title: Transcription Factor 4 Maintains Endothelial Cell Identity by Inhibiting Endothelial to Mesenchymal Transition

city: Boston

first: Kaifu

last: Chen

state: MA

address: 300 Longwood Ave

department: Cardiology

institute: Boston Children's Hospital

summary: Endothelial-to-mesenchymal transition (EndoMT) is essential for embryonic heart development and contributes to many disease-causal pathobiological processes. It is unclear how the balance between endothelial cell (EC) identity and EndoMT mediators is regulated to drive this transition. This study identifies TCF4 as a critical EC identity gene. TCF4 knockdown in ECs impairs EC phenotype and function, and induces EC identity transition towards mesenchymal-like state. This discovery suggests that TCF4 functions as a guardian of EC identity against EndoMT. Mechanistically, TCF4 binds directly to the promoter of TGFB1 and SNAI1, leading to the repression of their expression. TCF4 expression is consistently downregulated in three EndoMT models. TCF4 downregulation diminishes its inhibitory effect on the TGFB signaling pathway, leading to upregulation of SNAI1 and TGFB1, and subsequently enhancing EndoMT. This, in turn, further suppresses TCF4 expression. Consequently, the TCF4-TGFB1 feedback loop is formed to intensify the EndoMT process. We demonstrate that introducing exogenous TCF4 disrupts this TCF4-TGFB1 feedback loop of EndoMT, rescuing EC phenotype and function under TGFB1 stimulation, as well as ECs from heart failure patients. Our results reveal a key role of TCF4 in safeguarding EC identity and preventing EndoMT, suggesting a therapeutic potential of TCF4 for EndoMT-related cardiovascular diseases.

overall_design: CUT&RUN analysis of TCF4 and SNAI1 in HUVECs to identify their binding peaks.

first: Gaopeng

last: Xian

first: Rongbin

last: Zheng

first: Lili

last: Zhang


title: 4-Acetylantrocamol LT3 Suppresses Colorectal Cancer Growth and Metastasis via PI3K/AKT and MAPK Pathway Modulation

status: Public on Dec 03 2025

city: Taipei

first: I-CHUAN

last: YEN

address: No.161, Sec. 6, Minquan E. Rd., Neihu Dist.

department: school of pharmacy

country: Taiwan

institute: National Defense Medical Center

type: Expression profiling by high throughput sequencing

summary:
Background:
Colorectal cancer (CRC) remains one of the leading causes of cancer-related mortality worldwide. Despite advances in targeted therapies, drug resistance and limited efficacy in KRAS-mutant CRC continue to present clinical challenges. Antrodia cinnamomea, a medicinal fungus, has demonstrated anti-tumor properties, yet the mechanisms of its triterpenoid compound 4-acetylantrocamol LT3 (LT4) remain unclear.
Methods:
We investigated LT4’s effects in HCT116 CRC cells using cell viability, colony formation, and migration assays. Western blotting was employed to examine key signaling pathways. Transcriptome profiling via RNA sequencing was followed by KEGG/GO enrichment and protein–protein interaction (PPI) network analyses using STRING, CytoHubba, and MCODE. Molecular docking with PI3Kγ (PDB: 1E7U) was conducted to evaluate LT4’s binding affinity.
Results:
LT4 significantly inhibited HCT116 cell proliferation and migration, induced a mesenchymal-to-epithelial transition, suppressed PI3K/AKT/mTOR and ERK signaling, and activated GSK3β/FoxO and p38/p21 axes. It also reduced COX-2 and anti-apoptotic proteins (Bcl-2, Bcl-XL), while impairing mitochondrial stability (COX IV). Transcriptomic analysis identified the PI3K-Akt pathway as the most significantly enriched signaling cascade. Network topology analyses highlighted SLC3A2, CCND1, PSAT1, and CHAC1 as central nodes, linking LT4’s effects to nutrient signaling, redox homeostasis, and serine metabolism. Molecular docking confirmed that LT4 stably occupied the ATP-binding pocket of PI3Kγ with a binding energy comparable to KWT and a conformation similar to Antroquinonol.
Conclusion:
This study is the first to comprehensively demonstrate LT4’s multi-target anti-CRC effects, highlighting its potential as a therapeutic agent, especially in KRAS-mutant CRC.

overall_design: To evaluate the biological effects of LT4 in colorectal cancer, HCT116 cells were subjected to cell viability, clonogenic, and migration assays. Western blotting was performed to assess LT4-induced modulation of key signaling pathways. Transcriptomic analysis was carried out through RNA sequencing, followed by functional enrichment analyses including KEGG and Gene Ontology (GO). Protein–protein interaction (PPI) networks were constructed and analyzed using STRING, CytoHubba, and MCODE to identify central regulatory nodes. Additionally, molecular docking was conducted to assess the binding affinity of LT4 to PI3Kγ (PDB ID: 1E7U), providing insights into potential target engagement.


title: Characterization of miRNA expression in 3D cultured cells

city: CDMX

first: Stephanie Iraiz

last: Nuñez Olvera

address: Circuito, Mario de La Cueva s/n

country: Mexico

institute: Universidad Nacional Autónoma de México

summary:
A Comprehensive miRNA-lncRNA-mRNA Corregulation Network in 3D Cultures of Luminal B Breast Cancer
Three-dimensional (3D) cell cultures offer advantages over traditional 2D models by better replicating tumor biology. In this study, we examined the effects of 3D culture on miRNA expression in BT-474 luminal B breast cancer cells. Microarray analysis revealed significant differences: 82 miRNAs were upregulated and 119 downregulated in 3D conditions. A regulatory network was constructed involving four miRNAs consistently downregulated (miR‑92a‑3p, miR‑539‑5p, miR‑18a‑5p, miR‑130a‑3p), potentially influencing MAPK signaling, ECM remodeling, and estrogen receptor activity. These results highlight how 3D systems improve understanding of breast cancer biology and may help uncover novel therapeutic targets.

overall_design: We compared 3D and 2D cultures of the BT-474 using the Affymetrix GeneChip miRNA 4.0 platform. Data processing was performed with the Affymetrix GeneChip Command Console Software v4.0. All samples were analyzed in triplicate.

first: S

middle: I

last: Nuñez-Olvera

first: C

last: López-Camarillo


title: In situ multi-modal characterization of pancreatic cancer reveals tumor cell identity as a defining factor of the surrounding microenvironment. [RNA-Seq]

city: Cambridge

first: Brian

last: Rabe

address: 250 Water St

country: USA

institute: Bristol Myers Squibb

summary: Pancreatic ductal adenocarcinoma is heterogeneous, with low tumor purity, a prominent microenvironment, and complex architecture, which preclude the identification of shared tumor-intrinsic and stromal biology within and across patients. We overcame these challenges by achieving necessary resolution and context through the application of complimentary genomics, pathology and machine learning approaches to characterize primary untreated tumors from 39 patients. We capture 340K spatial low-bulk and 530K spatial single-cell transcriptomes and observe a spectrum of classical-to-basal tumor subtypes present within all patients. We find each subtype has distinct regulators, stromal neighborhoods, microenvironment, extracellular matrix and histology corresponding to multiple immunosuppressive and therapy resistance mechanisms. We define key tumor heterogeneity features including the presence of mixed KRAS mutations and tertiary lymphoid structures; identifying biomarkers that distinguish the latter from lymph nodes. Lastly, leveraging patient, cell and mouse data, we determine which aspects of tumor biology are recapitulated in bulk datasets and reductionist models.

overall_design: RNAseq characterization of Panc0203, Panc0403, Panc1, AsPC1, and PACADD-188 cells in normoxia vs hypoxia (1%O2) over the course of 14 days

first: Anna

last: Lyubetskaya

first: Andrew

last: Kavran

first: Yulong

last: Bai

last: Fisher

first: Alba

last: Font-Tello

first: Anne

last: Lewin

first: Hannah

last: Pliner

first: Yunfan

last: Fan

first: Lauren

last: Giampapa

first: Yelena

last: Cheng

first: Chao

last: Dai

first: Ruifeng

last: Hu

first: Tom

last: Lila

first: Alexandre

last: P Alloy

first: Mike

last: Mason

first: Constance

last: Brett

first: Todd

first: Fayaz

last: Seifuddin

first: Steven

last: Vasquez Grinnell

first: Soren

middle: R

last: Stahlschmidt

first: Yilin

last: Zhao

first: Ryan

last: Golhar

first: Isaac

last: Neuhaus

first: Daniel

last: Carrera

first: Carlos

last: Rios

first: Pradeep

last: Kar

first: Abhishek

last: Shukla

first: Rachael

last: Bashford-Rogers

first: Matthew

middle: J

last: Meyer

first: Enas

last: Abu Shah

first: Lara

last: Heij

first: Shivan

last: Sivakumar

first: Jimena

last: Trillo Tinoco

first: Benjamin

first: Konstantinos

last: Mavrakis

first: Eugene

last: Drokhlyansky


title: Effect of D419N mutation on STAT6 transcription factor activity, in EuMyc murine lymphoma cells

city: Montréal

first: Madelyn

last: Abraham

state: QC

address: 3755 Chemin de la Cote Sainte Catherine, Lab E504

country: Canada

institute: Lady Davis Institute for Medical Research

summary: To investigate how mutation of STAT6 at residue D419 impacts gene expression in EuMyc lymphoma tumour cells

overall_design: EuMyc cells which are STAT6 WT or D419N mutant, were transplanted into C57BL6 mice. After 11 days, once tumours have formed in the cervical and inguinal lymph nodes, tumour cells were isolated with CD19 microbeads, and subject to bulk RNAseq

first: Alexandre

last: Benoit

first: Koren

middle: K

last: Mann


title: STING-induced blood-brain barrier opening in combination with radiation therapy potentiates anti-glioma immune and therapeutic activity monitored with [18F]-FLT PET

city: Chicago

first: Shashwat

last: Tripathi

state: Illinois

address: 302 e Huron St

department: Neurosurgery

institute: Northwestern

summary: Radiation therapy (RT) is the standard of care for glioblastoma but is not curative. Triggering the cGAS/STING pathway with potent agonists such as 8803 exerts marked activity across high-grade glioma preclinical models through the induction of anti-tumor immune responses. To determine if the combination of 8803 with radiation therapy (RT) warrants consideration in the upfront treatment setting and to clarify the underlying mechanisms of therapeutic activity, C57BL/6 mice harboring intracerebral CT-2A or QPP8v high-grade gliomas were treated with fractionated RT (2 Gy daily for 5 days), intratumoral 8803, or both regimens. The treatment with 8803 with RT resulted in 80% long-term and undefined median survival (MS) relative to monotherapy (control MS: 25; 8803 MS: 36; RT MS: 38 days) in the high-grade CT-2A glioma model (combination vs. control p<0.0001), but not in the radiation-resistant QPP8v model. CRISPR gene editing was used to knock out (KO) the STING pathway in CT-2A glioma tumor cells to model the epigenetic silencing of STING expression in human glioblastoma. In this setting, the combinatorial therapeutic effect has been maintained, highlighting that the direct contribution of  immune system in mediating survival benefit. The 8803-mediated STING activation was visualized longitudinally using  [18F]-FLT uptake. In CT-2A-bearing mice, maximum peak of the [18F]-FLT uptake was observed at 72-96 hours after 8803 administration. Sc-RNA sequencing of the CT-2A glioma during the therapeutic window identified a nitric oxide synthase gene signature in the Inflam-TAM(2) population associated with combinatorial efficacy. However, the therapeutic effect of 8803, RT, or the combination of RT + 8803 was not ablated in the NOS2 background mice, indicating that this pathway is not a major contributor to therapeutic activity. scRNA sequencing revealed that 8803 treatment reprograms the blood-brain barrier (BBB) through changes in the PECAM and CD147 pathways in the endothelial cell. A single intracranial injection of 8803, but not RT monotherapy, in non-tumor bearing C57BL/6J mice, induced diffuse bi-hemispheric blood-brain barrier (BBB) opening, shown by fluorescent imaging up to 24 hours, but not in STING KO background mice. In summary, a 8803, combined with RT, triggers distinctive anti-glioma immune reactivity, facilitates brain immune infiltration through the opening of the BBB, and warrants consideration for clinical trials in the up-front setting for glioblastoma that can be monitored with [18F]-FLT  PET imaging.

overall_design: At designated time points, tumor-bearing mice were euthanized and brains collected following cardiac perfusion and chopped up using a scalpel, dissociated, and suspended using a mixture of IMDM 1X (Corning) containing 2% inactivated FBS (Millipore Sigma), collagenase (100 μg/mL) and DNase (20 units/mL). Samples were incubated for 35–40 minutes at 37°C with agitation. The tissue was filtered through a 70 μm nylon cell strainer (BD Biosciences) and then underwent centrifugation at 4°C. Half of the pellet representing the whole TME was resuspended in culture media, and the other half in a 20 mL mixture of 5.4 mL Percoll Plus (GE Healthcare) overlaid with 12 mL 1X PBS and 0.6 mL 10X PBS (Corning) for immune enrichment. The tube was centrifuged at 800g for 10 minutes at 4°C, with 9 acceleration and 0 deceleration. After centrifugation, the immune-enriched cell pellet was collected, washed, mixed with the whole TME samples at a ratio of 1:1, stained with Trypan blue dye (MilliporeSigma), and counted using a Countess II FL automated cell counter in a Countess cell-counting chamber (Invitrogen, Thermo Fisher Scientific). Post-library preparation cells were sequenced using the Illumina NovaSeq. Preprocessing of raw sequencing files included alignment to mm10 reference using Cell Ranger (v3.1.0). Next, ambient mRNA and doublets were removed using SoupX (v.1.3.0) and sDblFinder (v1.4.0), respectively. Then, a standard Seurat R Package workflow was applied (34). Cells were cleaned using a mitochondrial DNA threshold of 10% and a UMI range of 100 to 5000. In addition to Seurat functions, the Harmony algorithm was used for batch correction (35). Non-tumor cell clusters were annotated using three parallel methods: 1) comparison against known cell markers; 2) examination of DEGs against the Human Protein Atlas; and 3) singleR package, an automated cell assignment algorithm. Differential abundance testing was conducted using the MiloR package (36).

first: Tripathi

last: Shashwat


title: ABC1K2 is involved in stress response and glucosinolate modification during seed development in Arabidopsis thaliana

city: Verona

first: Elisa

last: Gecchele

address: viale del lavoro

country: Italy

institute: DiamanteSB srl

summary: The Activity of BC1 complex Kinases (ABC1K) family is a ubiquitous group of proteins that share a highly conserved ABC1 domain (unrelated to the ATP-Binding Cassette – ABC – transporter proteins), whose precise function is still undetermined. The ABC1K proteins are included among the atypical protein kinases due to their lack of many features characterizing canonical eukaryotic protein kinases; despite this, they share a structurally similar kinase fold domain and have been reported to exhibit kinase activity. The Abc1k genes in plants show different functions compared to those in yeast. For instance, in wheat, TaABC1 is involved in a hypersensitive response to fungal pathogens and confers enhanced tolerance to abiotic stresses when overexpressed in Arabidopsis. In rice 15 ABC1K genes were identified, nine of which were localized in chloroplasts and some of them were affected by NaCl, high temperature, methyl viologen, abscisic acid and cadmium. We describe the characterisation of the knock-out mutant lines at the gene ABC1K2, corresponding to the locus At5g24970 in the A. thaliana genome, according to the proposed classification of Lundsquit et al., 2013. The gene seems to be expressed during embryogenesis (as for GUS assay), and ABC1K2 mRNA is not detectable in leaves, shoots or roots. Mutant lines have been analysed, and although the lack of ABC1K2 does not influence the overall plant fitness, development and reproduction, mutant seeds show a reduced ABA content, an increased seed size and mass as well as a reduced seed pigmentation, different accumulation of ABA and glucosinolates.

overall_design: Siliques of both wild-type and abc1k2 plants were collected at all developmental stages and sampled together. Siliques were frozen in liquid nitrogen, and valves were removed after freeze-opening, leaving developing seeds. To minimise biological variation, three pools of siliques were analysed from each plant

last: Fasani

first: Sofia

last: Cardin

first: Mauro

last: Commisso

first: GianPietro

last: Di Sansebastiano

first: Antonella

last: Furini

first: Giovanni

last: DalCorso


title: Basis for Lineage-Determining Pioneer Factors Targeting Distinct Repressed Chromatin States

city: Philadelphia

first: Kenneth

last: Zaret

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Pioneer transcription factors target compact, transcriptionally silent chromatin, thereby enabling gene activation in development, regeneration, and cell reprogramming.   However, silent chromatin is heterogenous, varying in nucleosome mobility, nucleosome compaction, and repressive histone modifications, and how pioneer factors may overcome these different chromatin barriers is unknown.  We systematically compared the chromatin targeting of 13 embryonic transcription factors and found that the DNA binding domain (DBD) type predicts whether a pioneer factor targets low-turnover nucleosomes in compact chromatin, dynamic nucleosomes in compact chromatin, or function as non-pioneer factors targeting accessible chromatin.  By contrast, non-DBD domains enable targeting of repressed chromatin marked by H3K9me3 or H3K27me3.  Fusions of different non-DBD segments of heterochromatin-targeting pioneer factors onto SOX2 can expand binding of Sox2 target motifs, including within heterochromatin, and improve cellular reprogramming.  Our study unveils how different forms of silent chromatin are coordinately targeted by lineage-specifying factors.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for V5-tagged transcription factors after 48 ectopic expression in hBJ fibroblasts

first: Andrew

last: Katznelson


title: SOX10 regulates melanoma metastasis through the IRF1-ITGA3/EphA2-FAK pathway.

city: Toyama

first: Satoru

last: Yokoyama

state: Toyama

address: 2630 Sugitani

country: Japan

institute: Univeristy of Toyama

summary: Melanoma heterogeneity is associated with an enhanced metastatic potential. Although an invasive state with MITFlow/AXLhigh in the melanoma subpopulation has been identified using a single-cell RNA-seq analysis, the mechanisms by which these cells acquire their invasiveness remains unclear. In the present study, we identified the gene set related to cell migration as one of the enriched gene ontologies after the knockdown of SOX10 in melanoma. We demonstrated that the knockdown of SOX10 induced melanoma migration independent of MITF reduction or AXL induction. An in silico analysis and in vitro analysis revealed that ITGA3 and EphA2 were downstream molecules for SOX10-mediated migration, and were required for adhesive and random motile abilities, respectively. In addition, the oncogenic activation of MAPK was required for increased random motility through EphA2 phosphorylation at the Ser 897 residue. We also demonstrated the significance of IRF1 in the induction of both ITGA3 and EphA2 after the knockdown of SOX10. The FAK inhibitor, defactinib, suppressed metastasis in vivo. In summary, the present study showed that the reduced expression of SOX10 induced melanoma metastasis through the IRF1-ITGA3/EphA2-FAK pathway and also suggests the potential of FAK inhibitors as candidate drugs for the treatment of melanoma metastasis.

overall_design: RNAseq was performed using Illumina NovaSeq 6000 on siRNA-transfected A2058 melanoma cells


title: Prenatal Glucocorticoid Exposure Disrupts a Subcluster Microglia Maturation Leading to ASD-like Behavior

city: Hangzhou

first: Baixiu

last: Zheng

state: Zhejiang

address: Yuhangtanglu

country: China

institute: Zhejiang University

summary: Prenatal glucocorticoid exposure, whether due to pharmacological treatment or stress-induced maternal overproduction, has been associated with an increased risk of autism spectrum disorders (ASD), yet the underlying neurodevelopmental mechanisms remain poorly understood. Here, we report that late-pregnancy exposure to dexamethasone resulted in ASD-like behaviors in adolescent offsprings, accompanied by an increased density of immature dendritic spines and imbalance of neurotransmission in hippocampus. Single-cell RNA sequencing uncovered a significant expansion of MRC1+ microglia derived from border-associated macrophages (BAM) following prenatal exposure, with arrested maturation into homeostatic microglia. Strikingly, this population exhibited selective F13a1 upregulation. Early postnatal inhibition of F13A1 restored microglial maturation and ameliorated behavioral abnormalities and dendritic spine deficits. Elevated levels of F13A1 were also observed in the plasma of postnatal rats and in the umbilical cord blood of human females exposed to prenatal glucocorticoids, suggesting its potential value as a biomarker.

overall_design: Single-cell RNA sequencing of microglia isolated from hippocampus of rats' embryo on gestational day 20 with prenatal dexamethasone exposure or not. Each sample contained 7 male embryos.


title: Fluvastatin protects Leydig cells in orchitis through direct activation of Peroxiredoxin 1

city: Shanghai

first: Fan

last: Dong

address: 845 Lingshan Road

department: Department of Reproductive Medicine

institute: Shanghai Jiao Tong University School of Medicine

summary: Orchitis caused by infection is one of the most important causes of male infertility, which can cause an imbalance of the oxidation/antioxidation system. Appropriate antioxidant therapy may be effective in alleviating testicular damage. Previous studies found that peroxiredoxin 1 (PRDX1) is involved in the regulation of oxidative stress and inflammation, and is highly expressed in testis. Therefore, selecting an effective PRDX1 agonist might become an attractive strategy in the treatment of orchitis related to oxidative stress. In the current study, we identified the effective agonist of PRDX1. Leydig cells were used to find the antioxidant role and mechanisms of the agonist in vitro. Models of orchitis in wild-type and Prdx1-/- mice were employed to confirm the anti-orchitis effect of the agonist. We found that fluvastatin (FV), a classical cholesterol-lowering drug, could directly bind PRDX1 to activate its enzyme activity. FV played a protective and antioxidant role on H2O2-treated Leydig cells by improving cell viability and testosterone level, inhibiting apoptosis, and reducing reactive oxygen species level and inflammatory factors in a PRDX1-dependent manner. FV could also decrease oxidative stress and inflammation levels of testes in mice models, thereby reducing the damage on testicular steroidogenesis and spermatogenesis caused by orchitis. FV was an effective agonist of PRDX1, which showed antioxidant and anti-inflammatory impact in orchitis. Our results may shed light on the antioxidant treatment of orchitis and male infertility.

overall_design: We analyzed the gene expression profiling of H2O2-treated primary mouse Leydig cells followed by fluvastatin (FV) treatment with or without the transfection of PRDX1 small interfering RNA (siprdx1). The primary mouse Leydig cells were divided into six groups with different treatments before RNA-seq. In brief, primary mouse Leydig cells were transfected with either siprdx1 or siNC, and then treated with or without 200 μM H2O2 for 30min, followed by 5 μM FV or 0.1% DMSO treatment for 6 hours. Consequently, groups (1) siNC; (2) siNC+H2O2; (3) siNC+H2O2+FV; (4) siprdx1; (5) siprdx1+H2O2; (6) siprdx1+H2O2+FV were employed for RNA-seq (each n=3).


title: The Impact of Lithium Chloride Pretreatment on MicroRNA Expression Levels in Exosomes Derived from Human Umbilical Cord Mesenchymal Stem Cells

city: Dalian

first: zhao

last: wang

state: Liao Ning

address: 222 Zhongshan Road, Xigang District, Dalian City

department: Dermatology Department

institute: The first affiliated hospital of  Dalian medical university

type: Non-coding RNA profiling by high throughput sequencing

summary: Exosomes are extracellular vesicles, 30~150 nm in diameter, characterized by a phospholipid bilayer membrane structure and secreted by cells through the endosomal pathway. These vesicles carry diverse bioactive molecules, including DNA, RNA, lipids, and metabolites, and play crucial roles in mediating intercellular communication and facilitating material transport.Various physical and chemical pretreatment methods, such as hypoxia, ultrasound, and specific compounds, have been shown to reprogram exosomes, increase the yield of engineered exosome preparations, or alter their contents, including RNA expression levels.LiCl, a small-molecule agonist of the Wnt pathway, upregulates Wnt signaling by inhibiting GSK-3β, thereby mimicking Wnt signal transduction, maintaining the differentiation potential of hUC-MSCs, and promoting their proliferation.This sequencing result suggested that LiCl-pretreated HUCMscs derived exosomal mirnas were indeed altered

overall_design: miRNA sequencing of human umbilical cord mesenchymal stem cell-derived exosomes in lithium chloride pretreated group and untreated group

first: Lin

last: Gong

first: Zhao

last: Wang


title: Transcriptomic analyses of normal human pancreatic acinar cells

city: Gainesville

first: Jason

middle: Orr

last: Brant

state: FL

address: 2197 Mowry Rd

department: Biostatistics

institute: University of Florida

summary: A cohort of 69 normal human pancreatic acinar cell specimens was collected from islet transplantation centers. Total RNA was isolated from uncultured pancreatic acinar cells, and sequencing was performed using Illumina NGS platforms. The resulting transcriptome data for each specimen were analyzed.

overall_design: RNAseq profiling of uncultured normal human pancreatic acinar cells. After adding Matrigel, it was immediately removed from the uncultured Day 0 samples by centrifugation at 4°C before solidification. In contrast, Day 6 samples underwent 6 days of ADM incubation at 37°C before Matrigel removal and subsequent collection.

first: Corey

last: Perkins

first: Jinmai

last: Jiang

middle: O

first: Kalyanee

last: Shirlekar

first: Thomas

last: Schmittgen


title: Epigenetically regulated expression of ALDH1 by anthracyclines causes an adaptive oxidative response and drug resistance in AML

city: Marseille

first: Nori

last: SADOUNI

address: 169 Avenue Luminy

country: France

institute: TAGC INSERM U1090

summary: To investigate drug-induced epigenetic resistance in AML, the K562 cell line was selected due to its responsiveness to anthracyclines and its ease of genetic manipulation. Daunorubicin (DNR) was chosen as a model drug because of its pivotal role in AML treatment. DNR treatment of K562 cells induced expression of all three ALDH1 isoforms. To explore the activation of cis-regulatory elements, ChIP-Seq with H3K27Ac was performed on K562 cells treated or not with DNR for 18 hours.

overall_design: In vitro and in vivo validation of daunorubicin-induced enhancers associated to drug resistance in Acute Myeloid Leukemia.

first: Francesco

last: Leonetti

first: Sladana

last: Kosanovic

first: Iris

last: Manosalva

first: Rocio

last: Rebollidos-Rios

first: Céline

last: Baier

first: Muhube

last: Yazir

first: Andrada

last: Constantinescu

first: Charbel

last: Souaid

first: Raquel

last: Pequerul

first: Yasmine

last: Labiad

first: Regis

last: Costello

first: Jaume

last: Farrés

first: Guillaume

last: Martin

first: Meritxell

last: Alberich-Jorda

first: Salvatore

last: Spicuglia

first: Mileidys

last: Perez- Alea


title: Multiomics-based insights into tomato adaptation to multifactorial stress combination

city: Columbia

first: Sameep

last: Dhakal

state: MO

address: 1201 Rollins St.

department: Institute for data science and Informatics

institute: University of Missouri

summary: Multifactorial stress combination (MFSC) represents a major threat to crop productivity under climate change scenarios. While the physiological effects of MFSC have been studied, its impact on gene expression and primary metabolism remains poorly understood in tomato plants. In this study, we performed an integrative transcriptomic and metabolomic analysis of tomato (Solanum lycopersicum) plants exposed to combinations of up to six low-intensity abiotic stresses. RNA-seq analysis revealed a stress complexity-dependent increase in differentially expressed genes (DEGs), including 258 core transcripts and 155 transcription factors uniquely regulated under 4-, 5-, and 6-stress conditions. Heat-specific analysis identified 103 uniquely regulated transcripts, including two key transcription factors (Zinc Finger TF32 and a B3-domain family protein) suggested as central regulators of different combinations involving heat stress. Our findings define a conserved, stress-complexity-dependent molecular architecture in tomato and identify candidate markers for improving crop resilience under MFSC.

overall_design: The experimental design to study wild-type tomato (Moneymaker) responses to MFSC included the following stresses: Nitrogen deficiency (N-), heat stress (HS), salinity (S), high light (HL), heavy metal as cadmium treatment (Cd), and the herbicide paraquat (PQ) were applied up to a combination of all six factors. HL, HS, S and PQ were combined in all their possible combinations of 2-, 3- and 4-factors and Cd and N- were added to 4-factor combination to generate 2 different groups of 5-factor stresses, and all of them simultaneously generate the 6-MFSC. N deficiency was applied by watering plants with a half strength Hoagland solution with 10% of N (Ca(NO₃)₂) content one week after transplanting the plants. One week after the starting of the N-deficiency stress, plants with and without N deficiency were watered with half strength Hoagland solution containing each stressor(s): S (75 mM NaCl), PQ (1 µM PQ), Cd (10 µM CdSO4), S+PQ (75 mM NaCl + 1 µM PQ), S+PQ+N- (75 mM NaCl + 1 µM PQ + 10% N), S+PQ+Cd (75 mM NaCl + 1 µM PQ + 10 µM CdSO4) and S+PQ+Cd+N- (75 mM NaCl + 1 µM PQ + 10 µM CdSO4 + 10% N). Following 15 days of stress treatments, a group of CT plants and a group of plants subjected to each of the individual and combined stresses were transferred to growth chambers and were subjected to HL (700 µmol m-2s-1) and/or HS (37ºC). The tissue sampled from tomato plants were young leaves. All experiments were repeated three times with at least 8 plants per stress treatment.

first: Lidia

last: S Pascual

first: Abdul

last: Ghani

first: Zhen

last: Lyu

first: Manish

last: Sridhar Immadi

first: Mohit

middle: S

last: Verma

first: Trupti

last: Joshi

first: Aurelio

last: Gómez-Cadenas

first: Ron

last: Mittler

first: Sara

last: Zandalinas


title: Mega-scale single-cell profiling reveals novel biomarkers associated with acute GvHD after allogeneic hematopoietic stem cell transplantation

city: Hamburg

first: Immo

last: Prinz

address: Martinistraße 52, Building N25

department: Institute of Systems Immunology

country: Germany

summary: Alloreactive T cells mediate graft-versus-leukemia (GvL) reactions and acute graft-versus-host disease (aGvHD) in AML patients following allogeneic hematopoietic stem cell transplantation. To investigate biomarkers that identify alloreactive T cells associated with either beneficial GvL or detrimental aGvHD, we collected graft samples and two post-transplant follow-up blood samples (day 30 and day 100) of ten AML patients undergoing hematopoietic stem cell transplantation and profiled over 777,000 CD45+ leukocytes in total by combinatorial barcoding-based mega-scale single-cell RNA sequencing. Using immune receptor sequences as intrinsic clonal barcodes, we observed that especially CD8+ graft-derived T cells persisted and displayed enhanced proliferation, clonal expansion, and likely alloreactivity. Notably, patient-derived peripheral leukocytes that survived the conditioning, as identified by sex-chromosome-related genes, were primarily CD4+ T helper cells. MDGA1 expression on T cells and NK cells emerged as a novel biomarker potentially associated with aGvHD. Additionally, we observed a significant deficiency of ADGRG1 expression, a marker of alloreactive cytotoxic T cells, by αβ and γδ T cells from relapsed patients. In conclusion, mega-scale single-cell monitoring of graft and hematopoietic immune cell reconstitution allowed us to demonstrate that MDGA1 and ADGRG1 may function as complementary biomarkers expressed by distinct circulating T cells that are associated with divergent outcomes in AML patients, enabling precise risk stratification of alloHSCT outcomes and presenting potential therapeutic targets.

overall_design: Ten adult ( > 18y) patients with AML in complete remission who underwent alloHSCT with peripheral blood stem cell grafts (matched unrelated, n = 8; matched related, n = 2) in the Department for Stem Cell Transplantation of University Cancer Center Hamburg-Eppendorf from December 2021 to May 2022 were included in this study (Table 1). The study was approved by ethics commission of the Medical Chamber of Hamburg and was performed according to the approved study protocol (version 1.1 from 01.11.2021). Written informed consent was obtained from all participants. The majority of patients received myeloablative conditioning (n = 7) with ATG-based immunoablation (n = 9). After a median follow-up of 20 months (18–22), three patients died (relapse, n = 2; NRM, n = 1). The relapses occurred on days +149 and +622. Five patients developed acute GvHD (II-IV) at a median of 57 days (19–136). The eight patients remained alive in complete remission at the last follow-up. Peripheral blood stem cell graft samples were collected at the time of transplantation and were cryopreserved on the next day. The PBMC samples of recipients were collected at day +30 (D30) and day +100 (D100) and were cryopreserved on the same or the following day. Mononuclear cells were isolated using a Ficoll gradient and cryopreserved in DMSO until they were used for single cell analysis. All DAPI− (Thermo Fisher Scientific Cat# D1306) (RRID:AB_2629482) live cells were sorted from frozen PBMC samples at the flow cytometry core facility of University Medical Center Hamburg-Eppendorf (RRID:SCR_017156). The sorted cells were fixed and permeabilized using Evercode™ Cell Fixation v2 (Parse Biosciences, Cat. ECF2001) following the manufacturer’s protocol. Fixed cells were stored at −80 °C. All samples were then processed together to prepare single-cell libraries using one Evercode™ WT Mega v2 Kit (Parse Biosciences, Cat. ECW02050), according to the manufacturer’s instructions. Fifteen sub-libraries were sequenced on the Illumina NovaSeq 6000 S4 flow cell platform (RRID:SCR_016387) using PE150 chemistry with a sequencing depth of 25,000 reads per cell.

first: Zheng

last: Song

first: Evgeny

last: Klyuchnikov

first: Anita

last: Badbaran

first: Nicolaus

last: Kröger


title: Müller glia-mediated protection of retinal ganglion cells from ethambutol-induced neurotoxicity through brain-derived neurotrophic factor

first: Yu-Hui

last: Wong

state: Taiwan

address: (NYCU) No. 155, Sec. 2, Linong St., Beitou Dist.

institute: National Yang Ming Chiao Tung University

summary: Ethambutol (EMB)-associated optic neuropathy is the most common toxic optic neuropathy and poses a significant visual threat worldwide. This study aimed to investigate the neuroprotective roles of Müller glia, the most abundant macroglia in the retina, and their associated growth factors in supporting retinal ganglion cells (RGCs) under EMB-induced toxicity. Induced RGC-like cells (iRGCs), differentiated from human induced pluripotent stem cells, and Müller glial cell line MIO-M1 were used as cellular models. RNA sequencing revealed that EMB significantly disrupted neurotrophin and BDNF-associated pathways in iRGCs. Co-culture with MIO-M1 cells markedly enhanced the survival of iRGCs during EMB exposure. mRNA of BDNF and nerve growth factor (NGF) were elevated in MIO-M1 cells, while only BDNF improved the survival and morphological integrity of iRGCs under EMB treatment. Administration of BDNF also improved the survival of RGC in mouse retinal explants. The pro-survival effect of BDNF was suppressed by GNF5837, a pan-TRK inhibitor. Among the three downstream effectors of BDNF signaling, AKT was most prominently activated by BDNF in EMB-treated iRGCs, compared to ERK and PLCγ1. Furthermore, the protective effect of BDNF was blocked by the AKT inhibitor MK-2206 but not by the ERK inhibitor GDC-0094. Müller glia confer neuroprotection to RGCs under EMB-induced stress, primarily via BDNF signaling. AKT functions as the key downstream effector mediating this protective response. These findings suggest that the BDNF-AKT signaling may serve as a promising therapeutic target for EMB-associated optic neuropathy.

overall_design: The response of week 4 iRGCs to EMB was investigated by using RNA sequencing.

first: Hui-Chen

last: Cheng

first: An-Guor

last: Wang

first: Shih-Wei

last: Chen

first: Yong-Lin

last: Yang

first: Hsien-Chia

last: Juan

first: Roxanne Hsiang-Chi

last: Liou

first: Jenn-Yah

last: Yu


title: Modeling myocardial physiological growth using human pluripotent stem cell derived cardiomyocytes and 3D cardiac microtissues

first: Chang

last: Liu

address: Nanchen Road 333

institute: Shanghai University

summary: Prior work suggests that exercise-responsive molecules may mediate exercise-induced myocardial physiological growth and promote functional recovery after ischemia- reperfusion injury in adult mice. Based on these findings, multiple mouse models of myocardial physiological growth have been successfully established. However, an in vitro model of physiological growth in cardiomyocytes derived from human embryonic stem cells (hESC-CMs) has not been successfully developed. To address this gap, we generated an inducible hESC cell line with forced Cbp/P300 Interacting Transactivator with Glu/Asp Rich Carboxy-Terminal Domain 4 (CITED4) gene expression, and differentiated those hESCs towards cardiomyocytes. The results showed that CITED4 expression increased cell size and proliferation in hESC-CMs, and promoted cardiomyocyte proliferation in 3D cardiac microtissues. Forced expression of CITED4 induced activation of Protein kinase B (also known as AKT1) signaling, which was necessary for CITED4-induced proliferation of hESC-CMs and 3D cardiac microtissues, while mTOR signaling mediated both proliferation and physiological hypertrophy induced by CITED4. In an in vitro model mimicking ischemia-reperfusion, CITED4 expression inhibited cardiomyocyte apoptosis in hESC-CMs and 3D cardiac microtissues, and this effect was mediated by activation of mTOR signaling. In conclusion, we successfully generate a physiological growth model in hESC-CMs and 3D cardiac microtissues. Moreover, physiological growth induced by CITED4 is mediated by activation of the mTOR signaling, which is necessary to promote proliferation and physiological hypertrophy, and to alleviate apoptosis after ischemia- reperfusion injury in hESC-CMs and 3D cardiac microtissues.

overall_design: We generated an inducible hESC cell line with forced Cbp/P300 Interacting Transactivator with Glu/Asp Rich Carboxy-Terminal Domain 4 (CITED4) gene expression via lentivirus transfection followed by fluorescence activated cell sorting. We then differentiated those hESCs towards cardiomyocytes.Divided into two groups, the control group and the group with Doxy, RNA sequencing was carried out.


title: Differential contribution of TFE3 isoforms to cell motility and invasion

city: Bethesda

first: Pablo

last: Contreras

state: MD

address: 50 South Dr.

institute: NIH

summary: We and other have previously reported that TFE3 migrates as two distinct bands of approximately 72 and 82 kDa in SDS-PAGE. Interestingly, whereas the smaller form of TFE3 is always present in cell lysates, the higher molecular weight form appears only after specific stress conditions, such as prolonged starvation. A recent report suggested that the 82 kDa form does in fact corresponds to TFE3 full length (TFE3-L). It was proposed that the control of TFE3 stability may constitute the main mechanism of TFE3 regulation. There is, however, a critical question that remains to be addressed regarding the role of the 72 kDa TFE3 short isoform (TFE3-S). TFE3-S is expressed at high levels in most cell types and its expression remains constant both under control and stress conditions. Characterizing the nature and regulation of TFE3-S, as well as its potential transcriptional activity and selectivity, is therefore essential to fully understand TFE3 regulation.

overall_design: To investigate the transcriptional capability of TFE3-L and TFE3-S, we generated adenovirus (Ad) expressing either recombinant (r)TFE3-L or rTFE3-S. ARPE-19 cells were infected for 30 hours with Ad-rTFE3-L, or Ad-rTFE3-S or Ad-Null as a negative control to compare.

first: José

middle: A

last: Martina

first: Katie

last: Rollins

first: Euteum

last: Jeong

first: Alberto

last: Rissone

first: Rosa

last: Puertollano


title: TSniffer: Unbiased de novo identification of RNA editing sites and quantification of editing activity in RNA-seq data

city: Rochester

first: Christian

middle: Karl

last: Pfaller

state: MN

address: 200 First Street SW

department: Molecular Medicine

institute: Mayo Clinic

summary: RNA editing by adenosine deaminases acting on RNA (ADARs) is an evolutionarily conserved posttranscriptional modification essential for organismal development and normal cell function. Three catalytically active ADARs are conserved in mammals: two isoforms of ADAR1 referred to as ADAR1-p150 and ADAR1-p110, as well as ADAR2. All recognize and edit double-stranded RNA (dsRNA) structures but demonstrate target specificity and selectivity that dictate the unique essential biological functions of the three enzymes. The editing activity of ADAR1-p150 suppresses autoimmune responses against self-RNA structures, whereas ADAR1-p110 and ADAR2 have other primary functions. To better understand the mechanism of target selection by ADARs, we developed TSniffer, which allows accurate de novo identification of edited transcripts and quantification of the extent of editing within each transcript. We found that 17-40% of protein coding transcripts in mice, ferrets, and humans are edited by ADARs. Individual transcripts can harbor hundreds and thousands of editing sites, mostly within inverted retrotransposable elements. For human transcripts, we found differential editing by ADAR1 and ADAR2, aligning with a supportive role for ADAR2, while some targets were dominantly edited by ADAR1. Relying only on RNA-seq data and reference genome, TSniffer represents a novel tool to decipher the role of ADAR editing in different physiological states including disease models. Its unbiased approach is suitable for any organism.

sample_organism:
Homo sapiens
Mustela putorius furo

platform_organism:
Homo sapiens
Mustela putorius furo

overall_design: We analyzed RNA-seq datasets from wild type (WT) and ADAR-deficient mouse and human samples, GTEx datasets of human brain, and of ferret PBMCs.

first: Maike

last: Herrmann

first: Yvonne

last: Krebs

first: Francisco

middle: M

last: Acosta

first: Sebastian

last: Parusel

first: Oliver

last: Siering

first: Felix

middle: G

last: Andres

first: Biruhalem

last: Taye

first: Csaba

last: Miskey


title: Spatial dynamics of the tumor microenvironment associated with emerging resistance to targeted therapy in EGFR-mutated non–small cell lung cancer

city: Fukuoka

first: Satoshi

last: Nakamura

state: Fukuoka

address: 3-1-1, Maidashi, higashi-ku

department: Respiratory Medicine

institute: Kyushu University

summary: Epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKIs) provide therapeutic benefit in EGFR mutation–positive non–small cell lung cancer, but some individuals develop early resistance. We performed spatial transcriptomics analysis of pre- and posttreatment tumor samples from the same patients to explore the underlying mechanisms of such early resistance. The proportion and activation of fibroblasts increased in association with the development of early resistance, whereas a distinct tumor cell cluster showed activation of tumor necrosis factor–α signaling via the NF-B pathway even before treatment. Also in the early resistance sample, specific tumor cell clusters interacted with immune and stromal cells. Immature tertiary lymphoid structures (TLSs) were enriched in the early resistance sample, whereas mature TLSs were observed in the long-term response sample. These findings implicate tumor heterogeneity and an inflammatory tumor microenvironment in early EGFR-TKI resistance, providing insight into potential therapeutic strategies to improve treatment outcomes.

overall_design: Spatial transcriptome of paired samples from 4 patients before and after osimertinib treatment with VisiumHD and StarDist processing

last: Nakamaura

first: Daisuke

last: Shibahara

first: Kentaro

last: Tanaka

first: Yasuyuki

last: Kishikawa

first: Mikiko

last: Hashisako

first: Keita

last: Nakatomi

first: Noriaki

last: Nakagaki

first: Mikihiro

last: Kohno

first: Koichi

last: Azuma

first: Ritsu

last: Ibusuki

first: Kohei

last: Otsubo

first: Yasuto

last: Yoneshima

first: Eiji

last: Iwama

first: Yoshinao

last: Oda

first: Isamu

last: Okamoto


title: IFITM3-MET interaction drives osimertinib resistance through AKT pathway activation in EGFR-mutant non–small cell lung cancer

city: Kyoto

first: Akira

last: Watanabe

state: Kyoto

address: Rm504, Miyako Bldg, 233, Isa-cho, kamigyo-ku

institute: CyberomiX Inc

summary: Despite an initial favorable response of EGFR mutant non–small cell lung cancer (NSCLC) to osimertinib, an EGFR tyrosine kinase inhibitor (TKI), resistance inevitably develops. We here performed transcriptomics analysis of pretreatment specimens and identified IFITM3 as a gene specifically upregulated in tumors that develop early resistance to osimertinib. Immunohistochemistry confirmed patients with IFITM3-positive tumors experienced a shorter progression-free survival. Spatial transcriptomics and other analyses further revealed that IFITM3 expression was increased in response to cytokines derived from the tumor microenvironment (TME) during osimertinib treatment. IFITM3 was found to promote the development of osimertinib resistance through interaction with MET and activation of the AKT pathway. Furthermore, combined treatment with a MET inhibitor suppressed the development of osimertinib resistance in a mouse model. Our findings thus reveal that upregulation of IFITM3 represents a previously unrecognized mechanism of osimertinib resistance, and they suggest that targeting the IFITM3-MET axis may improve treatment outcomes.

overall_design: We performed RNA-seq analysis of PC-9 cells (EGFR-mutant NSCLC cell line) stably depleted of IFITM3 with a specific shRNA and corresponding control cells.

first: Atsushi

last: Shimauchi

first: Hiromu

last: Kawano

first: Shun

last: Mizusaki


title: IFITM3-MET interaction drives osimertinib resistance through AKT pathway activation in EGFR-mutant non–small cell lung cancer II

overall_design: We analyzed formalin-fixed, paraffin-embedded (FFPE) tumor sections and clinical data for 32 individuals with EGFR mutant NSCLC who received osimertinib monotherapy as a first-line treatment between January 2016 and April 2023 across eight institutions. We defined short and long PFS as <12 and >20 months, respectively, on the basis of the results of a previous clinical study of osimertinib treatment. RNA-seq analysis was performed for 32 patients with a short PFS (n = 10) or long PFS (n = 22) who had sufficient RNA available, with these individuals constituting the discovery cohort.

first: Satoshi

last: Nakamura


title: Unraveling the Molecular Mechanisms of Total Fertilization Failure: Insights into Transcriptional Dysregulation

city: Doha

first: Mohamed Nadhir

last: Djekidel

state: Doha

address: Gharafa

department: Translational Medicine Department

country: Qatar

institute: Sidra Medicine

summary: Background Fertilization involves interactions between sperm and metaphase II (MII) oocyte, initiating a cascade of events including oocyte activation, calcium release, resumption of meiosis, and zygote formation. Total fertilization failure (TFF), characterized by disruption of any of these processes, occurs in 1-3% of intracytoplasmic sperm injection (ICSI) cycles. The genetic basis of TFF remains largely unexplored. Methods We recruited a familial case of TFF. We assessed sperm parameters, binding ability, and fertilization outcomes using molecular assays and confocal microscopy. The whole genome sequencing and comprehensive genetic analyses were performed on the patients and family members to identify potential loss-of-function variants in genes involved in oogenesis and fertilization. Additionally, single-cell RNA sequencing of the patient's MII oocytes was conducted to assess transcriptomic profile. Two ICSI cycles were performed, one of which included assisted oocyte activation (AOA) using a calcium ionophore. Integrated bioinformatic analysis using RNA-seq and ATAC-seq was used to map genome-wide regulatory landscape in normal oocytes and early embryos. An enhancer-mediated gene regulatory network (eGRN) was constructed to assess the impact of mutations on transcription factor binding and gene   regulation across the different GO BP and Reactome pathways. Results Despite normal sperm parameters in the husband and the absence of genetic variants related to oocyte activation in both partners, RNA-seq revealed aberrant expression of genes involved in meiosis, zona pellucida biogenesis, and oocyte activation. RNA-seq and ATAC-seq data identified 22 key transcription factors whose binding is significantly affected by the mutational landscape of the patient’s oocytes and that may disrupt downstream pathways involved in oogenesis, fertilization, and early embryonic development. ZNF121, TFAP2D, VEZF1 and YY1 were the top 4 hub TFs discovered in GO terms network. Additionally, TFAP2D, YY1, ZFP28 and ZNF121 were the most connected TFs to different Reactome pathways. Conclusions Our findings suggest that transcriptional dysregulations play a central role in total fertilization failure (TFF), by impacting downstream gene expression. Although, assisted oocyte activation with calcium ionophore helped successfully achieve fertilization, leading to the development of an 8-cell embryo. The insights from our study provide valuable opportunities for targeted interventions and potential therapeutic strategies in reproductive medicine.

overall_design: low-input RNA sequencing (RNAseq) at the single-oocyte resolution level of inseminated MII oocytes of an infertile patient.

first: Manar

last: Ata

first: Fadi

last: Choucair

first: Maria

last: Esteves

first: Fatima

last: Al Ali

first: Shoaib

last: Nawaz

first: Lina

last: El Taha

first: Oleksandr

last: Soloviov

first: Abbirami

last: Sathappan

first: Elbay

last: Aliyev

first: Khalid

last: Fakhro

first: Johnny

last: Awwad

first: Matteo

last: Avella


title: The Retinal Determination Gene Network can confer chemoresistant properties to AML [THP1_chip_rna]

city: Manchester

first: Georges

last: Lacaud

state: England

address: Wilmslow Raod

department: Stem Cell Biology

country: United Kingdom

institute: Cancer Research UK Manchester Institute

summary: SIX1 is a target of MLL-AF9 and MOZ-TIF2 fusions in murine models of AML. SIX1 is also expressed in a subset of human AML cell lines. Being a transcription factor we have studied the functional loss of SIX1 in this cell line.

overall_design: ChIP sequencing of  1x10^8 formaldehyde crosslinked WT THP1 cells, using IgG as an isotype control. CRISPR CAS9 generated THP1 cells were also transduced with two guides targeting exon 1 and 2 of the SIX1 gene. Cells were sorted for guide expression and sequenced at 24, 48 and 72hrs to understand the dynamic gene changes upon SIX1 loss.

first: Liam

last: Clayfield

first: Divya

last: Mailk

first: Anne

last: Largeot

first: Renaud

last: Mevel

first: Muhammad

middle: Z

last: Fadlullah

first: Rahima

last: Patel

first: Martyna

last: Szpakowska

last: Maqbool

first: Michael

last: Lie-a-ling

first: Andy

last: Chevigne

first: Jessica

last: Whittle

first: Pascal

last: Maire

first: Tim

middle: C

last: Somervaille

first: Heide

middle: L

last: Ford

first: Valerie

last: Kouskoff

last: Lacaud#


title: Coincident evolution and functional adaptation of the Caenorhabditis-restricted genes ivph-3 and gon-14

city: Baltimore

first: Nikita

middle: Sudhir

last: Jhaveri

address: 3400 N Charles Street

department: Biology

institute: Johns Hopkins University

summary: Poorly conserved or taxonomically-restricted genes represent a sizable portion of most genomes. Many of these genes participate in essential processes and can contribute to evolutionary innovation in species. However, identifying which genes are biologically important and uncovering their functions remains a significant challenge, since routine tools reliant on gene ontology or sequence orthology are of limited use. Here we evaluate two genes of the Caenorhabditis-restricted class of LIN-15B-domain-encoding genes, ivph-3 and gon-14, and compare their in vivo functions in two species, C. elegans and C. briggsae. We show that within the Elegans supergroup of Caenorhabditis, ivph-3 and gon-14 exhibit sequence constraints distinct from other family members, including maintenance of a one-to-one orthology and a higher degree of stabilizing selection. Coincidentally, mutants for either of the genes exhibit strong phenotypic defects that are similar within-species (C. elegans or C. briggsae), but with notable differences when comparing between species. These findings highlight the genetic and genomic features associated with the evolution of a taxonomically restricted gene family, and suggest mechanisms by which specific family members adapt to fulfill essential biological functions.

overall_design: RNA-seq profiling of C. briggsae wild strain AF16 and mutant Cbr-ivph-3 hermaphrodites at L3 larval stage.

first: Bhagwati

middle: P

last: Gupta

first: Helen

last: Chamberlin


title: A pathogenic GATA2 zinc finger mutation restricts chromatin occupancy in human erythroid progenitor cells

city: Madison

first: Bresnick

last: Emery

state: WI

address: 600 Highland Avenue

institute: University of Wisconsin Madison

summary: The transcription factor GATA2 regulates hematopoietic stem and progenitor production and function via interactions with other regulatory proteins at gene enhancers and promoters.  Genome-wide patterns of GATA2 chromatin occupancy differ by cell type; dynamically controlled by levels of GATA2 and associated proteins.  During erythroid differentiation, gene expression networks that drive the process are established upon displacement of GATA2 from regulatory elements by the related transcription factor GATA1.  Herein, we map sites of GATA2 chromatin occupancy in the human erythroid progenitor cell line HUDEP-2 and define the genes regulated by GATA2 in these cells.  Additionally, we show that a human pathogenic GATA2 mutation, T354M, restricts GATA2 occupancy to a subset of chromatin sites.

overall_design: Cut & Tag to detect GATA2 chromatin binding was performed on wild-type and GATA2-deficient HUDEP-2 cells following lentiviral expression of HA-tagged GATA2 or HA-tagged GATA2(T354M).

first: Kirby

middle: D

last: Johnson

first: Philippos

last: Tsourkas

first: Vu

last: Tran

first: Emery

middle: H

last: Bresnick


title: ZDHHC12 palmitoylates HDAC8 and promotes the development of hepatocellular carcinoma associated with a diet high in saturated fatty acids

city: Changsha

first: Huaiyuan

last: Liang

address: 183 Renmin Middle Road

institute: Institute of Urological Cancer, Central South University

summary: Excessive intake of saturated fatty acids (SFAs), which are prevalent in diets high in fried foods and red meat, poses a significant threat for hepatocellular carcinoma (HCC). Herein, we found via Mendelian randomization (MR) analysis that SFAs could be one of the factors leading to HCC. However, the role and associated mechanism of SFAs in HCC progression remain poorly understood. Palmitic acid (PA) is the most common type of SFA. We therefore chose PA as an example of SFAs for our study. We identified zinc finger DHHC-type palmitoyltransferase 12 (ZDHHC12) as a key protein involved in the promotion of HCC progression by PA, which was accomplished by maintaining the stability of the recognized HCC-promoting gene histone deacetylase 8 (HDAC8). Mechanistically, supplementation with PA led to the upregulation of ZDHHC12 expression via activation of the transcription factor SWI/SNF-related BAF chromatin remodeling complex subunit ATPase 4 (SMARCA4). ZDHHC12 mediated the palmitoylation of HDAC8 at cysteine 244, thereby preventing the lysosomal degradation of HDAC8, which promoted the progression of HCC. In conclusion, this study revealed that ZDHHC12 was a key protein in palmitic acid-mediated HCC progression and that targeting HDAC8 could inhibit this process. These findings offer a potential therapeutic strategy for HCC patients with a high intake of saturated fatty acids, especially palmitic acid.

overall_design: Transcriptome sequencing data of tumor samples from 15 patients with hepatocellular carcinoma on a high red meat diet and 15 patients with hepatocellular carcinoma on a normal diet

first: Xin

last: Jin

first: Yvlong

last: Hong


title: The Retinal Determination Gene Network can confer chemoresistant properties to AML

first: Georges

last: Lacaud

summary: HoxA9, Six1 and Eya1 are targets of MOZ-TIF2 and MLL-AF9 fusion proteins in murine models. Hoxa9 overexpression can induce AML in murine HSPCs with a latency of ~6-9 months. Co-overexpression of RDGN members Six1 or Eya1 with Hoxa9 can enhance the differentiation block and colony forming potential of HoxA9 alone in vitro. RNA-seq was carried out on these lines to establish genetic pathways responsible for these chages in leukemogenicity. Benzarone is a potent EYA1 inhibitor. We wanted to assess if this drug was able to reverse the leukemogenic properties that EYA1 adds to HOXA9.

overall_design: Murine c-Kit+ cells were isolated from the bone marrow of female C57BL/6 mice. Cells were maintained in MT2 media  for 1 day before being retrovirally transduced with flourescent reporter plasmids encoding HoxA9 alone, or together with Six1/Eya1. Lines were  established in methylcellulose culture for 3 weeks before being cell sorted for their reporter construct and squenced. HOXA9_EYA1 lines were treated with either 5ug Benzarone or a DMSO (vehicle) control for 72hrs before RNA was extracted and samples sent for sequencing. HOXA9 alone (4 samples), HOXA9+SIX1 (4 samples).

first: Liam

last: Clayfield

first: Divya

last: Mailk

first: Anne

last: Largeot

first: Renaud

last: Mevel

first: Muhammad

last: Fadlullah

first: Rahima

last: Patel

first: Martyna

last: Szpakowska

last: Maqbool

first: Michael

last: Lie-a-ling

first: Andy

last: Chevigne

last: Whittle


title: Cancer-associated fibroblast-derived CCL5 promotes cisplatin resistance in neuroendocrine prostate cancer

first: Bo

last: Liu

state: Select a state...

address: 160 Pujian Road

department: Urology

institute: Renji Hospital, School of Medicine, Shanghai Jiao Tong University

summary: Chemoresistance remains a significant challenge in the treatment of neuroendocrine prostate cancer (NEPC), a highly aggressive and lethal subtype of prostate cancer. Here, we identify a tumor-stromal interaction mediated by the CCL5/CCR5 signaling axis that drives cisplatin resistance. Cisplatin-induced DNA damage promotes a cGAS-STING–dependent senescence program in cancer-associated fibroblasts (CAFs), resulting in the secretion of CCL5, a key senescence-associated secretory phenotype factor. CAF-derived CCL5 binds to CCR5 on tumor cells, promoting the formation of a CCR5/β-arrestin1/p85 complex that activates the PI3K/AKT signaling pathway. This activation enhances DNA repair, protecting tumor cells from cisplatin-induced apoptosis. Pharmacologic inhibition of the CCL5/CCR5 pathway using maraviroc, an FDA-approved CCR5 antagonist, sensitizes NEPC cells to cisplatin treatment and significantly prolongs survival in an NEPC mouse model. These findings establish the CCL5/CCR5 axis as a critical mediator of tumor-stromal crosstalk and provide a promising therapeutic strategy for overcoming chemoresistance in NEPC.

overall_design: We collected and performed RNA sequencing on tumors from five NEPC mice in the PBS group and five NEPC mice in the cisplatin treatment group to investigate the associated molecular changes.

first: Qi

last: Wang


title: Decoding transcriptional regulation in response to visible light in vertebrates

city: Eggenstein-Leopoldshafen

first: Alessandra

last: Boiti

address: Hermann-von-Helmholtz-Platz 1

institute: Karlsruhe Institute of Technology

summary: Sunlight influences various physiological processes, including circadian clock regulation and DNA repair via D-box enhancer elements. However, the broader transcriptional effects of visible light remain unclear. To investigate this, we compared light-mediated gene expression in zebrafish (Danio rerio) and the blind Somalian cavefish (Phreatichthys andruzzii), a species that evolved in perpetual darkness and lacks light-dependent circadian and DNA repair responses. We performed RNA sequencing of zebrafish and cavefish embryonic cell lines exposed to blue light (468 nm, for up to 6 hours), followed by gene ontology analysis and functional validation via bioinformatic, in vitro, and in vivo approaches. We revealed a light-dependent activation of a set of mitochondrial and heme metabolism genes via D-box enhancer elements. This transcriptional response was absent in cavefish cells. Further analysis revealed that while all zebrafish and cavefish PAR-bZip factors can activate the D-box, cavefish homologs exhibit diminished activity, suggesting an evolutionary reduction in light responsiveness. The D-box emerges as a key regulator of light-driven transcription in zebrafish, extending its role beyond circadian and DNA repair pathways to metabolic and mitochondrial processes. These findings provide insights into the evolution of light-sensing transcriptional mechanisms and lay the groundwork for future studies on their physiological implications.

sample_organism:
Danio rerio
Garra andruzzii

platform_organism:
Danio rerio
Garra andruzzii

overall_design: RNA-seq pofiling of wild type zebrafish (D. rerio) embryonic cell line (PAC-2) and Somalian cavefish (P. andruzzii) embryonic cell line (EPA) exposed to 0h, 1h, 3h, 6h of blue light, 3 replicates each.

first: Hanna

last: Weber

first: Daniela

last: Vallone

first: Nicholas

last: Foulkes


title: Unique Mycobacterium tuberculosis-specific blood immune signatures in sarcoidosis: implications for clinical diagnosis

city: La Jolla

first: Leila

middle: Y

last: Chihab

state: CA

address: 9420 Athena Circle

institute: La Jolla Institute for Immunology

summary: Sarcoidosis is a granulomatous systemic inflammatory disease predominantly affecting lungs. It shares histopathological, clinical and immune features with tuberculosis (TB). There are currently no diagnostic tests to formally identify sarcoidosis; clinicians first need to rule out the presence of other diseases, including TB. We characterized Mycobacterium tuberculosis (Mtb)-specific immune responses in blood of pulmonary sarcoidosis patients in comparison to active tuberculosis (ATB), Mtb-sensitized and non-sensitized healthy controls using flow cytometry and transcriptomics. We found that sarcoidosis was associated with i) a marked reduction in the frequency of antigen-reactive T cells in response to both Mtb peptides and Mtb lysate, ii) increased frequency of monocytes ex vivo and after in vitro stimulation, and iii) increased expression of phagocytic genes compared to Mtb-infected and healthy cohorts. Combination of Mtb-specific T cell and monocyte gene or flow cytometry signatures in Mtb-stimulated PBMC could efficiently distinguish sarcoidosis from ATB with high specificity and sensitivity, and to a lower extent from Mtb-sensitized and non-sensitized healthy controls. These biomarkers offer promising aspects for developing effective diagnostic tests for sarcoidosis, in particular for differential diagnosis from tuberculosis.

overall_design: Bulk RNA-seq analysis of sorted CD4 memory T cells and whole PBMC from 60 IGRA-,  48 Sarcoidosis, 59 IGRA+, and 57 ATB subjects following ex vivo stimulation with epitopes specific to Mycobacterium tuberculosis, DMSO control, or a polyclonal (CD3/CD28) positive control.

first: Leila Y

first: Gregory

last: Seumois

first: Bjoern

last: Peters

first: Julie G

last: Burel


title: Transcriptional profiling of the striatum from METH self-administered rats, including those after 12 and 24 hours of abstinence.

city: Daegu

first: Taekwon

last: Son

address: 61, Cheomdan-ro, Dong-gu

department: Korea Brain Bank

country: South Korea

institute: Korea Brain Research Institute

summary: This study aimed to identify transcriptome markers for diagnosis in each phase of METH self-administration and abstinence after METH self-administration, and to investigate the role of these markers. In addition, we aimed to identify transcriptomes involved in resistance to drug-seeking behavior in a group that did not show drug-seeking behavior after METH self-administration, and to elucidate their roles. We identified an impressive transcriptomes in the striatum of rats during repeated METH administration and abstinence phases.

overall_design: Gene expression profiling of the striatum in five groups of rats: 16 days of saline self-administration, 16 days of METH self-administration, 12-hour abstinence, 24-hour abstinence, and non-addicted, following 16 days of methamphetamine self-administration.

first: Won-Jun

last: Jang

first: Sooyeun

last: Lee

first: Chul-Ho

last: Jeong


title: The IL-33 and IL-4Rα blocking antibodies, itepekimab and dupilumab, modulate distinct and common inflammatory mediators in asthma - mouse data

city: Tarrytown

first: Kaitlyn

last: Gayvert

state: NY

address: 777 Old Saw Mill River Rd

department: Molecular Profiling & Data Science

institute: Regeneron Pharmaceuticals

summary: Biologics that target IL-4Ra or IL-33 pathways have demonstrated clinical efficacy in asthma and chronic obstructive pulmonary disease (COPD), highlighting the importance of IL-4, IL-13 and IL-33 in respiratory diseases. Despite this, there are limited studies that link preclinical models to human disease and evaluate disease biology in the setting of clinical trials. To address these gaps, we evaluated transcriptional, cellular and pathophysiological processes driven by IL-4/ IL-13 and IL-33 using human innate cells in vitro, a mouse model of airway inflammation and a Bronchial Allergen Challenge (BAC) in house dust mite (HDM)-sensitized individuals with mild asthma. Using the HDM mouse model of airway inflammation, we show that blockade of either IL-4Ra or IL-33 at the peak of type 2 (T2) inflammation leads to inhibition of airway inflammation and remodeling. While the combination of dupilumab and itepekimab was not additive, blockade of both IL-33 and IL-4Ra in a severe, late-phase mixed T1/T2 inflammation reduced all measured parameters. Consistent with some of these observations in mice, blocking either IL-33 or IL-4Ra in the context of T2 airway inflammation suppressed sputum gene expression in individuals with mild persistent asthma post-BAC. Overall, these results highlight that IL-33 and IL-4/IL-13 are key drivers of airway inflammation and remodeling and provide insight into the differences in targeting IL-4Ra or IL-33 pathways in asthma independently or in combination.

overall_design: All mouse experiments were conducted in compliance with protocols approved by the Institutional Animal Care and Use Committee of Regeneron Pharmaceuticals. Female, 8–12-week-old mice in a hybrid 129S6/C57BL/6 background were used for all studies. For assessing dupilumab, itepekimab and combo in mice, endogenous IL‐4Rα ectodomain, IL‐4 and IL-33 in mice were replaced with their corresponding human sequences. Mice were exposed to house dust mite extract (HDM) intranasally three times a week for either 4, 15 or 19 weeks to induce different phases of airway inflammation. The effect of IL-33 and IL-4R-alpha blockade was assessed using Itepekimab (anti-IL-33), dupilumab (anti-IL-4Ra) or a control antibody starting prophylactically at day -3, at the peak of type 2 inflammation at 4 weeks post HDM exposure or after the onset of chronic inflammation at 11 weeks post HDM through the end of the study.

first: Wei Keat

last: Lim

first: Seblewongel

last: Asrat


title: TSniffer: Unbiased de novo identification of RNA editing sites and quantification of editing activity in RNA-seq data [re-analysis]

first: Christian

last: Pfaller

relation:
Reanalysis of: GSM3167406
Reanalysis of: GSM3167414
Reanalysis of: GSM2474527
Reanalysis of: GSM2474528
Reanalysis of: GSM2474529
Reanalysis of: GSM3854153
Reanalysis of: GSM3854154
Reanalysis of: GSM3854155

sample_organism:
Homo sapiens
Mus musculus

overall_design:
We analyzed RNA-seq datasets from wild type (WT) and ADAR-deficient mouse and human samples, GTEx datasets of human brain, and of ferret PBMCs.

The re-analysis details are provided in the 'readme_re-analysis_details.txt', 'sample_to_processed_data_file.txt' files.

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The table below lists GEO accessions reused/reanalyzed for this study.
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The following re-analyzed samples are from GTEx data series (dbGaP phs000424):

Sample title SRA Experiment BioSample BioProject
GTEx, human brain, donor 1 SRX1153214 SAMN03878157 PRJNA75899
GTEx, human brain, donor 2 SRX1153642 SAMN03877474 PRJNA75899
GTEx, human brain, donor 3 SRX1155861 SAMN03878313 PRJNA75899

first: Maike

last: Herrmann

first: Yvonne

last: Krebs

first: Francisco

last: Acosta

first: Sebastian

last: Parusel

first: Oliver

last: Siering

first: Felix

last: Andres

first: Biruhalem

last: Taye

first: Csaba

last: Miskey


title: In situ multi-modal characterization of pancreatic cancer reveals tumor cell identity as a defining factor of the surrounding microenvironment [Spatial Transcriptomics]

city: Cambridge

first: Brian

last: Rabe

state: MA

address: 250 Water St

institute: Bristol Myers Squibb

summary: Pancreatic Ductal Adenocarcinoma (PDAC) is heterogeneous with low tumor purity, prominent microenvironment and complex architecture, which preclude identification of shared tumor intrinsic biology within and across patients. We overcame these challenges by applying spatial omics approaches – providing necessary resolution and context – to primary untreated PDAC tumors from 39 patients capturing 340K low-bulk and 530K single-cell spatial transcriptomes. We observe a spectrum of classical-to-basal tumor subtypes present within all patients. We identify a distinct population of proliferative tumor cells enriched for the DNA synthesis-condensation-mitosis transcriptional network suggesting this subset disproportionately contribute to tumor growth. Furthermore, we characterize the microenvironment surrounding each tumor subtype and observe that basal identity is contextually defined by collagen, hypoxic adaptation and fibroblast neighbors expressing activated stroma and interferon stimulated gene therapy resistance signatures. Lastly, leveraging orthogonal patient, cell and mouse data, we determine which aspects of PDAC biology are recapitulated in bulk datasets and reductionist models.

overall_design: PDAC tumors, resected following FOLFIRINOX neoadjuvant treatment, were FFPE embedded, and sectioned for spatial transcriptomic analysis using Visium for FFPE (human probeset v2)

first: Anna

last: Lyubetskaya

first: Andrew

middle: J

last: Kavran

first: Yulong

last: Bai

last: Fisher

first: Hannah

last: Pliner

first: Alba

last: Font-Tello

first: Anne

last: Lewin

first: Ruifeng

last: Hu

first: Alexandre

last: Alloy

first: Yelena

last: Cheng

first: Chao

last: Dai

first: Yunfan

last: Fan

first: Constance

last: Brett

first: Todd

first: Lauren

last: Giampapa

first: Sören

middle: R

last: Stahlschmidt

first: Fayaz

last: Seifuddin

first: Steven

last: Vasquez Grinnell

first: Daniel

last: Carrera

first: Carlos

last: Rios

first: Tom

last: Lila

first: Pradeep

last: Kar

first: Abhishek

last: Shukla

first: Rachael

last: Bashford-Rogers

first: Lara

last: Heij

first: Mike

last: Mason

first: Ryan

last: Golhar

first: Isaac

last: Neuhaus

first: Enas

last: Shah

first: Jimena

middle: T

last: Tinoco

first: Benjamin

last: Chen

first: Shivan

last: Sivakumar

first: Konstantinos

last: Mavrakis

first: Eugene

last: Drokhlyansky


title: The IL-33 and IL-4Rα blocking antibodies, itepekimab and dupilumab, modulate distinct and common inflammatory mediators in asthma - human mast cell and eosinophil data

first: Kaitlyn

last: Gayvert

overall_design: Human mast cells were differentiated in vitro from bone marrow-CD133+ cells as previously described. Briefly, bone marrow-CD133+ cells were cultured in StemSpan SFEM media (StemCell) in the presence of 50ng/mL IL-6 (PeproTech), 100ng/mL SCF (PeproTech) and 1ng/mL IL-3 (R&D Systems) for 3 weeks, followed by treatment with IL-6 and SCF for 4 more weeks. Purity of in vitro-generated mast cells was confirmed by CD117 and FceRI expression by flow cytometry and mast cell morphology was confirmed by cytospin preparations and May-Grünwald/Giemsa staining (Sigma). Human eosinophils were isolated from buffy coats using MACSxpress Eosinophil Isolation Kit (Miltenyi) and red blood cells were removed by MACSxpress Erythrocyte Depletion Kit (Miltenyi). Cell purity was confirmed by CD45, CD15 and Siglec-8 surface staining and analysis by flow cytometry. Purified eosinophils and mast cells were cultured in RPMI-1640 (Gibco) with 10% Fetal Bovine Serum (Life Technologies) and treated with IL-4, IL-13, or IL-33 (R&D Systems) at 100nM in 2-5 donors overnight (eosinophils) or 48hrs (mast cells) at 37°C. Cells were harvested and suspended in TRIzol (Life Technologies) for RNA extraction. Untreated mast cells and eosinophil samples were also collected as control.

first: Wei Keat

last: Lim

first: Seblewongel

last: Asrat


title: Urinary Extrecellular Vesicles miRNA Expression in Patients with Gitelman Syndrome: The Role of Hsa-let-7d-3p

city: Taipei City

first: MIN-HSIU

last: CHEN

address: No. 161, Sec. 6, Minquan E. Rd., Neihu Dist.

institute: National Defense Medical University

summary: Gitelman syndrome (GS) is a hereditary renal disorder caused by SLC12A3 mutations, resulting in salt-wasting and electrolyte imbalances. This study profiled miRNA expression in urinary extracellular vesicles (uEVs) and renal tissues from GS patients to explore the role of miRNA in renal tubular regulation. We aim to indetify the differnital expressed miRNA that may regulate renal transporters.

overall_design: Urine samples were collected from 23 genetically confirmed GS patients and 23 healthy controls for uEV isolation, and renal biopsy tissues were obtained from 3 GS patients. Total RNA was extracted from uEVs ( uEVs combined into 4 GS groups vs 4 healthy control groups) and renal tissues, and small RNA sequencing was performed using the Illumina NextSeq 550 platform.

first: Chih-Chien

last: Sung

first: Chao-Ting

first: Min-Hsiu

first: Shih-Hua

last: Lin

first: Hsin-Yi

last: Chang

first: Yi-Jwo

last: Lo

first: Kuan-Chieh

last: Peng

first: Che-Chung

last: Huang


title: The genome wide mapping of H3K4kme3, H3K27ac and H3K27me3 in Ctcf f/f and Ctcf Δ/Δ CALM-AF10 AML cells [CTCF RNA-seq]

city: Toyoake

first: Yoko

last: Kuroki

address: 1-98 Denngakugakubo Kutsukake-cho

institute: Fujita Health University

summary: CALM (Clathrin Assembly Lymphoid Myeloid Leukemia)-AF10, a fusion gene frequently observed in acute myeloid leukemia (AML), is caused by the t(10;11)(q13;q14) translocation, and is associated with poor prognosis. In this study, we demonstrate that the CCCTC-binding factor (CTCF) is crucial for both the initiation and maintenance of CALM-AF10-induced AML (CALM-AF10 AML). To investigate the role of CTCF in CALM-AF10 AML, we used hematopoietic stem and progenitor cells (HSPCs) from conditional knockout (KO) mice and immortalized them by introducing the CALM-AF10 fusion gene to generate CALM-AF10 AML models. Our in vivo experiments revealed that CTCF deficiency significantly prolonged the survival of CALM-AF10 AML mice. Similarly, in vitro analyses showed that CTCF KO inhibited the colony-forming ability of CALM-AF10 AML cells and induced differentiation into macrophage-like cells. RNA sequencing (RNA-seq) of CTCF KO cells identified that the most downregulated gene was Transglutaminase 2 (TGM2). Chromatin immunoprecipitation followed by sequencing (ChIP-seq) showed that increase in levels of trimethylation of histone H3K27 as well as decrease in levels of trimethylation of histone H3K4 and acetylation of histone H3K27 were observed at the transcription start site (TSS) of the Tgm2 gene after CTCF KO. Knocking down (KD) TGM2 using small hairpin RNA (shRNA) in both CALM-AF10 AML cells and the human leukemic cell line U937, which expresses the CALM-AF10 fusion gene, resulted in reduced colony-forming ability and cell proliferation, alongside differentiation into macrophage-like cells. These results mirrored those observed with CTCF KO. Furthermore, treatment with GK921, a TGM2 inhibitor, yielded similar effects. Taken together, our findings suggest that CTCF regulates the expression of TGM2 by altering histone modifications at its TSS, thereby contributing to the maintenance of the undifferentiated state in CALM-AF10 AML. Given the efficacy of TGM2 inhibitors, such as GK921, against CALM-AF10 AML, TGM2 represents a promising therapeutic target for this leukemia subtype.

overall_design: Conditional Ctcf knockout (cKO) mice were generated to investigate the role of CTCF in CALM-AF10-driven acute myeloid leukemia (AML). The leukemia cells purified from the bone marrow of the leukemia model were treated with 4-hydroxytamoxifen to knock out Ctcf.

first: Issay

last: Kitabayashi


title: The genome wide mapping of H3K4kme3, H3K27ac and H3K27me3 in Ctcf f/f and Ctcf Δ/Δ CALM-AF10 AML cells [Tgm2 RNA-seq]

overall_design: We established murine CALM-AF10 leukemia model. To investigate the role of Tgm2 in the leukemia cells expressing CALM-AF10, The leukemia cells purified from the bone marrow of the leukemia model were trasduced with shRNA against Tgm2 to knockdown the expression of  Tgm2.


title: Decoding the molecular complexity of lacrimal gland  governing corneal wound closure in vivo

city: Montpellier

first: Frederic

last: Michon

address: 80, rue Augustin Fliche

department: Institute for Neurosciences of Montpellier

institute: Inserm

summary: The cornea, the transparent outermost layer of the eye, possesses exceptional wound healing capabilities essential for vision preservation. The complexity of the corneal microenvironment is central to its rapid healing; however, the molecular mechanisms orchestrating this process remain poorly defined, limiting therapeutic advancements. Here, we elucidate the extensive remodeling of the corneal molecular landscape following physical injury. Multi-omics analyses—including transcriptomic, epitranscriptomic, and proteomic profiling—uncover significant induction of epithelial cell plasticity driving wound closure. Moreover, lacrimal gland ablation further suppresses Pax6 expression, highlighting its regulatory role. Our multi-omic approach uniquely reveals bilateral remodeling of the molecular environment, a phenomenon constrained by an intact tear film. Collectively, our findings identify novel molecular factors critical to corneal healing, significantly advancing the understanding of epithelial plasticity. These insights will facilitate the translation of cell plasticity research into innovative strategies for tissue and organ regeneration.

overall_design: We compared the transcriptomic signatures of murine corneas during wound healing

first: Kuony

last: Alison

first: Michon

last: Frederic


title: The genome wide mapping of H3K4kme3, H3K27ac and H3K27me3 in Ctcf f/f and Ctcf Δ/Δ CALM-AF10 AML cells [ChiP-seq]

overall_design: Chromatin immunoprecipitation DNA sequencing (ChIP-Seq) of genome wide H3K4 and H3K27 trimethylation as well as H3K27 acetylation in Ctcf f/f and Ctcf Δ/Δ CALM-AF10 AML cells


title: ChIP-seq analysis for STAT3 targets downstream of LIF signaling in liver ischemia-reperfusion injury

city: Wuhan

first: Ran

last: Liu

state: Hubei

address: 1277 Jiefang avenue

institute: Union hospital, Tongji medical college, Huazhong university of science and technology

summary: LIF is a pleotropic cytokine and its role in liver ischemia-reperfusion injury (IRI) remains unexplored. Utilizing wildtype (WT) and myeloid cell-specific knockout (KO) mice, we demonstrate that the transcription of LIF is activated in myeloid cells and promotes LIFR-induced STAT3 activation in hepatocytes during liver IRI. To understand the downstream targets of STAT3, we performed ChIP-seq analysis.

overall_design: WT and KO mice underwent 1 h ischemia/6 h reperfusion injury and liver samples were collected. The samples were then analyzed with STAT3 ChIP-seq.

first: Liu

last: Ran

first: Gu

last: Jinyang


title: Metabolic reprogramming by PRDM16 drives cytarabine resistance in acute myeloid leukemia

city: Yokohama

first: Junji

last: Ikeda

state: Kanagawa

address: 3-9, Fukuura, Kanazawa-ku

department: Pediatrics

institute: Yokohama City University

summary: Acute myeloid leukemia (AML) patients with high PRDM16 expression frequently experience induction failure and have a poor prognosis. However, the molecular mechanisms underlying these clinical features are elusive. We found that murine AML cells transformed by MLL::AF9 fusion and oncogenic short-isoform Prdm16 overexpression (hereafter, MF9/sPrdm16) exhibited resistance to cytarabine (AraC), but not to anthracycline, both in vitro and in vivo. Intriguingly, MF9/sPrdm16 cells displayed a gene expression signature of high oxidative phosphorylation (OxPHOS) and increased mitochondrial respiration. The inhibition of mitochondrial respiration with metformin or tigecycline abrogated AraC resistance in MF9/sPrdm16 cells via an energetic shift toward low OxPHOS status. Furthermore, sPrdm16 upregulated c-Myc and the glutamine transporter Slc1a5, activating TCA cycle and glutaminolysis. Of note, both OxPHOS and MYC-target gene signatures were significantly enriched in AML patient samples with high PRDM16 expression. Together, we showed that PRDM16 overexpression activates mitochondrial respiration through metabolic reprogramming via c-MYC-SLC1A5-Glutaminolysis axis, thereby conferring AraC resistance on AML cells. These results suggest that targeting mitochondrial respiration might be a novel treatment strategy to overcome chemoresistance in AML patients with high PRDM16 expression.

overall_design: We first transduced murine bone marrow cells with retroviral MLL::AF9 vector. Subsequently, we transduced murine normal bone marrow cells or MLL::AF9 AML cells with either mock or sPrdm16-expressing retroviral vector. To explore molecular basis of chemoresistance driven by sPrdm16 expression, we performed RNA-seq using these cells.

first: Hiroyoshi

last: Kunimoto


title: Comprehensive evaluation on the effect of spatial fractionation on anti-tumor immune response: the case of proton minibeam radiotherapy for glioblastoma.

city: Orsay

first: Lorea

last: Iturri

address: Rue Henri Becquerel

institute: Institut Curie

summary: Treating radioresistant tumors like glioblastoma multiforme (GBM) remains a challenge exacerbated by their immunosuppressive nature. Radiation therapy has an immunomodulatory (immunosuppressive or immunostimulatory) role.  The nature of the effects would depend on the total dose, dose per fraction, dose delivery method and treatment length. It is well-known that conventional fractionation schemes (2 Gy per fraction during several weeks) are mainly immunosuppressive and that hypofractionation tips the balance towards immune stimulation. However, the use of hypofractionation is restricted in bulky tumours, i.e. gliomas, due to the high risk of toxicity. Therefore, finding new strategies leading to more favourable immune responses while reducing normal tissue toxicities could be a game-changer. This is the case of proton minibeam radiation therapy (pMBRT). However, its immunomodulatory effects are not fully understood. To explore this, we conducted an in-depth characterization of the immune response to a curative dose of pMBRT in a preclinical orthotopic rat model of glioblastoma. Our findings revealed a close association between pMBRT and the immune response. pMBRT increased lymphocyte density in tumors more effectively than conventional proton therapy. Single-cell transcriptomics identified several immune cell types and unique transcriptional changes in tumor immune cells post-pMBRT, including increased antibody production, chemotactic cytokine expression, and interferon responses. These results underscore the critical role of adaptive immunity, specifically T cells, in pMBRT's mechanism. The potential of pMBRT to trigger an anti-tumor immune response in a single radiotherapy session with minimal damage to healthy tissue makes it a promising candidate for future clinical trials and radio-immunotherapy combinations.

overall_design: Rat immune cells infiltrated in RG2-[D74] glioblastoma were isolated for analysis after cranial irradiation treatment with conventional proton therapy (Conv-PT) or pMBRT

first: Miriam

last: Riquelme-Perez

first: Pierre-Emannuel

last: Bonté

first: Sarah

last: Potiron

first: Christel

last: Goudot

first: Marjorie

last: Juchaux

first: Elise

last: Brisebard

first: Cristèle

last: Gilbert

first: Julie

last: Espenon

first: Ramón

last: Ortiz

first: Annalisa

last: Patriarca

first: Ludovic

last: de Marzi

first: Sebastián

last: Amigorena

first: Yolanda

last: Prezado


title: Single cell RNA sequencing data of CD45+ colonic cells derived from wild-type and VISTA-KO mice after oral treatment of dextran sulfate sodium.

city: Guangzhou

first: Binfeng

last: Chen

address: 58 Zhongshan Second Road

institute: Department of Rheumatology, The First Affiliated Hospital, Sun Yat-sen University

summary: To evaluate VISTA's function upon immune response in colitic mice,  colonic immune cells from wild-type and VISTA-KO mice with dextran sulfate sodium induced colitis were used for single cell RNA sequencing.

overall_design: We isolated colonic cells from wild-type and VISTA-KO mice treated with dextran sulfate sodium. The CD45+ immune cells were further isolated through flowcytometry sorting procedure. The single cell RNA sequencing was then applied to analyse the role of VISTA upon immune response in colitic mice. Sample tags were used for wild-type or VISTA-KO annotation since all immune cells were pooled into one sample for sequencing process.


title: Clonally expanded effector CD4+ cytotoxic T lymphocytes are associated with severe neurological adverse events after immune checkpoint inhibitor therapy

city: Berlin

first: Ambre

middle: Manon

last: Giguelay

state: Berlin

address: Hannoversche Str. 28

department: Cell Biology/Single Cells

institute: Berlin Institute for Health

summary: Immune checkpoint inhibitor (ICI) therapies present a pillar of modern cancer therapy but can cause severe and potentially fatal neurological immune-related adverse events (n-irAEs). Here, we performed single-cell RNA sequencing and T cell receptor profiling of PBMCs of a cohort of 17 cancer patients receiving ICI therapy. Our data suggest alterations in regulatory T cell frequencies and B cell states, and a significant enrichment of clonally expanded CD4+ cytotoxic T lymphocytes (CD4+ CTLs) with an effector gene expression profile in n-irAE patients.

overall_design:
5'scRNAseq and TCR-seq analysis of PBMCs from cancer patients with or without neurological immune adverse events (n-irAEs), before or after immume checkpoint inhibition therapy

***************************************************************
Submitter states that missing raw data are being made available for controlled access in EGA.
***************************************************************

first: Patrick

last: Maschmeyer

first: Leif

last: Ludwig


title: TGF-b signaling in infarct fibroblasts prevents adipocyte conversion through Smad-independent mechanisms

city: NYC

first: Izabela

last: Tuleta

address: 1545 Rhinelander Ave, Apt. 3K

institute: Albert Einstein College of Medicine

summary: The adult mammalian myocardium has very limited endogenous regenerative capacity; thus, repair of the heart after myocardial infarction is dependent on timely activation of matrix-secreting reparative fibroblasts and myofibroblasts that deposit a collagenous matrix network, thus replacing dead cardiomyocytes and protecting the heart from catastrophic rupture or excessive dilation. Infarct fibroblasts undergo dynamic phenotypic transitions critical for the reparative response. During the proliferative phase of cardiac repair, the abundant myocardial fibroblast-like cells undergo myofibroblast conversion, expressing contractile proteins such as alpha-smooth muscle actin, and secrete large amounts of extracellular matrix proteins. As the scar matures, myofibroblasts become de-activated and convert to matrifibrocytes, fibroblast-like cells that lack expression of myofibroblast markers, such as  and periostin and express genes encoding specialized matricellular and tendon proteins. Cardiac repair is dependent on retention of fibroblast identity and cell specification throughout the healing response. Defects in the reparative cellular response, resulting in infiltration of the infarct with fatty or calcified tissue, have been reported in both experimental models of and in human patients with myocardial infarction. However, the cellular mechanisms responsible for these perturbations remain enigmatic. In the current study, we discovered that disruption of TGF-b signaling specifically in infarct fibroblasts triggers their conversion to adipocytes, resulting in extensive infiltration of the scar with adipose tissue.

overall_design: To examine the effects of fibroblast-specific TbR2 loss on the transcriptional profile of infarct fibroblasts, we harvested PDGFRα+ fibroblasts from FTbR2 KO and TbR2 fl/fl infarcts 7 days after coronary occlusion and we performed RNA-seq. 4 samples in each group.

first: Harikrishnan

last: Venugopal

first: Nikolaos

last: Frangogiannis


title: Effect of medical treatment on malignant transformation to clear cell carcinoma in endometriosis patients: A comparative study on gene expression using next generation sequencing (NGS)

city: Seoul

first: YunSoo

last: Chung

address: Yonseiro 50-1, Yonsei University College of Medicine

department: OBGY

institute: Severance Hospital

summary: The cause of endometriosis remains unknown, but the most compelling explanation involves the growth of endometrial glands and stroma outside the uterine cavity. Approximately 10% of women of reproductive age are affected by endometriosis, and those with endometriosis have a 50% higher risk of developing ovarian cancers compared to those without the condition. The possibility of endometriosis transforming into ovarian clear cell carcinoma (OCCC) has been suggested, and molecular-level analyses are progressing to verify this hypothesis. Recent emphasis on the importance of long-term dienogest treatment for endometriosis is due to the fact that ovarian cyst surgery decreases ovarian reserve. Medical treatment is also important to reduce the recurrence rate. This study aims to perform a molecular-level analysis of dienogest on endometriotic ovarian tissue at the molecular level. This could enhance current treatments for endometriosis and potentially delay its malignant transformation.

overall_design: To evaluate gene expression in endometriosis without any treatment before surgery, and endometriosis with dienogest treatment before surgery were compared. Gene expression profiling, particularly RNA sequencing, will be conducted. Differentially expressed genes (DEGs) will be identified to pinpoint target genes associated with an increased likelihood of OCCC development from endometriosis.

first: Yun Soo

first: Jung Eun

last: Sim

first: Jin Kyung

last: Baek

first: Euna

last: Choi

first: Heeyon

last: Kim

first: Yong Jae

last: Lee

first: Bo Hyon

last: Yun

first: Seok Kyo

last: Seo


title: A spatially resolved atlas of gastric cancer characterises a lymphocyte aggregated region [bulk RNA-seq]

city: Beijing

first: Zemin

last: Zhang

address: No.5 Yiheyuan Road, Haidian District

institute: Peking University

summary: The tumour microenvironment (TME) is a focal point in cancer immunotherapy: its cellular composition and spatial organisation, especially the distribution of lymphocytes, can affect the clinical outcomes of cancer patients. In addition, the function of a cell differs depending on its spatial location and interaction with neighbouring cells. Here, by integrating single-cell transcriptomics with spatial transcriptomics, we survey how the spatial distribution of different cell types varies across diverse histological regions of gastric cancer. Notably, tertiary lymphoid structures (TLSs), a tissue architecture harbouring lymphocytes more than any other region within the TME, possess great potential in modulating anti-tumorigenic immunity by elevating an array of genes (FDCSP and CCL19) principally involved in lymphocyte recruitment and activation.  Our findings advance the understanding of TLSs in contributing to anti-tumorigenic immunity in a spatially resolved context, which could be further leveraged as a predictive marker for immunotherapy response.

overall_design:
We built a high-resolution single-cell transcriptomic atlas by sequencing cells derived from four different tissue sources, including surgically resected tumour (denoted as T), histologically normal adjacent tissue (N), lymphoid node (L), and peripheral blood (P), from a cohort of 27 treatment-naive donors with GC, covering two clinical phenotypes — subtype (diffuse, indeterminate, and intestinal) and stage (I, II, and III). In addition, 19 tumour samples were assayed by 33 ST sections, covering three categories of sampling locations in the tumour (core, in-between, and edge).
After dichotomising tumour samples into Groups A and B based on their cellular composition using ST, we performed RNA-seq on the remaining tumour samples to verify the findings revealed by ST.
*** Submitters state that they are not permitted to submit raw data (to GEO) by Ministry of Science and Technology, China***

first: Sen

last: Gao


title: A spatially resolved atlas of gastric cancer characterises a lymphocyte aggregated region [Spatial Transcriptomics]

overall_design:
Nineteen tumour samples were assayed by 33 ST sections, covering three categories of sampling locations in the tumour (core, in-between, and edge). In addition, we assayed 39 replicates from the main study cohort using ST.
*** Submitters state that they are not permitted to submit raw data (to GEO) by Ministry of Science and Technology, China***


title: A spatially resolved atlas of gastric cancer characterises a lymphocyte aggregated region [scRNA-seq]

overall_design:
We built a high-resolution single-cell transcriptomic atlas by sequencing cells derived from four different tissue sources, including surgically resected tumour (denoted as T), histologically normal adjacent tissue (N), lymphoid node (L), and peripheral blood (P), from a cohort of 27 treatment-naive donors with GC, covering two clinical phenotypes — subtype (diffuse, indeterminate, and intestinal) and stage (I, II, and III).
*** Submitters state that they are not permitted to submit raw data (to GEO) by Ministry of Science and Technology, China***


title: Single-nucleus multiomic profiling of mouse substantia nigra across age

city: San Diego

first: Kangli

last: Wang

address: 9500 Gilman Drive

institute: University of California San Diego

summary: We used single-nucleus multiomic sequencing (snRNA-seq + snATAC-seq) to analyze the dynamic transcriptional regulation in mouse substantia nigra cell types across aging.

overall_design: Chromium Single-Cell Multiome ATAC + Gene Expression for mouse substantia nigra in four age stages of 2, 6, 12, and 18 months.

first: Allen

first: Bing

last: Ren