed set, although the mechanism by which seeds acquire seasonal timing information is unclear. Here we show that loss of maternal like heterochromatin protein 1 (LHP1) causes an inability of progeny seeds to sense temperature and that this is linked mechanistically to reduced ABA levels in seeds and hyperaccumulation of free nitrate. Remarkably, single cell transcriptomics reveals that in both maternal fruit and seed tissues, the effect of small changes in temperature closely phenocopies the lhp1 mutant phenotype and ABA biosensor imaging reveal large fluxes of maternal ABA into seeds is modulated by temperature cues. We show that temperature activates ABA production in leaves and that maternal ABA is necessary and sufficient for progeny seeds to acquire seed dormancy. Thus, we reveal that the climate experience of mother plants causes adaptation of progeny behaviour via hormone transport during seed set.

overall_design: single nucleus RNA-seq was performed on whole developing siliques including seeds at the bend cotyledon stage of embryo development. Plants were grown in controlled long day conditions at 16°C D/14°C N. with a single day transfer to 22°C for the relevant samples to match developmental stage. Plants are WT Col-0 or homozygous lhp1-6 in the Col-0 background.

first: Xiaochao

last: Chen

first: Steven

last: Penfield


title: Dual targeting CDK4/6 and CDK7 augments tumor response and anti-tumor immunity in breast cancer

city: New York

first: Hee Won

last: Yang

state: NY

institute: Columbia University

summary: CDK4/6 inhibitors (CDK4/6i) have significantly improved the prognosis for hormone-positive (HR+) breast cancer patients. However, the emergence of drug resistance severely limits their long-term efficacy, and CDK4/6i monotherapy remains largely ineffective against triple-negative breast cancer (TNBC). Here, we demonstrate that combining CDK4/6i with CDK7 inhibitors (CDK7i) offers a promising therapeutic strategy to overcome resistance in both HR+ breast cancer and TNBC. Kinetic analyses reveal that CDK7i primarily targets RNA polymerase II-mediated transcription, a key driver of CDK4/6i resistance by amplifying E2F activity following the degradation of the retinoblastoma protein. Consequently, the combination of CDK4/6i and CDK7i synergistically suppresses E2F activity and inhibits the growth of drug-resistant tumors. Furthermore, this combination stimulates immune response pathways and cytokine production in cancer cells, enhancing anti-tumor immunity. These findings provide critical insights into evolving CDK inhibition strategies and highlight the therapeutic application of CDK7i in breast cancer management.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Bulk RNA-Seq was performed on the MDA-MB-231 cell line, and scRNA-Seq was conducted on tumors extracted from an AT3-OVA syngeneic mouse model.

first: Sungsoo

last: Kim

first: Eugene

last: Son

first: Haram

last: Park

first: Minah

first: HeeWon