title: TREM2+ Macrophage Infiltration Underlies Breast Cancer Lung Metastasis due to Paclitaxel Treatment [ATAC-seq]

first: Yuqi

last: Xing

state: Beijing

address: Peking University

institute: Peking University

summary: Metastasis is a major cause of breast-cancer-related death and frequently occurs following paclitaxel neoadjuvant chemotherapy failure. Tumor microenvironment contributes to metastasis, while the role of specific host cells in lung metastases induced by paclitaxel (PTX) treatment remains poorly understood. Here, we demonstrate that PTX neoadjuvant chemotherapy promotes triggering receptor expressed on myeloid cells-2 (TREM2)-positive macrophage infiltration in the breast cancer tissues of patients. Meanwhile, we also show that more TREM2-positive macrophage infiltrates in breast cancer tissues of patients with lung -metastasized. Genetic TREM2 deficiency decreases breast cancer lung metastases induced by PTX treatment in vivo, suggesting that TREM2-positive macrophages are essential for PTX-promoting lung metastasis of breast cancer. We further reveal that PTX promotes tumor cell secretion of fibroblast growth factor 2 (FGF2), triggering TREM2 transcription via upregulating its transcriptional factor early growth response-1 (EGR1) in macrophages. Increased TREM2 activates epithelial-mesenchymal transition (EMT)-related cytokine secretion in macrophages, inducing tumor cell lung metastases. Targeting TREM2 significantly suppressed lung metastasis in breast-cancer-bearing mice. Our findings establish that tumor-cell-derived FGF2 induced by paclitaxel treatment upregulates TREM2 in myeloid macrophages, which in turn promotes the EMT of neighboring tumor cells through cytokine secretion. Our results highlight TREM2 as a potential therapeutic target to mitigate lung metastasis due to PTX treatment.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: ATAC-seq of BT549-D, BT549-P, BT549-PB, BT549-NP, BMDM-D, BMDM-P, BMDM-PB, BMDM-NP were harvested and analyzed

first: Hongquan

last: Zhang

first: Jun

last: Zhan


title: TET-dependent signaling of β-cell underlies intrauterine hyperglycemia-induced glucose intolerance in offspring [scRNA-seq]

status: Public on Dec 31 2025

city: Shanghai

first: Jiahang

last: Mo

address: No.131 Dong'an Road

department: Institute of Reproduction and Development

country: China

institute: Obstetrics and gynecology Hospital of Fudan University

type: Expression profiling by high throughput sequencing

summary: Epidemiologically, gestational diabetes mellitus (GDM) increases offspring’s diabetes risk. Intrauterine hyperglycemia (IHG) is a typical characteristic of GDM, impairing offspring’s glucose tolerance and insulin secretion, but the underlying mechanisms remain unclear. Here, we found IHG downregulates DNA demethylases Tet2/3 in fetal pancreatic islets. Pancreas-specific Tet2/3 double knockout (DKO) recapitulates the IHG effects. scRNA-seq analysis shows IHG or DKO downregulates β-cell signature while upregulating δ-cell signature.

overall_design: To investigate the mechanisms of impairing offspring’s glucose tolerance and insulin secretion in IHG offspring. Pancreatic islets from Tet2/3 double knockout mouse and IHG offspring was analyzed using scRNA-seq.


title: Visualize and quantify rDNA instabilities in mammalian cells and mouse models

city: New York

first: Shan

last: Zha

state: NY

address: 1130 Saint Nicholas Ave.

country: USA

institute: Columbia University

summary: Ribosomal DNA (rDNA) encodes the 18S, 5.8S, and 28S RNA components of ribosomes, accounting for up to 70% of cellular transcription activities. Despite its central role in cellular function and known association with cancer and aging, quantifying rDNA instability in mammals remains challenging due to its repetitive organization and inherent heterogeneity. In this study, we developed murine rDNA FISH probes and genomic tools tailored for laboratory strains. The results confirmed the locations of rDNA clusters, uncovered marked inter-/intra-strain and inter-cell heterogeneity at rDNA loci in inbred mice and unstressed cells, and identified sources of spontaneous, replication-associated DNA double-strand breaks within rDNA. Focused mini-screens using DNA repair-deficient cells uncovered distinct contributions of homologous recombination, non-homologous end-joining, and the ATM-mediated DNA damage response in safeguarding rDNA stability. Together, these findings and tools provide a robust framework for assessing rDNA instability in mammalian cells and animal models with utility in aging and cancer research.

overall_design: End-Seq of purified and activated (24 or 28 h with anti-CD40 and IL4) (S phase) or quiescent (G1 phase) CD43–splenic B cells to map replication-dependent single-ended DNA DSB in primary cells, without external DNA damage.

first: Xiaolu

last: Zhu

first: Demis

last: Menolfi

first: Brian

middle: J

last: Lee


title: Asymmetric Division in a Two-Cell-Like State Rejuvenates Embryonic Stem Cells

city: Guangzhou

first: Man

state: Guangdong

address: No.9, XingDaoHuanBei Road, Guangzhou International Bio-island, Haizhu District

department: Department of Basic Research

institute: Guangzhou Laboratory

summary: An intriguing question in biology is whether all cells age. Embryonic stem cells (ESCs) stand out as rare normal cells capable of indefinite in vitro passage. However, it remains unclear how ESC lineage immortality is achieved and whether individual ESCs are immortal. Using long term live-cell imaging to follow fates of single ESCs, we show here that lineage renewal of ESCs can be attributed to a sporadic state characterized by the expression of markers found in two-cell embryos. During this state, cells undergo asymmetric divisions, giving rise to one dying branch, and one that reverts to the pluripotent state. Importantly, the latter lineage exhibits signs of rejuvenation, including reduced DNA damage and enhanced chimeric efficiency. These findings underscore the crucial role of asymmetric cell division in maintaining the long-term health of the ESC lineage against mounting damage within individual cells.

overall_design: To trace the fate of 2C-like cells, we established a mouse embryonic stem (mES) cell line expressing a MERVL promoter driven GFP reporter (MERVL::GFP) to mark the 2C-like state, and H2B-mIFP to track cells. The MERVL::GFP signal strongly correlates with endogenous MERVL-Gag protein staining.

first: Mingwei

last: Min


title: Differential regulation of genes in response to exogenous ganglioside GM2 treatment in Cancer cells.

city: Kolkata

first: Kaushik

last: Biswas

state: WB

address: Block EN-80 Sector V, Salt Lake, College More

department: Department of Biological Sciences

country: India

institute: Bose Institute

summary: Gangliosides have been implicated in various diseases including but not limited to cancer. Overexpression of one of these gangliosides, namely ganglioside GM2 has been associated with several cancers like Glioblastoma (GBM), Renal Cell Carcinoma (RCC) and several others. Despite the definite role of GM2 in tumor-induced host immune suppression has been extensively studied, not much was known regarding its involvement in the alteration of tumor cell behaviour. Our laboratory established that ganglioside GM2 plays a pivotal role in promoting migration and invasion of cancer cells and in inducing epithelial-mesenchymal transition (EMT) primarily by acquiring anoikis resistance and anchorage independence. Our initial data indicates that GM2's pro-tumorigenic function may be elaborated through modulation of a diverse, yet distinct signaling pathways. To address this, we undertook this task of mapping the differential regulation of genes in response to exogenous GM2 treatment in HeLa cells.

overall_design: RNA-seq profiling of GM2 treated (1hour treatment in serum starved condition) and non treated condition (only serum starved condition) in HeLa wild type cells.

first: Barun

last: Mahata

first: Elora

last: Khamrui

first: Aishwarya

last: Ray

first: Arijita

last: Sarkar

first: Zhumur

last: Ghosh


title: The microbial tryptophan metabolite indole acts on the gastrointestinal tract to improve glucose homeostasis in a mouse model of diabetes by enhancing GLP-1 secretion and L cell differentiation

city: Cambridge

middle: Yee Hong

last: Lam

address: Box 289 Addenbookes Hospital, Hills Road

department: Metabolic Research Laboratories

country: United Kingdom

institute: University of Cambridge

summary: Aims/hypothesis: Growing evidence implicates gut microbiota-derived metabolites in metabolic homeostasis. Indole, a microbial tryptophan metabolite, has been reported to enhance Glucagon-like peptide-1 (GLP-1) secretion in vitro, and its derivatives have been inversely associated with risk of type 2 diabetes (T2D). We hypothesised that indole acts via the gastrointestinal tract to modulate glucose homeostasis, and aimed to test this hypothesis using in vitro and in vivo models. Methods: The acute effects of indole on GLP-1 secretion in vitro, and on glucose tolerance and hormone secretion in mice, were determined. Subsequently, the effects of indole on intestinal epithelial cell fate and L-cell differentiation in murine ileal organoids and in vivo were studied. Finally, the utility of chronic indole administration in a murine model of T2D was explored. Results: Indole stimulated in vitro GLP-1 secretion in a concentration-dependent manner, and improved acute glucose control in vivo. Additionally, we demonstrate that indole drives enteroendocrine L-cell differentiation in murine ileal organoids, resulting in increased L-cell density and longer-term glucoregulatory benefits in vivo. Finally, sub-chronic indole administration improved glucose tolerance and insulin sensitivity in diabetic mice. Conclusions/interpretation: Our findings identify indole as an anti-diabetic molecule that acts on the gut, and raise the possibility of incorporating indole into nutraceutical supplements to aid in the treatment or prevention of T2D. This highlights the importance of gut microbiota-derived metabolites in metabolic health and opens new avenues for developing novel strategies to combat T2D.

overall_design: RNASeq profiling of mouse liver tissue after subchronic treatment with either Indole (20mg/kg) or water (vehicle control)

first: Phyllis

last: Phuah

first: Kevin

middle: G

last: Murphy

first: Giles

middle: S

last: Yeo

middle: Y


title: FOXF2 regulates pericyte function required for pericyte-endothelial signaling during neonatal hyperoxic lung injury [scRNA-seq]

city: Chengdu

first: Hua

last: He

state: Sichuan

address: 2222 Xinchuan Rd

institute: West China Second University Hospital Sichuan University

summary: Pulmonary vascular development is essential for alveolarization, and disruption of this process contributes to bronchopulmonary dysplasia (BPD) pulmonary pathology. Proper vascular development requires an orchestration of many cell types within the lung. However, the mechanisms by which pericytes support the endothelium in the postnatal lung remain poorly understood. Here, we identify FOXF2 as a critical transcription factor that governs pericyte maturation and function during postnatal lung development and regeneration. FOXF2 expression in pericytes increases postnatally and is selectively downregulated following neonatal hyperoxic injury. Pdgfrb-CreER mediated Foxf2 deletion in pericytes leads to pericyte hyperplasia, impaired migration, reduced expression of angiogenic factors such as ANGPTL4, and exacerbated alveolar simplification in a neonatal murine model of BPD. Transcriptomic and genomic studies demonstrate that FOXF2 maintains chromatin accessibility at pro-angiogenic loci and modulates paracrine signaling essential for endothelial regeneration. Loss of FOXF2 disrupts pericyte–endothelial crosstalk, impairing angiogenesis and alveolar repair during injury. Our study identifies FOXF2 as a central transcriptional regulator of pericyte-driven vascular niche function in the neonatal lung and underscores the pathogenic role of dysfunctional pericytes in BPD.

overall_design: Single-cell RNA sequencing (scRNA-seq) libraries were generated from CD45⁻ cells sorted from control and Foxf2 cKO lungs using the Chromium Next GEM Single Cell 5' Reagent Kit v2 (10x Genomics).


title: A distinct mechanism governs translation initiation and its regulation in Staphylococcus aureus [Ribo-Seq]

city: Strasbourg

first: Stefano

last: Marzi

address: 2 allée Konrad Roentgen

department: UPR9002 - IBMC

country: France

institute: CNRS

summary: Retapamulin-assisted ribosome profiling (Ribo-Ret) reveals translation initiation sites at a translatome-wide scale. Here we employed Ribo-Ret in S. aureus, utilizing either MNase or RNAse 1 for ribosomal protected footprint (RPF) generation, significanlty improving the obtainable resolution at translation start sites with the latter. The improved resolution helped to identify precise start codon selection, revealing distinct features of the S. aureus translation initiation mechanism as well as multiple unrecognized small open reading frames (sORFs). Furthermore, we identified novel regulators of the translation initiation step in this major human pathogen.

overall_design: For the MNase as well as the RNase 1 Ribo-Ret experiments, two biological replicates were analyzed for Retapamulin-treated and untreated samples. These samples were processed and analyzed by our method for ribosome profiling in S. aureus.

first: Maximilian

middle: P

last: Kohl

first: Roberto

last: Bahena-Ceron

first: Béatrice

last: Chane-Woon-Ming

first: Maria

last: Kompatscher

first: Matthias

last: Erlacher

first: Pascale

last: Romby

first: Bruno

last: Klaholz


title: Unravelling the tumorigenesis mechanisms of oncocytic cell tumors: discoveries from a comparative omics studies

city: Vizela

first: Marta

middle: Patrícia

last: Ferreira

state: Braga

address: Rua da junuqeira, Santo Adrião

country: Portugal

summary: Transcriptome analysis of  thyroid tumors from frozen tissue sections.

overall_design: We performed an extensive comparative analysis of transcriptomic between oncocytic cell tumors (5 oncocytic adenoma-OA and 7 oncocytic carcinoma -OCA) and mitochondrion-rich neoplasms (2 oncocytic subtype of papillary thyroid carcinoma-O-PTC and 4 low-risk neoplasms with oncocytic morphology), irrespective of their biological behavior. Our focus was to explore molecular distinctions within these two tumor categories characterized by oncocytic morphology.

first: Sule

last: Canberk

first: Luisa

last: Pereira

first: Carla

last: Oliveira

first: Paula

last: Soares

first: Valdemar

last: Máximo


title: Finding Sorafenib-Responding Signature in Hepatocellular Carcinoma (HCC)

city: Houston

first: Han

last: Liang

address: 1515 Holcombe Blvd

institute: The University of Texas MD Anderson Cancer Center

summary: Sorafenib has been a cornerstone in hepatocellular carcinoma (HCC) therapy; however, its efficacy is limited, and identifying patients that will respond to sorafenib is challenging.  Gene expression data from 33 HCC tumors treated with sorafenib were analyzed to construct a prediction model aimed at identifying patients with greater benefit from sorafenib treatment. The analysis of transcriptome data revealed a 50-gene signature, KUSS50 (Korea University Sorafenib Signature with 50 genes), that exhibited high predictive power in identifying patients responded to sorafenib treatment in a training cohort. Extensive validation across 2 independent cohorts (IMbrave150 and BIOSTORM) given sorafenib demonstrated KUSS50's high specificity in predicting sorafenib response. Genomic analyses identified distinct molecular characteristics linked with KUSS50 subtypes, including an increased mutation rate and activation of ferroptosis, suggesting increased baseline ferroptotic activity in HCCs, which may sensitize them to sorafenib. The benefit subtype also overlapped with those in previously defined genomic HCC subtypes associated with stemness and aggressiveness. Conversely, the non-benefit subtype correlated with -catenin mutations and increased tumor purity, underscoring the biological significance of the signature. In conclusion,  KUSS50 is a clinically actionable biomarker for optimizing HCC patient selection for treatment with sorafenib, providing an opportunity to improve outcomes. Further exploration of KUSS50's underlying biology, particularly the involvement of ferroptosis in sorafenib sensitivity, could provide additional therapeutic insights.

overall_design: All patients underwent liver biopsy analysis prior to sorafenib use, and total RNA was obtained from their formalin-fixed, paraffin-embedded tissue blocks. Total RNA was extracted from slides containing tissue sections from these blocks using a Purigen Biosystems Ionic Purification System, and the DV200 values (representing the percentage of fragments >200 nucleotides) exceeded 15%. mRNA expression data for HCCs in the study patients were subsequently generated on the Illumina NovaSeq 6000 platform, employing S4-xp-200 lanes with a sequencing depth of 50 million reads per sample. The quality of the raw reads was checked using FastQC (v0.11.5) and summarized using MultiQC (v1.7). FASTQ files were mapped to the human reference genome (GRCh38) using STAR (v2.7.10a), and gene expression level was quantified using RSEM (v1.3.3) with default parameter settings.

first: Sun Young

last: Yim

first: Yitao

last: Tang

first: Ji Hoon

last: Kim

first: Ju-Seog

last: Lee


title: Narrow-band ultraviolet B induces peripheral regulatory T cells to exert antigen-specific immune suppression [RNA-seq]

city: Taipei

first: Yungling

middle: Leo

address: Sec. 2, Academia Rd.

department: Institute of Biomedical Sciences

country: Taiwan

institute: Academia Sinica

summary: Narrow-band ultraviolet B (UVB) is a commonly used therapy for autoimmune diseases. While alloantigen immunization combined with NB-UVB has been shown to induce antigen-specific regulatory T cells (Tregs), the underlying mechanism remains elusive. We used Treg RNA-seq from psoriasis-like mice model to investigate differentially expressed genes under UVB treatemnt.

overall_design: The backs of mice were shaved before initiation of psoriasiform dermatitis. Aldara treatment was performed by daily applying 60 mg Aldara cream containing 5% imiquimod (IMQ) on the backs of mice. The mice were exposed to NB-UVB every other day for 3 times. The dorsal skin of mice presented erythema and scaling and the psoriasis-like dermatitis was in remission when mice receiving NB-UVB irradiation. Treg cells were isolated from mice skin with or without UVB treatment for RNA-seq.

first: Chun-Hao

last: Lu


title: Narrow-band ultraviolet B induces peripheral regulatory T cells to exert antigen-specific immune suppression [scRNA-seq]

summary: Narrow-band ultraviolet B (UVB) is a commonly used therapy for autoimmune diseases. While alloantigen immunization combined with NB-UVB has been shown to induce antigen-specific regulatory T cells (Tregs), the underlying mechanism remains elusive. Single-cell RNA sequencing analysis of patient PBMCs showed that UVB suppressed negative regulators of Treg development, thereby promoting CD4+ T differentiation into Tregs.

overall_design: We collected blood samples from psoriasis patients before and after UVB treatmet. Cells were isolated from whole blood to preform single-cell RNA sequencing (scRNA-seq).


title: Characterization of the global bovine microRNAome of peripheral blood mononuclear cells isolated from Mycobacterium bovis exposed cattle

city: Edinburgh

first: Elisabeth

middle: Margaretha Diana Louise

last: van der Heijden

state: Midlothian

address: Easter Bush Campus

department: Division of Immunology

institute: The Roslin Institute, The University of Edinburgh

type: Non-coding RNA profiling by high throughput sequencing

summary: Accurate diagnostics are urgently needed for bovine TB in cattle – an economically devastating disease posing a re-emerging threat to veterinary and public health worldwide. MicroRNAs, post-transcriptional regulators of gene expression, are involved in a wide range of biological processes and immunological pathways, and have emerged as promising diagnostic biomarkers for numerous diseases. In human TB, microRNAs have been widely studied, but not much is currently known about their role in bovine TB. The aim of this study was to investigate the diagnostic potential of microRNAs in bTB through comprehensive analysis of their expression profiles in disparate states of M. bovis (BCG) exposure. We used a state-of-the-art RNA sequencing approach to characterize the global microRNAome of peripheral blood mononuclear cells isolated from cattle that were either unvaccinated, BCG-vaccinated, unprotected or protected. A total of 468 microRNAs were detected across all samples, none of which were uniquely expressed in any group. Significant differential expression between groups was observed for 3 microRNAs (bta-miR-6122-3p, bta-miR-3533 and bta-miR29b) in various comparisons. Subsequent target analysis of bta-miR-29b, a candidate biomarker of disease in human tuberculosis, revealed that several genes (ACVR2A, PIK3R1, TBX21, TGFBR1 and TGFBR2) involved in a number of relevant T-cell and immune signaling pathways, were amongst the predicted targets. Overall, this study provides evidence that microRNAs could be a promising novel biomarker for bovine TB diagnostics.

overall_design: PBMC were isolated from whole blood of cattle in previous study (doi: 10.3389/fimmu.2020.588180). The present study compared two groups of animals: unvaccinated controls and vaccinated with live M. bovis BCG (Danish SSI 1331; 0.5 mL 4.6 x 10^6). Animals were vaccinated at T=0 and challenged endobronchially with virulent M. bovis (AF2122/97; 10^4 CFU) after 9 weeks. Samples used in this study were taken 8 weeks after vaccination (week 8) and 8 weeks after challenge (week 17). Samples were selected on the basis of presence (VL) or absence (NVL) of lesions at PM. Animals were subsequently grouped according to their immunological and infection status (“status”): controls (unvaccinated, prior to challenge), vaccinated (BCG-vaccinated, prior to challenge), unprotected (unvaccinated, post-challenge, VL) and protected (BCG-vaccinated, post-challenge, NVL).

first: Anna

last: Karagianni

first: Lindert

last: Benedictus

first: Sabine

last: Steinbach

first: Tom

last: Holder

first: Femke

last: Broere


title: Analysis of organoid-derived microglia implicates microglial dysfunction in C9ORF72 ALS/FTD

city: Utrecht

first: Roland Jeroen

last: Pasterkamp

state: Utrecht

address: Universiteitsweg 100

department: Translational Neuroscience

country: Netherlands

institute: UMC Utrecht

summary: Amyotrophic lateral sclerosis (ALS) is an adult-onset neurodegenerative disease characterized by loss of upper and lower motor neurons and progressive muscle wasting. Accumulating evidence indicates a role for non-neuronal cells in ALS pathogenesis, but their exact role and mechanism-of-action remain incompletely understood. A hexanucleotide (GGGGCC) repeat expansion (HRE) in C9ORF72 is the most common genetic cause of ALS (C9-ALS) and a frequent cause of frontotemporal dementia (FTD). Several lines of experimental evidence support a role for the immune system and microglia in C9-ALS/FTD, and, dependent on experimental settings and species used, both reduced and increased microglial activity have been reported. To further study microglia in C9-ALS/FTD in the context of a complex, three-dimensional disease environment, we developed cerebral organoids that innately develop microglia derived from induced pluripotent stem cells (iPSCs) of C9ORF72 patients and controls. To define changes in C9-organoid derived microglia (oMG) activational state due to C9-HRE, we performed RNA sequencing from four C9 iPSC lines and four healthy controls (HC).

overall_design: iPSC derived cerebral organoids were generated as previously described (Ormel et al., 2018). Organoid derived microglia cells were isolated from day 64 cerebral organoids using CD11b-coated beads. Around 10-12 organoids were used per line. Sequencing was performed on C9-oMGs (n=4) and HC-oMGs (n=4).

first: Tijana

last: Ljubikj

first: Mayte

last: Mars

first: Astrid

middle: T

last: van der Geest

first: Nils

last: Bessler

first: Channa

middle: E

last: Jakobs

first: Xynthia

last: van den Oetelaar

first: Marina

last: de Wit

first: R


title: Gene expression dynamics at the single cell level in mouse lung cells

city: Paris

first: Olivier

last: Mirabeau

address: 25-28 rue du Docteur Roux

institute: Institut Pasteur

summary: We performed single-cell RNA sequencing (scRNA-seq) to dissect the heterogeneity of lung cells from mice exposed to papain, with or without co-administration of TLR ligands or bacterial extracts, identify key transcriptional signatures associated with type 2 inflammation, and uncover molecular changes induced by cross-regulatory signals.

overall_design: Experimental design : To assess acute effects, long-term changes, and recall responses induced by allergen exposure and cross-regulation, we performed scRNA-seq on whole lung cells from mice under six conditions:  1.Acute Phase (Day 3): Papain or papain+CpG, analyzed 3 days after administration. 2.Long-Term Phase (6 Weeks): Papain or papain+CpG, analyzed 6 weeks post-administration (no recall). 3.Long-Term Phase with Recall: Papain or papain+CpG, followed by a secondary papain challenge at 6 weeks.

first: Jaechan

last: Ryu

first: Victoire

last: Baillet

first: Gérard

last: Eberl


title: Integrated transcriptomic and epigenomic profiling of mouse lung cells at the single-cell level

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Our previous scRNA-seq data suggest that immune and stromal cells exhibit memory properties that contribute to the long-term regulation of lung allergic responses, which are cross-regulated by the co-administration of TLR ligands or bacterial extracts. To further investigate these mechanisms, we performed single-cell multiome sequencing (scMulti-omics) to integrate transcriptomic and epigenomic profiling, focusing on the characterization of immune and stromal cell populations during long-term resolution.

overall_design: To assess long-term changes induced by allergen exposure and cross-regulation, we performed scMulti-omics on whole lung cells from mice under four conditions: Long-Term Phase (6 Weeks): Control, papain, papain+CpG or papain+OM85, analyzed 6 weeks post-administration (no recall).


title: Decoding the Effects of Bexarotene treatment on brain of AD-like model mice: A Single-Cell Transcriptomic and Chromatin Accessibility Analysis [scRNA-seq]

city: Pittsburgh

first: Iliya

last: Lefterov

state: PA

address: 130 De Soto St

department: Environmental and Occupational Health

institute: University of Pittsburgh

summary: Ligand activation of nuclear receptor has been linked with therapeutic implications in Alzheimer's Disease. In this study, we used AD mouse model treated with Bexarotene, an RXR agonist and performed scRNA-seq and snATAC-seq using the brain tissue. We reavealed changes in chromatin architure in brain of AD-lie mouse model in response to RXR ligand and  link those changes to the initiation of transcriptional programs at a single-cell resolution.

overall_design: We used an AD mouse model treated with Bexarotene, an RXR agonist. scRNA-seq and snATAC-seq were performed using mouse brain 10-day post-treatment to assess brain transcriptome and chromatin accessibility change in response to RXR activation.


title: TCR Cis-Proximity-Guided LAG-3 Suppression of T Cell Activation and Autoimmunity [bulk RNA-seq]

first: Jun

last: Wang

address: 550 1st Ave

institute: NYU Grossman School of Medicine

summary: Therapeutically targeting pathogenic T cells in autoimmune diseases has been challenging. LAG-3, an inhibitory receptor specifically expressed on activated T cells, binds to MHC-II as its canonical ligand. Using artificial antigen-presenting-cells reconstituting cognate or non-cognate peptide-MHC-II, we discovered that MHC-II interaction alone is insufficient for LAG-3's function. Instead, LAG-3's proximity to TCR but not CD4 coreceptor, facilitated by cognate peptide-MHC-II, is crucial in mediating T cell suppression. Mechanistically, LAG-3 forms condensate with TCR signaling component CD3ε through its intracellular FSAL motif and disrupts CD3ε/Lck association. To enhance LAG-3's proximity to TCR complex, an Fc-attenuated LAG-3/TCR bispecific antibody was generated, transforming LAG-3 antagonists into LAG-3-dependent potent suppressors of both CD4 and CD8 T cells, and alleviating autoimmune symptoms in mouse models. Our findings reveal a unique checkpoint cis-modulatory mechanism and provide potential strategies, distinct from PD-1 agonists and others, for T cell-driven autoimmune diseases that lack effective and well-tolerated immunotherapies.

overall_design: To understand transcriptional differences between OT-I T cells activated with SIINFEKL presented on APCs and treated with BiTS, BiTS(mut) or isotype.

first: Wang

last: Jun

first: Du

last: Jasper

first: You

last: Jia

first: Yin

last: Weiwei


title: Effects of chemotherapy on the elimination of various viruses and viroids from grapevine

city: Godollo

first: Eva

last: Varallyay

address: 4 Szent-Györgyi Albert Street

department: Institute of Plant Protection

country: Hungary

institute: Hungarian University of Agriculture and Life Sciences

summary: Our experiments investigated the effects of various known chemotherapeutic agents (2-thiouracil, ribavirin and zidovudine) on grapevine for the elimination of several different viruses and viroids. Viruses and viroids were identified by small RNA HTS in the mother plants of different grapevine cultivars, and RT-PCR verified the results. Among  the tested agents, ribavirin had the broadest elimination effect on most viruses. It proved to be particularly effective against GFkV, GLRaV-4, GPGV and GRSPaV, however, as a single treatment it was not able to eliminate GFLV. In our experiments, ribavirin also showed very low efficacy against GLRaV-1 and GVA viruses. The application of 2-TU caused high phytotoxicity, with only 25% efficacy against GLRaV-4 among the viruses tested. Zidovudine failed to eliminate any of the viruses we tested. However, the combination of ribavirin and zidovudine was able to eliminate GFLV, though with low efficacy (12.5%). In contrast, the combination of ribavirin and 2-TU has been shown to be very effective against GRSPaV and GPGV. Compared to ribavirin, zidovudine and 2-thiouracil did not demonstrate significant virus elimination efficacy in the case of tested viruses. In our experiments ribavirin could not remove HSVd and GYSVd-1 viroids. To the best of our knowledge, no prior studies have been published the successful use of ribavirin or other chemotherapeutic agents against GLRaV-4, and this is the first publication of a successful application of 2-TU and zidovudine against grape viruses .

overall_design: virome was determined by sRNA HTSfor each grapevine plants

first: Mihaly

last: Turcsan

first: Robert

last: Olah

first: Nikoletta

last: Jaksa-Czotter

first: Zsuzsanna

middle: N

last: Galbacs

first: Krisztina

first: Diana

last: Sardy


title: VAPB Promotes Osteogenic Differentiation in Aortic Valve Interstitial Cells via Activation of the SMAD Signaling Pathway

city: Jinan

first: Xiaolin

last: Liu

address: 6699 Qingdao Road,Jinan, Shandong Province CHINA

institute: Shandong Provincial Hospital Affiliated to Shandong First Medical University

summary: Calcific aortic valve disease (CAVD) is increasingly affecting the aging population and is involved in the osteogenic reprogramming of valvular interstitial cells (VICs). However, the exact underlying molecular regulatory mechanisms remain unclear. Vesicle-associated membrane-protein-associated protein B (VAPB) mediates the generation of contact sites between the endoplasmic reticulum (ER) and other cellular membranes. However, the role of VAPB in CAVD remains unclear. This study was to elucidate the relationship between vesicle-associated membrane protein-associated protein B (VAPB) and aortic valve calcification at both tissue and cellular molecular levels, exploring potential regulatory mechanisms. The expression levels of VAPB were assessed using immunohistochemical analysis. Osteogenic differentiation and calcification levels of valve interstitial cells (VICs) were assessed through alizarin red staining, calcium content quantification, and the detection of the osteogenic marker RUNX2. Gene set enrichment analysis was used, and immunoprecipitation was performed. VAPB expression was significantly upregulated in the aortic valve leaflets of patients with calcific aortic valve disease (CAVD) compared to normal aortic valves. VICs with VAPB overexpression exhibited a significant increase in calcium content (p < 0.001) and upregulation of the transcription factor RUNX2 and the osteogenic markers osteocalcin and osteopontin at both mRNA and protein levels (p <0.01). Conversely, VAPB knockdown reduced osteogenic differentiation in VICs. Furthermore, VAPB overexpression led to the enhanced expression of p-SMAD1/5/9 through activation of the SMAD signaling pathway (p < 0.05), while inhibition of the SMAD pathway abrogated the pro-calcification effects of VAPB. Dual immunofluorescence staining demonstrated colocalization of VAPB with SMAD1/5/9, and immunoprecipitation confirmed an interaction between VAPB and SMAD1/5/9. The findings indicate that VAPB promotes osteogenic differentiation in aortic valve interstitial cells by activating the SMAD signaling pathway.

overall_design: RNA-seq profiling of wildtype human VICs  and their  knockdown derivatives (shVAPB) cultured in osteogenic medium for 3 days

first: Kai

last: Xing

first: Qiang

last: Zheng

first: Ting

last: Li

first: Xiaochun

last: Ma

first: Tao

last: Zhang

last: Sun

first: Jian

last: Song

first: Zhengjun


title: High-salt diet induces melanoma re-differentiation

city: Bonn

first: Clivia

last: Lisowski

address: Venusberg-Campus 1

country: Germany

institute: Universität Bonn

summary: A High-salt diet induces immune-independent re-differentiation, metabolic shut down and cell-cycle arrest of melanoma through upregulation of MITF, TSC2 and p18, leading to metabolic shutdown, cell cycle arrest and melanogenesis as well as re-differentiation.

overall_design: Female C57BL/6J mice aged 8-12 weeks were exposed to a normal salt diet (NSD) (or a high salt diet (HSD) for one week before s.c injection of B16-OVA melanoma cells and tumor growth was followed for 14 days while maintaining the respective diets. On day 14 mice were sacrificed and 3' mRNA-Sequencing was performed on isolated tumor cells (ex vivo) to investigate the impact of HSD on B16-OVA melanoma growth.


title: A genome-wide CRISPRa screening to functionalize lncRNAs in CDK4/6i response [siRNA_RNAseq]

first: Da

last: Yang

address: 308 Salk Pavilion

summary: RNA-seq data for candidate genes identified from CRISPR activation screen for regulation of CDK4/6i response

overall_design: Total RNA-seq data for candidate genes knockdown in MCF-7 cells

first: Wang

last: Yifei

first: Zhao

last: Yueshan

first: Zhang

last: Min

first: Yang

last: Da


title: TREM2+ Macrophage Infiltration Underlies Breast Cancer Lung Metastasis due to Paclitaxel Treatment

city: Beijing

first: Yuqi

address: Peking University

institute: Peking University

summary: Metastasis is a major cause of breast-cancer-related death and frequently occurs following paclitaxel neoadjuvant chemotherapy failure. Tumor microenvironment contributes to metastasis, while the role of specific host cells in lung metastases induced by paclitaxel (PTX) treatment remains poorly understood. Here, we demonstrate that PTX neoadjuvant chemotherapy promotes triggering receptor expressed on myeloid cells-2 (TREM2)-positive macrophage infiltration in the breast cancer tissues of patients. Meanwhile, we also show that more TREM2-positive macrophage infiltrates in breast cancer tissues of patients with lung -metastasized. Genetic TREM2 deficiency decreases breast cancer lung metastases induced by PTX treatment in vivo, suggesting that TREM2-positive macrophages are essential for PTX-promoting lung metastasis of breast cancer. We further reveal that PTX promotes tumor cell secretion of fibroblast growth factor 2 (FGF2), triggering TREM2 transcription via upregulating its transcriptional factor early growth response-1 (EGR1) in macrophages. Increased TREM2 activates epithelial-mesenchymal transition (EMT)-related cytokine secretion in macrophages, inducing tumor cell lung metastases. Targeting TREM2 significantly suppressed lung metastasis in breast-cancer-bearing mice. Our findings establish that tumor-cell-derived FGF2 induced by paclitaxel treatment upregulates TREM2 in myeloid macrophages, which in turn promotes the EMT of neighboring tumor cells through cytokine secretion. Our results highlight TREM2 as a potential therapeutic target to mitigate lung metastasis due to PTX treatment.

overall_design: D tumor and  P tumor were harvested and analyzed using Singleron GEXSCOPE® protocol by GEXSCOPE® Single-Cell RNA Library Kit (Singleron Biotechnologies).

first: Hongquan

first: Jun

last: Zhan


title: Transcription factor occupancy is affected by genetic variation in the white adipose tissue of C57BL6/j and 129S1/SvImJ mice [ATAC-seq]

city: Kuopio

first: Juho

middle: Mikael

last: Mononen

address: Yliopistonranta 1E

department: Faculty of Health Sciences

country: Finland

institute: University of Eastern Finland

summary: Most of the disease associated genetic variants identified in genome wide association studies have been mapped to the non-coding regions of the genome. One of the leading mechanisms by which these variants are thought to affect disease susceptibility is by altering transcription factor (TF) binding. Even though inbred mouse strains have been commonly used to investigate polygenic diseases, less is known on how their genetic differences translate to the level of gene regulation and chromatin landscape. Here, we investigated how genetic variation affects chromatin accessibility, a commonly used proxy for TF binding, and how this relates to gene regulation in the epididymal white adipose tissue (eWAT) of C57BL/6J and 129S1/SvImJ mice fed either chow or high-fat diet. We show that differences in chromatin accessibility are almost exclusively strain-specific and driven by genetic variation. In addition, we integrate ATAC-seq (chromatin accessibility) and H3K27ac ChIP-seq (active regulatory regions) data to show that tissue-specific TFs are commonly found in the active regulatory regions hosting TF binding motif altering variants in eWAT. By incorporating footprint analysis, we also show that TF occupancy is consistent with TF binding motif scores at the genetically altered loci. In addition, we validate these findings by extending the footprint analysis to ATAC-seq and H3K27ac ChIP-seq data obtained from the liver. Also, we employ RNA-seq to show that differentially expressed genes are collocated with differentially accessible regions hosting genetic variants. Overall, our findings highlight the connection between differential chromatin accessibility, TF binding and genetic variation and their role in the gene regulation across metabolically central tissues of a mouse model for polygenic obesity.

overall_design: We generated  5-7 ATAC-seq libraries from the 4 groups: 129S1/SvImJ and C57BL/6J on either chow or high-fat diet

first: Mari

last: Taipale

first: Sami

last: Heikkinen


title: Impact of lysine, methionine, and histidine deficiencies on gene expression and upstream transcriptional regulators in bovine mammary epithelial cells: an RNA-sequencing analysis

city: GUELPH

first: Boning

state: ON

address: 50 Stone Road East

department: Animal Biosciences

country: Canada

institute: University of Guelph

summary: Essential amino acids (EAA) may alter bovine mammary epithelial cell functions by impacting mRNA expression of genes through their upstream transcription factors. This study investigates the transcriptional responses in bovine mammary epithelial cells under EAA deprivation (lysine, methionine, and histidine) using RNA-sequencing and pathway analysis. Differential expression genes with absolute log2 fold change ≥ 1 and a false discovery rate of < 0.05 were considered differentially expressed. QIAGEN Ingenuity Pathway Analysis identified kinetochore metaphase signaling pathway as the most significant across all treatments, suggesting a strong link to cell proliferation and apoptosis during EAA deficiency. Activation of activating transcription factor 4 (ATF4) regulates genes involved in amino acid transport, stress response, and apoptosis. Interferon signaling emerged as a novel pathway activated by EAA deficiency, contributing to reduced cell proliferation and protein synthesis. In contrast, the RAS/RAF/MEK/ERK signaling pathway was unaffected. Hypoxia-inducible factor 1α (HIF1A) increased expression, suggesting an anti-proliferative role. Downregulation of Forkhead box protein M1 (FOXM1), a key cell cycle progression factor, likely contributed to slower cell proliferation. Additionally, tumor suppressor p53 (TP53) and ER stress-related transcription factor DNA damage inducible transcript 3 (DDIT3) were identified as mediators of apoptosis. These findings reveal a complex network of transcriptional regulators and signaling pathways influenced by EAA availability, providing new insights into the regulation of milk protein synthesis and potential strategies for optimizing milk production in dairy cows.

overall_design: To identify potentially novel transcription factors that mediate the effects of essential amino acid deficiency on mammary cell activity, we used a genome-wide approach based on RNA-sequencing of gene expression in bovine mammary epithelial cell exposed to lysine, methionine, or histidine deprivation for 60 h.

first: David

last: Innes

first: Eduardo

last: Ribeiro

first: Sergio

middle: A

last: Burgos

first: John

last: Doelman

last: Cant


title: Overabundant endocannabinoids in neurons are detrimental to cognitive function

city: San Antonio

first: Chu

last: Chen

state: Texas

address: 7703 Floyd Curl Dr

department: Cellular and Integrative Physiology

institute: UT Health San Antonio

summary: In the brain, 2-Arachidonoylglycerol (2-AG) is the most abundant endogenous cannabinoid. Enhancing 2-AG signaling by inhibiting monoacylglycerol lipase (MAGL) in astrocytes, the primary enzyme that degrades 2-AG in the brain, produces anti-inflammatory and neuroprotective effects in neurodegenerative diseases. However, the effects of neuronal MAGL inhibition and the responsible molecular mechanisms are largely unclear. To address this question, behavioral tests were performed and hippocampal nuclei were isolated from cell type-specific MAGL knockout (KO) mice. Our behavioral and electrophysiological results showed that cognitive and synaptic functions were impaired in neuronal MAGL-KO mice. Using single-nucleus RNA sequencing analysis, we show here that neuronal MAGL KO mice display distinct gene expression profiles of synaptic DEGs in neurons and glial cells

overall_design: Single nucleus transcriptomics of hippocampus from WT and transgenic mice were analyzed by snRNA-seq.

first: Chen

last: Chu

last: Jian

first: Hu

last: Mei

first: Zhu

last: Dexiao


title: DNA-damaging chemotherapy reshapes cardiac-resident macrophage composition and function

city: St Louis

first: Ruijun

last: He

state: Missouri

address: 660 S Euclid Ave

department: Cardiology

institute: Washington University School of Medicine

summary: Heart failure and ischemic heart disease represent prevalent causes of death among cancer survivors. Despite extensive use of conventional chemotherapies, a limited understanding of how these agents affect the cardiac immune landscape exists. Using mouse models, we show that DNA-damaging agents selectively deplete cardiac-resident macrophages through activation of p53 signaling and resultant necroptosis and apoptosis. Genetic lineage tracing, transcriptomic profiling, and functional studies revealed that recruited monocytes progressively reconstitute the cardiac-resident macrophage compartment, were transcriptionally distinct from embryonic-derived cardiac-resident macrophages, and conferred protection from subsequent hypertensive and ischemic cardiac injury in mice. Monocyte-derived resident-like cardiac macrophages suppressed inflammation and attenuated adverse myocardial remodeling through a type I interferon-dependent mechanism. Collectively, these findings highlight unrecognized effects of DNA-damaging chemotherapies on the cardiac immune landscape and shed light on our understanding of monocyte plasticity and resident macrophage dynamics.

overall_design:
We collected hearts from 20 adult mice that were randomly grouped into 4 groups, PBS+Sham, CBP+ Sham, CBP +AngII/PE, and PBS+AngII/PE (each group has 5 mice of mixed gender). Mice were injected with Carboplatin (45 mg/kg, i.p., twice a week) or equal volume of PBS for two weeks. Then, all the mice underwent 4-week recovery. Next, we implanted osmotic minipump subcutaneously to each mouse. The minipump will either infuse Angiotensin II (1.5mg/kg/d) and PE (50mg/kg/d), or Saline (Sham group) for 7 days. Seven days after the minipump implantation, the CD64+ cardiac mononuclear phagocytes (CD45+CD11b+Ly6G–Ly6Clo) were sorted through FACS. Ten thousand cells from each group were pooled to make Single-cell barcoded cDNA libraries using 10X Genomics 3‘v1kit following manufacturer’s manual.
GTAC core of WUSM conducted the quality control, sequencing, and alignment through cellRanger. Further analysis was performed using R studio (Seurat, DEseq2, ggplot2). The obtained single-cell RNA sequencing data contain 21681 features across 38066 samples. After being filtered as mitochondrial gene proportion(prompt) < 10.0%, nCounts of RNA<30000, and nFeature RNA counts< 7000 & >500, 20290 features across 17438 samples remained. We utilized graph-based clustering and UMAP (Uniform Manifold Approximation and Projection) visualization of the combined four groups (Dim=1:80, resolution=0.6, normalized by SCTransform). According to the feature genes of each cluster, the contamination from cardiomyocytes, endothelial cells, fibroblasts, lymphocytes were found and removed together with two junk clusters. The proliferating cells, monocytes, and mono-phagocytes including Dendritic cells and macrophages are kept for further analysis.

first: Andrew

last: Koenig

first: Kory

last: Lavine

first: Pan

last: Ma


title: TCR Cis-Proximity-Guided LAG-3 Suppression of T Cell Activation and Autoimmunity [scRNA-seq]

city: New York

first: Jun

last: Wang

overall_design: To understand transcriptional and population differences in the livers of hepatitis mice treated with PBS or BiTS.

first: Wang

last: Jun

first: Du

last: Jasper

first: You

last: Jia

first: Lu

last: Catherine

first: Lin

last: Meng-ju


title: Serial and regional assessment of the right ventricular molecular and functional response to pressure-loading

city: Toronto

first: Michael

middle: Bradley

last: Dewar

state: Ontario

address: 661 University Avenue

department: Physiology

institute: University of Toronto

summary: Background: Right ventricular(RV) function determines outcomes in RV pressure-loading. A better understanding of the time-course and regional distribution of RV remodeling may help optimize targets and timing for therapeutic intervention. We sought to characterize RV remodeling between zero and 6-weeks after initiation of RV pressure-loading. Methods and results: Thirty-six rats were randomized to either sham surgery or to pulmonary artery banding(PAB). After echocardiography and conductance catheter studies, groups of rats were euthanized at 1-week, 3-weeks, and 6-weeks after sham surgery, or induction of RV pressure-loading, for RV histological, RNA and molecular analysis. A vigorous inflammatory response characterized by increased RV inflammatory cytokines, chemokines and macrophage markers was observed at 1-week following PAB. Metabolic changes, TGF-β1 canonical signaling, collagenous fibrosis deposition and apoptosis were already significantly increased by 1-week after PAB. Genes marking fibroblast activation were upregulated at 1-week but not 6-week post-PAB surgery. Mitochondrial dysfunction as evidenced by increased PDK activity and decreased PDH phosphorylation significantly at 6-week post PAB. These processes preceded the development of overt myocardial hypertrophy and impaired echo parameters of systolic and diastolic function which occurred significantly from 3-weeks after PAB. Conclusion: RV myocardial inflammation, metabolic shift, metabolic gene transcription and pro-fibrotic signaling occur early after initiation of pressure-loading when RV pressures are only moderately elevated, before the development of overt myocardial hypertrophy and dysfunction, suggesting that adaptive hypertrophy and maladaptive remodeling occur simultaneously. These results suggest that therapeutic intervention to reduce adverse RV remodeling may be needed earlier and at lower thresholds than currently employed

overall_design: Young male Sprague-Dawley rats were subjected to either sham surgery (thoracotomy) or pulmonary artery banding to induce right ventricle (RV) pressure overload. The RVs were then dissected at either 1-week or 6-weeks post-surgery and stored at -80°C. Finally, RNA was isolated from whole-RV samples and prepared for bulk RNA-sequencing.

first: Kana

last: Yazaki

last: Duaz

first: Yohei

last: Akazawa

first: Mei

last: Sun

first: Golam

last: Kabir

first: Jean-Francois

last: Dejardin

first: Kim

last: Connelly

first: Mark

last: Friedberg

first: Scott

last: Heximer


title: A genome-wide CRISPRa screening to functionalize lncRNAs in CDK4/6i response [activation_RNAseq]

first: Da

last: Yang

overall_design: Total RNA-seq data for candidate genes activation in MCF-7 cells

first: Yifei

first: Yueshan

last: Zhao

first: Min

last: Zhang


title: GeoMx DSP- profiling of mouse spleen

city: Novato

first: Fei

last: Wu

state: CA

address: 8001 Redwood Blvd

institute: Buck Institute for Research on Aging

summary: GeoMx DSP- profiling of mouse spleen

sample_organism:
Mus musculus
synthetic construct

platform_organism:
Mus musculus
synthetic construct

overall_design: Mouse spleen from young and old C57BL/6 mice were compared using spatial transcriptomics. Areas of interaction between t- and b-lymphocytes were selected explicitly for ROI selection.

first: Nicolas

last: Martin

first: Serban

last: Ciotlos


title: scRNAseq of the BM immunophenotypic HSC fraction with tracing random DNA-barcode 20 weeks after transplantation

city: minato-ku

first: Tsuyoshi

last: Fukushima

state: tokyo

address: siroganedai 4-6-1

department: Cell therapy

country: Japan

institute: Institute of Medical Science

summary: Random DNA barcode could identified the functional atributes in  immunophenotypic HSC fraction. Combined scRNA-seq with tracing random DNA-barcode could identifed specific molecular signature of the theses functional atributes.

overall_design: HSCs were transduced random DNA barcode and transplantaed to lethal-irradiated mice. BM immunophenotypic HSCs were isolated by FACS 20 weeks after transplantation and analyzed using scRNA-seq.

first: Trine

last: Kristiansen

first: David

last: Scadden


title: Astrocyte-microglia signaling controls developmental thalamocortical synapse refinement

city: Durham

first: Kristina

last: Sakers

state: NC

address: 307 Research Dr

institute: Duke University

summary: Synapse formation and elimination are two crucial processes that concurrently take place in the developing brain. Astrocytes and microglia have been shown to control both processes. However, it is largely unknown how these two major glial cell types of the central nervous system (CNS) communicate to balance synapse formation and elimination. Astrocytes secrete a synaptogenic protein called Hevin/SPARCL1, which induces the formation and plasticity of thalamocortical synapses in the mouse visual cortex. Hevin does so by physically localizing to synaptic clefts and bridging the thalamic axon/cortical dendrite via its interactions with presynaptic Neurexin1a and postsynaptic Neuroligin1b. Here, we found that in addition to this synaptogenic function, Hevin directly signals to microglia cells by interacting with Toll-like Receptors (TLRs) TLR4 and TLR2. This signaling occurs when Hevin is proteolytically cleaved producing an active C-terminal fragment. This fragment is sufficient to upregulate TLR2 expression in microglia and increase microglia phagocytic activity in vivo. This signaling is required for proper refinement of thalamocortical synapses in early postnatal development and for early life ocular dominance plasticity.

overall_design: Microglia were isolated from P7-P9 mouse forebrains via Magnetic Activated Cell-Sorting using Cd11b microbeads. 40-80k cells were plated in each well of a 96 well tissue culture plate. Cells were treated with recombinant proteins at 500nM final concentration. LPS treatment was done at a final concentration of 50ng/mL. OxPAPC treated cells was performed at a final concentration of 15ug/mL. Control cells received additional growth media equivalent to the treatment volume. Microglia were cultured for 6 hours after treatment and then collected and pelleted. RNA was extracted from the cell pellets. RNA was sent to MedGenome for RNA-sequencing library generation and sequencing. Libraries were generated using the Illumina TruSeq stranded mRNA kit and then sequenced on a NovaSeq.

first: Juan

last: Ramirez

first: Evelyn

last: Hardin

first: Crystal

last: Colon-Ortiz

first: Richa

last: Hanamsagar

first: Carina

middle: L

last: Block

first: Sandeep

middle: K

last: Singh

first: Staci

middle: D

last: Bilbo

first: Cagla

last: Eroglu


title: An absolute quantification atlas of small non-coding RNAs across mammalian tissues and cell lines

city: Shanghai

first: Wen

last: Xiao

address: 320 Yueyang Road

department: Institute of Biochemistry and Cell Biology

institute: Shanghai Institutes for Biological Sciences, CAS

summary: The low quantitative accuracy of conventional small noncoding RNA sequencing (sncRNA-seq) methods due to extensive ligation bias commonly limits functional investigation of microRNAs (miRNAs) and PIWI-interacting RNAs (piRNAs). Here, we developed 4NBoost, a single-tube sncRNA-seq protocol designed to minimize bias in the estimated absolute quantification of miRNA and piRNA transcripts through the incorporation of quantitative exogenous RNA spike-ins. With 4NBoost, we profiled sncRNA expression across 20 murine tissues, 18 macaque tissues, and 24 widely used cell lines, as well as 4 Arabidopsis tissues, to establish a comprehensive quantitative reference atlas. Compared with existing small RNA databases, our data revealed substantial biases in miRNA abundance, strand selection, and tissue-specific expression at both individual and family levels. To further extend its utility, we employed machine learning to model and correct biases in conventional datasets, effectively recovering ground truth transcript abundances. All 4NBoost data and the accompanying bias-correction model are freely available via SmRNAQuant (http://wulg-lab.sibcb.ac.cn/SmRNAQuant/), a web-based repository for exploring sncRNA expression. Together, the 4NBoost, bias-correction model, and SmRNAQuant provide powerful resources to advance sncRNA research.

sample_organism:
Arabidopsis thaliana
Macaca fascicularis
Homo sapiens
Mus musculus

overall_design:
Absolute quantification of miRNA and piRNA expression profiles in common tissues and cell lines using 4NBoost.
Pleaes note that total 242 samples are used for formal analysis, and their processed expression profiles are provided in the 'absolute quantification of miRNA expression for each sample.xlsx'.

first: Yuli

last: Zheng

first: Hongdao

first: Beiying

last: Xu

first: Ruiwen

first: Ligang


title: Study title: B Cells Promote T Cell Immunosenescence and Mammalian Aging Parameters - B and T Cell Singlet and PIC Single Cell RNA Seq

first: Fei

last: Wu

summary: The goals of this experiment were two-fold: 1) To understand changes in splenic B and T cells at the transcriptomic level, and 2) to identify unique physically interacting B-T cells and their molecular signatures in young and aged mice.

overall_design: Singlet B/T cells and B-T PICs were isolated from the spleens of WT aged mice and young controls via fluorescence-activated cell sorting (FACS) and subsequently analyzed using single cell RNA sequencing.

first: Daniel

last: A Winer

first: Saad

last: Khan

first: Mainak

last: Chakraborty


title: The selective RRM2 inhibitor TAS1553 is synergistic with multiple CHK1 inhibitors in neuroblastoma

city: Ghent

first: Sarah-Lee

last: Bekaert

state: No state

address: Corneel Heymanslaan 10

country: Belgium

institute: UGent

summary: Tumor cells experience high replication stress, driving genomic instability. Recent studies reveal that neuroblastoma, a pediatric tumor, heavily relies on the ATR-CHK1 signaling pathway. Our prior work identified RRM2, part of the ribonucleotide reductase (RNR) complex, as a key target in neuroblastoma. In this study, we assessed the effects of the RNR-disrupting compound TAS1553 on neuroblastoma cells. Both in vitro and in vivo, TAS1553 inhibited cell growth and triggered apoptosis. Additionally, TAS1553 synergized with CHK1 inhibitors prexasertib and SRA737, increasing replication stress and DNA damage. We also observed these effects in Ewing sarcoma, osteosarcoma, and rhabdomyosarcoma. Notably, TAS1553 downregulated RNA splicing factors, suggesting potential for combination therapies with splicing inhibitors.

overall_design: Neuroblastoma cells (IMR32 and CLBGA) were treated with TAS1553, SRA737, prexasertib and DMSO. Three or four biological replicates.

first: Iris H.

last: Nelen

first: Soetkin

last: Leys

first: Fanny

last: De Vloed

first: Fien

last: Martens

first: Shunya

last: Ohmura

first: Thomas G. P.

last: Grünewald

first: Frank

last: Speleman

first: Annelies

last: Van Hemelryk

first: Lisa

last: Depestel

first: Kaat

last: Durinck


title: Molecular Profile of Interleukin-17RA Blockade by Brodalumab in Japanese Patients with Psoriasis: Results from the ESPRTI study

first: James

last: Krueger

address: 1230 York Avenue

department: Center for Clinical and Translational Science

institute: The Rockefeller University

summary: Brodalumab, an anti-interleukin-17 receptor antibody, is presumed to be effective in psoriasis due to its action on the IL-17 pathway. This study is an analysis of an exploratory intervention study (ESPRIT) conducted in Japanese patients with moderate to severe plaque psoriasis. The efficacy of brodalumab was analyzed by clinical changes and modulation of skin inflammation by changes in gene expression in the skin and protein expression in blood samples.

overall_design: The study was conducted at five sites in Japan from March 2020 to March 2022. Eligible patients were at least 18 years of age at the time of consent and had moderate to severe plaque psoriasis, psoriasis skin severity (PASI) score >10 or body surface area (BSA) >10%. Healthy volunteers are selected whose age and sex were similar to those of psoriasis patients. Brodalumab dosing was consistent with the label: 210 mg subcutaneously at Week 0, 1, and 2, and every 2 weeks thereafter until 12 weeks. The primary efficacy endpoints were: (i) clinical changes in terms of PASI score and PASI score 0 achievement rate at Week 12, (ii) molecular profile changes from Week 0 (baseline) to Week 12, and (iii) changes in inflammation-related and cardiovascular risk factors at Week12.

first: Akimichi

last: Morita

first: Mona

last: Uchida-Yamada

first: Yasumasa

last: Kanai

first: Sandra

last: Garcet


title: A genome-wide CRISPRa screening to functionalize lncRNAs in CDK4/6i response

first: Da

last: Yang

institute: University of Pittsburgh

summary: Aberrant cell cycle regulation is one of central hallmarks for cancer, and cyclin-dependent kinase inhibitors (CDKi) have showed promising clinical outcome in treating ER+/HER2- breast cancer patients. There are also increasing pre-clinical and clinical studies trying to expand the usage of CDKi to more cancer types. However, the underlying mechanism of high individual variability in clinical response remains unclear. LncRNAs are a group of long non-coding RNAs, which have emerged as regulators and biomarkers for cancer therapeutic outcome. In this study, we first performed a CRISPR activation screen of 9744 lncRNAs in breast cancer cells treated with Palbociclib. We identified 144 and 152 lncRNAs that lead to Palbociclib sensitivity and resistance (FDR<0.05), respectively. Further pharmacogenomic analysis from 41 breast cancer cell lines suggested 34 lncRNAs as potential regulators for Palbociclib response (p<0.05). Targeted screen of overlapped lncRNAs and positive control protein-coding genes was performed to further narrow down the hits. Interestingly, we observed a significant association between cancer cell proliferation and Palbociclib response from both screens. Experimental validation of the screen demonstrated that activation of lncRNA CSS1, CSS2 and CSS3 lead to Palbociclib sensitivity. Mechanically, RNA-seq analysis suggested that they may promote cell cycle progression and downregulate cancer stemness. Collectively, our study characterized novel lncRNAs involved in CDK4/6i response which can act as biomarkers for CDK4/6i treatment in cancer patients.

overall_design: CRISPR activation sgRNA library targeting lncRNAs was transduced in MCF-7 cells and treated with Palbociclib before sequencing to determine sgRNA distribution

first: Yifei

last: Wang

first: Zehua

first: Yueshan

last: Zhao

first: Min

last: Zhang


title: Chromatin remodeling at the C-REPEAT BINDING FACTOR cluster controls growth retardation at low ambient temperature

city: Austin

first: Sibum

last: Sung

state: TX

institute: University of Texas at Austin

summary: Temperature profoundly impacts plant growth and development. Response to temperature by plants is one of most crucial ecological factors determining the natural distribution of species, and the yield potential of crops. Among various temperature responses of plants, there remains a gap in understanding molecular mechanisms underlying growth retardation caused by low temperature. Here, we addressed genetic and epigenetic determinants that mediate growth retardation under low ambient temperature in plants. Transcriptome changes mediated by low ambient temperatures include upregulation of a series of regulatory genes, consequently resulting in growth retardation. Our study identified a regulatory network in which a Polycomb protein, VERNALIZATION INSENSITIVE 3-LIKE 1 (VIL1), and a transcription factor, C-REPEAT BINDING FACTOR 1 (CBF1), operate to control growth under suboptimal low temperature. Under suboptimal low ambient temperature, VIL1 controls dynamic chromatin remodeling through transient chromatin loop formation and nucleosome rearrangement at the CBF cluster. Our study provides insights into how plants reprogram growth and development in response to suboptimal low ambient temperatures.

overall_design: To investigate the molecular basis of suboptimal low ambient temperature-mediated growth retardation in WT and vil1 mutants, we performed RNA-sequencing (RNA-seq) analysis using whole rosettes at growth stages of 1.12 -1.13 (when 12 or 13 rosette leaves are greater than 1mm) of both WT and vil1 mutants grown at 12℃ or 22℃ in short day and compared the two transcriptomes.

first: Junghyun

last: Kim


title: Pulmonary surfactant protein D reduces lung cancer progression associated with decreased IL-4/STAT6 signaling

city: Odense M

first: Kim

last: Ravnskjaer

address: Campusvej 55

department: Department of Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

summary: Pulmonary surfactant protein D (SP-D) is an endogenous innate immune factor known to be involved in several immune related diseases and has also been linked to lung adenocarcinoma cell growth. By analyzing single-cell, bulk, and spatial transcriptomics of human clinical samples, we have demonstrated significantly reduced expression in lung cancer cells compared to healthy cells, along with a distinct localization of SP-D expression in stromal areas adjacent to the tumor cells and at the periphery. Interestingly, a near-complete loss of SP-D expression was observed in metastatic tissue, suggesting its association with a more aggressive and metastatic phenotype. In this context, we show that SP-D re-expression in A549 adenocarcinoma cell line significantly decreased tumor growth and spontaneous metastasis formation in vivo and furthermore, that intranasal administration of recombinant SP-D signicantly reduced lung tumor burden. Mechanistically, we demonstrated that SP-D supresses interleukin 4 (IL4)/IL13 signaling pathways. Intriguingly, our data revealed that recombinant SP-D binds directly to the IL4 receptor, leading to the effective inhibition of the IL4 signaling pathway. Collectively, these findings demonstrate that SP-D acts as a tumor supressor inhibiting both tumor growth and metastatic progression potentially through blokage of the IL4/STAT6 signaling pathway. This provides a rationale of SP-D as a promising therapeutic agent for modulating crucial signaling pathways involved in cancer development and progression.

overall_design: A549 cells were treated in triplicates with recombinant human SP-D protein (10µg/ml) og vehicle for 48h.

first: Ali

last: Mohammadi

first: Grith

last: Soerensen

first: Mohammed

last: Inayatullah

first: Behzad

last: Mansoori

first: Mikkel

last: Terp


title: Gene expression profile at single cell level of endothelial cells (ECs) from LPS-injected PPARD-ECWT or PPARD-ECKO mouse lung

city: Shatin

first: XiaoYu

last: TIAN

state: Hong Kong

address: Rm208, LKIBSB, Area 39, Chinese University of Hong Kong

country: Hong Kong

institute: Chinese University of Hong Kong

summary: Vascular hyperpermeability is one of the hallmarks of sepsis and endotoxemia, which contributes to tissue inflammation and organ dysfunction. The peroxisome proliferator-activated receptor delta (PPARδ) is an anti-inflammatory transcription factor, while its role in endothelial barrier function remains unclear. We use single cell RNA-sequencing analysis to profile the gene expression of mouse lung ECs regulated by PPARD in endotoxemia.

overall_design: Mouse received i.p. injection of LPS (5 mg/kg) for 18 h, and mouse lung CD45-CD326-CD144+CD31+ ECs were collected by flow cytometry sorting for scRNA-seq.

first: Xiao

last: Tian

first: Huiling

last: Hong


title: S1PR3 modulates the hyper-proliferation of keratinocytes in psoriasis by activating STAT3 in PKA/Src dependent manner

city: Nanjing

first: Hongwei

address: No. 22, Hankou Road

department: School of Medicine

institute: Nnanjing University

summary: Background: Abnormal lipid metabolism influences the occurrence and development of psoriasis. Moreover, persistent activation of STAT3 signaling pathway in epidemies contributes to psoriasis. However, the molecular mechanism of lipid metabolism and STAT3 activation is unclear. Methods: Imiquimod (IMQ)-induced mouse psoriasis-like model was established to access the potential treatment of FTY720. The function of SIP receptors 3 (S1PR3) was determined by S1PR3 siRNA in HaCaTs and S1pr3 knock out in mice. RNA-seq in HaCaTs was undertaken to explore the downstream target of S1PR3. ChIP assay was applied to explore the transcription factor on S1PR3 promoter.  Findings: The upregulation of S1PR3 in the lesion from psoriasis patients and IMQ-induced mice was observed. Moreover, the pan-S1PR modulator FTY720 ameliorated the lesion in IMQ-induced mice, which was mediated by internalizing S1PR3. S1PR3 knocking downing both in vivo and in vitro significantly suppressed the hyper-proliferation of keratinocytes in a P-STAT3-dependent manner. We found that upregulated-S1PR3 expression maintained STAT3 activation in psoriasis through both short and long term. Namely, S1PR3 enhanced early STAT3 activation via promoting the binding of P-Src to gp130, and long STAT3 activation by reducing Src. Ultimately, Upregulated-S1PR3 was due to STAT3 binding to S1PR3 promoter in psoriatic skin.

overall_design: Utilize RNA-seq to investigate the transcriptome profile of HaCaT treated with IL-6 or IL-6 plus TY52156 for 24 hours.

first: Panpan

last: Lian

first: Zhiqiang

last: Huang


title: Study title: B Cells Promote T Cell Immunosenescence and Mammalian Aging Parameters- 5’ single cell transcriptomics with VDJ T cell receptor analyses on splenic CD3+ cells from aged µMT and WT mice

first: Fei

last: Wu

summary: The goals of this experiment were two-fold: 1) To understand changes in splenic  T cells at the transcriptomic level from aged µMT and WT mice, and 2) to understand TCR diversity and clonality in aged µMT and WT mice

overall_design: T cells isolated from spleens of aged µMT and WT mice via fluorescence-activated cell sorting (FACS) and subsequently analyzed using single cell RNA sequencing.

first: Daniel

last: A Winer

first: Saad

last: Khan

first: Mainak

last: Chakraborty


title: RNAi-mediated regulation of alg-3 and alg-4 coordinates the spermatogenesis developmental program in C. elegans [small RNA-seq]

city: Arlington

first: Alicia

middle: Kathryn

last: Rogers

address: 1225 W Mitchell Street

department: Department of Biology

institute: University of Texas at Arlington

summary: Developmental coordination of gene regulatory networks is necessary for maintaining fertility. Inappropriate activation or silencing of genes responsible for promoting the totipotent germ cell fate into oocytes and/or sperm can have detrimental effects on an organism’s reproductive potential. Spermatogenesis and oogenesis are temporally separated within the germline tissue during the L4 and adult developmental stages, respectively. Yet, it remains unclear how these developmental programs are robustly executed, particularly during stressful conditions. Here we show evolutionarily conserved RNA interference (RNAi) pathways act to restrict expression of spermatogenesis genes to the L4 developmental stage during heat stress. We performed differential expression analysis of mRNA-seq and small RNA-seq libraries from L4 and adult-stage wild-type and mut-16 mutants, which lack a critical RNAi pathway protein, grown at permissive (20ºC) and elevated temperature (25ºC). Our analyses revealed spermatogenesis-enriched gene expression is developmentally mis-regulated in a small RNA-dependent manner at elevated temperature. Many of the mis-regulated spermatogenesis genes are targets of the ALG-3/4 pathway, which is critical for thermotolerant male fertility. We found that the genomic loci of alg-3 and alg-4 are targeted by small RNAs, and that during heat stress, MUT-16-dependent small RNAs are required for L4 stage-specific expression of the Argonautes, ALG-3 and ALG-4. These findings indicate that RNAi pathways are essential for properly coordinating the developmental program of spermatogenesis during heat stress. We propose that appropriate expression of spermatogenesis genes is achieved through small RNA-mediated genetic switches that regulate the expression of ALG-3 and ALG-4 to control ALG-3/4 pathway function throughout development. Moreover, this work provides key insights into the different molecular mechanisms that RNAi pathways employ to maintain both maternal and paternal germ cells’ reproductive potential, and further highlights the complexities and importance of RNAi-mediated gene regulation in development.

overall_design: 8 mRNA-seq and 8 small RNA-seq libraries were generated and analyzed. Each genotype per condition were generated in duplicate.


title: scATAC-seq of mouse 3,5-diethoxycarbonyl-1,4-dihydrocollidine (DDC) induced liver injury model

city: Cincinnati

first: Emily

middle: R

last: Miraldi

state: OH

address: 3333 Burnet Avenue

department: Immunobiology

institute: Cincinnati children hospital

summary: Regulatory T cells (Tregs) were shown to protect from cholestatic liver injury. Here we investigate whether amphiregulin (AREG), a ligand for epithelial growth factor receptor (EGFR) which promotes epithelial repair, mediates innate Treg functions in cholangiopathies. Mice were fed with diet containing 0.1 % of the xenobiotic 3,5-diethoxycarbonyl-1,4-dihydrocollidine (DDC) for 14 days to induce sclerosing cholangitis, followed by a 28-day recovery period (without DDC). Liver mononuclear and epithelial cells were enriched and subjected to single-cell sequencing at four time points: baseline, at day 14 of DDC treatment, and following a 14- or 28-day recovery period from 14 days of DDC treatment.

overall_design: For our time course, 8-week wild type C57Bl/6 mice were fed with 5058 chow admixed with 0.1% DDC for 14 days and then allowed to recover for an additional 14-28 days (5058 chow without DDC).  Liver mononuclear and epithelial cells were enriched and subjected to single cell sequencing at four time points: baseline, at day 14 of DDC treatment, and following a 14- or 28-day recovery period from 14 days of DDC treatment.

first: Alexander

middle: G

last: Miethke

first: Joseph

last: Wayman

first: Ramesh

last: Kudira

first: Zi

last: Yang


title: miR184 and miR499 in HSPC proliferation and differentiation

city: Pittsburgh

first: Partha

last: Dutta

address: 200 Lothrop Street

department: Medicine

summary: We observed that platelet-derived extracellular vesicles (pEV) are enriched in miR184 and miR499. These pEVs are taken up by hematopoietic stem and progentior cells (HSPC). We wanted to know the effects of miR184 and miR499 on HSPC proliferation and differentiation.

overall_design: We transfected mouse hematopoietic stem and progenitor cells with control miR, miR184, or miR499. Two days after the transfection, mRNA was extracted and RNAseq was performed.

first: Lee

last: Ohayon

first: Xinyi

last: Zhang


title: Genome-wide mapping of the chromatin enrichment of CEBPB in NCM460 cell

city: Hong Kong

first: Jian

last: Yan

state: Hong Kong Special Administrative Region

address: 83 Tat Chee Avenue, Kowloon

department: Department of Biomedical Sciences

institute: City University of Hong Kong

summary: In this study, the region harboring the SNP rs2643219 was found to be a putative enhancer.ChIP-qPCR shown that the CEBPB can bind the region. So, ChIP-seq was carried out in colon epithelium-derived NCM460 cells to validate the binding of CEBPB to the genomic region and discover candidate loci interacting with the putative enhancer.

overall_design: CEBPB ChIP-seq on human NCM460 cells. Two independently replicative experiments were performed (rep1 and rep2), and input was used as control.

first: Yong-Qiang

last: Ning

first: Wen-Ju

last: Sun


title: High-throughput RNA-sequencing of preadipocyte subsets in obese mice

first: Chunxing

last: Zheng

address: 320 Yueyang Rd.

institute: Shanghai Institute of Nutrition and Health

summary: We identified a population of obesity-promoted adipogenic preadipocytes that co-expressed Fabp4 and ICAM-1. Fabp4-Cre;mTmG mice were treated with high-fat diet for 16 weeks. The inguinal adipose tissues were collected and digested to obtain vascular and stromal fractions (SVF). The mature adipocytes, CD31-CD45-Sca-1+PDGFR-α+ICAM-1+EGFP+, CD31-CD45-Sca-1+PDGFR-α+ICAM-1+EGFP-, CD31-CD45-Sca-1+PDGFR-α+ICAM-1- cell population were isolated for RNA-seq.

overall_design: Total RNA of four cell populations form two independent experiments were pooled together for RNA sequencing.

first: Qian

first: Yufang

last: Shi

first: Ying

last: Wang


title: Axon guidance genes are regulated by TDP-43 and RGNEF through the rate of long-intron processing.

city: Trieste

first: Maurizio

last: Romano

address: Via A. Valerio 28

department: Department of Life Sciences

country: Italy

institute: University of Trieste

summary: Rho guanine nucleotide exchange factor (RGNEF) is a guanine nucleotide exchange factor (GEF) mainly involved in regulating the activity of Rho-family GTPases. It is a bi-functional protein, acting both as a guanine exchange factor and as an RNA binding protein. RGNEF is known to act as a destabilising factor of neurofilament light chain mRNA (NEFL). Most importantly, RGNEF inclusions in the spinal motor neurons of ALS patients co-localise with TDP-43, the major RNA binding protein aggregating in the brain and spinal cord of ALS patients. Therefore, it can be hypothesized that loss-of-function of both proteins, following their aggregation, may contribute to motor neuron death/survival in ALS patients. To further characterise their relationship, we compared the transcriptomic profiles of neuronal-like cells depleted of TDP-43 and RGNEF demonstrating that these two factors predominantly act in an antagonistic manner when regulating the expression of axon guidance genes. From a mechanistic point of view, our experiments show that the effect of these genes on the processivity of long introns can explain their action. Taken together, our results show that the loss-of-function of factors co-aggregating with TDP-43 can potentially affect the expression of commonly regulated neuronal genes in a very significant manner, acting as potential disease modifiers. This finding further highlights that neurodegenerative processes at the RNA level are the result of combinatorial interactions between different RNA binding factors that can co-aggregate in neuronal cells. A deeper study of these complex scenarios may lead to a better understanding of pathogenic mechanisms occurring in patients, where more than one specific protein may be aggregated in their neurons.

overall_design: Analysis of RGNEF-mediated transcription profile in human neuroblastoma (SH-SY5Y) cell line.

first: Sara

last: Cappelli

first: Emanuele

last: Buratti


title: scRNA-seq of mouse 3,5-diethoxycarbonyl-1,4-dihydrocollidine (DDC) induced liver injury model

first: Emily

last: Miraldi

summary: Regulatory T cells (Tregs) were shown to protect from cholestatic liver injury. Here we investigate whether amphiregulin (AREG), a ligand for epithelial growth factor receptor (EGFR) which promotes epithelial repair, mediates innate Treg functions in cholangiopathies. Mice were fed with diet containing 0.1 % of the xenobiotic 3,5-diethoxycarbonyl-1,4-dihydrocollidine (DDC) for 14 days to induce sclerosing cholangitis, followed by a 28-day recovery period (without DDC). Liver mononuclear and epithelial cells were enriched and subjected to single-cell sequencing at six time points: baseline, at days 7 or 14 of DDC treatment, and following a 7-, 14- or 28-day recovery period from 14 days of DDC treatment.

overall_design: For our time course, 8-week wild type C57Bl/6 mice were fed with 5058 chow admixed with 0.1% DDC for 14 days and then allowed to recover for an additional 7-28 days (5058 chow without DDC). Liver mononuclear and epithelial cells were enriched and subjected to single-cell sequencing at six time points: baseline, at days 7 or 14 of DDC treatment, and following a 7-, 14- or 28-day recovery period from 14 days of DDC treatment.

first: Alexander


title: Chronic intermittent hypoxia in DEN-induced rat model of HCC

city: La Tronche

first: Sophie

last: Rousseaux

address: Bd de la Chantourne

department: IAB

institute: INSERM-UGA

summary: Using RNA-seq analysis, we investigated whether obstructive sleep apnea (OSA)-related chronic intermittent hypoxia (IH) can influence HCC progression and aggressiveness.

overall_design: 7-week-old Fischer 344 male rats were treated weekly with intra-peritoneal injections of 50 mg/kg DEN for 14 weeks in order to develop HCC. Nodule/tumor number and size were evaluated by ultrasound, and the animals were then divided into two equivalent groups (n=9/group). During the following period of 6 weeks, the rats were exposed to intermittent hypoxia (IH group) or to normoxia (N group) during eight hours of the daytime sleeping period of rats.

first: Florent

last: Chuffart

first: Zuzana

middle: M

last: Jilkova

first: Lydie

last: Carreres


title: NanotRNA-seq of Human WT and TRMT5 KO samples

city: Barcelona

first: Eva Maria

last: Novoa

address: Dr. Aiguader 88

country: Spain

institute: Center for Genomic Regulation

summary: tRNA samples from WT and TRMT5 KO OCI-AML2 cell lines and synthetic tRNA samples were sequenced using NanotRNA-seq.

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: NanotRNA-seq of WT and TRMT5 KO OCI-AML2 cell lines and synthetic tRNA samples

first: Eva

first: Oguzhan

last: Begik

first: Cornelius

last: Pauli

first: Michaela

last: Frye


title: Immune Checkpoint B7x Promotes Immune Evasion and Resistance to PD-1/PD-L1 Blockade in Bladder Cancer

status: Public on Dec 30 2025

city: Bronx

first: Deyou

state: NY

address: 1301 Morris Park Avenue

department: Department of Genetics

country: USA

institute: Albert Einstein College of Medicine

summary: Cancer cells adopt multiple strategies to avoid detection and destruction by the immune system, including exploiting immune checkpoint pathways. B7x (B7-H4, B7S1, or VTCN1), a member of the B7/CD28 family, is frequently expressed in advanced bladder cancer (BC), yet its role in BC progression and resistance to therapy remains poorly understood. Resistance to PD-1/PD-L1 immune checkpoint blockade immunotherapy significantly limits durable responses, with only 20%–25% of patients with muscle-invasive BC achieving long-term benefits. Here, we demonstrated that B7x mRNA and protein expression were associated with poor survival outcomes in muscle-invasive BC patients and mouse models of BC. Stable expression of B7x in immune-competent BC mouse models resulted in enhanced tumor growth and splenomegaly, driven by the exclusion and suppression of tumor-infiltrating anti-tumor immune cells and the enrichment of pro-tumor and immunosuppressive cells. Consistently, in the IMvigor210 clinical trial, high B7x mRNA expression was correlated with poorer survival in muscle-invasive BC patients treated with PD-L1 blockade. Notably, combination therapy targeting B7x alongside PD-1/PD-L1 or CTLA-4 blockade reduced tumor burden and overcame resistance to monotherapy. These findings establish B7x as a substantial driver of immune evasion in BC and highlight its potential as a therapeutic target to improve immune checkpoint blockade efficacy in muscle-invasive BC.

overall_design: Given the significant tumor growth-enhancing effect of B7x observed in BBN963 and, to a lesser extent, UPPL1541 tumors, but not in MB49, we conducted bulk RNA-seq on BBN963, UPPL1541, and MB49 cell lines (n = 5) to identify immunomodulatory factors contributing to their sensitivity to B7x.

first: Marc

middle: C

last: Pulanco

first: Xiang Yu

last: Sankin

first: Xingxing

last: Zang


title: 3D genome landscaping of in vitro totipotent cellular models [CUT&Tag]

city: Hangzhou

first: Zheting

last: Zhang

state: Zhejiang

address: Dunyu load

department: school of life science

country: China

institute: Westlake University

summary: Totipotent embryos lack higher-order genome architecture. In this study, we profile the 3D genome architecture of two putative totipotent cellular models, ciTotiSCs and TBLCs. Notably, both ciTotiSCs and TBLCs retain TADs and structurally resemble ICM/ESCs more closely than totipotent embryos. While TADs and compartmentalization are positionally conserved, they weaken upon acquisition of totipotency. Integrative analysis of epigenetic and Hi-C data further reveal that pluripotency genes undergo coordinated epigenetic landscape remodeling and contact domain reorganization, driving pluripotency suppression. Conversely, totipotency gene activation appears to operate through distinct, yet undefined mechanisms. This study establishes the first functional link between 3D genome folding and totipotency-pluripotency transitions while proposing a revised framework for evaluating in vitro totipotency models.

overall_design: CUT&Tag libraries targeting CTCF, H3K27ac, H3K4me3, H3K27me3 and H3K9me3 were prepared from the ESC and the two mouse 2C-like cell lines generated from it, the ciTotiSCs and the TBLCs.

first: Yu

last: Fu


title: 3D genome landscaping of in vitro totipotent cellular models [RNA-seq]

overall_design: RNA-seq libraries were prepared from the ESC and the two mouse 2C-like cell lines generated from it, the ciTotiSCs and the TBLCs.


title: 3D genome landscaping of in vitro totipotent cellular models [ATAC-Seq]

overall_design: ATAC-seq libraries were prepared from the ESC and the two mouse 2C-like cell lines generated from it, the ciTotiSCs and the TBLCs.


title: 3D genome landscaping of in vitro totipotent cellular models [Hi-C]

overall_design: Hi-C libraries were prepared from the ESC and the two mouse 2C-like cell lines generated from it, the ciTotiSCs and the TBLCs.


title: Transcriptional regulation of temporal dynamics in human neurogenesis and neuronal maturation [scRNA-seq]

city: Hefei

first: lingling

last: zhu

address: JinZhai Road

institute: University of Science and Technology of China

summary: Human pluripotent stem cells (hPSCs) provide a valuable platform for studies of human neuronal differentiation, but the mechanisms regulating the timing of this process remain poorly understood. This study compares two differentiation systems with distinct timing of differentiation, transcription factor (TF)-induced forward programming and stepwise cellular differentiation. Our analyses reveal that divergent cellular trajectories drive distinct neurogenesis timing. Multi-omic analysis identifies crucial gene regulatory networks (GRNs) that govern cell fate determination and timing control. Modulation of these GRNs modulates neurogenesis and timing of neuronal maturation. Specifically, OLIG family TFs, enriched in the TF-induced system, promoted cell cycle exit through NOTCH signaling regulation; conversely, ablation of these TFs delayed neurogenesis. In contrast, NEUROD2 overexpression accelerated neuronal maturation through precocious activation of maturation gene modules. Collectively, these findings illuminate characteristics of the cell-intrinsic mechanisms that govern timing of differentiation; the studies also offer a framework for investigation into, and the rational design of, timing-controlled in vitro differentiation strategies.

overall_design: We performed scRNA-seq on cells over the time course of TF-induced forward programming (hPSCs female and male cell lines, with mRNA or dox inducbile NEUROG1, NEUROG2, NEUROD1 overexpression induced neurogenesis) and stepwise cellular differentiation (dual-SMAD inhibition).Taken together, these data indicate that TF-induced forward programming represents a distinct differentiation shortcut from hPSCs to neuronal fate. In order to further decipher the regulatory landscape underlying the drastic cell fate changes, several experiments were performed including high-resolution time-course RNA expression profiling, chromatin accessibility analysis, and TF binding profiling by CUT-TAG (NEUROG1, NEUROG2, and NEUROD1). We next aimed to infer GRNs that may play a crucial role in facilitating rapid neurogenesis (OLIG1, OLIG2, OLIG3) and subsequent neuronal maturation (NEUROD2, MSC). To gain mechanistic insights, scRNA seq of cells induced from OLIG KO cell line, TF binding profiling by ChIP (OLIG2) and CUT-TAG (NEUROD2, MSC) were performed.


title: Transcriptional regulation of temporal dynamics in human neurogenesis and neuronal maturation [ATAC-seq]


title: Chromatin accessibility and transcriptome in human neuronal model exposed to Parkinson's environmental toxins [RNA-Seq]

city: Changsha

first: Jingchao

last: Hong

address: Xiangya Street

institute: Central South University

summary: Parkinson's disease is a complex neurodegenerative disorder where environmental factors play a predominant role in sporadic cases. While environmental toxins are implicated in PD pathogenesis via epigenetic pathways, the specific alterations in chromatin accessibility induced by these toxins remain poorly characterized. To address this gap, we established in vitro models using the human neuroblastoma cell line SH SY5Y, a well established neuronal model, exposed to the PD associated environmental toxins rotenone and MPP+. We performed RNA sequencing to profile the transcriptome and Assay for Transposase-Accessible Chromatin sequencing to map genome-wide chromatin accessibility landscapes under toxin exposed conditions. This integrated dataset provides a comprehensive resource detailing both gene expression and chromatin accessibility dynamics in response to PD relevant environmental neurotoxins and will facilitate investigations into transcriptional regulation, biomarker discovery, and the epigenetic basis of environmentally linked sporadic PD.

overall_design: SH-SY5Y cells (ATCC) were cultured in DMEM/F12 (1:1) medium (Gibco, MA, USA) supplemented with 10% fetal bovine serum (Gibco, MA, USA). Cells were plated in 6-well plates at a density of 5 × 105 cells/mL and incubated overnight at 37°C with 5% CO2. Experimental groups were treated with 5 mM MPP⁺ (Selleck, Houston, USA) and 10 μM rotenone (Sigma, Saint Louis, USA).  Negative control (NC) wells received equivalent volumes of dimethyl sulfoxide (DMSO) vehicle (Sigma, Saint Louis, USA). After 24-hour exposure, cells were harvested for RNA sequencing and ATAC-seq analyses. Three biological replicates per group (NC, MPP⁺, Rotenone) were processed for RNA-seq, while two replicates per group were analyzed by ATAC-seq

first: Juanjuan

last: Huang


title: Human Aging Lung Cell Atlas

city: New Haven

first: Ruben

last: De Man

state: CT

address: 333 Cedar St

institute: Yale School of Medicine

summary: Age is a substantial risk factor and is associated with worse prognosis in nearly all lung diseases. We performed scRNAseq to profile transcriptional changes in the aging human lung at single-cell resolution.

overall_design: Samples were collected from cryopreserved human lung samples and analyzed using scRNAseq.

first: De Man

last: Ruben

first: Rosas

last: Ivan

first: Kaminski

last: Naftali


title: Chromatin accessibility and transcriptome in human neuronal model exposed to Parkinson's environmental toxins [ATAC-Seq]


title: ChIP-seq experiment of transcription factor NFAT in Diaphorina citri

status: Public on Dec 24 2025

city: Fuzhou

first: You

last: Li

state: Fujian

address: No.15 Shangxiadian Road

institute: Fujian Agriculture and Forestry University

summary: ChIP-seq experiment of transcription factor NFAT in Asian citrus psyllid Diaphorina citri. This experiment will figure out what gene was transcripted by NFAT in Diaphorina citri

overall_design: The CHIP-Seq experiment included three biological replicates for each condition ( NFAT antibody and control IgG) .

last: Du

first: Mengle

last: Sun

first: Taiyun

last: Wei


title: Ketogenic diet dampens excitatory neurotransmission by shrinking synaptic vesicle pools

status: Public on Dec 29 2025

city: Philadelphia

first: Yemin

last: Lan

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

summary: The ketogenic diet (KD) is a common dietary intervention for treating seizures in intractable childhood epilepsies and has been proposed to improve disease outcome in neurodegenerative disorders. Despite its clinical applications, we know little about how this diet impacts brain circuitry and neuronal function to elicit its protective effects. Here, we examined the impact of the KD on hippocampal function through integrative analysis of gene expression, epigenetics and neurotransmission.  We found that KD induces profound transcriptional reprogramming of the hippocampus, including altered expression of numerous synaptic genes. Proteomic analysis of histone variants and post-translational modifications also revealed significant changes in activating and repressive epigenetic marks in the hippocampus of KD mice. To determine how transcriptional and epigenetic rewiring of the hippocampus under KD impacts neurotransmission, we performed electrophysiological recordings to examine synaptic dynamics and synaptic summation at CA3-CA1 synapses. We found that KD diminishes synaptic gain and dampens short-term plasticity at excitatory synapses, resulting in reduced summation of synaptic inputs at the circuit level. We determined that the dampening of synaptic gain was due to a reduction in size of the readily releasable as well as the total of synaptic vesicles in excitatory but not inhibitory synapses. Our findings show that the ketogenic diet triggers synaptic remodeling in the hippocampus, driven by broad transcriptional and epigenetic changes that reduce synaptic vesicle pools and short-term plasticity at excitatory synapses ultimately dampening excitatory synaptic gain and integration at the circuit level. These synaptic adaptations may represent a major mechanism underlying the anti-epileptic effects of this diet.

overall_design: ChIP-seq analysis of H3K4me1 histone modifications in the hippocampus of mice fed either a chow or ketogenic diet.

first: Marion

middle: I

last: Stunault

first: Pan-Yue

last: Deng

first: Anjali

last: Yadav

first: Erica

last: Periandri

first: Francisca

last: de Luna Vitorino

first: Michael

last: Thomsen

first: Jasmin

last: Sponagel

first: Amelia

middle: J

last: Barfield

first: Renzelle

last: Ponce

first: Layla

last: Foroughi

first: Benjamin

last: Garcia

first: Gabor

last: Egervari

first: Vitaly

last: Klyachko

first: Ghazaleh

last: Ashrafi


title: Global stabilization of the transcriptome in mitotic cells [RNA-Seq]

status: Public on Dec 23 2025

city: Cambridge

first: Ekaterina

last: Khalizeva

state: MA

address: 455 Main St

department: Biology

institute: Whitehead Institute

summary: In the presence of cell division errors, mammalian cells can pause in mitosis for tens of hours with little to no transcription, while still requiring continued translation for viability. These unique aspects of mitosis require substantial adaptations to the core gene expression programs. During interphase, the homeostatic control of mRNA levels involves a constant balance of transcription and degradation, with a median mRNA half-life of ~2–4 hours. If such short mRNA half-lives persisted in mitosis, cells would be expected to rapidly deplete their transcriptome in the absence of new transcription. Here, we report that the transcriptome is globally stabilized during prolonged mitotic delays. Median mRNA half-lives are increased >4-fold in mitosis compared to interphase, thereby buffering mRNA levels in the absence of new synthesis. Moreover, the poly(A)-tail-length profile of mRNAs changes in mitosis, strongly suggesting a partial mitotic repression of deadenylation. In contrast, the machinery required for siRNA-mediated mRNA degradation remains active. We further show that mitotic mRNA stabilization is dependent on cytoplasmic poly(A)-binding proteins PABPC1&4. Depletion of PABPC1&4 and consequently reduced mRNA stability disrupts the maintenance of mitotic arrest, highlighting the critical physiological role of mitotic transcriptome buffering.

overall_design: RNA-seq data from transcription inhibition timecourses in HeLa cells arrested in mitosis, G2, or G1 using double thymidine block followed by STLC, RO3306, or STLC release respectively. One timecourse experiment only contained STLC-arrested cells without additional transcriptional inhibition. Also included are PAL-seq data from the STLC timecourse and the G2-vs-M timecourse in the presence of actinomycin D. RNA-seq data from HCT116 PABPC1&4-AID cells arrested in mitosis, with or without IAA-induced PABPC1&4 depletion (0 h and 4 h post-IAA addition)

first: Arash

last: Latifkar

first: Kehui

last: Xiang

first: Jimmy

last: Ly

first: Iain

last: Cheeseman

first: David

middle: P

last: Bartel


title: Early Radial Extracorporeal Shockwave Stimulation on Proximal Tibial Circular Osteotomy Site Enhanced Heterotopic Skin Wound Healing via Small Extracellular Vesicles

city: Changchun

first: Tiecheng

last: Yu

state: Jilin

address: Xinmin Street No.1

department: Department of Orthopaedics

institute: the First Hospital of Jilin University

summary: Wound healing represents a complex biological process necessitating innovative therapeutic approaches, particularly for chronic wounds such as diabetic foot ulcers (DFUs). Inspired by the regenerative effects of tibial bone transport for DFUs, we explored whether radial extracorporeal shockwave therapy (rESWT) at the tibial circlularr osteotomy site (TOE) could enhance wound healing in rats. We found that TOE accelerated dorsal foot wound healing via small extracellular vesicles (sEV). This sEVs showed strong regenerative effects and modulated macrophage polarizations in vitro and in vivo. Single-cell sequencing revealed mesenchymal stem cells as the likely sEV source, with rESWT triggering sEV release through ATP/P2X7R/p38MAPK pathway. Proteomic analysis identified five differentially expressed proteins in sEVs, with Thbs1-enhanced sEVs enhancing wound healing by promoting IL4-induced M2 macrophage polarization. This innovative approach represents a promising alternative strategy for wound management, with potential for future DFU treatment.

overall_design: Single-cell RNA sequencing (scRNA-seq) was performed on all nine samples from circular osteotomy tissues at the proximal tibia to elucidate the cellular origins of the pro-healing sEVs derived from TOE. We established a 3-mm circular osteotomy model at the proximal tibia (TO model) and a concurrent 4-mm full-thickness cutaneous wound on the ipsilateral dorsum of the foot in Sprague-Dawley rats (n=9, 6-8 weeks old). Shock wave therapy was administered to the osteotomy site on postoperative days 2 and 4. Tissue samples from the proximal tibial osteotomy site were collected at 4 and 24 hours after each shock wave session (TOE group), with non-treated osteotomy site samples (TO group) serving as controls. An additional baseline sample (TO_2d_0h) was obtained prior to shock wave intervention on postoperative day 2. Single-cell RNA sequencing (scRNA-seq) was subsequently performed on all nine samples.

first: Xiaoping

last: Xie

first: Songqi

last: Bi

first: Bang

last: Su

first: Rongqi

last: Zhou

first: Xudong

last: Li