title: PSPC1 selectively controls tumorigenesis and oncogenic transcription in acute myeloid leukemia [RNA-seq]

first: Pinpin

last: Sui

department: Molecular Medicine

summary: Acute myeloid leukemia (AML) is an aggressive hematopoietic malignancy characterized by the blockage of myeloid cell differentiation and uncontrolled proliferation of immature myeloid cells. Here, we show that paraspeckle component 1 (PSPC1) is aberrantly overexpressed in AML and high level of PSPC1 expression is associated with poor survival in AML patients. We demonstrate that PSPC1 loss dramatically suppresses leukemia maintenance and initiation/development as well as self-renewal of leukemia stem cells (LSCs) but has no effect on normal hematopoiesis. Mechanistically, PSPC1 interacts with PU.1, and they co-occupy the chromatin, especially at promoter regions proximal to transcription start site (TSS). Recruitment of PSPC1 and PU.1 on co-bound regions was dependent on each other to regulate target genes expression such as NDC1, a prognostic marker in multiple tumors. Collectively, our findings uncover a selective and crucial role of PSPC1 in AML and highlight its potential as a promising therapeutic target for myeloid malignancies.

overall_design: RNA-seq for OCIAML5 and MOLM13 with or without PSPC1/PU.1 knockdown (n=2 for each group).

first: Mingjiang

last: Xu

first: Juyeong

last: Hong


title: Innervation and cargo-specific axonal transport impairments in FUS-ALS mice with gain and loss of function [RiboTag]

status: Public on May 29 2025

city: London

first: Pietro

last: Fratta

address: Queen Square

country: United Kingdom

institute: University College London

type: Expression profiling by high throughput sequencing

summary: Mutations in the RNA-binding protein FUS cause aggressive, early-onset forms of amyotrophic lateral sclerosis (ALS), leading to the progressive degeneration of the neuromuscular system. These mutations drive nuclear depletion and cytoplasmic mislocalisation of FUS, resulting in both loss and gain of function. We investigated these mechanisms and their impact on key pathophysiological processes in vivo, using a novel FUS-ALS mouse model. Adult mice presented widespread transcriptomic alterations consistent with nuclear loss of function, while translatome analysis revealed specific deficits associated with aberrant FUS-dependent cytoplasmic partitioning and gain of function. Mutant FUS expression selectively impaired neuromuscular junction (NMJ) innervation in FUS-ALS females. However, NMJ reinnervation following sciatic nerve crush was equally perturbed in homozygous mutants of both sexes, indicating impaired regeneration and damage responses. Additionally, we observed cargo-specific alterations in axonal transport, a process critical for neuronal function and maintenance; in vivo mitochondrial transport was impaired in homozygous FUS-ALS mice, whereas the retrograde transport of signalling endosomes was again only affected in mutant females, strengthening the link between endosomal transport impairment and NMJ denervation in ALS. Altogether, our findings establish FUS-ALS homozygous mice as a valuable model for investigating early cellular impairments driving ALS pathology, and identify broader and sex-dependent motor neuron dysfunction in FUS-ALS pathogenesis.

overall_design: In vivo motor neuron RiboTag-seq and total RNA-seq performed on from spinal cords of 3-month-old Fus+/+ and Fus∆14/∆14 mice. Animals express Chat-cre/Rpl22HA and derive from   C57BL/6J × DBA/2J intercrossing and are F1.

first: Rebecca

last: Simkin

first: Andrew

last: Tosolini

first: Alla

last: Mikheenko

first: Agnieszka

last: Ule

first: Wenanlan

last: Jin

first: Bernadett

last: Kalmar

first: Mhoriam

last: Ahmed

first: Qiuhan

last: Lang

first: Franciane

last: Lirot

first: Martha

last: McLaughlin

first: David

last: Villarroel-Campos

first: Linda

last: Greensmith

first: James

last: Sleigh

first: Thomas

last: Cunningham

first: Giampietro

last: Schiavo

first: Elizabeth

last: Fisher

first: Nicol

last: Birsa


title: Innervation and cargo-specific axonal transport impairments in FUS-ALS mice with gain and loss of function [RNA-seq]

first: Pietro

last: Fratta

overall_design: spinal cord RNA-seq from Fus+/+ and Fus∆14/∆14 (1 and 3 month old) and Fus-/- (3 month old). All animals derive from C57BL/6J × DBA/2J intercrossing and are F1.

first: Rebecca

last: Simkin


title: Engineering Sonogenetic EchoBack-CAR T cells

city: Los Angeles

first: Peixiang

last: He

state: California

address: 1002 Childs Way

country: USA

institute: USC

summary: Chimeric antigen receptor (CAR) T cell therapy marks a significant advancement in oncology, offering the promise of durable remissions in hematological malignancies. However, solid tumors present formidable challenges, including on-target off-tumor toxicity, exhaustion, and limited persistence of therapeutic T cells. Here, we engineered sonogenetic EchoBack-CAR T cells using a highly heat-sensitive promoter, evolved through a sort-seq platform, and integrated it with a positive feedback loop from CAR signaling pathways that enables the conversion of tumor engagement into CAR production, resulting in long-lasting CAR expression upon remote stimulation by focused ultrasound (FUS). EchoBack-CAR T cells with a high-affinity single-chain variable fragment (scFv) targeting disialoganglioside GD2 (EchoBack-hGD2CAR) exhibited potent cytotoxicity and persistence in an in vitro glioblastoma spheroid model. In both subcutaneous and orthotopic glioblastoma models in mice, EchoBack-hGD2CAR T cells achieved robust and safe tumor suppression without off-tumor toxicity. Through single-cell RNA sequencing, we uncovered a distinctive transcriptomic landscape that underscores the enhanced cytotoxicity and reduced exhaustion of EchoBack-CAR T cells after chronic antigen stimulation compared to standard CAR T cells that constitutively express CAR. The EchoBack-CAR can also be generalized and extended to treat prostate cancer by targeting prostate-specific membrane antigen (EchoBack-PSMACAR), demonstrating a remarkable tumor suppression but minimal off-tumor toxicity to healthy tissues. Collectively, these findings not only highlight the potential of EchoBack-CAR T cells to promote solid tumor immunotherapy via ultrasound remote control but also present a modular approach adaptable to various cancer targets, poised to mitigate the limitations of current CAR T cell therapies.

overall_design: EchoBack CAR-T cells and standard CAR-T cells were rechalleneged with glioblastoma cancer cells daily at a E:T ratio of 1:2 for 10 days to achieve chronic antigen stimulation in vitro. EchoBack and standard CAR-T cells were isolated by FACS and analyzed using scRNA-seq

first: Longwei

last: Liu

first: Fengyi

last: Ma

first: Yuxuan

last: Wang

first: Yingxiao


title: Thermally adapted Escherichia coli keeps transcriptomic response during temperature upshift exposure

city: Cuernavaca

first: Gilberto

last: Pérez Morales

state: Morelos

address: Avenida Universidad 2001, Colonia Chamilpa

department: Cellular Engineering Department

country: Mexico

institute: Instituto de Biotecnología - Universidad Nacional Autónoma de México

summary: The heat-shock response is a cellular protection mechanism against sudden temperature upshifts extensively studied in Escherichia coli. However, the effects of thermal evolution on this response remain largely unknown. In this study, we investigated the early and late physiological and transcriptional responses to temperature upshift in a thermotolerant strain under continuous culture conditions. Adaptive laboratory evolution was performed on a metabolically engineered E. coli strain (JU15), designed for D-lactic acid production, to enable cellular growth and fermentation of glucose at 45 °C in batch cultures. The resulting homofermentative strain, ECL45, successfully adapted to 45 °C in a glucose-mineral medium at pH 7 under non-aerated conditions. The thermal-adapted ECL45 retained the parental strain’s high volumetric productivity and product/substrate yield. Genomic sequencing of ECL45 revealed eight mutations, including one in a non-coding region and six within the coding regions of genes associated with metabolic, transport, and regulatory functions. Transcriptomic analysis comparing the evolved strain with its parental counterpart under early and late temperature upshifts indicated that the adaptation involved an inactive stringent response. This mechanism likely contributes to the strain’s ability to maintain growth capacity at high temperatures.

overall_design: The analysis compared the early (15 min) and late (three residence times) transcriptomic response of two strains (a parental and thermal adapted strain) during the temperature upshift from 37 °C to 45 °C in a chemostat culture.

last: Pérez-Morales

first: Alfredo

last: Martínez


title: Multi-omics analyses in cows and their female progeny in the context of direct and time-lagged heat stress effects

city: Wenzhou

first: Tong

last: Yin

address: Luchengqu Guantanglu38-9

country: China

institute: Zhejiang Key Laboratory of Dairy Cattle Genetic Improvement and Milk Quality Researc

summary: A heat stress (HS) cattle research design was implemented to study HS effects on the three different “omics features” methylations, gene expressions and metabolic pattern from a direct perspective in pregnant cows and from an indirect time-lagged intergenerational perspective in offspring (the respective F1 and as F1 offspring before calving). In this regard, German Holstein dairy cows and their calves were blood sampled for DNA and RNA extraction and for metabolic phenotyping, and allocated to HS and respective control groups (the cows (dams) as well as their calves) according to a temperature-humidity threshold of 60.

overall_design: German Holstein dairy cows and their female calves were allocated to heat stress and respective control groups (the cows (dams) as well as their calves) according to a temperature-humidity threshold of 60

first: Kathrin

last: Halli

first: Christian

last: Koch

first: Stefan

last: Krebs

first: Sven

last: König


title: Single-cell transcriptomic profiling of Botrylloides diegensis of a whole colony

city: Dunedin

first: Megan

middle: J.

last: Wilson

state: Otago

address: 56 Hanover St

department: Anatomy

country: New Zealand

institute: University of Otago

summary: In this study, we performed single-cell RNA sequencing (scRNA-seq) of an entire B. diegensis colony, including zooids, buds, and vascular tunics, to resolve cellular heterogeneity and identify cell and tissue markers.

overall_design: Colonies were fixed in a mix of methanol and acetic acid (ACME), filtered, FACS sorted and loaded on a 10X Chromium Next GEM Single Cell 3ʹ v3 Kit.

first: Berivan

last: Temiz

first: Michael

last: Meier

last: J. Wilson


title: ABHD18 is essential for cardiolipin remodeling and its inhibition restores mitochondrial function in Barth Syndrome [RNA-Seq]

city: Toronto

first: Jason

last: Moffat

state: Ontario

address: 686 Bay Street

department: Genetics and Genome Biology

country: Canada

institute: Hospital for Sick Children

summary: Cardiolipin (CL) is the signature phospholipid of the inner mitochondrial membrane, where it stabilizes the electron transport chain protein complexes. The final step in CL biosynthesis concerns its remodeling: the exchange of nascent acyl chains with longer, unsaturated chains. However, the enzyme responsible for cleaving nascent CL has remained elusive. Here, we describe ABDH18 as the candidate de-acylase in the CL biosynthesis pathway. Accordingly, ABHD18 converts CL into monolysocardiolipin (MLCL) in vitro and its inactivation in cells and mice results in accumulation of nascent CL in serum and tissues. Strikingly, ABHD18 deactivation rescues the mitochondrial defects in cells and the morbidity and mortality in mice associated with Barth Syndrome. This rare genetic disease is characterized by the build-up of MLCL due to inactivating mutations in TAFAZZIN (TAZ), which encodes the final enzyme in the CL remodeling cascade. We also identified a selective, covalent small molecule inhibitor of ABHD18 that restores TAZ mutant phenotypes in patient fibroblasts and fish embryos. This study highlights a striking example of genetic suppression of a monogenic disease revealing a canonical enzyme in the CL biosynthesis pathway.

overall_design:
RNA-seq
WT HAP1 cells cultured in DMEM (minimal) + 10% FBS
WT HAP1 cells cultured in IMDM + 10% FBS
TAZ mutant HAP1 cells cultured in DMEM (minimal) + 10% FBS
TAZ mutant HAP1 cells cultured in IMEM + 10% FBS

first: Sanna

last: Masud

first: Kevin

middle: R

last: Brown


title: 3D bioprinting of human liver models with biliary branching morphogenesis for hepatotoxicity, regeneration and NASH

status: Public on May 30 2025

city: Beijing

first: Rui

last: Yao

address: Haidian District

institute: Tsinghua University

summary: The study of liver disease and drug discovery has been constrained by a lack of liver tissue with intrahepatic bile ducts (IHBD) network. Here we created functional bioprinting human liver with IHBD through precise temporal-spatial regulation via biochemical and mechanical cues. To investigate the regulatory mechanisms of the cell microenvironment of the human liver on the biliary branching morphogenesis, biomimetic liver tissue formation, and physiological function, transcriptome analysis of model A and model B was performed and compared with 2DD and PHH cells.

overall_design: For 2D differentiated HepaRG cell (2DD) culture, HepaRG cells were maintained for 2 weeks in the growth medium and then shifted to the growth medium supplemented with 2% DMSO for the next 2 weeks. To obtain bioprinting liver models A and B, uniformly sized hepatobiliary aggregates (HBAs) were used as building blocks. HBAs were readily produced and non-destructively harvested after 7-day culture within the 3D printing alginate/gelatin scaffolds with HepaRG growth medium. The alginate, gelatin solution, and the HBAs were gently and uniformly mixed. Lego-livers were cultured with low concentration medium A or high concentration medium B for 14 days to obtain model A or B, respectively. Primary human hepatocyte (PHH) was bought from the company and cultured for 3 days as instructed. The samples for RNA-seq were collected in TriZol.

first: Yao

last: Rui


title: PSPC1 selectively controls tumorigenesis and oncogenic transcription in acute myeloid leukemia [ChIP-seq]

city: San Antonio

first: Pinpin

last: Sui

state: TX

address: 8403 Floyd Curl Dr., STRF

institute: UT health San Antonio

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: ChIP-seq for OCIAML5 with IgG, PSPC1 or PU.1 antibody to identify the genome occupancy of PSPC1 and PU.1.

first: Mingjiang

last: Xu

first: Juyeong

last: Hong


title: CD4+ tissue resident memory Th17 cells drive IL-17A-mediated joint pathology in Spondyloarthritis

city: OXFORD

first: Feng

last: Liu

address: Green Templeton College, 43 Woodstock Road

institute: University of Oxford

summary: Interleukin (IL)-17A plays a central role in driving joint pathology in Spondyloarthritis (SpA). In this study, synovial tissues from patients with Axial SpA and Psoriatic arthritis were analyzed using single-cell RNA sequencing and spatial RNA profiling to pinpoint the cellular source of IL-17A. The results revealed that IL-17A expression is exclusively localized to CD4⁺CXCR6⁺ tissue resident memory Th17 (TRM17) cells, which interact with activated CLEC10A⁺ dendritic cells within the joint. These interactions coincide with an enhanced IL-17A response signature in both sublining and lining fibroblasts. Furthermore, in vitro-generated TRM17-like cells from blood memory CD4⁺ T cells recapitulated the in situ characteristics by producing IL-17A in response to T cell receptor stimulation, while IL-23 selectively amplified TCR-mediated IL-17F and IFN-γ production. Importantly, perturbation of the epigenetic regulator BRD1 impaired the generation of TRM17-like cells. These findings underscore the predominant role of TRM17 cells as the source of IL-17A in SpA and suggest that targeting BRD1 or depleting TRM17 cells may offer promising therapeutic strategies for achieving long-term disease remission.

overall_design: Synovial tissues from patients with spondyloarthritis (SpA) were analyzed by single-cell RNA sequencing, including five axial SpA (AxSpA) and six psoriatic arthritis (PsA) samples. Due to national regulations governing genetic data, three of the five AxSpA datasets generated at Shanghai Sixth People’s Hospital are not deposited in the GEO repository; these datasets are available upon request through a formal data access application.


title: Characterization of chicken peripheral blood mononuclear cells (PBMCs) during AIV prime vaccinations at single-cell resolution

city: Xi'an

first: Hai

last: Li

address: No.76 Yanta West Road

department: Department of Pathogenic Microbiology and Immunology

institute: Xi'an Jiaotong University

summary: We performed scRNA-seq for PBMCs isolated from 35-day old healthy male SPF chicken at the onset or upon vaccination with live-attenuated or inactivated AIV vaccines.

overall_design: PBMC samples freshly isolated from 35-day-old healthy male SPF chickens were subjected to scRNA-seq using the 10 × Chromium platform.


title: PPIase dPPIL4 regulates high-amplitude PERIOD oscillations in Drosophila

city: Suwon-si

first: Eun Young

last: Kim

address: 164 Worldcup-ro

country: South Korea

institute: Ajou University School of Medicine

summary: Peptidyl-prolyl cis/trans isomerases (PPIases) accelerate proline peptide bond isomerization, affecting substrate protein function. In this study, through RNAi-based behavioral screening of PPIases in Drosophila melanogaster, we identified CG5808, termed Drosophila Peptidyl-Prolyl cis/trans Isomerase-like 4 (dPPIL4), as crucial for circadian rhythm regulation. Knockdown of dppil4 in clock cells lengthened the circadian rhythm period and decreased rhythmicity, accompanied by a significant reduction of core clock protein PERIOD (PER). Dppil4 knockdown downregulated per transcription and reduced phosphorylation at Ser5 in the RNA polymerase II C-terminal domain, critical for transcription elongation. In addition, dPPIL4 stabilized Cullin1 of the Skp1-Cullin1-F-box protein complex, a key regulator of PER degradation. Our findings suggest that dPPIL4 supports high-amplitude PER oscillation by enhancing both synthesis and degradation processes in a timely manner.  In conclusion, our study underscores the importance of high-amplitude PER oscillations in PER for robust circadian rhythms and highlights the critical role of dPPIL4 in this process.

overall_design: Control flies and dppil4 knock-down flies (with knockdown in clock cells) were entrained under a 12:12 light-dark cycle. On the fourth day of entrainment, flies were collected at ZT8 and ZT16. Fly heads were isolated for RNA extraction, followed by RNA-sequencing.

first: So Who

last: Kang


title: Sperm-derived circRNA-1572 regulates embryogenesis and zygotic genome activation by targeting CCNB2 via bta-miR-2478-L-2 [ncRNA-seq]

city: Xianyang

first: Yanfang

last: Wu

state: Shaanxi

address: No. 22, Xinong Road, Yangling District

department: College of Veterinary Medicine

institute: Northwest A&F University

type: Non-coding RNA profiling by high throughput sequencing

summary: This study identified circRNA-1572, which is delivered by sperm into the oocyte during fertilization, whose downregulation resulted in developmental arrest and inhibition of ZGA during porcine embryogenesis. Moreover, we elucidated that sperm-derived circRNA-1572 competitively binds to bta-miR-2478-L-2 through a “sponge” mechanism to target and regulate cyclin B2 expression, thereby modulating the distribution of F-actin in early pig embryos, ensuring proper chromosome segregation during mitosis, and facilitating normal embryo cleavage, maternal RNA degradation (MRD), and ZGA.

overall_design: This study identified circRNA-1572, a sperm-derived circRNA delivered into oocytes during fertilization, through whole-transcriptome sequencing of porcine metaphase II (MII) oocytes, purified mature sperm, and in vitro fertilized pronuclear (PN) embryos. Functional assays confirmed circRNA-1572 competitively binds to bta-miR-2478-L-2 through a “sponge” mechanism, regulating the expression of the target gene cyclin B2 (CCNB2). Knockdown (KD) of circRNA-1572 or overexpression of bta-miR-2478-L-2 resulted in reduced CCNB2 mRNA and protein levels, along with altered F-actin distribution and aberrant chromosomal organization, leading to increased developmental arrest and compromised zygotic genome activation (ZGA) during early porcine embryogenesis. Importantly, these phenotypes were rescued upon supplementary mRNA of CCNB2. Moreover, SMART-seq analysis revealed KD of CCNB2 resulted in delayed degradation of maternal transcripts in 2-cell embryos and delayed initiation of ZGA in 4-cell.


title: Sperm-derived circRNA-1572 regulates embryogenesis and zygotic genome activation by targeting CCNB2 via bta-miR-2478-L-2 [SMART-seq]


title: miRNA Differential Expression Profile Analysis and Identification of Potential Key Genes in Active Tuberculosis

city: Shah Alam, Selangor, Malaysia

first: Yang

last: Jun

state: selangor

address: setia alam

country: Malaysia

institute: UiTM

summary:
Background: Tuberculosis (TB), caused by Mycobacterium TB (MTB), remains a significant global health issue, particularly in developing nations. MicroRNAs (miRNAs) are non-coding RNAs (ncRNAs) that modulate immune responses and play a pivotal role in the pathogenesis of MTB by altering host immune defenses. Insights into the regulatory functions of these miRNAs have revealed mechanisms through which MTB evades immune surveillance and establishes persistent infections, highlighting the critical role of miRNA networks in TB pathogenesis.
Objective: The purpose of this study was to analyze miRNA expression in plasma from TB patients, to predict target genes, and to construct regulatory networks to elucidate the roles of miRNAs in TB pathogenesis.
Methods: This study recruited six participants, comprising three patients with active TB and three healthy controls (HCs). High-throughput sequencing was employed to profile miRNAs. Differentially expressed miRNAs (DEMs) were identified, and their target genes were predicted using the TargetScan and miRWalk databases. The Gene Ontology (GO) and KEGG databases facilitated the construction of regulatory pathway networks. Additionally, the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) analyzed protein-protein interaction (PPI) networks for genes enriched in immune-related pathways, highlighting key genes.
Results: The study identified 23 DEMs, with 17 upregulated and 6 downregulated. PRKCB was recognized as a potential diagnostic target. Analyses using GO and KEGG identified pivotal pathways implicated in TB pathogenesis, particularly involving miRNAs hsa-let-7a-5p and NovelmiRNA-41 in the PRKCB-related regulatory network.
Conclusion: We identified 23 DEMs and a key gene, PRKCB, associated with TB pathogenesis. The MAPK and chemokine pathways were identified as central to the regulatory mechanisms of MTB infection, presenting new possibilities for the development of early diagnostic and therapeutic strategies.

overall_design: miRNA-seq profiling of human serum that were collect from 3 patients with active tuberculosis and 3 healthy control.

first: Dan

last: Hanliang

first: Chen

last: Yeng

first: Zou

last: Linrong

first: Liu

last: Shanshan

first: Wang

last: Feng

first: Maslinda

middle: B

last: Musa


title: The genomic instability mechanism of histone oncogenic mutation H2BE112K in Schizosaccharomyces pombe genetic analysis

city: 南京

first: Ruifan

last: Zhu

address: 江苏省南京市栖霞区仙林街道南京师范大学生命科学学院

institute: 南京师范大学

summary: To investigate the different of gene expression between E112K、E112K clr6-1 and wild strain, and then, we performed the gene expression analysis from the RNA-Seq data.

overall_design: Gene expression analysis of the  E112K and E112K clr6-1 mutant strain was compared with the wild-type.

first: Gang


title: Sperm-derived circRNA-1572 regulates embryogenesis and zygotic genome activation by targeting CCNB2 via bta-miR-2478-L-2 [miRNA-seq]


title: single-cell ATAC-sequencing of human aortic media that was composed by vascular smooth muscle cells

city: Xiamen

first: Wei

last: Shen

state: Fujian

address: 2999 Jinshan Rd, Huli District

institute: Xiamen University

summary: single-cell ATAC-sequencing was performed on vascular smooth muscle cells isolated from human aortic media

overall_design: The isolated human aorta media was isolated, dounced, lysed and washed to retrieve cell nuclei for scATAC-Seq.


title: Deletion of Smooth Muscle ZFP36 Promotes Neointimal Hyperplasia in Mice

city: Jinan

first: lei

last: wang

address: 07 Wenhua xi road, Jinan, Shandong

institute: Qilu hospital Shandong University

summary: Platelet-derived growth factor (PDGF-BB) released from the injured intima induces the proliferation and migration of vascular smooth muscle cells (VSMCs), which is the key mechanism of neointimal hyperplasia. Zinc finger 36 (ZFP36), a widespread RNA-binding protein, is important for pathological processes in many diseases. In this study we investigated the role of ZFP36 in VSMCs proliferation, migration and neointimal hyperplasia in mice. We generated smooth muscle-specific Zfp36 knockout (Zfp36SMKO) mice, and established restenosis mouse models by ligation of left carotid artery in Zfp36SMKO mice. We showed that the expression levels of ZFP36 were significantly decreased in human atherosclerotic coronary arteries and murine injured carotid arteries compared with controls. Compared to control Zfp36fl/fl mice, Zfp36SMKO mice displayed accelerated neointimal hyperplasia. In cultured mouse VSMCs, PDGF-BB (20 ng/mL) significantly downregulated ZFP36 expression through KLF4 binding site in Zfp36 promoter. We revealed that ZFP36 could bind to the mRNA of cell migration-inducing protein (CEMIP) and promoted its degradation in VSMCs, thereby reducing the expression of CEMIP protein. Knockdown of Cemip inhibited VSMCs proliferation and migration induced by Zfp36 knockout, thereby suppressing neointimal hyperplasia in Zfp36SMKO mice. We conclude that vascular smooth muscle ZFP36 has a protective effect against neointimal hyperplasia by reducing CEMIP expression. ZFP36 is downregulated by vascular injury and PDGF-BB treatment, which promotes VSMCs proliferation and migration and neointima formation. The results suggest that targeting ZFP36 may represent a novel therapeutic strategy for preventing or treating neointimal hyperplasia and related cardiovascular diseases.

overall_design: RNA-seq profiling of human aortic smooth muslce cells (HASMCs) which were transfected with vector adenovirus (Ad-CTR) as controls or ZFP36 adenovirus (Ad-ZFP36) to overexpress ZFP36 and treated with PDGF-BB.

first: Lei

last: Wang

first: Lifan

last: He

first: Xiao

last: Xiong

first: Zhinan

first: Mi

last: Tian

first: Guangqing

last: Cao

first: Huixia

last: Lu

first: Xiaoping

last: Ji

first: Yanling

last: Zhang

first: Pavel

last: Kovarik

first: Wencheng

first: Yan


title: Histone modification changes during RASMCs' transformation into macrophage-like cells

summary: We report histone modification status of H3K4me1, H3K4me2, H3K4me3 and H3K27ac within rat vascular smooth muscle cell at de-differentiated state (induced by DAPT treatment), inflammatory state (induced by cholesterol treatment) and macrophage-like state (induced by combined treatment of DAPT and cholesterol)

overall_design: Primary rat aortic smooth muscle cells were treated by NOTCH inhibitor DAPT, soluble cholesterol or both of them for 48 hrs to achieve cell state transformations


title: The temporal refinement of Dach1 is a key step in the functional maturation of primary somatosensory neurons

city: GOSSELIES

first: Abdulkader

last: AZOUZ

address: Rue Adrienne Bolland, 8

country: Belgium

institute: Université Libre de Bruxelles

summary: During somatosensory neurogenesis, neurons are born in an unspecialized transcriptional state, with several transcription factors following a broad-to-restricted expression dynamic as development proceeds, supporting neuron subtype identities. The relevance of this temporal refinement remains however unclear, these broad-to-restricted transcription factors being selectively involved in neurons in which they are ultimately maintained. Here we found that Dach1 encodes for a bona fide broad-to-restricted transcription factor retained and required in tactile somatosensory neurons. Within developing nociceptors, we demonstrate that Prdm12 contributes to Dach1 extinction. Using genetic approaches to prevent its temporal restriction during somatosensory development, we reveal that Dach1 refinement is a prerequisite for the appropriate transcriptional maturation of somatosensory subtypes from which it becomes ultimately excluded. These findings highlight the essential role played by Dach1 during somatosensory neuron development. They further demonstrate that the broad-to-restricted temporal pattern followed by several transcription factors is physiologically relevant to achieve appropriate transcriptional maturation of somatosensory neurons.

overall_design: ChIP-seq of V5-Prdm12 in knock-in mice

first: Tunde

last: Szemes

first: Alba

last: Sabate San Jose

last: Azouz

first: Maren

last: Sitte

first: Gabriela

last: Salinas Riester

first: Younes

last: Achouri

first: Sadia

last: Kricha

first: Laurence

last: Ris

first: Kristy

last: Red Horse

first: Eric

middle: J

last: Bellefroid

first: Simon

last: Desiderio


title: Mitochondrial Dysfunction Fuels Drug Resistance in Adult T-cell Acute Lymphoblastic Leukemia

city: Grenoble

first: Florent

last: Chuffart

state: La Tronche

address: Site Santé - Allée des Alpes

country: France

institute: IAB - INSERM (U1209) - CNRS (UMR5309)

summary: Following our previous work indicating that a decreased mitochondrial activity is an important feature of tumour aggressiveness in adult T-ALL, we assembled the largest known tumour bank, consisting of 133 samples, to uncover the underlying mechanism. Transcriptomic analysis of these tumours showed that down-regulation of mitochondrial activity plays a central role in mediating the activation of ABCB1, a gene associated with multidrug resistance. Furthermore, our research identified de novo lipid synthesis and lipid accumulation as key mechanisms facilitating ABCB1 activation in T-ALL. Lipid accumulation, together with down-regulation of β-oxidation, promote the activation of lipogenic transcription factors, LXRs, which are the strong drivers of ABCB1 gene activation. This knowledge not only allows us to better understand the biology of aggressive T-ALL, but also to shed light on the mechanisms underlying tumour resistance to induction chemotherapy. We propose that in patients with tumours exhibiting low mitochondrial activity, the inhibition of de novo lipogenesis and restriction of dietary fats, such as caprylic acid, could mitigate the treatment resistance.

overall_design: Bone marrow (BM) samples containing high percentages of leukemic blasts from newly-diagnosed adult T-ALL patients were collected at the Hematology Department of Ruijin hospital, Shanghai Jiaotong university school of medicine. Diagnoses were assigned based on the World Health Organization Classification of Haematolymphoid Tumours: Lymphoid Neoplasm and NCCN Guidelines Version 2.2024-Acute Lymphoblastic Leukemia

first: Shanshan

last: Guo

first: Ekaterina

last: Bourova-Flin

first: Sophie

last: Rousseaux

first: Lijun

last: Peng

first: Duohui

last: Jing

first: Jian-Qing

last: Mi

first: Saadi

last: Khochbin

first: Jin

last: Wang


title: STAU1 exhibits oncogenic characteristics and modulates alternative splicing and gene expression in A549 lung adenocarcinoma cells

city: Urumqi

first: Ling

last: Zhang

state: Xinjiang

address: No. 91 Tianchi Road

institute: People's Hospital of Xinjiang Uygur Autonomous Region

summary: Staufen double-stranded RNA-binding protein 1 (STAU1) assumes a significant role in cancer development and is correlated with survival outcomes in patients with lung cancer. Nevertheless, its specific functions and molecular mechanisms in lung adenocarcinoma (LUAD) remain insufficiently explored. In our research, we established a STAU1 knockdown expression model within the A549 cell line. We discerned that the knockdown of STAU1 significantly suppressed the proliferation, invasion, and migration of A549 cells and enhanced the level of cell apoptosis. Through RNA-seq analysis, we identified 197 differentially expressed genes (DEGs) and 1,362 STAU1-Regulated alternative splicing Events (ASEs). The DEGs were specifically enriched in cell adhesion pathways, while the ASE genes were mainly associated with cell division and the cell cycle. Our study implies that STAU1 possesses oncogenic characteristics and may modulate DEGs and ASEs to affect the proliferation, invasion, and migration of A549 cells. This research provides novel insights that might contribute to the diagnosis and treatment of LUAD.

overall_design: We established a STAU1 knockdown model in the A549 cell line and integrated it with RNA-seq data to thoroughly disclose the biological functions of STAU1 in A549 cells and analyze the alterations in the transcriptome subsequent to STAU1 Knockdown.

first: Zhen

first: Xue

middle: M

last: Wei

first: Lin

last: Niu


title: H2A.Z distribution and chromatin accessibility within human aortic smooth muscle cell [HASMC_ScienCell_CutTag]

first: Wei

last: Shen

summary: We report the genome wide distribution of H2A.Z and  chromatin accessibilty profile within human aortic smooth cells

overall_design: Cut&Tag for H2A.Z and ATAC-Seq was performed on human aortic smooth muscle cell(obtained from ScienCell)


title: Transcriptome accessment of RASMC after H2a.z knockdown [RASMC_H2azKD_RNASeq]

summary: We report transcriptome of RASMCs after H2a.z knockdown. H2a.z knockdown cells were fruther treated with cholesterol.

overall_design: RNA-Seq was performed on RASMCs and RASMCs with H2a.z knockdown. H2a.z knockdown cells were fruther treated with cholesterol.


title: An erythroid-biased FOShi hematopoietic multipotent progenitor subpopulation contributes to adaptation to chronic hypoxia

city: Tianjin

first: Peng

last: Wu

address: 288 Nanjing Road

institute: IHCAMS

type: Methylation profiling by high throughput sequencing

summary: Single-cell transcriptome analysis revealed an enrichment of Fos+ MPP subpopulations in mouse bone marrow under hypoxic conditions. To validate the biological characteristics and hypoxia stress response of the Fos+ MPP subpopulation, we used Fos-2A-tdTomato mice to establish a HAPC model. We then sorted Fos+ and Fos- MPP cells for low-input DNA methylation sequencing analysis.

overall_design: The DNA methylation experiment consisted of six groups: normoxic control, hypoxia for 2 weeks, hypoxia for 4 weeks, hypoxia for 12 weeks, hypoxia for 12 weeks followed by normoxic recovery for 5 weeks, and hypoxia for 12 weeks followed by normoxic recovery for 5 weeks and re-exposure to hypoxia. For each group, 3-4 mice were used for DNA methylation sequencing. Fos+ and Fos- MPP cells were sorted for low-input DNA methylation sequencing.

first: Weili

last: Liu

first: Xiaoru

first: Jinhua

first: Lingling

last: Pu

first: Lihong

last: Shi


title: Proteotranscriptomic Characterization of Human Retinoblastoma

city: Freiburg

first: Clemens

last: Lange

address: Kilianstraße 5

department: Klinik für Augenheilkunde

country: Germany

institute: Uniklinik Freiburg

summary: Background: Retinoblastoma is a rare pediatric eye cancer caused by mutations in the RB1 gene, which regulates retinal cell growth. Early detection and treatment are critical for pre-venting vision loss and improving survival outcomes. This study aimed to perform an inte-grated proteotranscriptomic characterization of human retinoblastoma to provide a deeper understanding of disease biology and to identify novel therapeutic targets. Methods: Paired tumor and adjacent retinal tissue samples were dissected from seven eyes affected by retinoblastoma. The global transcriptome and proteome were determined using RNA sequencing and liquid chromatography-mass spectrometry from the same samples. The spatially resolved cellular landscape was assessed using Imaging Mass Cytometry (IMC). Results: The correlation between RNA and protein level was moderate (Pearson’s R = 0.339, p < 10-16) with variations across different pathways. While biological processes like visual perception were similarly regulated on the RNA and protein level, others, such as cell cycle processes and glycolysis were predominantly active at the protein level. IMC identified more than 67,000 single cells in distinct clusters, including antigen presenting cells, T cells, stroma cells, vascular cells and two clusters of proliferating and CD44/c-Myc positive tumor cells. In retinoblastoma, we observed increased apoptotic signals in T cells and higher ex-pression of CD68 in antigen presenting cells compared to control tissue. Conclusions: Retinoblastoma's key biological processes are predominantly regulated at either the RNA or protein level, underscoring the value of an integrated proteotranscriptomic approach. Elevated caspase 3 activity in tumor-associated T cells may indicate potential im-mune escape mechanisms and CD44+ and high-c-Myc-expressing tumor cells may repre-sent cancer stem cells with possible involvement in metastasis, warranting further validation. Our multilayered approach could pave the way for enhanced molecular assessments and novel targeted therapies for human retinoblastoma.

overall_design: Retinoblastoma (n=7) and control (n=5) tissue from eyes with retinoblastoma.

first: Julian

last: Wolf

first: Rozina

last: Hajdu

first: Stefaniya

last: Boneva

first: Lucas

last: Stürzbecher

first: Claudia

last: Auw-Haedrich

first: Wolf

last: Lagrèze

first: Hansjürgen

last: Agostini

first: Thomas

last: Reinhard

first: Stefan

last: Tholen

first: Oliver

last: Schilling

first: Günther

last: Schlunck

first: Bertram

last: Bengsch


title: ABHD18 is essential for cardiolipin remodeling and its inhibition restores mitochondrial function in Barth Syndrome [CRISPR]

first: Jason

last: Moffat

summary: Cardiolipin (CL) is the signature phospholipid of the inner mitochondrial membrane, where it stabilizes the electron transport chain protein complexes. The final step in CL biosynthesis concerns its remodeling: the exchange of nascent acyl chains with longer, unsaturated chains. However, the enzyme responsible for cleaving nascent CL has remained elusive. Here, we describe ABDH18 as the candidate de-acylase in the CL biosynthesis pathway. Accordingly, ABHD18 converts CL into monolysocardiolipin (MLCL) in vitro and its inactivation in cells and mice results in accumulation of nascent CL in serum and tissues. Strikingly, ABHD18 deactivation rescues the mitochondrial defects in cells and the morbidity and mortality in mice associated with Barth Syndrome. This rare genetic disease is characterized by the build-up of MLCL due to inactivating mutations in TAFAZZIN (TAZ), which encodes the final enzyme in the CL remodeling cascade. We also identified a selective, covalent small molecule inhibitor of ABHD18 that restores TAZ mutant phenotypes in patient fibroblasts and fish embryos. This study highlights a striking example of genetic suppression of a monogenic disease revealing a canonical enzyme in the CL biosynthesis pathway.

overall_design: We performed genome-wide CRISPR knockout screens with the TKOv3 CRISPR library in human HAP1 cells with mutations in TAZ, or TAZ and ABHD18 combined to assess enhancers and suppressors of TAZ dysfunction phenotypes

first: Sanna

last: Masud

first: Kevin

last: Brown


title: G-quadruplex stabilizer CX-5461 effectively combines with ionizing radiation to selectively target ATRX-deficient malignant glioma

city: Houston

first: Sharvari

last: Dharmaiah

address: 2130 W. Holcombe Blvd.

institute: MD Anderson Cancer Center

summary: Mutational inactivation of ?-thalassaemia/mental retardation X-linked (ATRX) represents a defining molecular feature in large subsets of adult and pediatric malignant glioma. ATRX deficiency gives rise to abnormal G-quadruplex (G4) DNA secondary structures at GC-rich regions of the genome, altering chromatin accessibility and enhancing DNA damage. Building on earlier work, we sought to assess the extent to which pharmacological G4 stabilization selectively enhances DNA damage and cell death in preclinical models of ATRX-deficient glioma. In this study, we assessed the extent to which G4 stabilization impacted genome-wide deposition of H3.3 in patient-derived glioma stem cells (GSCs). In order to evaluate the overlap of these H3.3 deposition sites with regions of the genome that bind ATRX, we performed cleavage under targets and tagmentation (CUT&Tag) for ATRX using GSC line TS 543. Our analyses show that G4 stabilizer CX-541 disrupts H3.3 deposition at regions of the genome that frequently bind ATRX.

overall_design: Global genomic profiling analyses of ATRX CUT&Tag sequencing data for patient-derived glioma stem cell line (GSC) TS 543, which was conducted in triplicates.

first: Prit

last: Malgulwar

middle: T

last: Huse


title: Epigenetic priming of embryonic enhancer elements coordinates developmental gene networks [scNMT]

city: Cambridge

first: Sarah

last: Inglesfield

address: Babraham Research Campus

department: Bioinformatics

institute: The Babraham Institute

summary: Embryonic development requires the accurate spatiotemporal execution of cell lineage-specific gene expression programs, which are controlled by transcriptional enhancers. Developmental enhancers adopt a primed chromatin state prior to their activation; however how this primed enhancer state is established, maintained, and how it affects the regulation of developmental gene networks remains poorly understood. Here, we use comparative multi-omic analyses of human and mouse early embryonic development to identify subsets of post-gastrulation lineage-specific enhancers which are epigenetically primed ahead of their activation, marked by the histone modification H3K4me1 within the epiblast. We show that epigenetic priming occurs at lineage-specific enhancers for all three germ layers, and that epigenetic priming of enhancers confers lineage-specific regulation of key developmental gene networks. Surprisingly in some cases, lineage-specific enhancers are epigenetically marked already in the zygote, weeks before their activation during lineage specification. Moreover, we outline a generalisable strategy to use naturally occurring human genetic variation to delineate important sequence determinants of primed enhancer function. Our findings identify an evolutionarily conserved program of enhancer priming and begin to dissect the temporal dynamics and mechanisms of its establishment and maintenance during early mammalian development.

overall_design: Supernumerary human blastocysts, cryopreserved at D5 or D6

first: Christopher

middle: D

last: Todd

first: Jannat

last: Ijaz

first: Fereshteh

last: Torabi

first: Oleksandr

last: Dovgusha

first: Stephen

last: Bevan

first: Olivia

last: Cracknell

first: Tim

last: Lohoff

last: Clark

first: Ricard

last: Argelaguet

first: Juliette

last: Pearce

first: Ioannis

last: Kafetzopoulos

first: Alice

last: Santambrogio

first: Jennifer

last: Nichols

first: Ferdinand

last: von Meyenn

first: Ufuk

last: Guenesdogan

last: Schoenfelder

last: Reik


title: Depletion of WWP1 increases Adrb3 expression and lipolysis in white adipose tissue of obese mice

city: Noda

first: Yoshikazu

last: Higami

state: Chiba

address: 2641, Ymazaki

department: Faculty of Pharmaceutical Science

country: Japan

institute: Tokyo University of Science

summary: Obesity is defined as abnormal or excessive fat accumulation of body fat and contributes to several metabolic disorders. White adipose tissue (WAT) stores energy in the form of triglycerides and releases energy as free fatty acids and glycerol through a process called lipolysis. People with obesity have impaired catecholamine-stimulated lipolysis, but comprehensive understanding of this lipolysis is still unclear. WW domain-containing E3 ubiquitin ligase 1 (WWP1) is a member of the HECT-type E3 family of ubiquitin ligases and is associated with several diseases. We previously showed that WWP1 expression was increased in WAT of obese mice. In this study, we investigated the function of WWP1 in WAT of obese mice by analyzing the phenotype of Wwp1 knockout (KO) mice fed a high-fat diet. The mRNA levels of beta-3 adrenergic receptor (Adrb3), which were decreased with a high-fat diet, were increased by Wwp1 KO in WAT. Moreover, Wwp1 KO mice showed increased phosphorylated hormone-sensitive lipase levels in WAT and plasma non-esterified fatty acid concentrations. In contrast, noradrenaline and its metabolism were not altered in WAT of obese Wwp1 KO mice. These findings indicate that WWP1, which is increased in adipocytes because of obesity, is a candidate for suppressing the Adrb3 signaling pathway and lipolysis independently of noradrenaline metabolism.

overall_design:
Mice with global KO of Wwp1 (Wwp1-/-mice) and wild-type (WT) Wwp1+/+ mice were generated by mating Wwp1fl/fl/Wwp2+/+ (Wwp1fl/fl) mice, which were obtained by crossing Wwp1fl/+/Wwp2fl/+ mice with CAG-Cre mice. Wwp1fl/+/Wwp2fl/+ mice were obtained by crossing Wwp1fl/fl/Wwp2fl/fl and C57/BL6 (Wwp1 Knocuout (KO)) mice [Hoshino et al., FEBS Open Bio 2020].
At 5 weeks old, WT and Wwp1 KO mice were divided into two groups: the ND group or HFD group. The Charles River Formula-1 diet and High-Fat Diet 32 (25.5% crude protein, 32.0% crude lipid and 2.9% crude fiber; CREA, Tokyo, Japan) were fed as the ND and HFD, respectively. At 15 weeks old, mice were euthanized under isoflurane anesthesia (Mylan, Canonsburg, PA, USA) and epididymal white adipose tissue (eWAT) were collected. Then, we performed RNA-seq. using eWAT derived from ND-WT, ND-Wwp1 KO, HFD-WT and HFD-Wwp1 KO.

first: Nozaki

last: Yuka

first: Ose

last: Yuko

first: Ohmori

last: Chinatsu

first: Mizunoe

last: Yuhei

first: Kobayashi

last: Masaki

first: Saitoh

last: Akiyoshi

first: Higami

last: Yoshikazu


title: Transcriptomic profiling of right ventricular remodeling in CTEPH pig model

city: 91400 Orsay

first: Florent

last: Dumont

state: Ile de France

address: 17 avenue des sciences

institute: Université Paris-Saclay

summary: To better understand the molecular mechanisms of right ventriuclar dysfunction in CTEPH pig model, a RNA sequencing analysis was performed in RV tissues collected from 5 CTEPH pigs and 5 sham opereted pigs.

overall_design: mRNA profiles for Sham and CTEPH pig right ventricle

first: Fabrice

last: Antigny

first: Olaf

last: Mercier


title: Follicular development of fetal gonads under the skin of adult mice

city: TianJin

first: Liu

last: Chang

address: Weijin Road

institute: Nankai University

summary: Adult ovarian tissues or biopsies isolated from patients prior to chemotherapy or irradiation can reconstitute ovarian functions when transplanted either in the abdomen or subcutaneously. This approach avoids invasive surgery and potential risks associated with internal procedures. We investigated whether functional ovaries could develop subcutaneously from early E12.5 fetal gonads without entering meiosis in mouse model. Unexpectedly, the subcutaneously transplanted fetal gonads failed to undergo folliculogenesis, showing meiotic deficiencies, DNA repairdefects, and elevated apoptosis. Thes meiotic defects were partly due to variations in temperature and oxygen concentration. However, in vitro culture of the gonads at 37C allowed completion of meiotic prophase I. After subcutaneous transplantation, the in vitro cultured E12.5 gonads successfully underwent folliculogenesis, restoring endocrine functions. This suggests potential for using pluripotent stem cell technologies to rejuvenate ovarioids from fetal gonad-like cells, enhancing  endocrine recovery and health span.

overall_design: This dataset contains single-cell RNA sequencing data from subcutaneous graft and renal capsule graft tissues. The tissues were harvested 4 days post-grafting for analysis of gene expression profiles.


title: Effect of MEKi on NF1 pseudarthrosis primary cells

city: Dallas

first: Jonathan

last: Rios

address: 2222 Welborn Street

institute: Scottish Rite for Children

summary: Background: Neurofibromatosis type 1 (NF1) is a genetic condition predisposing children to fracture pseudarthroses. MEK inhibitors are FDA-approved or under study for the treatment of malignant pathologies associated with NF1, though their potential to treat pseudarthrosis is largely unknown. Methods: Primary cells cultured from control bone (i.e., iliac crest) or fracture pseudarthroses from children with NF1 were treated with vehicle or the MEK inhibitors trametinib or selumetinib. Gene expression was evaluated by transcriptome sequencing (RNAseq), and activation of the downstream signaling pathway was evaluated by western blotting. Results were replicated in an independent cohort of patient pseudarthrosis-derived primary cells. Results: We confirmed increased MAPK signaling in pseudarthrosis samples compared to patient-matched control samples. Pseudarthrosis samples were reproducibly associated with reduced expression of gene signatures implicated in osteoblast differentiation, skeletal development, and formation of the extracellular matrix. Expression of these gene signatures was significantly rescued following treatment with selumetinib, and to a lesser extent trametinib, concomitant with reduced MAPK signaling activation. Conclusions: Our study utilized patient-derived primary cells to demonstrate the molecular signatures associated with fracture pseudarthrosis and how this molecular dysregulation was reversed with MEK inhibitor treatment. Clinical relevance: MEK inhibitors may be repurposed to promote healing of fracture pseudarthroses in children with NF1.

overall_design: Primary cells were cultured from two cohorts of patients. The first cohort includes cells cultured from patient-matched control or fracture pseudarthrosis bone, while the second cohort includes only cells cultured from pseudarthrosis bone. All samples were treated with vehicle (dmso) or the MEK inhibitors trametinib or selumetinib prior to expression proviling by RNA-sequencing.

first: Rios

last: Jonathan

first: Paria

last: Nandina


title: Interferon-dependent R-loop Induction by Zika Virus Contributes to Growth Attenuation [ZIKV_Bruseq]

city: Atlanta

first: Bing

last: Yao

address: 615 Michael Street

department: Department of Human Genetics

institute: Emory University

summary: Zika virus (ZIKV) infection in human neural progenitors triggers DNA damage and activates DNA damage response, leading to cell cycle arrest that can retard brain development. Here we link the ZIKV- induced S phase arrest to replication fork stalling and R-loop induction. DRIP-seq reveals that ZIKV infection induces R-loops at specific loci strongly enriched in the interferon-stimulated genes (ISGs). Bru-seq results further indicate that nascent ISGs transcripts are prone to R-loop induction upon infection. Knockout of interferon receptor eliminated the R-loops on ISGs and partially rescued S phase arrest in infected cells. And overexpression of RNaseH1 reduced ZIKV-mediated DNA damage and cell cycle arrest. We conclude that unscheduled expression of ISGs induced by ZIKV alters R-loop homeostasis and perturbs replication fork progression, leading to fork stalling and eventually DNA damage. IFN- dependent R-loop induction represents a previously unknown, nucleic acid-based mechanism for cell cycle arrest.

overall_design: human glioblastoma SNB-19 cells were treated by MR and PR ZIKV virus and subjuct for Bru-seq, untreated Mock control were used for comparison

first: Yijing

last: Zhao

first: Yangping

last: Li

first: Yilin

last: Wang

first: Hengli

last: Tang


title: H2a.z, pol II and histone modification status within RASMC [RASMC_CutTag]

first: Wei

last: Shen

summary: We report genome wide distribution of H3K27me3, H2a.z and pol II within RASMC. We also report genome wide distribution of H3K27ac, H3K4me3, pol II within RASMC after H2a.z knockdown down

overall_design: Cut&Tag sequencing was performed on RASMCs before or after H2a.z knockdown for various proteins and histone modifications


title: Epigenetic priming of embryonic enhancer elements coordinates developmental gene networks [scPBAT]

first: Sarah

last: Inglesfield

first: Christopher

last: Todd

first: Jannat

last: Ijaz

first: Fereshteh

last: Torabi

first: Oleksandr

last: Dovgusha

first: Stephen

last: Bevan

first: Olivia

last: Cracknell

first: Tim

last: Lohoff

last: Clark

first: Ricard

last: Argelaguet

first: Juliette

last: Pearce

first: Ioannis

last: Kafetzopoulos

first: Alice

last: Santambrogio

first: Jennifer

last: Nichols

first: Ferdinand

last: von Meyenn

first: Ufuk

last: Guenesdogan

first: Stefan

last: Schoenfelder

first: Wolf

last: Reik


title: BMP4 induces a p21-dependent cell state shift in glioblastoma linking mesenchymal transition to senescence

city: Uppsala

first: Bengt

last: Westermark

address: Dag Hammarskjölds väg 20

country: Sweden

institute: Uppsala University

summary: Bone morphogenetic protein 4 (BMP4) has emerged as a potential glioblastoma therapy due to its anti-proliferative effect via SOX2 downregulation and differentiation promotion. However  BMP4 responses vary across and within tumors. Our previous data indicate that BMP4 induces a mesenchymal-like cell state  which is associated with therapy-resistance and tumor recurrence  similar to senescence in cancer. In this study  we investigated BMP4?s potential to induce senescence in primary glioblastoma cells  including proneural- and mesenchymal-like clones derived from the same tumor. BMP4 treatment induced senescence-associated genes and phenotypic changes  such as cell enlargement  senescence-associated-?-gal expression  lamin B1 downregulation  and elevated p21 levels. Importantly  the most robust senescence induction was observed in the mesenchymal-like clone  compared to its proneural counterpart. Notably  mesenchymal-like cells displayed elevated basal levels of p21 and other senescence-associated markers  suggesting a convergence of mesenchymal and senescent traits. p21 knockout abolished BMP4-induced senescence  maintaining proliferation and cell size despite SOX2 downregulation. Additionally  senolytic treatment effectively eliminated senescent cells through apoptosis  thereby favoring survival of cells retaining normal p21 levels.  Our findings demonstrate BMP4?s ability to induce p21-dependent senescence in glioblastoma  particularly in therapy-resistant mesenchymal-like cells. These insights provide potential therapeutic strategies targeting senescence pathways in this challenging disease.

overall_design: The human glioblastoma cell line U3065MG and two clonal derivates (clone-271 and clone-475) were used in the study. Cells were treated with recombinant BMP4  protein (Thermo Fisher Scientific) at 10 ng/ml between 7-33 days. For knockout of the p21 gene, the p21 Waf1/Cip1 CRISPR/Cas9 KO plasmids (sc-400013) and the p21-specific homology-directed repair (HDR) plasmid containing puromycin resistance gene and RFP gene (sc-400013-HDR) were transfected into cells according to the manufacturer’s recommendations (Santa Cruz). For siRNA experiments, cells were seeded one day prior to siRNA transfection using Lipofectamine RNAiMAX (Thermo Fisher Scientific), overnight. siRNA used were Smad4 Silencer Select Pre-designed siRNA (1 nM, #4390824, ID s8403) and negative control siRNA (#4390843) (Thermo Fisher Scientific). After 2 days, BMP4 was added to the cultures. Cells were re-transfected on day 8 and used for analyses on day 12 and 14. For senolytic experiments, navitoclax (ABT-263, Selleck Chemicals) was used at a 1000 nM concentration.

first: Mia

last: Niklasson

first: Erika

last: Dalmo

first: Anna

last: Segerman

first: Veronica

last: Rendo


title: An alternative transcription factor isoform controls AML chemoresistance [Cut&Run]

city: Farmington

first: Harshpreet

last: Chandok

state: CT

address: 10 Discovery Dr

institute: The Jackson Laboratory

summary: Aberrant splicing is a hallmark of many cancers, including Acute Myeloid Leukemia (AML), but its role in post-treatment relapse remains poorly understood. Here, we analyzed the alternative splicing landscape of 19 AML patients during chemotherapy treatment. We found an upregulation of the long isoform of the transcription factor RUNX1 (also known as RUNX1C) in relapsed cohorts, which conferred chemotherapy resistance. Notably, these patients showed elevanted intragenic DNA methylation at the RUNX1 proximal promoter, thereby activating RUNX1C transcript through its alternative distal promoter. Mechanistically the N-terminus region of RUNX1C is required to promote chemoresistance by regulating a distinct RUNX1 transciptional program. Among these target genes, B-cell translocation gene 2 (BTG2) mediates a quiescent-like phenotype by deadenylating ribosomal RNAs to reduce global protein synthesis. Lastly, we harnessed orthogonal RNA-targeting strategies to target RUNX1C isoform, which led to augmented chemotherapy efficacy. Collectively, our finidngs delineate a transcriptional circuity orchestrated by a transcription factor isoform that underpins chemotherapy responsiveness and a potential therapeutic strategy to mitigate disease recurrence.

overall_design: To determine any unique binding sites for different RUNX1 isoforms, MOLM-13 cells were infected with lentiviral constructs expressing each isoform individually. This construct contained a GFP reporter and 1x10^6 cells per replicate were sorted on a BD FACS Aria Fusion. After sorting, cells were subjected to CUT&RUN using the CUTANA™ kit from Epicypher. Libraries were generated using Epicypher's CUTANA™ CUT&RUn LIbrary Prep Kit. All procedures followed the manufacturer's protocol.

first: Han

last: Cuijuan

first: Wang

last: Eric


title: Combined single-cell RNA-sequencing and single-cell bisulfite-sequencing reveal key regulatory mechanisms associated with oocyte in vitro maturation in pig [scBS-seq]

city: Murcia

first: Francisco

last: Huertas

address: C/ Campus Universitario de Espinardo Nº7 (Edificio CEEIM)

country: Spain

institute: Marbyt - Smart Solutions for Biotechnology

summary: In vitro maturation (IVM) is a critical step in current animal in vitro embryo production protocols. However, in vitro matured oocytes often exhibit lower developmental competence than their in vivo counterparts, and the molecular mechanisms underlying successful maturation remain unclear. In this study, we compared the developmental competence up to the blastocyst stage of IVM and in vivo matured porcine oocytes (N=397) and also analysed simultaneously their gene expression and DNA methylation profiles at single cell resolution (N=40) using RNA sequencing and bisulfite sequencing. Our final aim was to find the associations between the developmental and molecular differences between the two groups of oocytes. All the oocytes were obtained by aspiration of either ovarian follicles between 3-6 mm diameter, and the subsequent IVM, or ovarian follicles from 8-10 mm diameter, with no need of maturation (in vivo matured oocytes). Significant differences were found at day 2 for cleavage rates (58.2 ± 3.0 and 45.7 ± 4.4, P = 0.010) and at day 7 for the blastocyst rates (31.4 ± 3.7 and 47.5 ± 6.6, P = 0.014) for IVM and in vivo groups, respectively, but not for the total cell number per blastocyst (48.1 ± 1.9 and 48.2 ± 2.7). Using the in vivo group as a reference, 1297 and 476 differentially expressed genes (DEGs) were down-regulated and up-regulated, respectively, in the IVM group. The up-regulated DEGs in IVM oocytes were mainly associated with organelle organization, DNA methylation, and cell cycle processes; down-regulated genes were mainly enriched in ribosomal RNA processing, protein synthesis, oxidative phosphorylation and metabolomic processes such as glycosyl and aldehyde compound pathways. The global percentage of methylation was similar between the IVM and in vivo groups, but 321, 344, and 843 differentially methylated regions (DMRs) were detected (P < 0.05) in CpG islands, promoters and coding regions, respectively. Integrative analysis of RNA-sequencing and DNA methylation data identified the main methylated regions and genes that define each group. A total of 236 loci and 296 genes defined the IVM group, while 856 loci and 688 genes were related to the in vivo group. In addition, in the IVM group, we found a higher number of negative correlations between gene expression and DNA methylation, while the in vivo group showed higher number and stronger positive correlations. Taken together, these results indicate a discrete effect of IVM on the DNA methylation landscape in mature porcine oocytes, but these changes seem to have a greater impact on gene expression regulation.

overall_design: Ovaries from Landrace-Large-White gilts were collected at the slaughterhouse and transported to the laboratory (within 60 minutes) in saline solution containing 100 µg/mL kanamycin sulphate at 38.5°C, washed once in 0.04% cetrimide solution (w/v) and then twice in saline. Then, the IVM protocol was the same as in Romero-Aguirregomezcorta et al. (2024). As for the in vivo matured oocytes, the contents of follicles of 8-10 mm diameter were aspirated and washed twice in Dulbecco's PBS supplemented with 1 mg mL-1 PVA. All IVM and in vivo matured COCs were identified under a stereomicroscope and mechanically detached from the cumulus cells using an automatic pipette set to a volume of 200 microlitres. To do this, the COCs were gently aspirated and repeatedly ejected into the Petri dish until the zona pellucida was visualised free of cumulus cells at 50x magnification. Only oocytes with a visible polar body under the stereomicroscope were selected and snap frozen in LN2 and stored at -80°C until use (n = 20 IVM and 20 in vivo matured oocytes).

first: Pilar

last: Fuster Coy

first: Laura

last: Abril-Parreño

first: Gavin

last: Kelsey

first: Antonio

last: Galvao

last: Huertas-López

first: Emilio

last: Serrano-López

first: David

last: Martínez-Moreno


title: A plasma 9-microRNA signature for lung cancer early detection: a multicenter validation

city: San Giovanni Rotondo (FG)

first: Fabrizio

last: Bianchi

state: Outside U.S. & Canada

address: Viale Padre Pio 7

country: Italy

institute: Fondazione IRCCS Casa Sollievo della Sofferenza

summary: Lung cancer is the most critical concern in oncology worldwide, due to its substantial morbidity and mortality rates. Low-dose computed tomography (LD-CT) screening is considered the best promising strategy to alter the fatal prognosis of this disease, in combination with effective minimally invasive molecular testing. Although, several approaches based on blood-borne biomarkers (e.g. ctDNA, CTC, proteins, antibodies and microRNAs) have been proposed to better identify at-risk populations, and characterize the nature of screening-detected nodules, their use has not been successfully implemented in clinical settings. To this end, we propose a signature of 9 circulating miRNAs derived from a robust multi-platform workflow with a multi-center design, for a total of 276 lung cancer and 451 non-cancer controls, based on the data from two European LD-CT screening cohorts (Poland and Italy).

overall_design: A total of 276 lung cancer and 451 non-cancer controls (plasma samples) were analyzed.

first: Elisa

last: Dama


title: Interferon-dependent R-loop Induction by Zika Virus Contributes to Growth Attenuation [U251 DRIP-Seq]

first: Bing

last: Yao

overall_design: IFNAR1 CRISPR Knockout in U-251 cell, KO and CTL cells were treated byZIKV virus or Mock control, samples were used for DRIP-seq

first: Yijing

last: Zhao

first: Yangping

last: Li

first: Yilin

last: Wang

first: Hengli

last: Tang


title: SIRT3 is required for the protective function of ketogenic diet on neural inflammation and neuropathic pain

city: Shanghai

first: Mengqiu

last: Deng

state: None Selected

address: 415 Fengyang Road

department: Department of Anesthesiology,

institute: Second Affiliated Hospital of Naval Medical University

summary: Chronic neural inflammation is the key pathology of neuropathic pain. The ketogenic diet (KD) has been shown to reduce neural inflammation and hyperexcitability in Alzheimer's disease. However, the function and mechanism of KD in neuropathic pain remains unclear. In this study, we first found that the KD production was decreased upon neuropathic pain induced by chronic constriction injury (CCI). Then we demonstrated that KD effectively alleviated CCI-induced thermal hyperalgesia and mechanical allodynia and relieved neuroinflammation by reducing microglia activation and pro-inflammatory cytokines. β-hydroxybutyrate (BHB), a major component of KD, reduced ROS production by enhancing mitochondrial membrane potential in microglia, thereby decreasing microglia-induced inflammatory responses. In vivo and in vitro experiments revealed that the expression of UCP2, SIRT3 and PGC-1α expression in the spinal dorsal horn was increased by KD. SIRT3-deficiency abolished the protective function of KD on neuropathic pain. Additionally, SIRT3 deficiency decreased BHB production due to the reduced expression of ketone body synthases in the liver and ketone body-utilizing enzymes in the spinal dorsal horn. These findings suggest that SIRT3 is a promising therapeutic target for neuropathic pain, particularly in the context of a ketogenic diet, which may inspire novel therapeutic strategies and potentially improve patient prognosis and quality of life.

overall_design: mRNA profiles of BV-2 cells from three groups (Control group, Medium group, and BHB group) were generated by RNAseq, with n=3, using Illumina Novaseq 6000 platform.

first: Yuanyuan

last: Fang

first: Yan

last: Chu

first: Ruifeng

last: Ding

first: Xiaoyi

last: Fan

first: Huawei

last: Wei

first: Honghao

last: Song

first: Guowei

last: Jiang

first: Hailing

last: Zhang

first: Chaofeng

last: Han

first: Hongbin

last: Yuan


title: Chromatin accessibility in human aortic smooth muscle cells

city: Xiamen

first: Wei

last: Shen

address: 2999 Jinshan Rd, Huli District

institute: Xiamen University

summary: We report the chromatin accessibilty profile within human aortic smooth cells

overall_design: ATAC-Seq was performed on human aortic smooth muscle cell (iCell, HUM-iCell-a009)


title: Transcriptome accessment of human aortic smooth muscle cell and rat aortic smooth muscle cell [HASMC_RASMC_RNASeq]

summary: We report the transcriptome within human aortic smooth muscle cell and rat aortic smooth muscle cell. Some of the cells were treated with cholesterol.

sample_organism:
Homo sapiens
Rattus norvegicus

platform_organism:
Homo sapiens
Rattus norvegicus

overall_design: RNA-Seq was performed on HASMC1 (obtained from ScienCell), HASMC2 (obtained from iCell) and RASMC before and after cholesterol treatment.


title: Interferon-dependent R-loop Induction by Zika Virus Contributes to Growth Attenuation [ZIKV_DENV_IFN_DRIPseq]

first: Bing

last: Yao

overall_design: human glioblastoma SNB-19 cells were treated by MR and PR ZIKV virus, DENV virus or interferon and subjuct for DRIP-seq, untreated Mock control were used for comparison


title: An alternative transcription factor isoform controls AML chemoresistance [LongRead_mRNA]

first: Harshpreet

last: Chandok

overall_design: To determine the role of BTG2 on mRNA stability, MOLM13 cells were transcuded with a cDNA to overexpress BTG2 or with an empty vector control, and mRNA was isolated for long-read sequencing.

first: Cuijuan

first: Eric


title: VGLL-fusions define a new class of intraparenchymal CNS schwannoma

city: Berlin

first: Simone

last: Schmid

address: Charitéplatz 1

department: Department of Neuropathology

institute: Charité-Universitätsmedizin Berlin

summary: This study is important as it identifies and characterizes a new class of benign CNS tumors, termed VGLL-altered intraparenchymal CNS schwannomas. These rare tumors, previously unclassified, resemble schwannomas but are found within CNS tissue. By analyzing 20 tumor samples using advanced molecular and histological techniques, the study reveals that these tumors have a distinct DNA methylation profile and frequently harbor VGLL3 or VGLL1 gene fusions. The findings offer a clearer understanding of their morphology, molecular characteristics, and behavior, with MRI showing well-defined, nodular tumors and clinical data indicating no recurrence during follow-up. This research enhances diagnostic accuracy and may inform treatment strategies for these rare intracerebral neoplasms, highlighting the need for their recognition as a separate tumor type in medical classifications.

overall_design: We analyzed 20 tumor samples by histology, targeted RNA Next-Generation Sequencing, DNA-methylation profiling (Illumina 450k and 850k Beadchips), copy number analyses, and single nucleus RNA sequencing. Clinical data, including age, sex, and disease progression, were collected. Presurgical MRI series were included when available.

first: David

last: Capper


title: miR-223-3p and miR-29a-3p induced transcriptional rewiring in lung adenocarcinoma cell lines

first: Fabrizio

last: Bianchi

summary: We investigated the biomolecular activity of miR-29a-3p/miR-223-3p in human lung adenocarcinoma (LUAD) by performing transcriptome profiling of H2023 (LUAD) cell line upon modulation of miR-29a-3p/miR-223-3p by mimic (QIAGEN) (OE) or antisense microRNA (KD).

overall_design: A total of six samples were analyzed with the following experimental conditions:  mimic miR-223-3p, mimic miR-29a-3p, mimic control. Experimental replicates were performed.


title: CSTF2 shortens polyA tail of CXCL10 and drives immune suppression in pancreatic cancer

city: Guangzhou

first: Zhou

last: yifan

state: 周一帆

address: 74 Zhongshan Second Road

institute: Sun Yat-sen University Cancer Center

summary: Alternative cleavage and polyadenylation (APA) has gained increasing attention in cancer biology, yet its role in tumor immunotherapy resistance remains largely unexplored. Here, we identify the cleavage stimulation factor 2 (CSTF2) in pancreatic ductal adenocarcinoma (PDAC) cells, an APA-related gene, as a novel suppressor of anti-tumor immunity. CSTF2 promotes tumor development by inhibiting the infiltration and function of TCRαβ+CD4–CD8–NK1.1– innate αβ T (iαβT) cells. Mechanistically, CSTF2 downregulates CXCL10 expression by promoting PolyA polymerase alpha (PAPα) binding to the 3' untranslated regions (3'UTR) of CXCL10 RNA, resulting in shortened PolyA tails and reduced RNA stability. Consequently, we identified Forsythoside B, a selective inhibitor of the RNA recognition motif (RRM) of CSTF2, effectively activates anti-tumor immunity and reverses immune checkpoint blockade (ICB) therapy resistance. Collectively, our findings unveil CSTF2 as a promising therapeutic target for sensitizing PDAC to ICB therapy.

overall_design: To evaluate the effects of Cstf2 KD on tumor microenvironment, we performed scRNA sequencing of tumor tissue from the KPC mice.

first: Jian

last: Zheng

first: Xiaowei

last: He


title: An alternative transcription factor isoform controls AML chemoresistance

overall_design: To investigate the functions of unique RUNX1 isoforms, MOLM-13 cells were infected with lentiviral constructs expressing each isoform individually. Three days after transduction, cells were collected and RNA isolated and polyA mRNAs were enriched and used to generate cDNA libraries. Barcoded libraries were then sequenced on a NovaSeq. Gene expression analysis was then performed on cells expressing RUNX1 Isoforms, compared to an empty vector control.

last: Wang


title: Signaling basis of gastric epithelial cell differentiation revealed by human and mouse organoids [ChIP-Seq]

city: Beijing

first: Ye-guang

last: Chen

address: Tsinghua Road, Medical Building

department: School of life science

institute: Tsinghua University

summary: The directed differentiation of adult gastric stem cells into specific epithelial cell types is crucial for gastric homeostasis. Although it is well appreciated that the niche plays a critical role in gastric epithelium cell differentiation, the relevant molecular factors and the underlying regulatory mechanisms remain poorly understood. In this study, by combining the knowledge of the niche cells obtained from single-cell RNA sequencing and manipulation of signaling pathways, we achieved efficient differentiation of various gastric epithelial cell types in mouse and human gastric organoids. These in vitro differentiated cells showed a similar gene expression profile to those in gastric tissues. Specifically, we showed that BMP4 signaling stimulates parietal cell differentiation, EGF and BMP4 signaling work together to enhance pit cell differentiation, while TGF-β inhibition facilitates chief cell differentiation. In addition, the small molecule Isoxazole 9, which has been shown to stimulate differentiation of neuronal cells, pancreatic β-cells, and intestinal enteroendocrine cells, promotes parietal and endocrine cell differentiation in gastric organoids. Our data also revealed the different requirements of parietal and chief cell differentiation between mouse and human. Together, our findings provide a mechanistic insight into gastric epithelial cell differentiation and uncover its similarities and differences between mouse and human.

overall_design: Gastric epithelial cells isolate from stomach in mice detected after 2 weeks after tamoxifen inducation of specific gene deletion, then according to the manufacturer’s instructions for ChIP-Seq.

first: Ye-Guang

first: Fan

last: Hong

first: Xiaodan

first: Shibo

last: Lin

first: Nanshan

last: Zhong

first: Ze

first: Mengxian

first: Haonan

last: Li

first: Yalong

first: Yuan

last: Liu

first: Lianzheng

last: Zhao

first: Hui

last: Liang

first: Hongwen

last: Zhou

first: Xiao

last: Yang


title: Pyroptosis of pulmonary fibroblasts through NLRC4 inflammasome leads to acuterespiratory failure

city: COLLEGE STATION

first: Yan

last: Zhang

state: Texas

address: 206 olsen blvd

institute: Texas A&M University

summary: The NAIP-NLRC4 inflammasome plays a pivotal role in the defense against bacterial infections. Thus far, the in vivo physiological function of the NAIP-NLRC4 inflammasome is acknowledged primarily as a driving force of inflammation and limited to immune cells. Acute lung injury and its severe manifestation, acute respiratory failure (ARF), are the leading cause of mortality in septic patients. Here we identify that the NAIP/NLRC4 inflammasome is highly and specifically expressed in pulmonary fibroblasts and that pyroptosis of pulmonary fibroblasts play a critical role in acute lung injury. We found that mice challenged with Gram-negative bacteria or flagellin developed lethal ARF, evident by a reduction in blood oxygen saturation, disruption of lung barrier function, and escalated inflammation. Flagellin-induced ARF was protected in caspase-1 or fibroblast-specific GSDMD deficient mice. These findings not only expand our knowledge on the (patho)physiological function of the NAIP-NLRC4 inflammasome, but also demonstrate an underappreciated role of inflammasome activation and pyroptosis in the development of ARF during sepsis.

overall_design: To detect the types of cells changing during inflammasome-dependent acute lung injury, we performed single-cell RNA sequencing of lung cells. C57BL/6 were divided into PBS and LFn-flagellin/PA treated groups. We then performed gene expression profiling using data from RNA-seq of these two group.

first: Jiaqian

last: Qi

first: Yinan

last: Wei

first: Zhenyu


title: SESN1 alleviates autoimmunity by potentiating STING autophagic degradation

city: Nanjing

first: Mingyu

last: Pan

state: Jiangsu

address: Long Mian 639 Nanjing

institute: China Pharmaceutical University

summary: STING, the pivotal adaptor protein of CGAS-STING signaling, is critical for type I IFN production of innate immunity. However, excessive or prolonged activation of STING is associated with autoinflammatory and autoimmune diseases. Thus, preventing STING from over-activation is important to maintain immune homeostasis. Here, we reported that SESN1 was essential to prevent the excessive activation of STING-mediated type I IFN signaling through autophagic degradation of STING.

overall_design: The mRNA profile of control or SESN1 knockdown Hela cells that stimulated with HTDNA  by deep sequencing.

first: Hongqiang


title: Human post-mortem skin samples from slow death and fast death

city: Pittsburgh

first: CHANDAN K

last: SEN

state: PA

address: 221 Republic Street

institute: University of Pittsburgh

type: Methylation profiling by genome tiling array

summary: Human death marks the end of organismal life under conditions such that the components of the human body continue to be alive. Such postmortem cellular survival depends on the nature (Hardy scale) of human death.  Slow and expected death typically result from terminal illnesses and includes a prolonged terminal phase of life. As such organismal death process unfolds, do cells of the human body adapt for postmortem cellular survival? Organs with low energy cost-of-living, such as the skin, are better suited for postmortem cellular survival. In this work, the effect of different durations of terminal phase of human life on postmortem changes in cellular gene expression was investigated using RNA sequencing data of 701 human skin samples from the Genotype-Tissue Expression database. Longer terminal phase (slow-death) was associated with a more robust induction of survival pathways (PI3K-Akt signaling) in postmortem skin. Such cellular survival response was associated with the upregulation of embryonic developmental transcription factors such as FOXO1, FOXO3, ATF4 and CEBPD. Upregulation of PI3K-Akt signaling was independent of sex or duration of death-related tissue ischemia. Analysis of single nucleus RNA-seq of post-mortem skin tissue specifically identified the dermal fibroblast compartment to be most resilient as marked by adaptive induction of PI3K-Akt signaling. Prospective studies depicted hypomethylation of PI3K-Akt signaling genes in slow compared to fast human death. Compared to fast death, slow death also induced angiogenic pathways in the dermal endothelial cell compartment of postmortem human skin. In contrast, specific pathways supporting functional properties of the skin as an organ were downregulated following slow death. Such pathways included melanogenesis and those representing the skin extracellular matrix. Efforts to understand the significance of death as a biological variable in influencing the transcriptomic composition of surviving component tissues has far-reaching implications including rigorous interpretation of experimental data collected from the dead and mechanisms involved in transplant-tissue obtained from dead donors.

overall_design: The Illumina Infinium MethylationEPIC array BeadChip (850K) was carried out by the Epigenomic Services from Diagenode (Cat nr. G02090000) from DNA isolated from human post-mortem skin samples

first: Ahmed

middle: S

last: Abouhashem

first: Kanhaiya

last: Singh

first: Chandan

middle: K

last: Sen


title: Signaling basis of gastric epithelial cell differentiation revealed by human and mouse organoids [RNA-Seq]

first: Ye-guang

last: Chen

overall_design: Bulk RNA profiles of stomach in mice detected after 2 weeks or 4 weeks after tamoxifen inducation of specific gene deletion.

first: Ye-Guang

first: Fan

last: Hong

first: Xiaodan

last: Wang

first: Shibo

first: Nanshan

first: Ze

first: Mengxian

first: Haonan


title: Human pancreatic beta cell transcriptomes from donors with and without T1D

city: Worcester

first: Mason

last: Tarpley

state: MA

address: 368 Plantation Street Albert Sherman Center, AS7.2049

department: Diabetes Center of Excellence

institute: UMass Chan Medical School

summary: We compared the transcriptome of bulk sorted T1D donor beta cells to those from non-diabetic donors.

overall_design: Isolated human donor islets were fiexed, permeabilized, and atained for hormones.  Beta cells were enriched by sorting for Insulin-positve cells and lysed for RNA purification. mRNA llibrarries prepared with either Nugen Ovation or Clotech SMARTER Pico kits were sequenced using Illumna NextSeq.  Sequnce data was process through the DolphinNext RNA-Seq pipeline and Harman was used normalize based on library kit.  DEBrowser was used to create differential gene expression lists.

first: David

last: Harlan

first: Sambra

last: Redick

middle: W

first: Sally

middle: C

last: Kent

last: Blodgett


title: Signaling basis of gastric epithelial cell differentiation revealed by human and mouse organoids [scRNA-Seq]

last: Lin

last: Zhong

last: Li

first: Yalong

first: Yuan

last: Liu

first: Lianzheng

last: Zhao

first: Hui

last: Liang

first: Hongwen

last: Zhou

first: Xiao

last: Yang


title: RNA-seq analysis of HEK293 and synphilin-1 overexpressing HEK293 cell line

city: Suwon

first: Gwang

last: Lee

state: Yeongtong-gu

address: 206 Worldcup-ro

department: Department of Physiology and Department of Biomedical Sciences

institute: Ajou University

summary: We report the gene expression profile of HEK293 cells and FLAG-tagged synphilin-1 overexpressing HEK293 cells (Synph-293 cells).

overall_design: RNA-sequencing was conducted to compare the gene expression in HEK293 and synphilin-1 overexpressing HEK293 cells (Synph-293 cell). 1 μg of total RNA of each sample was used for preparing the libraries using TruSeq Stranded mRNA Sample Prep Kit (Illumina, CA, USA). Then, RNAs were fragmented and synthesized as double-stranded cDNA through random hexamer priming. Following the end repair, A-tailing, and adapter ligation, cDNA libraries were amplified with PCR. The quality of cDNA libraries was evaluated with Agilent 2100 BioAnalyzer (Agilent Technologies, CA, USA). The quantification of cDNA libraries was conducted using KAPA library quantification kit (Kapa Biosystems, MA, USA). Following cluster amplification, sequencing progressed as paired-end (2×150bp) using Illumina Novaseq6000 (Illumina).


title: HBV-driven host chromatin accessibility changes affect liver metabolic pathways, iron homeostasis and promote a preneoplastic phenotype [RNA-seq]

city: Roma

first: Giuseppe

middle: Rubens

last: Pascucci

state: RM

address: Viale Regina Elena, 291

department: Center for Life Nano Science

institute: Istituto Italiano di Tecnologia

summary: Background and Aims: Complex host-virus interactions account for HBV-specific T and B cells dysfunction and the persistence of the viral cccDNA mini-chromosome, key features of HBV chronicity and challenges for HBV cure. The extent of HBV impact on liver transcriptome remains controversial. Transcriptional activation in eukaryotic cells has been tightly linked with disruption of nucleosome organization at accessible genomic sites of remodeled chromatin. We used ATAC-seq (Assay for Transposase Accessible Chromatin followed by high throughput sequencing) to detect early changes in chromatin accessibility in HBV-infected Primary Human Hepatocytes (PHHs). Results. ATAC-seq analysis revealed that after HBV infection an increasing number of genomic sites change their chromatin accessibility over time with a prevalent global reduction of accessibility (that is) partially prevented by inhibiting HBV transcription and replication. Motif Enrichment Analysis identified several TF involved in liver cell identity, glucose and lipid metabolism as potential regulators of differentially accessible genes 72h post-infection, when cccDNA transcription and viral replication are established. ATAC-seq and RNA-seq integration confirmed HBV infection impact on liver metabolism, the early establishment of a premalignant phenotype and identified a 39-genes liver iron signature modulated by chromatin accessibility changes. The upregulation of iron uptake genes translates in a significant increase of iron content in HBV-infected PHHs whereas iron chelation results in a drastic inhibition of cccDNA transcription and viral replication. Conclusions. Altogether our results show that HBV infection impacts on host cell chromatin landscape and specific transcriptional programs and that HBV modulates intracellular available iron to boost its replication.

overall_design: Primary Human Hepatocytes (PHHs) from 3 donors were infected with HBV or left un-infected (Mock) and cultured for 2h and 72h. RNA was extracted and sequenced on a NextSeq 500 Illumina platform. PHHs from an additional donor were treated with interferon (IFN) or left un-stimulated (Mock). For this second experiment, RNA was extracted and sequenced on a NovaSeq 6000 Illumina platform.

first: Vincenzo

last: Alfano

first: Giacomo

last: Corleone

first: Massimiliano

last: Cocca

first: Francesca

last: De Nicola

first: Océane

last: Floriot

first: Alexia

last: Paturel

last: Casuscelli Di Tocco

first: Michel

last: Rivoire

first: Massimo

last: Levrero

last: Guerrieri


title: GPNMB is a marker of invasive quiescent differentiated melanoma cells driven by tumor niche reprogramming

city: Milano

first: Marine

last: Melixetian

address: via Adamello 16

institute: European Institute of Oncology

summary: We provide evidence of the existence of a slow cycling melanoma population isolated in vivo from melanoma PDXs using the H2B-GFP system. Single cell transcriptomic analysis unveils a significant transcriptional heterogeneity of GFP-retaining slow cycling cells, defining a quiescent subpopulation of cells. These cells show a different phenotype in primary tumors and matched metastases, suggesting that tumor niche pressure drives a transcriptional reprogramming of quiescent cells during melanoma progression.

overall_design: Primary and metastatic melanoma MM13 and MM27 H2B-GFP PDX were sorted using fluorescence-associated cell sorters (Aria and Melody, BD Bioscience) to isolate GFP positive and GFP negative populations and analyzed using ScRNAseq.

first: F

last: Lotti

first: M

last: Meliksetyan

first: L

last: Landrancone


title: Transcriptional analysis of TDC in a fluorescent reporter model

first: Michela

last: Riba

address: via Olgettina 60

department: COSR, Center for Omics Sciences

institute: IRCCS, Ospdale San Raffaele

summary: TDC are hematopoietic cells that combine dendritic cell (DC) and conventional T cell markers and functional properties. To investigate the gene expression profile of TDC, we performed a bulk RNA sequencing (RNAseq) on TDC from Zbtb46-GFP reporter mice.

overall_design: TDC were sorted from splenocytes of naïve homozygous Zbtb46-GFP mice along with conventional T cells and DC as controls.

first: Alessandra

last: Fiore

first: Paolo

last: Provero

first: Mirela

last: Kuka


title: Psychological stress increases susceptibility to Staphylococcus aureus infection by the action of TGFβ to suppress immune acting fibroblasts [scRNA-Seq]

city: San Diego

first: Hung

last: Chan

state: CA

address: 9452 Medical Center Drive,ACTRI Bldg, L1W420

institute: UCSD

summary: Psychological stress results in increased susceptibility to infection yet the mechanisms responsible for this major healthcare burden are incompletely understood. In mice, stress induced by restraint increases infection by Staphylococcus aureus while adrenalectomy or chemical inhibition of adrenergic signaling blocks this response. Single-cell transcriptomics and lipidomic profiling of the skin after stress reveal fibroblasts undergoing adipogenesis are the major cell type responding to stress. Fibroblasts are critical to the increase in infection as adrenaline inhibits fibroblast Camp expression and bacterial killing, and stress did not increase infection in mice that lack Camp in fibroblasts. The suppression of the antimicrobial function of Camp in fibroblasts occurs due to activation of TGFβ signaling and is critical to the capacity of stress to increase susceptibility to infection since treatment of mice with a neutralizing TGFβ antibody or a TGFβ receptor inhibitor restores expression of Camp and alleviates increased susceptibility to infection. These data show that susceptibility to infection after psychological stress is due to a brain-skin axis that induces TGFβ and subsequently inhibits host defense by immune acting fibroblasts in the dermis. This identifies TGFβ as an unexpected target that can ameliorate increased bacterial infections associated with stress.

overall_design: scRNA-seq of infected mouse skin in the presence or absence of restraint stress with or without TGFβ receptor inhibitor (SB-431542)


title: Hepatic Dyrk1b regulates whole body glucose homeostasis

first: Lianju

last: Li

state: China

address: Xujiahui Road

institute: Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases

summary: Illuminating the mechanisms controlling glucose homeostasis may deepen our understanding of the pathogenesis of T2DM and provide new therapeutic strategies for T2DM in future. As reported, Dyrk1b is a pleiotropic protein and its genetic mutations associate with blood glucose levels. Yet, the role of Dyrk1b in glucose metabolism is not well understood. Herein, we find that hepatic Dyrk1b overexpression in mice impairs the glucose tolerance and insulin resistance, whereas global Dyrk1b deficiency improves glucose metabolism of mcie. Dyrk1b overexpression in vitro blunts insulin signalling and glucose uptake. Collectively, our study uncovers a novel link between hepatic Dyrk1b and whole body glucose homeostasis.

overall_design: For better understanding of Dyrk1b’s function, RNA-seq analyses were performed for Hepa1-6 cells infected with adenovirus overexpressing mouse Dyrk1b (Ad-Dyrk1b) or control adenovirus (Ad-EGFP).

first: Jiqiu

last: Wang

first: Ruixin

last: Liu

first: Guang

last: Ning


title: Psychological stress increases susceptibility to Staphylococcus aureus infection by the action of TGFβ to suppress immune acting fibroblasts [RNA-Seq]

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Bulk RNA-sequencing was performed on fibroblasts cultured in adipocyte differentiation medium (ADM) with or without adrenaline treatment [in vitro]. Additionally, peri-lesional skin tissues were analyzed from sham-operated mice and adrenalectomized (ADX) mice infected with Methicillin-resistant Staphylococcus aureus (MRSA) at day 2 post-infection. [In vivo]


title: Hepatic Dyrk1b regulates whole body glucose homeostasis by modulating Wbp2 expression

summary: Illuminating the mechanisms controlling glucose homeostasis may deepen our understanding of the pathogenesis of T2DM and provide new therapeutic strategies for T2DM in future. As reported, Dyrk1b is a pleiotropic protein and its genetic mutations associate with blood glucose levels. Yet, its role in glucose metabolism remains to be established. Herein, we invetigate the role of Dyrk1b in glucose metabolism and the underlying mechanisms. We find that hepatic Dyrk1b overexpression in mice impairs the glucose tolerance and insulin resistance, whereas global Dyrk1b deficiency improves glucose metabolism of mcie. Dyrk1b overexpression in vitro blunts insulin signalling and glucose uptake. Quantitative proteomic analyses further reveal that Wbp2 is a putative target of Dyrk1b. Importantly, hepatic Wbp2 restoration rescues the glucose homeostasis in Dyrk1b overexpression mice. Additionally, ATAC-seq analyses indicate Dyrk1b’s role in remodelling hepatic chromatin landscape. Collectively, our study uncovers a novel link between hepatic Dyrk1b and whole body glucose homeostasis via modulation of hepatic Wbp2 expression.

overall_design:
To elucidate the impact of Dyrk1b overexpression on chromatin modification and chromatin DNA binding, we performed assay for transposase-accessible chromatin using sequencing (ATAC-seq) analysis on livers from Dyrk1b overexpression and control mice.
*** Submitter states that raw data were lost.


title: Three germline lncRNAs promote PUM protein condensation and germline differentiation

city: Jerusalem

first: Yonatan

last: Tzur

address: Givat-Ram

country: Israel

institute: Hebrew University of Jerusalem

summary: Long-non-coding RNAs (lncRNAs) are highly expressed in gonads yet, given the lack of fertility defects in most knockouts, their role is unclear. Here, we report the overlapping roles of three lncRNAs in Caenorhabditis elegans fertility, whereby they bind and sequester FBF-2, an inhibitor of germ-cell differentiation. Deletion of the lncRNAs leads to additive reduction in progenitor-cells and progeny. FBF-2 destabilizes mRNAs, and in the lncRNAs deletion strain, the level of these mRNAs is significantly lower. FBF-2 is present in germ-cells, both diffused in the cytoplasm and in peri-nuclear condensates, and lncRNAs deletion reduces FBF-2 condensation. Moreover, the deletion reduces FBF-2 association to P granules, evolutionarily conserved phase-separated condensates. Our work demonstrates that lncRNAs cooperate to establish optimal fertility; hence the full effect is only evident in multiple knockouts. These findings support a model that the lncRNAs spatially restricts pro-proliferation factors into phase-separated granules and release mRNAs required for differentiation.

overall_design:
Comparative transcriptomics between WT and fbf-2 mutants and between WT and a mutant in 3 lincRNA genes

Compartive transcriptomics between fbf-1 and fbf-1Xtriple mutants

first: Roni

last: Falk

first: Noa

last: Gilad

first: Hanna

last: Achache

first: Ilanit

last: Sopher-Levi

first: Yisrael

last: Rappaport

first: Reut

last: Shantai

first: Hasan

last: Ishtayeh

first: Kayla

last: Nennig-Kniaz

first: Laura

last: Wolovelsky

first: Oren

last: Ram


title: HBV-driven host chromatin accessibility changes affect liver metabolic pathways, iron homeostasis and promote a preneoplastic phenotype [ATAC-seq]

first: Giuseppe

last: Pascucci

overall_design: Primary Human Hepatocytes (PHHs) from 2 donors were infected with HBV, left un-infected (Mock) or infected with HBV and treated with interferon (INF) and cultured for 2h and 72h. Assay for Transposase-Accessible Chromatin (ATAC) was performed and sequenced on a NextSeq 500 Illumina platform.

first: Vincenzo

last: Alfano

first: Giacomo

last: Corleone

first: Massimiliano

last: Cocca

first: Francesca

last: De Nicola

first: Océane

last: Floriot

first: Alexia

last: Paturel

last: Casuscelli Di Tocco

first: Michel

last: Rivoire

first: Massimo

last: Levrero

last: Guerrieri


title: Human pancreatic islet responses to cytokine treatment

first: Mason

last: Tarpley

summary: We performed CITE-Seq on isolated human donor islets cultured 48hrs in the presence or absence of a cytokine cocktail. Major cell types were identified based on gene expression and changes in gene expression in beta cells were examined.

overall_design: CITE antibody labeling, cell partitioning and library construction using antibodies from BioLegned and 10x Chrmium 3' technology.

first: David

last: Harlan

first: Sambra

last: Redick

first: Sally

last: Kent


title: Hight througput RNA sequencing in a cohort of HBV related HCC and healty liver samples

city: Lyon

address: 151 Cours Albert Thomas

institute: Université Claude Bernard Lyon 1, Inserm UMR 1350 - PaThLiv

summary: RNA samples from matched tumour (T) and non tumour (NT, at least 2 cm distant from the T) tissues of 10 HBV-related HCC patients from 3 French clinical centres (Lyon Croix Rousse and Toulouse Hospitals and the French National Biological Resource Centres) have been retrospectively studied (Agreement DC-2008−235). RNAs from normal liver tissue samples of HBV, HCV and HIV negative adult patients undergoing lobectomy or segmental liver resection for medically required purposes unrelated to this research program at the Centre Leon Bérard (CLB) cancer center (ministerial agreements #AC-2013−1871 and DC-2013−1870) were used as controls. Signed informed written consents in compliance with the requirements of the local ethical committee were obtained from all patients before surgery.

overall_design: To investigate the impact of chronic HBV on HCC we generated RNA-seq data to identify differentially expressed genes among tumors

first: Claude

last: Caron de Fromentel

first: Philippe

last: Merle


title: Development and validation of a microbiota signature to predict prognosis in nasopharyngeal carcinoma

first: Liu

state: GuangDong

address: 651 Dongfeng Road East

summary:
To investigate the risk bacteria in the regulation of NPC, we established RNA-seq in NPC tissues with high/low abundance of risk bacteria.
We then performed gene expression profiling analysis using data obtained from RNA-seq of NPC tissues with high/low abundance of risk bacteria.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for NPC tissues with high/low abundance of risk bacteria.

first: Xirong

last: Tan

last: Liu