title: Profibrotic monocyte-derived alveolar macrophages as a biomarker and therapeutic target in systemic sclerosis-associated interstitial lung disease [Northwestern]

status: Public on Jul 31 2025

city: Chicago

first: Alexander

middle: V

last: Misharin

state: Illinois

address: 303 E Superior St

department: Pulmonary and Critical Care

country: USA

institute: Northwestern University

type: Expression profiling by high throughput sequencing

summary: Interstitial lung disease (ILD) is present in over 60% of patients with systemic sclerosis (SSc) and is the leading cause of SSc-related deaths. Profibrotic monocyte-derived alveolar macrophages (MoAM) play a causal role in the pathogenesis of pulmonary fibrosis in animal models where their persistence in the niche requires signaling through the Colony Stimulating Factor 1 Receptor (CSF1R). We hypothesized that the presence and proportion of MoAM in bronchoalveolar lavage (BAL) fluid from patients with SSc-ILD may be a biomarker of ILD severity. To test this hypothesis, we performed BAL in 9 prospectively enrolled patients with SSc-ILD on imaging and 13 healthy controls and analyzed the cellular fraction using flow cytometry and single-cell RNA sequencing. Compared to healthy controls, patients with SSc-ILD showed increased abundance of MoAM and interstitial macrophages in BAL fluid that was associated with worse lung function and lung disease on imaging. We identified changes in the MoAM transcriptome as a function of treatment with mycophenolate, an effective therapy for SSc-ILD.

overall_design:
Bronchoalveolar lavage (BAL) fluid from 10 patients 5 heathy volunteers was obtained at the bronchoscopy suite of Northwestern Memorial Hospital or Yale New Haven Hospital.l. Single cell RNA-seq libraries were prepared with 10x 3' gene expression kit. Libraries were sequenced on Illumina NovaSeq 6000. Gene expression matrices were generated with 10x Cell Ranger v3.1.0 (exon-only mode) software and reads were mapped to GRCh38.84 reference genome (10x Genomics Cell Ranger Human 1.2.0 GRCh38 reference).

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Protected Health Information: fastq files have been omitted.
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first: Nikolay

middle: S

last: Markov

first: Anthony

middle: J

last: Esposito

first: Maxwell

last: Schleck

first: Radmila

last: Nafikova

first: Zhan

last: Yu

first: Ziyan

last: Lu

first: Monique

middle: E

last: Hinchcliff


title: Unlocking the diagnostic power of plasma extracellular vesicle miR-200 family in pancreatic ductal adenocarcinoma

city: Aarhus N

first: Morten

middle: T

last: Veno

state: DK

address: Aabogade 15

country: Denmark

institute: Omiics ApS

type: Non-coding RNA profiling by high throughput sequencing

summary: Background Distinguishing benign from malignant pancreaticobiliary disease is challenging because of the absence of reliable biomarkers. Circulating extracellular vesicles (EVs) have emerged as functional mediators between cells. Their cargos, including microRNAs (miRNAs), are increasingly acknowledged as an important source of potential biomarkers. This multicentric, prospective study aimed to establish a diagnostic plasma EV-derived miRNA signature to discriminate pancreatic ductal adenocarcinoma (PDAC) from benign pancreaticobiliary disease. Methods Plasma EVs were isolated using size exclusion chromatography (SEC) and characterised using nanoparticle tracking analysis, electron microscopy and Western blotting. EV-RNAs underwent small RNA sequencing to discover differentially expressed markers for PDAC (n = 10 benign vs. 10 PDAC). Candidate EV-miRNAs were then validated in a cohort of 61 patients (n = 31 benign vs. 30 PDAC) by RT-qPCR. Logistic regression and optimal thresholds (Youden Index) were used to develop an EV-miR-200 family model to detect cancer. This model was tested in an independent cohort of 95 patients (n = 30 benign, 33 PDAC, and 32 cholangiocarcinoma). Results Small RNA sequencing and RT-qPCR showed that EV-miR-200 family members were significantly overexpressed in PDAC vs. benign disease. Combined expression of the EV-miR-200 family showed an AUC of 0.823. In an independent validation cohort, application of this model showed a sensitivity, specificity and AUC of 100%, 88%, and 0.97, respectively, for diagnosing PDAC.

overall_design: Prospective single-centre cohort study recruiting patients with obstructive jaundice undergoing ERCP. Plasma samples in a smaller discovery cohort (n=20) underwent EV isolation by SEC and RNA sequencing performed to identify differentially expressed RNA biomarkers. RT-qPCR validation was performed and a biomarker profile was determined for PDAC and CCA.

first: Daniel

last: Liu

first: Puik

middle: R

last: Jisce

first: Patel

middle: Y

last: Bhavik

first: Venø

last: Morten

first: Vahabi

last: Mahrou

first: Mato Prado

last: Mireia

first: Webber

middle: P

last: Jason

first: Rees

last: Eleanor

first: Upton

middle: M

last: Flora

first: Bennett

last: Kate

first: Blaker

last: Catherine

first: Immordino

last: Benoit

first: Comandatore

last: Annalisa

first: Morelli

last: Luca

first: Sivakumar

last: Shivan

first: Swijnenburg

last: Rutger-Jan

first: Besselink

middle: G

last: Marc

first: Jiao

last: Long

first: Geert

last: Kazemier

first: Elisa

last: Giovannetti

first: Krell

last: Jonathan

first: Adam

last: Frampton


title: The MarR Family Transcription Factor SlyA Senses Iron and Respiratory Status in Enteric Bacteria

city: Seattle

first: William

middle: Ryan

last: Will

state: WA

address: 1959 NE Pacific Street

department: Laboratory Medicine and Pathology

institute: University of Washington

summary: SlyA and its homologs are conserved essential transcription factors in enteric bacteria, including Salmonella enterica and Yersinia pestis, in which they upregulate horizontally-acquired virulence genes. As members of the MarR family of transcription factors, they possess a small molecule binding pocket that allows the protein to undergo a conformational change upon ligand interaction that abrogates DNA binding. Although the original discovery of MarR was based on its ability to recognize xenobiotic compounds and promote their efflux, the conservation of the MarR family throughout Bacteria and Archaea suggests a more general function. Because SlyA is known to bind xenobiotic aromatic carboxylates, we performed a targeted analysis of aromatic metabolic genes in S. Typhimurium to identify potential endogenous ligands, including genes involved in essential cellular processes including iron metabolism, respiration, and aromatic amino acid and folate biosynthesis. We found that SlyA is promiscuously inhibited by multiple aromatic carboxylates including 2,3-dihydroxybenzoate, a precursor of iron-scavenging catecholate siderophores, and 4-hydroxybenzoate, a precursor of quinone-based electron-carriers, which allows it to sense changes in iron availability, respiration and growth on succinate. We suggest that SlyA and other MarR proteins sense bacterial metabolic status via the flux of aromatic carboxylates in biosynthetic pathways, allowing SlyA to function as a counter-silencer of horizontally-acquired genes that is exquisitely responsive to the metabolic state of the cell.

overall_design: RNA-seq analysis of Salmonella enterica serovar Typhimurium 14028s and isogenic slyA and tolC mutants. Late log phase (1.0 OD600) cultures were induced for 1 hour in N-minimal medium with 10 µM MgSO4.

first: W

first: Ferric

middle: C

last: Fang


title: HSPA1A can alleviate CFA-induced inflammatory pain by modulating macrophages

city: Guangzhou

first: Wenjie

last: Zhang

address: Guangzhou Medical University, No.1 Xinzao Road, Panyu District

department: School of Basic Medical Sciences

country: China

institute: Guangzhou Medical University

summary: Current clinical approaches for managing inflammatory pain are frequently accompanied by adverse effects, significantly compromising patients' quality of life. This study investigates the analgesic potential of murine HSPA1A protein administration in alleviating Complete Freund’s Adjuvant (CFA)-induced inflammatory pain. Findings indicate that HSPA1A mitigates CFA-induced mechanical allodynia positively correlated with macrophage abundance. Transcriptomic RNA sequencing suggests involvement of inflammation-associated pathways in plantar tissues after HSPA1A injection.

overall_design: This study investigates the analgesic potential of murine HSPA1A protein administration in alleviating Complete Freund’s Adjuvant (CFA)-induced inflammatory pain.Plantar tissues from HSPA1A-treated and control mice were collected.

first: Feiyu

last: Chen


title: The Lsm1-7 complex transiently interacts with the decapping machinery and plays a minor role in unstable mRNA degradation

city: Paris

first: Cosmin

last: Saveanu

address: 25-28 rue du docteur Roux

department: Genomes and Genetics

country: France

institute: Institut Pasteur

summary: Like-SM proteins (Lsm) assemble into heptameric complexes that are conserved in eukaryotes. The Lsm2-8 complex is involved in the function of spliceosomal RNAs, whereas the Lsm1-7/Pat1 complex associates with decapping complexes in the cytoplasm. It was proposed that the role of Lsm1-7 is to recruit the decapping machinery to unstable mRNA that are rapidly deadenylated. However, the role of deadenylation in RNA stability has been challenged by recent studies in yeast and other organisms. To better understand the potential role of Lsm1 in the degradation of unstable transcripts, we investigated the effects of rapid depletion of Lsm1 in an inducible degron system on transcripts degraded by decapping activation during nonsense-mediated mRNA decay (NMD). In contrast to previous studies that used deletion of LSM1, Lsm1 depletion, led to a slight increase in the abundance of NMD substrates, similar to what is observed following a minimal perturbation of decapping.

overall_design: RNA sequencing of samples from wt, inducible degron for DCP2, inducible degron for LSM1 strains at time 0 and after 60 minutes of treatment with IAA and beta-estradiol.

first: Laurence

last: Decourty

first: Abdelkader

last: Namane

first: Guilhem

last: Janbon


title: Impacts of Amylose Synthesis Knockout on Sorghum Seed Development and Grain Quality

city: Lubbock

first: Pallavi

last: Dhiman

address: 1006 Canton Avenue

institute: Texas Tech University

summary: Waxy sorghum seeds, defined by reduced amylose content in starch, offer the potential for improving grain quality in food and industrial applications. While waxy endosperms arising from non-functional waxy (wx) allele leading to the absence of Granule-bound starch synthase (GBSS) enzyme have been identified in sorghum, their broader effects on seed development and grain quality remain inadequately understood. To address this gap, we identified a novel wx loss-of-function allele, "wxe" in the mutant population of the sorghum reference genome line BTx623. Beyond reduced amylose content, wxe exhibited increased kernel hardness, elevated protein content, reduced endosperm-to-germ ratio, and decreased kernel weight compared to the wild-type. Integrating transcriptomic, metabolomic, and seed chemistry analyses revealed coordinated regulatory changes during seed development due to disrupted amylose synthesis. This included altered starch granule structure, enhanced lipid profiles, and reduced carbohydrate content. Differentially expressed genes and transcription factors related to starch metabolism provided insights into the regulatory mechanisms. Furthermore, metabolic profiling showed significant changes in the accumulation of compounds influencing flavor and nutritional properties. This study enhances our understanding of the molecular coordination of sorghum seed development and provides new insights into regulating seed development.

overall_design: Transcriptome profiling of endosperm was performed in Wily type Btx623 (samples designated as WT) and waxy mutant (samples designated as M) at 6, 11, 16, and 21 days post-anthesis to investigate the effects of GBSS1 gene knockout on seed development.

first: Shejal

last: Soumen

first: Deepti

last: Nigam

first: Scott R.

last: Bean

first: Xiaorong

last: Wu

first: Gunvant B.

last: Patil

first: Zhanguo

last: Xin

first: Yinping

last: Jiao


title: Genome-scale analysis of PCSK9 in PC12 cells reveals immune response modulation and alternative splicing of hypoxia response genes

city: Urumqi

first: Mengjie

last: Wang

state: Xinjiang Uygur Autonomous Region

address: No.137,Liyushan South Road

department: Department of Neurology

institute: First Affiliated Hospital of Xinjiang Medical University

summary: Background: Proprotein convertase subtilisin/kexin type 9 (PCSK9) is a potential RNA regulatory protein that plays an important role in cholesterol and fatty acid metabolism; however, the genome-wide regulation of gene expression and alternative splicing of PCSK9 remain unclear. Methods: PCSK9 overexpression experiments were performed in rat PC12 cells, and 330 genes were differentially expressed, including 209 upregulated and 121 downregulated genes. Results: The genes regulated by PCSK9 were enriched in immune response-related pathways, which showed enriched CCL2, Cxcl1, and Irf9. Moreover, genes with altered splicing patterns regulated by PCSK9 overexpression were enriched in pathways including the hypoxic response, and the alternative splicing of PKM and ARNT changed significantly. Conclusions: We found that PCSK9 may participate in the progression of ischemic stroke by activating the immune/hypoxia response. Thus, this study extends the functional roles of PCSK9 in ischemic stroke pathogenesis. Significance: PCSK9 involved into the progression of ischemic stroke, which could considered as a therapeutic target for improving ischemic stroke.

overall_design: We developed a PCSK9 overexpression model in the PC12 cell line, coupled with RNA sequencing (RNA-seq), to comprehensively elucidate the biological functions of PCSK9 in PC12 cells and to examine alterations in transcriptional profiles following PCSK9 overexpression. Additionally, we performed comparative gene expression profiling analysis of RNA-seq data between PC12 cells and their PCSK9-overexpressing derivatives.

first: Lei

last: Du

first: Jin

last: Lei

first: Jianhua

last: Ma


title: Nova-ST spatial transcriptomics of Lecanamab- and Lecanemab LALA-PG-treated xenotrasplanted human microglia [ST]

city: Leuven

first: Bart

last: de Strooper

address: Campus Gasthuisberg, Herestraat 49, bus 602

department: VIB-KU Leuven Center for Brain & Disease Research

country: Belgium

institute: KULeuven

summary: We investigated the effect of Lecanemab's Fc effector function on the transcriptomes of human microglia xenotransplanted in a mouse model of AD. We performed Nova-ST spatial transcriptomics analysis on xenografted mice treated with Lecanemab and Lecanemab LALA-PG, a human IgG1 variant designed to abolish Fc-mediated effector functions. We found that treatment with Lecanemab induced phagocytic and lysosomal reprogramming in the microglia surrounding plaques, an effect that was not present upon Lecanemab LALA-PG.

overall_design: Human embryonic stem cells (WiCell, #WA09) were differentiated into microglial precursors and grafted into AppNL-G-F Csf1rΔFIRE/ΔFIRE mice. At 4 months, the mice were chronically treated for 8 weeks with 10 mg kg−1 Lecanemab (n=2) or Lecanemab LALA-PG (n=2), dosed weekly intraperitoneally. One day after the final dose, mice were terminally anesthetized and Nova-ST spatial transcriptomics was performed on cryosections of the brains. Only the human (microglial) transcriptomes were analyzed.

first: Giulia

last: Albertini

first: Magdalena

last: Zielonka

first: Marie-Lynn

last: Cuypers

first: An

last: Snellinx

first: Ciana

last: Xu Ruchen

first: Suresh

last: Poovathinghal

first: Marta

last: Wojno

first: Kristofer

last: Davie

first: Veerle

last: van Lieshout

first: Katleen

last: Craessaerts

first: Leen

last: Wolfs

first: Emanuela

last: Pasciuto

first: Tom

last: Jaspers

first: Katrien

last: Horré

first: Lutgarde

last: Serneels

first: Mark

last: Fiers

first: Maarten

last: Dewilde

last: De Strooper


title: Effects of LpxC and lpxD disruption on Acinetobacter baumannii and phage interactions

city: Yangzhou

first: JIngchen

last: Hao

address: No. 136, Jiangyang Middle Road

institute: Yangzhou University

summary: LpxC and lpxD are involved in the synthesis of bacterial LPS and are essential for the maintenance of bacterial outer membrane integrity.Here, we show that loss of lpxC and lpxD affects energy metabolism in A. baumannii and is associated with bacterial-phage interactions.The lpxC and lpxD deficient strains showed significantly different changes compared with the parental strain under phage pressure.

sample_organism: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841

overall_design: RNAseq profiles of ATCC19606, lpxC and lpxD knockout strains and their exposure to phage stress

first: Jingchen


title: High-Throughput Sequencing Analysis of miRNAs in Pancreatic Ductal Adenocarcinoma

first: yu

last: chao

address: 106 Zhongshan 2nd Road

institute: Guangdong Provincial People's Hospital

summary: This study aimed to investigate the miRNA expression profiles in pancreatic ductal adenocarcinoma (PDAC) to identify novel potential diagnostic markers and therapeutic targets. Using high-throughput sequencing technology, we analyzed miRNA expression levels in 3 PDAC tissues with good prognosis (T1-T3) and 3 PDAC tissues with poor prognosis (T4-T6). The results revealed significantly distinct miRNA expression patterns between the two groups. Our study identified prognosis-associated miRNAs in PDAC and evaluated their potential as therapeutic targets.

overall_design: To systematically identify potential prognostic miRNA biomarkers, this study collected PDAC tissue samples from patients with good (T1–T3) and poor (T4–T6) prognoses. After total RNA extraction, high-throughput sequencing was performed to comprehensively profile differentially expressed miRNAs between the two groups.

first: Rufu

last: Chen


title: Targeted RNA-sequencing of testes from fetal rats exposed to dicyclohexyl phthalate informs potency and adverse outcome pathway development

city: Durham

first: Leah

last: Wehmas

state: NC

address: 109 T.W. Alexander Drive

institute: US EPA

summary: The US EPA is refining long-term animal testing to increase the pace of chemical risk assessments. One approach involves using benchmark dose (BMD) response modeling of gene expression data from short term adult animal studies to indicate longer term chemical risk. Whether this approach works with developmental and reproductive toxicants is less certain. Dicyclohexyl phthalate (DCHP) is a high production volume phthalate ester with known effects on testes. Despite knowledge on several key events in phthalate testicular dysgenesis, the molecular initiating event is still unknown. The present study aims to assess how well gene expression-based BMD analysis of fetal testes from an in utero exposure performs at predicting developmental and reproductive toxicity endpoints for DCHP while applying, whole transcriptome, targeted RNA-Sequencing (RNA-Seq) to  inform new molecular targets involved in phthalate-induced testicular dysgenesis. BMD analysis of targetd RNA-Seq data identified gene-set based BMD values that were 4 and 6-fold lower than development-related decreased anogenital distance and reproductive-related testis atrophy measures (101 and 144 mg/kg-day, respectively). Further analysis of top differentially expressed genes from targeted RNA-Seq identified Testin, Svs5, Lrrc39, etc. that may warrant further investigation in DCHP-induced testicular dysgenesis. Canonical pathway comparisons (Ingenuity Pathway Analysis) indicated suppression of steroid/cholesterol biosynthesis processes while biological function comparisons identified disrupted reproductive and genitourinary development processes across dose groups consistent with known DCHP effects. These results show promise in using targeted RNA-Seq from short-term in utero exposures to rapidly and quantitatively indicate developmental and reproductive effects, thereby helping EPA more quickly assess chemical impacts across a range of adverse effects. This abstract does not represent US EPA policy and mention of products does not constitute endorsement.

overall_design: Pregnant dams were exposed by oral gavage to 0 (corn oil vehicle), 100, 300, 600, or 900 mg/kg-day dicyclohexyl phthalate from gestational day 14 to 18. On gestational day 18, fetal rats were necropsied with testes collected and pooled by litter. There were 3 pooled testes samples per treatment except 900 mg/kg-day which had 2 pooled testes.

first: Miles

last: Crockett

first: Carolyn

last: Waterbury

first: Leonard

last: Gray

first: Justin

last: Conley


title: Profibrotic monocyte-derived alveolar macrophages as a biomarker and therapeutic target in systemic sclerosis-associated interstitial lung disease [Duke]

first: Alexander

last: Misharin

overall_design:
Bronchoalveolar lavage (BAL) fluid from 8 heathy volunteers was obtained at the bronchoscopy suite of Duke University Hospital. Single cell RNA-seq libraries were prepared with 10x 3' gene expression kit. Libraries were sequenced on Illumina NovaSeq 6000. Gene expression matrices were generated with 10x Cell Ranger v3.1.0 (exon-only mode) software and reads were mapped to GRCh38.84 reference genome (10x Genomics Cell Ranger Human 1.2.0 GRCh38 reference).

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first: Nikolay

last: Markov

first: Anthony

last: Esposito

first: Maxwell

last: Schleck

first: Radmila

last: Nafikova

first: Zhan

last: Yu

first: Ziyan

last: Lu

first: Robert

last: Tighe

first: Monique

last: Hinchcliff


title: Hidden stop codons dictate mRNA fate by ambushing ribosomal frameshifting

city: Kunming, Yunnan

first: fei

last: li

address: Dongwaihuan South Road, University Town, Chenggong District, Kunming City, Yunnan Province

institute: Yunnan university

summary: In eukaryotes, the intrinsic mRNA stability is generally dictated by codon usage bias, the uneven preferences for synonymous codons, in a translation-dependent manner. However, the conserved mechanism underlining this phenomenon remains elusive. Hidden stop codons (HSCs), which are stop codons located in the +1 or -1 frame relative to canonical open reading frames (ORF), are sidespread across all genomes but have long been overlooked. We demonstrate that in both fungi and mammals, HSCs play an important role in regulating mRNA decay across the genome by immediately terminating out-of-frame translations promoted by nonoptimal codons, primarily through +1 ribosomal frameshifting. In the filamentous fungus Neurospora, partially deleting HSCs via synonymous substitutions in the clock gene frequency disrupts the circadian rhythm due to increased mRNA stability. Similarly, in human cells, impaired translation termination caused by rapid depletion of eRF1 leads to globally increased stability of mRNAs enriched with non-optimal codons and HSCs, which are in part degraded through the NMD pathway via UPF1. Given that from yeasts to humans the occurrence of HSCs is genome-widely associated with the presence of nonoptimal codons, these findings suggest that in eukaryotes, HSCs might coevolve with codon usage to modulate mRNA stabilities via immediately terminating different levels of ribosomal frameshifting events promoted by nonoptimal codons.

sample_organism:
Neurospora crassa
Homo sapiens

platform_organism:
Neurospora crassa
Homo sapiens

overall_design:
SLAM-seq assay was performed for HCT116 cell line and N. crassa strains ( WT and upf1 KO) to observe mRNA decay profile.  Timepoints: 0, 10, 20, 40, 60 minutes.
Ribo-seq assay was performed for WT and eRF1 KD HCT116 cell line

first: Zhanbiao

last: Li

first: Shimin

last: Gong

first: Yunkun

last: Dang


title: Intrinsic de novo DNA methylation in early embryos enables the generation of semi-cloned mice from methylation-deficient androgenetic haploid stem cells

city: shanghai

first: Zhenyu

last: Shao

state: --- Select a state ---

address: Yueyang Road 320

department: Center for Excellence in Molecular Cell Science

institute: Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

type: Methylation profiling by high throughput sequencing

summary:
This SuperSeries is composed of the SubSeries listed below.
Abstract
Among all mammalian cell types, sperm cells exhibit one of the highest levels of DNA methylation, with ~80% of CpG sites being methylated. The role of this sperm hypermethylation in offspring development, aside from the methylation at the well-characterized H19-DMR and Dlk1-Dio3 intergenic germline DMR (IG-DMR) loci, remains largely unexplored. In mouse germ cells, removal of DNA methylation by deleting methyltransferase (Dnmt) genes causes meiotic catastrophe and infertility. To circumvent this limitation, we inactivated them instead in androgenetic haploid embryonic stem cells (AG-haESCs) lacking H19-DMR and IG-DMR to remove methylation prior to oocyte injection, and subsequently reactivated them in the resulting embryos during cleavage, to ensure Dnmt sufficiency. This strategy enabled the generation of viable offspring from unmethylated paternally-derived haploid cells. In the resulting embryos, the paternal genome rapidly reacquired methylation and was comparable to wild-type in post-implantation embryos. These semi-cloned embryos could develop to term and survived to adulthood, exhibiting near-normal morphological and physiological parameters. These findings indicate that the essential hereditary function of the paternal genome methylation is mainly restricted to the imprinted loci Igf2-H19 and Dlk1-Dio3, while methylation elsewhere appears dispensable for subsequent development, as de novo methylation activity intrinsic to the early embryo ensures epigenetic reprogramming for offspring development.

overall_design: Refer to individual Series


title: Viable semi-cloned mice derived from androgenetic haploid stem cells lacking DNA methylation [RNA-seq]

summary: Among all mammalian cell types, sperm exhibit the highest level of DNA methylation, with approximately 70–80% of CpG sites being methylated. The role of this paternal hypermethylation in embryonic developmental competence, aside from the well-characterized H19-DMR and Dlk1-Dio3 intergenic germline DMR (IG-DMR) loci, remains largely unexplored. In mouse male germ cells, the lack of DNA methyltransferase (Dnmt) causes a loss of methylation, leading to meiotic catastrophe and infertility. To circumvent this limitation, we used sperm-like androgenetic haploid embryonic stem cells (AG-haESCs) for oocyte injection to produce offspring. Using CRISPR/Cas9, we effectively inactivated Dnmt1, Dnmt3a and Dnmt3b in AG-haESCs and later reactivated them in the resulting embryos, overcoming Dnmt haploinsufficiency and enabling the generation of viable offspring from methylation-deficient haploid cells. In the offspring embryos, the paternal genome derived from Dnmt-inactivated AG-haESCs rapidly reacquired methylation and restored a methylome in post-implantation embryos comparable to that of wild-type AG-haESC counterparts. These semi-cloned embryos could develop to term and survived to adulthood, exhibiting near-normal morphological and physiological parameters. These findings indicate that the functional significance of paternal genome methylation is mainly restricted to the imprinted loci Igf2-H19 and Dlk1-Dio3, while methylation of the paternal genome elsewhere appears dispensable for normal development.

overall_design: Gene and transposon expression analysis of RNA-seq data

first: zhenyu

first: Yin

last: Wang


title: Envafolimab and Chidamide in combination with GEMOX as first-line treatment for advanced and metastatic biliary tract cancer (B-Enefits/SCOG-B001): A single-arm, exploratory, phase 2 trial

city: Suzhou

first: Mengyao

last: Wu

state: Jiangsu

address: No.899 Pinghai Road

institute: The First Affiliated Hospital of Soochow University

summary: BTC represents a rare malignancy with unfavorable prognosis. Here we conducted a single-arm, multicenter, prospective phase Ⅱclinical study (ChiCTR2400080783) to evaluate the efficacy and safety of envafolimab and chidamide in combination with gemcitabine plus oxaliplatin (GEMOX) as first-line treatment. 10×scRNA-seq was adopted to conduct an initial exploration into the potential mechanisms underlying the efficacy of the combination regimen.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Mice subcutaneous cholangiocarcinoma graft models were treated with chidamide at 0, 12.5, 25, and 50 mg/mL. To decipher the complexity of cellular diversity and evolutionary trajectory in immune cell composition in response to chidamide, we obtained one mice tumor of each group after treatment, and the tissues were subjected to scRNA-seq using the 10x Genomics single-cell library. Post-treatment tissue samples were obtained from patients who achieved PR after treatment through surgery or biopsy, and scRNA-seq was performed on two of them.


title: Single cell RNA sequencing data of femur bone marrow tissue derived from mice intramuscularly injected with a SARS-CoV2 mRNA vaccine

city: Seoul

first: Jae-Hun

last: Ahn

address: Daehak-ro 101, Jongro-gu

department: Biomedical Research Institute

country: South Korea

institute: Seoul National Universty Hospital

summary: SARS-CoV2 mRNA vaccine-induced side effects have been extensively reported in the clinical field. However, the potential toxicity of mRNA vaccines has not been fully identified. We aimed to clarify mRNA vaccine-induced bone marrow toxicity. Six-week-old CrlOri:CD1(ICR) female mice were used. A SARS-CoV2 S protein coding nucleoside-modified mRNA vaccine candidate or D-PBS (Negative control) was intramuscularly injected at left side femoral muscle twice at 2-week intervals (100 ug/head). Mice were sacrificed at 2 days post-secondary injection, and the bulk RNA sequencing for bone marrow of left side femur was performed. Notably, the mRNA vaccine induced significant decrease of erythroid cells in bone marrow. The bone marrow suppression was mediated by the complete mRNA vaccine, but not by mRNA alone or LNP alone. The RNA sequencing revealed that interferon-stimulated genes (ISGs), cell death-related genes and proteolysis-related genes were significantly upregulated, while erythrocyte development-related genes, hematopoietic cell differentiation-related genes and cytoskeleton-related genes were downregulated, in the bone marrow tissue of mRNA vaccine-injected mice compared to that of D-PBS-injected mice. These findings indicate that the mRNA template is involved in the mRNA vaccine-induced bone marrow suppression. We confirmed that the mRNA vaccine can cause pathological changes in bone marrow tissue. Although the underlying mechanism needs to be clarified, our findings suggest that mRNA vaccine-induced bone marrow suppression should be cautiously considered in the pre-clinical developmental process.

overall_design: Six-week-old CrlOri:CD1(ICR) female mice were used. A SARS-CoV2 S protein coding nucleoside-modified mRNA vaccine candidate or D-PBS (Negative control) was intramuscularly injected at left side femoral muscle twice at 2-week intervals (100 ug/head). Mice were sacrificed at 2 days post-secondary injection, and the Single cell RNA sequencing for bone marrow of left side femur was performed.

first: Jae-Hwan

last: Nam

first: Byeong-Cheol

last: Kang


title: A deep learning framework for the reconstruction of gene expression profiles derived from formalin-fixed paraffin-embedded samples

city: Amsterdam

first: Kristiaan

last: Lenos

address: Van der Boechorststraat 6B

department: Laboratory for Experimental Oncology and Radiobiology (LEXOR)

country: Netherlands

institute: Amsterdam UMC

summary: This dataset was applied to evaluate the performance of a deep learning framework, FFPERescuer, specifically designed to reconstruct gene expression profiles from RNA sequencing data derived from FFPE (formalin-fixed, paraffin-embedded) tumor tissues. The dataset includes a total of 12 RNA-Seq samples, comprising 10 FFPE tumor tissue samples from colorectal cancer (CRC) cases collected in Amsterdam, the Netherlands, with 2 duplicate samples included for reproducibility assessment. The corresponding gene expression profiles from fresh-frozen tumor tissues for these 10 cases are available in the dataset GSE33113, generated using microarray technology.

overall_design: Expression profiling by high throughput sequencing

first: Lingli

last: He

first: Kai

last: Song

first: Ying

first: Yujuan

last: Dong

first: Cherry Y N

last: Wong

first: Lin

last: Qi

first: Xianrui

last: Zhang

first: Tim

last: de Back

first: Clara

last: Elbers

first: Chenchen

last: Xu

first: Yinghan

first: Feng

last: Gao

first: Yufeng

last: Chen

first: Simon Siu-Man

last: Ng

first: Shentao

last: Zhou

first: Louis

last: Vermeulen

first: Xin


title: A single-cell assessment of intramuscular and subcutaneous adipose tissue in beef cattle

first: Mollie

last: Green

state: TX

address: 1006 Canton Ave, Room 109

summary: Intramuscular fat (IM; marbling) deposition is the deciding factor of beef quality grade in the U.S. Defining molecular mechanisms regulating adipogenesis in distinct anatomical areas in beef cattle is key to the development of strategies for marbling enhancement while limiting accumulation of excess subcutaneous adipose tissue (SAT; backfat). Our objective was to define the IM and SAT transcriptional heterogeneity at the whole tissue and single-cell levels in beef cattle. Longissimus dorsi muscle (9-11th rib) samples were collected from two harvested finished beef steers to dissect matched IM and adjacent SAT. Nuclei were isolated by dounce homogenization, then sequenced via bulk RNA sequencing (RNAseq) and single-nuclei RNA sequencing (snRNAseq) with 10x Genomics in an Illumina NovaSeq 6000. Analysis was conducted via Cell Ranger pipeline and Seurat in R Studio. By the expression of signature marker genes, snRNAseq analysis identified mature adipocytes (AD; ADIPOQ, LEP), adipose stromal and progenitor cells (ASPC; PDGFRA), endothelial cells (EC; VWF, PECAM1), smooth muscle cells (SMC; NOTCH3, MYL9) and immune cells (IMC; CD163, MRC1). We detected six cell clusters in SAT and nine in IM. Across IM and SAT, AD was the most abundant cell type, followed by ASPC, SMC, and IMC. In SAT, AD made up 50% of the cellular population, followed by ASPC (31%), EC (14%), IMC (1%), and SMC (4%). In IM depot, AD made up 23% of the cellular population, followed by ASPC with 19% of the population, EC with 28%, IMC with 7% and SMC with 12%. The abundance of ASPC and AD was lower in IM vs. SAT, while IMC was increased, suggesting a potential involvement of immune cells on IM deposition. Accordingly, both bulk RNAseq and snRNAseq analyses identified activated pathways of inflammation and metabolic function in IM. These results demonstrate distinct transcriptional cellular heterogeneity between SAT and IM depots in beef cattle, which may underly the mechanisms by which fat deposits in each depot. The identification of depot-specific cell populations in IM and SAT via snRNAseq analysis has the potential to reveal target genes for the modulation of fat deposition in beef cattle.

overall_design: Isolated nuclei from subcutaneous and intramuscular adipose tissue in 2 beef steers

first: Hunter

last: Ford

first: Alexandra

last: Tegeler

first: Oscar

last: Benitez

first: Bradley

last: Johnson

first: Clarissa

last: Barboza


title: Pathologic TPO-induced TPOR-CSF2RB signaling mediates Down syndrome abnormal myelopoiesis due to GATA1 mutant-dependent CSF2RB overexpression

city: Oxford

first: David

last: Cruz

address: John Radcliffe Hospital/Headley Way

department: Radcliffe Department of Medicine

country: United Kingdom

institute: MRC Weatherall Institute of Molecular Medicine, Oxford University

summary: Transient abnormal myelopoiesis (TAM) is a human myeloid leukemia that occurs in newborns with Trisomy 21, who acquire mutations in the transcription factor GATA1. TAM originates in the fetal liver but spontaneously regresses as hemopoiesis transitions from fetal liver to postnatal bone marrow, unless clonal evolution enables transformation of the TAM clone to Myeloid Leukemia of Down Syndrome. We sought to understand the developmental tissue restriction of TAM. We show that TAM cells are marked by high expression of the cytokine receptor CSF2RB, a direct target of GATA2. Oncogenic GATA1 fails to supress CSF2RB expression. Highly expressed CSF2RB directly interacts with the thrombopoietin receptor (TPOR). Specifically at high TPO levels, activation of JAK-STAT signalling by TPOR-CSF2RB complexes is amplified and distinct from that triggered by TPOR homodimers and drives TAM cell proliferation. CSF2RB-A455D, a previously identified pathogenic gain-of function variant seen in ML-DS, requires interaction with TPOR to induce cytokine-independent cell proliferation. Together, TPOR and CSF2RB jointly exploit TPO produced by the fetal liver to sustain developmentally restricted TAM cell proliferation

overall_design: 10x Genomics Chromium Next GEM Single Cell 5′ V2 Dual Index Kit  was used to perform scRNAseq on cord blood derived  KIT+ CD34- and KIT+ CD34+ TAM (n=3), Trisomy 21 (n=3), disomic (n=3) cells. CUT&TAG was perfomed in duplicates in CMK cells to measure GATA1s and GATA2 binding as well as H3K27ac. CUT&TAG was performed to measure H3K27ac  in 7 cell lines: CMK,  HEL, SET-2, TF-1, K-562, THP-1, and JURKAT cells 48 hours post lenti delivery of the empty vector or the GATA2 coding sequence. Bulk RNA sequencing was perfomred in triplicates on TF-1 cells expressing the TPOR and empty vector or TPOR and CSF2RB 3 hours post TPO treatment.

last: Cruz Hernandez


title: Stemness factor Mex3a times translation and protein trafficking to ensure robust differentiation of olfactory sensory neurons [Polysome]

city: New York

first: Rachel

last: Duffié

state: NY

address: Jerome L Greene Sciene Building

department: Biochemistry and Molecular Biophysics

institute: Columbia University

summary: During the switch from progenitor to terminally differentiated cell, cellular physiology must change to accommodate increased translation and trafficking of membrane-bound proteins. We identify stemness factor Mex3a, expressed in immature olfactory sensory neurons (OSNs), as a key factor in ensuring proper neuronal differentiation by regulating translation and trafficking of cell surface proteins in the context of Unfolded Protein Response (UPR) signaling. Loss of Mex3a in immature OSNs leads to defects in cilia structure, cell surface protein expression, and planar cell polarity in mature OSNs. Proteomics reveal a decrease in proteins related to vesicle organization. We identify putative RNA and ubiquitin targets of Mex3a and provide evidence that Mex3a can confer K27 ubiquitin linkage on targets. Finally, modulating cellular levels of Mex3a changes the recruitment of translational elongation factors to ribosomes with effects on translation. Our data reveal how a stemness factor regulates development post-transcriptionally and post-translationally to ensure robust differentiation.

overall_design: RNA-Seq from FAC sorted cell populations from the Main olfactory epithelium. All mice were transgenic for tetO-HyperTRIBE-mCherry or tetO-Mex3a-HyperTRIBE-mcherry constructs which were either driven by gg8-tTA (Nguyen et al. 2007, PMID: 18045541) or gg8-tTA and OMP-tTA (PMID: 15157418) drivers

first: Marko

last: Jovanovic

first: Stavros

last: Lomvardas

first: Lauren

last: Tang

first: Martin

last: Escamilla del Arenal


title: Transcriptomic Analysis of iPSC-derived Cortical Neurons Under TSA and Aβ Treatment

city: Indianapolis

first: Madeline

last: Peyton

state: IN

address: 410 W 10th St

institute: Indiana University

summary: This study investigates the transcriptional effects of TSA and Aβ oligomers on human neuronal cells using RNA sequencing of iPSC-derived cortical neurons subjected to various treatment conditions. The experimental design included four distinct groups: untreated control, TSA treatment alone, Aβ exposure alone, and combined TSA treatment and Aβ exposure. Each condition was evaluated with four biological replicates, with an additional technical replicate for each condition to assess reproducibility.

overall_design: RNA-seq analysis of iPSC-derived cortical neurons with 4 treatment conditions: (1) Control (untreated), (2) TSA treatment alone (60 ng/ml), (3) Aβ oligomer exposure alone (5 μM), and (4) Combined TSA pre-treatment (60 ng/ml for 24h) followed by Aβ oligomer exposure (5 μM). Cells were treated at DIV 4 and RNA was extracted using Total RNA Purification Kit. Four biological replicates per condition with additional technical replicates.

first: Travis


title: CRISPR screen using pseudotyped viruses identifies specific entry factors for viral infection

city: Brighton

first: Leandro

last: Castellano

address: Falmer, JMS Building

institute: University of Sussex

summary: To better prepare for future viral outbreaks, scalable and adaptable platforms to study emerging infections are essential. Understanding virus–host interactions, particularly the mechanisms of cell entry, is critical for developing effective therapeutics and vaccines. Current approaches often rely on live virus assays requiring high-containment facilities, limiting speed, scalability, and accessibility.  As a proof-of-principle, we developed a novel screening platform—Ceudovitox—using pseudotyped viruses (PVs) bearing the chikungunya virus (CHIKV) envelope protein. These PVs were engineered to express herpes simplex virus-1 thymidine kinase, enabling selective killing of infected cells with ganciclovir. A heterogeneous CRISPR-Cas9 knockout cell pool was then screened using this "killer" PV system, allowing identification of CHIKV entry factors via next-generation sequencing.

overall_design: Pooled CRISPR screen using pseudotype infection, in duplicate

first: Edward

last: Wright

first: Tom

last: Stiff

first: Elle

last: Campbell


title: Neuro-Glioblastoma Connectivity: Brain-Wide Mapping and Cholinergic Modulation of Tumor Progression

city: Chongqing

first: Yang

last: Yang

address: No. 30, Gaotanyan Street

institute: Southwest Hosptial

summary: This study explores the effect of long-range cholinergic input on glioblastoma (GBM) progression based on systematically mapping neuron-glioma connectivity via monosynaptic rabies virus tracing. To address the mechanism of cholinergic and glutamate inputs lead to increased GBM cell proliferation, we examined transcriptomic changes in patient-derived GBM cells at both early (3h) and chronic (24h) time points following brief exposure to glutamate, Cev, or their combination.

overall_design: Patient-derived GBM cells were exposed to vehicle, Cev (10 μM), a selective CHRM1/CHRM3 agonist, glutamate (Glu, 10 μM), or to a combination of Cev and Glu for 1-hour. Then, GBM cells were washed and replaced with fresh medium until lysis for sequencing at different time points. Total RNA was extracted from GBM cells at both early (3h) and chronic (24h) time points for bulk RNA-seq.


title: The function of Toll-like receptor 2 in control of transcriptome responses to the microbiome and microbiome composition

city: LEIDEN

first: Li

last: Liu

address: Verbeekstraat 29D

institute: Leiden University

summary: Background: Toll-like receptor 2 (TLR2) plays a pivotal role in innate immunity and has recently emerged as a criti-cal regulator of host-microbiome interactions. However, how TLR2 influences host transcriptional responses to colonized microbiome and microbial community dynamics remains largely unclear. Germ free (GF) and conven-tionalized zebrafish (Danio rerio) model provides a valuable system to study microbiome functions. Results: RNAseq analysis revealed that transcriptomic alterations resulted from tlr2 mutation were more extensive in the presence of the microbiome than under the GF condition, indicating that tlr2 mutation has a more pro-nounced impact on host transcriptional responses when microbial signals are present. KEGG enrichment analyses showed an enhanced host response to the energy metabolism in the presence of microbial stimuli resulting from tlr2 deficiency. In addition, microbiome colonization elicited a broader transcriptional response in tlr2 wild-type larvae than in the mutants, highlighting the essential role of tlr2 in regulating host transcriptomic programs in re-sponse to microbial signals. In terms of how tlr2 influences microbial composition, 16S rRNA gene sequencing showed that tlr2 mutants exhibited higher microbial diversity during early development, whereas adult microbial diversity was highest in wild-type males, indicating a developmental stage- and sex-specific restructuring of the gut microbiome. For larvae at the genus level, tlr2 mutant larvae showed increased Chryseobacterium and Flecto-bacillus but reduced Gracilibacteria abundance relative to wild-type controls. For adult gut samples, the relative abundance of Cetobacterium was lower, while genera such as Romboutsia, Aeromonas and Pseudarthrobacter were more abundant in tlr2 wild-type male group compared to other groups. Predicted functional analyses revealed that tlr2 deficiency induced complex alterations in microbial metabolic pathways, with distinct pathway enrichments observed between larval and adult stages. Conclusions: TLR2 not only modulates host transcriptional responses to microbial colonization but also shapes gut microbial diversity, composition, and metabolic potential. Our findings highlight the critical role of TLR2 in orchestrating immunometabolic homeostasis and provide new insights into its broader function in maintaining host-microbiota symbiosis across developmental stages.

overall_design: Germ free (GF) and conventionalized (CONVD) zebrafish larvae at 5 dpf from line tlr2 mutant and wild-type control were collected for RNAseq.

first: Herman

last: Spaink


title: MiR-29 enables immune evasion of colon cancer by regulating fucosylation-mediated Ras-GTP signal in CD8+ T cells

city: China

first: Yu qi

last: Wang

address: 17 Haidian District, Beijing

institute: China agricultural univercity

summary: Immune checkpoint blockade (ICB) therapies such as PD-1 antibodies  has shown remarkable clinical success in the control of tumor growth, yet only a fraction of patients benefits from such therapy. As a result, there is increasing interest in boosting the effectiveness of ICB by combining it with other treatments. Objectives: Screening critical microRNAs that inhibit colon tumor growth in concert with ICB based on the effectiveness of immunotherapy and the gene expression levels in colorectal patients and revealing the regulatory mechanism.

overall_design: We analyzed microRNAs, which are upregulated in colorectal patients, negatively correlated with immune score, and responsive to anti-PD-1 therapy using R language. Next, mice with conditional disruption of miR-29ab1 specifically in the intestinal epithelium were administered azoxymethane and dextran sodium sulfate to induce tumor formation. Furthermore, immune status in the tumor microenvironment was evaluated by flow cytometry immunofluorescence. Transcriptomics and metabolomics were performed to study the underlying mechanisms. We performed protein extraction and purification and luciferase assays to study genes and proteins that miR-29ab1 regulated in CD8+ T cells or CTLL-2 cells. Tissues were obtained, and histology and immunohistochemistry were used for analysis.

first: Guo

last: Huiyuan

first: Wang

last: Yuqi

first: Lu

last: Yao


title: scRNA-seq of Lecanamab- and IgG1-treated xenotrasplanted human microglia

first: Bart

last: de Strooper

address: Campus Gasthuisberg, Herestraat 49, bus 602

summary: We investigated the transcriptomic changes of human microglia xenotransplanted in a mouse model of AD upon treatment with Lecanamab (Lec) compared to control (IgG1). Single-cell RNA sequencing reveals that Lec treatment induces a transcriptional program in microglia that promotes amyloid plaque removal, involving pathways related to phagocytosis, metabolism, antigen presentation, unfolded protein response, and interferon response.

overall_design: Human embryonic stem cells (WiCell, #WA09) were differentiated into microglial precursors and grafted into AppNL-G-F and AppNL-G-F Csf1rΔFIRE/ΔFIRE mice. At 4 months, the mice were chronically treated for 8 weeks with 10 mg kg−1 Lecanemab or IgG1, dosed weekly intraperitoneally. One day after the final dose, mice were terminally anesthetized and human microglia were isolated for single-cell RNA-seq. Only the transcriptomes of the AppNL-G-F Csf1rΔFIRE/ΔFIRE mice were analyzed to evaluate the transcriptional response of human microglia cells to Lecanamab in this model.

first: Giulia

last: Albertini

first: Magdalena

last: Zielonka

first: Marie-Lynn

last: Cuypers

first: An

last: Snellinx

first: Ciana

last: Xu Ruchen

first: Suresh

last: Poovathinghal

first: Marta

last: Wojno

first: Kristofer

last: Davie

first: Veerle

last: van Lieshout

first: Katleen

last: Craessaerts

first: Leen

last: Wolfs

first: Emanuela

last: Pasciuto

last: Jaspers

first: Katrien

last: Horré

first: Lutgarde

last: Serneels

first: Mark

last: Fiers

first: Maarten

last: Dewilde

last: De Strooper


title: Viable semi-cloned mice derived from androgenetic haploid stem cells lacking DNA methylation [TAPS]

first: Zhenyu

last: Shao

overall_design: Methylation analysis of TAPS data

first: Yin

last: Wang


title: Innovative Thiosemicarbazones Down-Regulate N-Myc Expression in Neuroblastoma Cells via Transcriptional and Post-Transcriptional Mechanisms

city: Brisbane

first: Zhao

last: Deng

state: QLD

address: U131/79 Moray st, New Farm, QLD

country: Australia

institute: Griffith University

summary: Neuroblastoma (NB) is an aggressive solid childhood tumor. A key oncogenic effector in NB is the transcription factor, N-Myc, whose genetic amplification leads to poor prognosis. Previous studies have indicated that iron-binding ligands such as desferrioxamine (DFO) effectively down-regulate N-myc expression. However, the mechanism of how this occurs remains unknown and could provide clues to elucidating potential therapeutic interventions.    Herein, we mechanistically dissect the activity of a new class of iron-binding ligands that have entered clinical trials and show potent anti-proliferative activity against NB, namely the thiosemicarbazone, DpC. This was achieved using RNA sequencing (RNA-seq), where we have examined the effect of these ligands on gene expression in 3 NB cell-types with (Kelly and BE2-C) or without (SH-SY5Y) N-myc amplification.    RNA-seq revealed that DpC mimicked the effect of DFO on gene expression at a 20-fold lower concentration, up-regulating key N-Myc targets such as the metastasis suppressor NDRG1, which translocates to the nucleus upon treatment. DFO and DpC significantly reduced N-Myc mRNA in p53-mutant NB cells (Kelly, BE(2)-C). In contrast, DFO increased N-Myc mRNA in wild-type p53 SH-SY5Y NB cells, where it was demonstrated that MDM2 stabilized N-Myc mRNA.

overall_design: RNA-seq profiling of DFO or DpC-treated Neuroblastoma cells (SH-SY5Y, Kelly, BE(2)-C) related to untreated cells at 24 hours.

first: Des

last: Richardson


title: Establishment of Human Trophoblast Stem Cells from Term Smooth Chorion

city: Otsu

first: Takako

last: Hoshiyama

state: Shiga

address: Seta tsukinowacho

department: Department of Obstetrics and Gynecology

country: Japan

institute: Shiga University of Medical Science

summary: Human trophoblast stem (TS) cells, which were established from blastocysts and first-trimester placental villi, can differentiate into the all trophoblastic subtypes, extravillous trophoblast (EVT) cells and syncytiotrophoblast (ST) cells. We newly generated human TS cells from the term smooth chorion (Ch-TS cells). They has the potential  to differentiate into both ST and EVT cells as same as human TS cells derived from early placental villi. The transcriptomic profile of Ch-TS cells is also similar to conventional human TS cells.

overall_design: Comparative RNA-seq analyses for chorion TS cell lines, human TS cell lines and their differentiantial cell lines. HNES1, HNES3 and hDF cells were used as control.

first: Masanaga

last: Muto

first: Shoma

last: Matsumoto

first: Shunichiro

last: Tsuji

first: Masatsugu

last: Ema


title: Effect of ZYHT Recipe on transcriptome profiling of cancer cells

city: Wuhan

first: qingqing

last: li

address: No. 238 Jiefang Road, Wuchang District

department: Department of Respiratory and Critical Care Medicine

institute: Renmin Hospital of Wuhan University

summary: In order to explore the mechanism of ZYHT Recipe on gastric cancer, we performed a RNA-seq to explore the transcriptome profiling of gastric cancer cells treatment with or without ZYHT ,including three biological replicates per group.

overall_design: To compare gene expression between two groups, differential expression analysis was performed. We also investigated functional differences in DEGs, Gene Ontology (GO) analysis, Disease Ontolog (DO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were employed.

first: Peiwen

last: Duan


title: Viable semi-cloned mice derived from androgenetic haploid stem cells lacking DNA methylation [bisulfite-Seq]

overall_design: Methylation analysis of PBAT data


title: hnRNPL modulates synapsis gene and mTOR splicing to influence primordial follicle formation and activation

city: zhejiang

first: Siyu

last: Chen

address: zhejiang

institute: zhejiang university

summary: The primordial follicle pool established during the perinatal period, serves as the lifelong source of oocytes, with its depletion leading to premature ovarian failure. During the process of primordial germ cell (PGC) development and the formation of primordial follicles, germ cell development is regulated by precise transcriptional control, accompanied by extensive post-transcriptional alternative splicing (AS) events. The role of AS during PGC development and follicle formation remains poorly understood. In this study, we explore AS dynamics and identify hnRNPL, a splicing regulator, as a critical factor in primordial follicle pool formation. Using a conditional knockout (cKO) model, we demonstrate that loss of hnRNPL in pre-meiotic germ cells impairs splicing of genes involved in homologous synapsis and autophagy, leading to oocyte arrest, reduced follicle pool size, and accelerated ovarian aging. Excessive autophagy exacerbates oocyte atresia, further contributing to infertility. Our findings highlight hnRNPL as a key regulator of AS in oocyte development and suggest potential therapeutic targets for rescuing fertility in cases of disrupted primordial follicle formation.

overall_design: Examination of WT and hnRNPL flox/flox;Stra8-cre transcriptome in Ovarian tissues

first: Xing-Xing

last: Dai


title: Next Generation Sequencing Facilitates Quantitative Analysis of Col1a2+ stromal cells sorted from Col1a2-creERT;Bmpr1a and ctrl mice

first: li

last: zihao

address: dongchuan road 800

institute: shanghai jiao tong university

summary: We had one goal to perform this study: transcriptome of Col1a2+ stromal cells sorted from Col1a2-creERT;Bmpr1a and ctrl mice

overall_design: Comparison of transcriptome of Col1a2+ stromal cells sorted from Col1a2-creERT;Bmpr1a and ctrl mice

first: Zihao

last: Li


title: Single-cell RNA sequencing analysis of splenic immune cells from MEFV M694I knock-in mice reveals enhanced interferon responses and inflammatory pathway activation

city: Nagasaki

first: Tomohiro

last: Koga

address: 1-7-1 Sakamoto

institute: Nagasaki University

summary: This dataset contains single-cell RNA sequencing data from splenocytes isolated from MEFV M694I knock-in mice and wild-type controls. The analysis reveals distinct transcriptional signatures in immune cell populations, characterized by enhanced interferon responses in T cells and inflammatory pathway activation in monocytes.

overall_design: Single-cell RNA sequencing was performed on splenocytes from age-matched MEFV M694I knock-in mice and wild-type controls. Cells were processed using 10X Genomics Chromium Single Cell 3' v3.1 technology.

first: Kaori

last: Furukawa

first: Hirotaka


title: DHT-AR and D3-VDR regulation in LNCaP cells

city: Kaga, Itabashi-ku

first: Takao

last: Susa

state: Tokyo

institute: Teikyo University, School of Mediocine

summary: To analyze the regulatory mechanism of DHT and D3 via their respective nuclear receptors in LNCaP cells, we analyzed the effects of those hormones on LNCaP cells when they were treated with siRNA for their respective nuclear receptors.

overall_design: The number of samples analyzed was 9 (N=1). Control siRNA (siCT) and mixture of siRNA for the AR (siAR)and VDR (siVDR) were transfected into LNCaP cells. Each siRNA transfected cells were treated with vehicle (V), 10-7M of DHT or 10-7M of 1,25(OH)2D3 (D3), respectively.


title: Toxin-antitoxin deletions in Legionella pneumophila reveal unusual cell death and contact-dependent survival responses during genotoxic stress [Lp_growth_phase_RNAseq]

city: Toronto

first: Alexander

last: Ensminger

state: Ontario

address: 661 University Avenue

country: Canada

institute: University of Toronto

summary: Bacteria must contend with near constant environmental stresses, and to tolerate these cellular assaults, have evolved numerous stress response pathways and programs. One such strategy is the adoption of a dormant state, whereby cells restrict their growth and await a reversion to favourable conditions. A notable example of this is the formation of persister cells, which are a quiescent subpopulation that display increased tolerance to antibiotic killing. The genetics of persistence remain poorly understood, however bacterial genes called toxin-antitoxin (TA) systems have long been implicated in the persistence phenotype. TA systems are abundant genetic elements in bacteria that can function as growth toggling molecular switches, yet their role in persister formation is highly controversial. To address this, we constructed a pan-TA deletion strain (∆7TA) of the bacterial pathogen Legionella pneumophila to examine how a strain devoid of these genes tolerates cellular stress. We identified a single putative TA system (Lpg1604-05) that is activated specifically in response to genotoxic stress, however this system leads to cell death during stress rather than promoting survival. In the absence of Lpg1604-05, cells do not die during stress exposure and instead adopt a viable but non-culturable state. Strikingly, while persister survival during DNA stress is dramatically improved when Lpg1604-05 is deleted, this enhanced survival can be conferred to wild-type cells in a contact-dependent manner during co-culture with the deletion strain. This is dependent, however, on a sufficient proportion of the mixed population being deletion mutants. Despite having homology only to other TA systems, Lpg1604-05 displays non-canonical activity and we hypothesize that it has undergone exaptation, leading to integration into the cell’s stress response pathway and conservation within L. pneumophila’s core genome. Overall, our work demonstrates the stress-specific activation of a putative TA system and its involvement in facilitating cell death, rather than survival, during stressful conditions. These findings reveal both a new physiological function for TA systems in bacteria, as well as a heretofore undescribed phenomenon of contact-dependent survival within persister cells. This expands the functional scope of an omnipresent class of bacterial genes and suggests that domestication of mobilome genes may be an overlooked source of de novo genetic circuitry.

overall_design: These samples consist of wild-type (WT) Legionella pneumophila (LP) and a strain with a single TA system (lpg1604-05; DEL) deleted from its genome. Both strains were grown to two different growth phases to compare how their transcriptomes changed during stress exposure. Early exponential growth (OD1) and late exponential growth (OD3) were the time points when RNA was extracted for bulk sequencing. There are two biological replicates for each strain + growth phase.

first: Jordan

last: Lin

first: Alex


title: Toxin-antitoxin deletions in Legionella pneumophila reveal unusual cell death and contact-dependent survival responses during genotoxic stress [Lp_cipro_RNAseq]

overall_design: These samples consist of wild-type (WT) Legionella pneumophila (LP) and a strain with a single TA system (lpg1604-05; DEL16) deleted from its genome. Both strains were treated with genotoxic stress using the antibiotic ciprofloxacin to compare how their transcriptomes changed during stress exposure. Prior to stress exposure (T0), 1 hr of stress exposure (T1), and 6 hr of stress exposure (T2) were the time points when RNA was extracted for bulk sequencing. There are two biological replicates for each strain + time point.


title: Micro-C reveals MORC/ApiAP2-mediated links between distant, functionally related genes in the human malaria parasite

city: Parul

first: Parul

last: Singh

address: 25-28, rue du Docteur Roux

institute: Institut Pasteur

summary: Genome organization plays a significant role in silencing heterochromatinized genes in the most virulent human malaria parasite, Plasmodium falciparum. However, it remains unclear how heterochromatinized genes spatially cluster or if active genes are also organized in a specific manner. We used Micro-C to achieve a near-nucleosome resolution DNA-DNA contact map, which revealed new inter- and intrachromosomal heterochromatic and euchromatic structures in the blood stage parasite. We observed subtelomeric fold structures that facilitate interactions amongst heterochromatinized genes involved in antigenic variation. In addition, we identified long-range intra- and interchromosomal interactions amongst active, stage-specific genes. Both structures are mediated by AP2-P, an ApiAP2 transcription factor, and a putative MORC chromatin remodeler, and functional specificity is achieved via combinatorial binding with other sequence-specific DNA-binding factors. This study provides unprecedented insight into the organizational machinery used by this medically important eukaryotic parasite to spatially coordinate genes underlying antigenic variation and to co-activate stage-specific genes.

sample_organism:
Plasmodium falciparum
Plasmodium falciparum NF54
Plasmodium falciparum 3D7

overall_design:
MicroC experiment was performed on Wild type, Control and AP2-P knockdown samples to investigate the DNA-DNA interactions.
MicroC experiment was performed on Wild type samples to investigate the DNA-DNA interactions.

first: Jacques

last: Serizay

first: Justine

last: Couble

first: Sebastian

last: Baumgarten

first: Jessica

last: Bryant


title: Next Generation Sequencing Facilitates Quantitative Analysis of Epithelial cells sorted from Col1a2-creERT;Bmpr1a and ctrl mice

city: shanghai

summary: We had one goal to perform this study: transcriptome of Epithelial cells sorted from Col1a2-creERT;Bmpr1a and ctrl mice

overall_design: Comparison of transcriptome of Epithelial cells sorted from Col1a2-creERT;Bmpr1a and ctrl mice


title: Periosteum Signatures of Delayed Fracture Healing in Type 2 Diabetes at Single-Cell Resolution

city: 杭州

first: XING

last: JI

state: State

address: 余杭塘路866号

summary: Purpose: Periosteum is highly involved in bone generation. We used single cell RNA sequencing(scRNA-seq) to analyze the heterogenity of periosteum from db/+ and db/db mice, fractured or post-fractured, and the homology of periosteum from mice and human.

overall_design: scRNAseq of periosteum from db/+ and db/db mice, fractured or post-fractured, and T2DM patient

first: Xing

last: Ji

first: Jiahao

last: Luo


title: AVJ16 inhibits IGF2BP1 in lung adenocarcinomas and prevents tumor growth in mice

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: Igf2bp1 is an oncofetal RNA binding protein that is expressed in a wide variety of tumors.  We have recently described a small molecule inhibitor of Igf2bp1, termed AVJ16, that prevents binding of the protein to its RNA targets by directly associating with the protein.  Here, using a multi-omics approach, we have analyzed the effects of this inhibition on RNA binding (by eCLIP), RNA expression (by RNAseq), and protein expression (by mass spectrometry).  RNAs encoding members of several pro-oncogenic signalling pathways, including Hedgehog, Wnt, and PI3K-Akt, are downregulated by AVJ16 treatment, with a high correlation between reduced Igf2bp1 binding directly to the RNA, reduced expression levels of the RNA, and reduced protein expression.  AVJ16 treatment of lung adenocarcinoma (LUAD) cells in culture causes a strong reduction in proliferation, colony formation, invasion, and spheroid growth while enhancing apoptosis and cell death.  All of these effects are limited to cells expressing Igf2bp1. Chemoresistance has also been positively correlated with Igf2bp1 expression in cancer cells.  LUAD cells treated with AVJ16 show a pronounced reduction in vital dye efflux, considered to be a proxy for enhanced chemosensitivity.  In syngeneic LUAD xenografts in mice, IP injection of AVJ16 prevents growth of tumors, and incubation with AVJ16 induces cell death in human organoids from Igf2bp1-expressing LUADs but not from healthy lung tissue.  Taken together, these results suggest that AVJ16 is a promising candidate for mono- and/or adjuvant precision therapy directed against tumors expressing Igf2bp1.

overall_design: To elucidate the mechanisms of action of AVJ16 as an inhibitor of IGF2BP1, we assessed the effects of AVJ16 treatment on lung adenocarcinoma (LUAD). A comprehensive RNA sequencing analysis was conducted to identify alterations in RNA expression, H1299 cell line were treated for 48 hour thereby revealing the inhibitor’s widespread impact on RNA expression.

first: Nadav

last: Wallis

first: Tehila

last: Gershon

first: Sojod

last: Shaaby

first: Froma

last: Oberman

first: Myriam

last: Gruenwald

first: Deborah

last: Duran

first: Amandeep

first: Gilad

last: Vainer

first: Vladimir

last: Spiegelman

first: Arun

middle: K

last: Sharma

first: Joel

last: Yisraeli


title: Microenvironment T-Type calcium channels regulate neuronal and glial processes in glioblastoma

city: Charlottesville

first: Collin

last: Dube

state: Virginia

address: 21 Hospital Drive

institute: University of Virginia

summary: Glioblastoma (GBM) is the most primary common malignant brain tumor. The aim of this study was to elucidate the role of intrinsic and microenvironment T-type calcium channels (Cav3) in promoting tumor growth and progression.  Cav3.2 KO in the microenvironment led to significant reduction in GBM growth and prolongation of animal. Single-cell RNA sequencing showed that microenvironment Cav3.2 regulates neuronal and glial biological processes. Microenvironmental Cav3.2 downregulated numerous genes associated with regulating OPC cell state such as SOX10 and Olig2. Neuronal Cav3.2 promoted neuron/GSC synaptic connections and GSC growth. Treatment of GSCs with the Cav3 blocker mibefradil downregulated genes associated with neuronal processes. The combination of mibefradil with temozolomide and radiation significantly reduced tumor volume providing an additive effect compared to TMZ/radiation alone. Together these data reveal a role for microenvironmental Cav3 in promoting GBM tumor progression through regulating neuronal and glial processes particularly associated with the OPC-cell state. Targeting both intrinsic and microenvironment Cav3 with mibefradil significantly enhanced the anti-GBM effects of TMZ and radiation.

overall_design: WT or Cav3.2KO mice had GBM cells implanted which were harvested at day 24 for single-cell RNA-seq


title: The Mechanism Study of Intermittent Fasting in Glioblastoma Suppression via Gut Microbiota-mediated m6A Modification

city: Guangxi

first: Jun

last: Meng

address: ShuangYong Road

institute: Guangxi Medical University

summary: Glioblastoma Multiforme (GBM) is one of the most malignant tumors, characterized by high treatment costs and poor outcomes, thus urgently necessitating the development of new therapeutic approaches. Recent studies have found that intermittent fasting (IF) not only can suppress GBM among various tumors but also can reconstruct the gut microbiome and alter metabolism. However, the mechanism by which IF inhibits GBM is not yet fully understood. Using animal models, I discovered that IF can effectively suppress GBM and alter the gut microbiome. Furthermore, microbial metabolites such as methionine, m6A, and the m6A-targeted oncogene TGFB2 were also downregulated. Therefore, we hypothesize that IF, by reconstructing the gut microbiome, reduces the levels of microbial metabolite methionine, subsequently decreasing m6A in GBM, leading to the downregulation of the m6A-targeted oncogene TGFB2, thereby inhibiting the development of GBM.

overall_design: Lentivirus was used to induce a mouse glioblastoma model, and then the mice were subjected to intermittent fasting treatment and different experimental interventions on the basis of this treatment.

first: Yao

last: Lin

first: Xiaopeng

last: Hu

first: Zheng

last: Li

first: Dandan

last: Xiong

first: Yueqi

first: Xinyue

last: Xu

first: Hubin

last: Chen

first: Yi

last: Bao

first: Ziyi

last: Liu

first: Shuaiyi

last: Liang

first: Jiemei

last: Chu

first: Xuena

first: Xianning

last: Zhang

first: Sanqi

last: An


title: Transcriptional profiling of adult mushroom body neurons and whole head extracts of Drosophila melanogaster [Timecourse_RNA_Naive_Trx]

city: Halifax

first: Spencer

middle: Gordon

last: Jones

state: NS

address: 5850 College St

department: Biochemistry and Molecular Biology

institute: Dalhousie University

summary: We have analyzed transcript level changes in nuclei isolated from the adult mushroom body (MB) of Drosophila melanogaster, as well from whole-head (WH) nuclear extracts. MB and WH nuclei were isolated at five time-points across a 24-hour period.

overall_design: Examination of transcript levels in mushroom body (MB) and whole-head (WH) nuclei isolated from adult wild-type flies at five time-points across a 24-hour period. Genetic material was collected from pools of 50-60 fly heads with 3 replicates per condition.

first: Jamie

last: Kramer


title: The role of Serpinb2 and  underlying mechanisms in regulating vascular inflammation during wAMD

city: 广州

first: Min

last: Xie

state: 广东省

address: 广东省广州市天河区金穗路7号

department: State Key Laboratory of Ophthalmology

institute: Zhongshan Ophthalmic Center, Sun Yat-sen University

summary: wAMD is the leading cause of blindness in AMD, accounting for more than 90% of blindness caused by AMD. Choroidal neovascularization (CNV) is the most important pathological manifestation of wAMD. Inflammation is an important factor leading to CNV, but the key factors regulating the immunomodulation of vascular endothelial cells and their underlying mechanisms are not fully understood.Here, we identified SERPINB2 as an important regulator of endothelial inflammation by RNA-sequencing.

overall_design: To investigate the specific function of SERPINB2 in vascular inflammation, we established a mouse model of CNV and injected shRNA targeting SERPINB2. RPE-choroid complex were isolated at day 3. In addition, HUVECs (Human umbilical vein endothelial cells) with depletion of SERPINB2 by siRNAs for 48 hours were also used for RNA-seq.

last: Tian

first: Weisi

last: Lu


title: DHT-AR regulation in LNCaP cells and HOXC9 stably expressed LNCaP cells

first: Takao

last: Susa

summary: To analyze the regulatory mechanism of DHT in LNCaP cells (WT) and HOXC9 stably expressed LNCaP cells (C9), we analyzed the effects of 10-7M of DHT on LNCaP cells.

overall_design: The number of samples analyzed was 4 (N=1). Each cells were treated with vehicle (V) or 10-7M of DHT, respectively.


title: Expresson data from lncRNA LINC01929 knockdown in MCF7 and MDA-MB-231 breast cancer cell lines

first: Marie-Claire

last: Wasson

address: Rm 11-C1, 5850 College Street

summary: LncRNA LINC01929 was knocked down using anti-LINC01929 antisense oligonucleotides (ASOs) in the ER+ breast cancer cell line MCF7 and the triple-negative breast cancer cell line MDA-MB-231.

overall_design: To investigate the impact of lncRNA LINC01929 on the transcriptome of ER+ and triple-negative breast cancer, microarray analyses were conducted on MCF7 and MDA-MB-231 cell lines. Cells were treated with either control ASO or anti-LINC01929 ASO for 48 hours. Following the ASO treatment, the cells were collected and preserved in TRIzol reagent for subsequent RNA purification. The purified RNA samples were then sent to The Centre for Applied Genomics (TCAG), located at The Hospital for Sick Children in Toronto, Canada. The RNA samples underwent reverse transcription into complementary DNA (cDNA) and were subsequently hybridized to the Affymetrix Human Gene 2.0 ST microarray platform. The collected data was initially obtained in raw CEL format and subsequently processed using the Transcriptome Analysis Console (Affymetrix).

first: Paola

last: Marcato

first: Jaganathan

last: Venkatesh

middle: D


title: RNA-seq of B7H3_CAR_T cells loaded with oncolytic virus VSVΔ51

city: Guangzhou

first: Fan

last: Xing

state: Guangdong

address: No. 106 Zhongshan 2nd Road, Guangzhou, Guangdong Province, China

institute: Guangdong Provincial People's Hospital

summary: Oncolytic viruses (OVs) have been evaluated as an additional method to increase the efficacy of chimeric antigen receptor (CAR)-T cells in treating solid tumors.  Here, we designed a CAR moiety by inserting the CR2 and CR3 domains of low-density lipoprotein receptor, enabling specifically and significantly surface-loading of vesicular stomatitis virus (VSV) onto CAR-T cells. We used RNA sequence to study the global gene expression and identified differentially expressed genes in B7H3-CAR-T cells and CR2/3-B7H3-CAR-T cells loaded with loading VSVΔ51, aiming to identify the changed pathways that are influenced by the cross-connection between VSV-G protein and CR2/3-CAR moiety.

overall_design: For CAR-T cell construction, the activated CD3 positive human T lymphocytes were transduced with lentivirus carrying the B7H3-CAR and CR2/3-B7H3-CAR. To preload VSVΔ51, B7H3-CAR-T or CR2/3-B7H3-CAR-T cells were co-incubated with VSVΔ51 (MOI=10) on ice for 1 hour. Then the CAR-T cells were incubated in 37℃ for 3 hours. The samples used in the RNA sequence analysis were in triplicates.


title: FAM134B deficiency in HK-2 cells

city: Zhanjiang

first: Ji-Xin

last: Tang

address: No.57, Renmin Avenue

institute: Affiliated Hospital of Guangdong Medical University

summary: FAM134B, also known as RETREG1 or JK-1, was first identified in esophageal cancer and later identified as an ER autophagy receptor. The protein contains a Reticulon-homology domain(RHD) and an LC3 interaction region (LIR), where RHD is responsible for sensing and inducing ER membrane curvature, while LIR binds to LC3 on the phagocytic membrane, and the ER membrane and its contents are subsequently encapsulated into autophagosomes and transported to lysosomes for degradation. Now FAM134B, as one of the receptors involved in ER autophagy, has received more and more attention.We knocked down FAM134B in HK-2cells and researched which genes and pathways were been influenced.

overall_design: Bulk RNA-seq between WT HK-2 cells and TAX1BP1-KO HK-2 cells, each group has three biological duplication

first: Dong-Yi

last: LI

first: Ze-Sen

last: Feng

first: Hua-Feng


title: Transcriptomic Analysis of Nicotine on the Cardiovascular System Using a Diverse Population of Human Induced Pluripotent Stem Cell-derived Endothelial Cells

city: Palo Alto

first: Joseph

last: Wu

state: California

address: 240 Pasteur Drive

department: Cardiovascular Institute

institute: Stanford University

summary: Nicotine, the primary addictive component of tobacco, is linked to major adverse cardiovascular events (MACE) and increased mortality. The impact of nicotine across diverse populations is challenging to investigate in clinical studies due to individual variations in environmental exposures, the presence of other compounds in cigarettes and e-cigarettes, and differences in nicotine dosage and frequency. While animal models offer control over these variables, translating findings to human physiology remains complex. Induced pluripotent stem cells (iPSCs) present a promising alternative, leveraging each patient's unique genetic profile. In this study, we utilized iPSCs to explore the effects of nicotine on the cardiovascular system in a genetically diverse population. We derived endothelial cells (iPSC-ECs) from iPSCs of 20 healthy donors from diverse ancestries, including African, Caucasian, East Asian, and Hispanic, and exposed them to 1 µM nicotine for 48 hours. RNA sequencing analysis revealed significant interindividual variation in gene expression, while the nicotine-induced transcriptomic signature was consistent across individuals. A total of 399 differentially expressed genes (DEGs) were identified, with 303 downregulated and 96 upregulated genes. Pathway analysis indicated that upregulated genes were associated with cardiovascular diseases and nicotine addiction, whereas downregulated genes were linked to type 2 diabetes and respiratory disorders. Further analysis highlighted nicotine's effect on pathways related to atherosclerosis and type 2 diabetes. Notably, genes such as HMOX1 and HSPA6 were significantly downregulated upon nicotine exposure, findings validated by quantitative real-time PCR. This study underscores the utility of iPSC-ECs in modeling nicotine's direct impact on the endothelium, providing insights into its role in disease pathogenesis and offering potential avenues for the development of diagnostic markers and therapeutic interventions.

overall_design: Peripheral blood mononuclear cells (PBMCs) from 20 healthy donors (12 males and 8 females), including 5 African, 5 Caucasian, 5 East Asian, and 5 Hispanic participants, were reprogrammed into iPSCs at the Stanford Cardiovascular Institute Biobank using established protocols. We differentiated the iPSCs into iPSC-ECs and exposed them to 1 uM nicotine for 48h. The RNA was collected and submitted for bulk RNA sequencing.

first: Nerea

last: Jimennez-Tellez

first: Mingqiang

last: Wang

first: Yu

last: Liu

first: Damon

last: Williams


title: LncRNA and mRNA expression profile analysis defines the heterogeneity of pancreas islets

city: Fuzhou

first: Jinyan

last: Chen

address: No.7 Wusi Road

institute: Fufian Academy of Medical Sciences

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

summary: While the islet heterogeneity in size, number, architecture, cellular composition, and capillary density has been well studied in rodents and human, less is known about the islet heterogeneity in lncRNA and mRNA profile. To probe the heterogeneity of these molecular differences, microarray was used to examine lncRNA and mRNA expression profiles in islets from the head and tail regions of rat pancreas.

overall_design: Rat islets  from the head and tail regions of pancreas were isolated respectively using a modified method by common bile ductal collagenase infusion.Total RNA from the isolated islets was extracted using TRIzol Reagent. Microarray was used to examine lncRNA and mRNA expression profiles in islets from the head and tail regions of rat pancreas.

first: Peng

last: Huang


title: mIcroRNA sequencing of LINC01929 KD knockdown and control samples in MCF7 and MDA-MB-231 breast cancer cell lines

overall_design: To investigate the impact of lncRNA LINC01929 on the microRNA levels of ER+ and triple-negative breast cancer, small RNA-sequencing was conducted on MCF7 and MDA-MB-231 cell lines. Cells were treated with either control ASO or anti-LINC01929 ASO for 48 hours. Following the ASO treatment, small RNA was extracted with mirVana™ miRNA Isolation Kit (Invitrogen, Thermo Fisher Scientific) as per manufacturer’s instructions. Total RNA from same lysates was used to confirm knockdown of LINC01929 using qPCR as described. Samples were sent to TCAG for Illumina NovaSeq - SP flowcell.


title: Expression data from Adra1a, Adra1b and Adra1d KO mice treated with milnacipran.

city: Krakow

first: Grzegorz

last: Kreiner

address: Smetna 12

department: Dept. Brain Biochemistry

country: Poland

institute: Institute of Pharmacology

summary:
Investigation of the role of Adra1 subtypes and their impact on antidepressant drugs efficiency. Adra1a, Adra1b and Adra1d KO mice were chronically treated by antidepressant drug milnacipran.
Microarray experiment was applied to compare up and downregulated genes after chronic treatment of milnacipran itself on w/t animals and the effec of this drug when treated the mice with ablation of Adra1a, Adra1b or Adra1d genes, respectively.

overall_design: Control and Adra1a, Adra1b and Adra1d mice were treated 3 weeks by milnacipran, 1x daily. Mice were sacrified and brain tissue of hippocampus preserved in RNAlater, than RNA was extracted and hybridization on Affymetrix microarrays.

first: Irena

last: Nalepa


title: SON controls mouse early embryonic development by regulating RNA splicing and histone methylation

city: Chang Chun

first: Sheng

last: Zhang

address: xi an da lu 5333 hao

institute: Jilin University

summary: Thousands of genes are activated at later 2-cell embryos, which means that numerous pre-mRNAs are generated during this time. These pre-mRNAs must be accurately spliced to ensure that the mature mRNAs are translated to functional proteins. However, little is known about the roles of pre-mRNA splicing and cellular factors modulating pre-mRNA splicing during early embryonic development. Here, we report that downregulation of SON, a large Ser/Arg (SR)-related protein, reduced embryonic development and caused deficient blastomere cleavage. These embryonic developmental defects resulted from dysregulated nuclear speckle organization and pre-mRNA splicing of a set of cell-cycle-related genes. Furthermore, SON downregulation disturbed the transcriptome (2128 upregulation and 1399 downregulation) in 4-cell embryos. Increased H3K4me3, H3K9me3 and H3K27me3 levels were found in 4-cell embryos after SON downregulation. Taken together, those results demonstrate that accurate pre-mRNA splicing is essential for early embryonic development, and SON plays important roles on nuclear speckle organization, pre-mRNA splicing, the transcriptome establishment and histone methylation reprogramming during early embryonic development.

overall_design: In order to study the roles of SON on mice early embryonic development, we microinjeted siRNA of SON into zygotes to knockdown SON lelvel.


title: Normalization of vascular intussusception is essential for promoting lung regeneration over fibrosis (MeRIP-Seq)

city: Chengdu

first: Liyin

state: Sichuan

address: Remin nan Road

institute: Sichuan University

summary: Proliferation of vascular endothelial cells (ECs) is critical for providing sufficient cells lining the neo-vascular lumen after injury.  As compared with parenchymal cells, vascular ECs normally do not develop genetic mutation during injury. Therefore, epigenetic changes such as RNA modification in ECs might be essential for modulating vascular regeneration in damaged lungs. N6-methyladenosine (m6A) modification has been shown as a major mammalian internal mRNA modification.  However, the roles of RNA modification in the regulation of N6-methyladenosine (m6A) modification remain elusive. Here we examined m6A modification landscape in transcriptome-wide, and find that m6A is dynamically regulated during ECs proliferation after pneumonectomy (PNX). The result showed the number of m6A peaks in lung ECs 7 days post PNX was higher than that in sham group, and m6A-RIP sequencing revealed that the m6A peaks in Foxo1 exon 1 and exon 2 were increased on day 7 by PNX, suggesting that m6A methylation of these two exons in Foxo1 mRNA is increased in regenerating lung ECs after PNX.

overall_design: CD31+CD45- ECs were isolated from lung 0 day (Sham) and 7 days after PNX. The lung tissues were cut off and digested to get cell suspension. Immunomagnetic bead cell sorting was used to isolated mouse lung vascular ECs and magnetic beads were pre-coated with CD31 and CD45 antibody respectively. The endothelial cells were obtained as CD45 negative and CD31 positive cells.

first: Jie

last: Ma

first: Xu

first: Bi-Sen

last: Ding


title: Normalization of vascular intussusception is essential for promoting lung regeneration over fibrosis

summary: Proliferation of vascular endothelial cells (ECs) is critical for providing sufficient cells lining the neo-vascular lumen.  Moreover, expanding ECs need to undergo multiple steps to line new lumen,  functionalizing anti-thrombotic and anti-inflammatory interface that prevents extravasation of inflammatory cells, maintains blood perfusion, and facilitates cellular crosstalk. Therefore, productive angiogenesis in regeneration requires formation of endothelial tight junction, arrangement of endothelial apical lumen, and alignment of basolateral side juxtaposed with alveolar epithelial cells.  As a result, we used single cell RNA sequencing (scRNA-seq) to detect the function of diverse EC clusters.

overall_design: 7 days after PNX, wild type mice and their parallel control (Mettl3 KO) were harvested as well as Sham group. The lung tissues were cut off and digested to get cell suspension. Immunomagnetic bead cell sorting was used to isolated mouse lung vascular ECs and magnetic beads were pre-coated with CD31 and CD45 antibody respectively. The endothelial cells were obtained as CD45 negative and CD31 positive cells.


title: Alcohol-induced C/EBP β-driven VIRMA decreases oxidative stress and promotes pancreatic ductal adenocarcinoma growth and metastasis via the m6A/YTHDF2/SLC43A2 pathway

city: harbin

first: Lei

last: Gao

address: nagang street

institute: harbin medical university

summary: N6-methyladenosine (m6A) is implicated in tumorigenesis. To data, the role of VIRMA, an RNA methyltransferase in pancreatic ductal adenocarcinoma (PDAC) has not been clearly defined. The present study demonstrated that VIRMA was upregulated in PDAC. Overexpression of VIRMA accelerated PDAC proliferation and metastasis, whereas knockdown of VIRMA had an opposite effect. Mechanistically, VIRMA promoted the degradation of SLC43A2 mRNA via an m6A-YTHDF2 mechanism, and downregulation of SLC43A2 reduced phenylalanine absorption and oxidative stress, thus enhancing the progression of PDAC. In addition, alcohol induced the expression of C/EBP β, which bound to the promoter of VIRMA and boosted its transcription. The findings of the present study revealed a potential link between alcohol consumption, m6A and phenylalanine absorption in PDAC progression, providing a novel means to combat this disease.

overall_design: To reveal the m6A modified genes in pancreatic cancer cells, m6A-seq and mRNA-seq performed by deep sequencing, using Illumina HiSeq 4000.

first: Gang

first: Gaoyuan

last: Lv

first: Ziying


title: Genome‑wideBrain DNAMethylationandGeneExpression Patterns Unravel Epigenetic Reprogramming in Mesial Temporal Lobe Epilepsy

city: changsha

first: xi

last: zhang

state: hunan

address: xiangya road

institute: xiangya hospital, central south university

summary: Mesial temporal lobe epilepsy (MTLE) is the most common drug-resistant epilepsy in adults, characterized by hippocampus sclerosis. To date, the etiology of MTLE epileptogenesis and the  molecular mechanisms underlying hippocampus sclerosis remain largely unclear. Altered genome-wide DNA methylation patterns and differential gene expression have been reported to be involved in the pathophysiological mechanism of epileptogenesis. To discover epigenetic reprogramming patterns associated with MTLE, we used a higher-throughput microarray, Illumina Infinium 850 K BeadChip, and RNA sequence to analyze epigenome-wide DNA methylation and related gene expressions. We also performed an enrichment analysis to find differences between the patients and autopsy controls. Through data analysis we identified 1832 DNA differentially methylated sites, and ten differentially methylated regions in several chromosomes. The differentially methylated genes were found enriched in "synaptic vesicle", "synaptic vesicle exocytosis", "regulation of synaptic plasticity", "Parkinson's disease", and "Oxidative phosphorylation". Correlation analysis of RNA expression and DNA methylation revealed that 16/48 genes’ DNA methylation marks residing in the promoter region, and 32/48 were located within the gene body. These findings assist with a better understanding of the molecular pathogenesis of MTLE and aid in designing effective tailored interventions.

overall_design: to better understand the molecular pathogenesis of MTLE and to aid in designing effective tailored interventions.

first: Xi

first: Wenbiao

last: Xiao


title: Lysine-specific demethylase 6B promotes STAT1-mediated macrophages activation during atherosclerosis development

city: hangzhou

first: huan

last: chen

state: Zhejiang

address: Hangzhou, Zhejiang Province, China

institute: Zhejiang Chinese Medical University

summary: Atherosclerosis (AS) induced coronary heart disease is still the first killer threatening human health due to high morbidity and mortality. How N6-methyladenosine modification (m6A) in macrophage participates in atherosclerosis progression is still completely unclear. In this study, by performing meRIP-seq in macrophages during differentiation and activation processes, we aim to understand the landscape of m6A spectrum in macrophage from different stages. Moreover, we also find a large class of histone methylation modification enzymes were regulated by m6A modification. Western blot, qPCR and ChIP-seq results demonstrate m6A modification regulates Lysine-specific demethylase 6B (Kdm6b)-dependent macrophage activation. In mechanism, Kdm6b interacts and methylates Jak1 inducing its phosphorylation-mediated macrophage activation. Furthermore, RIP-qPCR detection indicates following macrophage differentiation and activation, both m6A writers Mettl3 and Rbm15 participates in m6A modification of Kdm6b mRNA. Finally, by performing atherosclerotic model on macrophage-specific Kdm6b knockout mice on Ldlr-/- background, we demonstrate Kdm6b promotes macrophage activation-mediated atherosclerosis by amplifying inflammation and destabilizing plaque. This study will provide a new understanding of the pathogenesis of AS and is expected to develop a new target for the treatment of AS.

overall_design: Comparative gene expression profiling analysis of RNA-seq data: Effects of GSKJ1 and IFNγ on genes in mouse bone marrow-derived macrophages


title: Comparative transcriptomic analysis ofcirculatingand muscle resident fibroadipogenic progenitors in middle cerebral artery occlusion (MCAO) mice.

city: guangzhou

first: li

last: ruijie

state: State...

address: sun yat-sen university

institute: sun yat-sen university

summary: Patients surviving stroke usually experience rapid muscle wasting and an increased risk of physical disability. Although multifactorial interactions including malnutrition, disuse, systemic catabolic imbalance and neurohormonal dysregulation are considered to contribute to the progression of stroke-related sarcopenia, the underlying mechanisms of this brain-muscle crosstalk remain elusive. Muscle-resident fibro/adipogenic progenitors (FAPs) are indispensable for maintaining muscle homeostasis and function as initial sensors of external perturbations. In the present study, we illustrate that FAPs rapidly respond to the overactive sympathetic nervous system (SNS), and egress from the muscle niche into circulation during the acute phase of stroke. In our study, we performed comparative transcriptomic analysis of circulating fibroadipogenic progenitors and muscle resident fibroadipogenic progenitors.

overall_design: RNA-Seq was performed from RNA samples extracted from fibroadipogenic progenitors obtained from peripheral blood and muscle of MCAO mice.

first: Yinong

first: Yilin

first: Ruijie

last: li


title: Microarray analysis in vessels from control rat (Wistar rat, WT) and transgenic rat (PKCbeta deletion rat, KO) with angiotensin II

city: Imabari

first: Masashi

last: Mukohda

state: Ehime

address: 1-3 Ikoinooka, Imabari

institute: Okayama University of Science

summary: Gene profiling in vessels

overall_design: Vessels were isolated from four male control (WT) and four male transgenic (KO) rats and treated with angiotensin II for 24 h.

first: Fumiyo

last: Saito


title: ChIP-seq comparing histone H3 acetylation state in Nipponbare WT rice and PINE1 knockout mutant

city: Milano

first: Vittoria

last: Brambilla

state: Milano

address: Via Celoria, 26

department: Agricoltural and environmental sciences

country: Italy

institute: University of MIlan

type: Genome binding/occupancy profiling by high throughput sequencing

summary: With this ChIP-seq we are comparing chromatine accessibility in the japonica rice variety Nipponbare and in pine1 mutant, a gene that may control stem elongation through chromatine remodelling. To check for differences in chromatine state between WT and pine1 we precipitated the acetylated chtromatine using an antiboyd against H3 acetylated at lysines 9 and 14 (H3K9/14ac)

overall_design: Nipponbare WT rice and pine1 knockout mutant plants were grown in long day conditions for 20 days. A total of 70 SAM were sampled for each genotype, in duplicate. Chromatine was then extracted from each sample and immunoprecipitated using H3K9/14ac Antibody.

first: Giulio

last: Vicentini

first: Giorgio

last: Perrella

first: Alessio

last: Baldini

first: Fabio

last: Fornara


title: Changes in gene expression of Pinus armandii seed kernels during the harvesting period (August to September)

city: Kunming

last: Li

state: Yunnan

address: Qingyun Street

institute: Southwest Forestry University

summary: The illumina NovaSeq6000 platform was utilized to generate mRNA profiles of Pinus armandii seednuts obtained in August and September. Total RNA was extracted from seed kernels from each month separately and pooled into three biological replicates for each condition. The concentration and purity of RNA (OD260/280 and OD260/230 ratios) were measured using a NanoPhotometer spectrophotometer. RNA concentration was examined for accurate quantification using a Qubit 2.0 Fluorometer, and then RNA integrity was accurately examined using an Agilent 2100 bioanalyzer.

overall_design: The  Pinus armandii cones were harvested at the end of August and the end of September, respectively, and then the seeds and the corresponding seed kernels were obtained separately, and the seed kernels at both stages were subjected to RNAseq analysis.

first: ChengZhong

last: He

first: Dan

last: Zong


title: Identification of Evolutionarily Conserved VSX2 Enhancers in Retinal Development [RNA-seq]

city: Memphis

first: Asha Jacob

last: Jannu

state: TN

address: Inspiration4 Advanced Research Center

department: Developmental Neurobiology

institute: St Jude Children's Research Hospital

summary: Super-enhancers (SEs) are expansive regions of genomic DNA that regulate the expression of genes involved in cell identity and cell fate. Recently, we found that distinct modules within a murine SE regulate gene expression of transcription factor Vsx2 in a developmental stage- and cell-type specific manner. In the present study, we examine the ability of these modules to drive retinal development between species. By inserting the human build of one Vsx2 SE module into a mouse with microphthalmia, eye size was rescued. To understand the implications of these SE modules in a model of human development, we generated human retinal organoids. Deleting one module results in small organoids, recapitulating the small-eyed phenotype of mice with microphthalmia, while deletion of the other module leads to a complete loss of ON cone bipolar neurons. This prototypical SE serves as a model for uncoupling developmental stage- and cell-type specific effects of neurogenic transcription factors with complex expression patterns. Moreover, by elucidating the gene regulatory mechanisms, we can begin to examine how dysregulation of these mechanisms contributes to phenotypic diversity and disease.

overall_design: Retinal organoids derived from hESC line H9 VSX2-GFP/CRX-TdTomato were generated using an established protocol from the Laboratory of Dr David Gamm. Each organoid was placed in one well of a 24-well plate (1 organoid/ 1 well) with 1mL of 3D Retinal Differentiation Media containing 1:1000 EC23 (3D RDM) and incubated at 37C. Media changes occurred weekly and Mycoplasma testing occurred every 2 months. After 100 days, 3D RDM media changes did not include EC23.

first: Victoria

last: Honnel

first: Jackie

last: Norrie

first: Asha

last: Jacob Jannu

first: Cody

last: Ramirez

first: Michael

last: Dyer