title: Transcriptomic impacts of TFIIB D207G editing in Jurkats during 6 h TRAIL treatment

city: Berkeley

first: Britt

last: Glaunsinger

address: RM 565, 1951 Oxford St

institute: University of California, Berkeley

summary: Cellular stressors often cause widespread repression of RNA polymerase II (RNAP II) activity, which is thought to facilitate a focused transcriptional output towards stress resolution. In many cases, however, the underlying regulatory mechanisms remain unknown. Here, we demonstrate that stress-induced downregulation of the general transcription factor TFIIB tempers expression of specific stimulus response genes. Following a variety of stressors, TFIIB is proteolytically cleaved between its cyclin folds at conserved aspartic acid residue D207 by caspases- 3 and 7. Cleavage in this portion of the protein significantly reduces the ability of TFIIB to form a TBP-TFIIB-DNA promoter complex in vitro. Using both overexpression and endogenous base-editing, we find that B and T cells that are unable to cleave TFIIB upregulate expression of a select gene set during apoptosis. These TFIIB-sensitive genes are primarily short, stimulus-responsive and proto-oncogenic loci, and cleavage of TFIIB temporally restricts their expression. Failure to cleave TFIIB during stress leads to aberrant lymphocyte proliferation during chemical perturbation. Hence, caspase targeting of TFIIB destabilizes transcription to tune gene expression, allowing for proper stress resolution.

overall_design: Using Jurkat T cells, which are sensitive to apoptotic stimuli, two different sgRNAs targeting the TFIIB D207 locus were validated (D207G-#1 and D207G-#2; also referred to as sgRNA1 and sgRNA2). A control dinucleotide base edit was made in the AAVS1 locus (Control/sgRNA3). Pooled populations with ≥ 85% editing at each target locus were validated by amplicon sequencing. Pooled populations were expanded for ≥ 10 days after delivery of A•G base editor RNA and the sgRNA, and then submitted to SLAM-sequencing (edit stability was monitored for all experiments and protein-level impacts were confirmed in parallel by western blotting). Cells were treated with SUPERKILLER TRAIL (Enzo) for 6 h and 4sU was pulsed on to label nascent RNA in the last 3 hours of this treatment. This was followed by RNA extraction, alkylation, library preparation, RNA-sequencing, and differential gene expression analysis.

first: Leah

last: Gulyas


title: Effect of ADAR1 silencing in human monocyte-derived macrophages

status: Public on Feb 01 2026

city: Huddinge

first: Niklas

last: Björkström

address: Alfreds Nobel Alle 8

country: Sweden

institute: Karolinska Institutet

type: Expression profiling by high throughput sequencing

summary: Adenosine deaminase acting on RNA 1 (ADAR1) regulates mRNA fate and function through adenosine-to-inosine (A-to-I) RNA editing and RNA-binding activities. While its role in innate immunity is well established, the broader regulatory functions of ADAR1 in macrophages remain poorly defined. Here, we systematically profiled ADAR1 expression across human immune cells and identified a marked enrichment in macrophages, driven by selective usage of an alternative transcription start site during monocyte-to-macrophage differentiation. ADAR1 binds, edits, and modulates key macrophage targets involved in efferocytosis, endocytosis, lysosomal processing, lipid metabolism, and proliferation in an isoform-specific manner. We further demonstrate that ADAR1 levels and activity are dynamically regulated in adipose tissue and liver during the progression of metabolic disease. Linked to this, macrophage specific ablation of ADAR1 co-cultured in organotypic 3D primary human spheroids and exposed to metabolic stress resulted in an exacerbated lipid accumulation phenotype. Finally, we identify a lipid-associated macrophage-specific upregulation of ADAR1 in adipose tissue following weight loss interventions, mechanistically driven by free fatty acids. These findings uncover a previously unrecognized role for ADAR1 in lipid-buffering, scavenging, and proliferative macrophage functions, extending its biological relevance beyond canonical interferon-mediated immunity and establishing ADAR1 as a key regulator of macrophage adaptation in metabolic disease.

overall_design: This dataset investigates the A-to-I RNA editome and transcriptome of macrophages with ADAR1 silenced using siRNAs targeting both isoforms or specifically the p150 isoform. Corresponding controls were transfected with negative control siRNAs. Samples were collected 48 hours post-transfection. Monocytes were isolated from peripheral blood mononuclear cells of healthy donors and differentiated into macrophages using M-CSF over 7 days.

first: Fardellas

last: Achilleas

first: Björkström

last: Niklas


title: Transcriptomic impacts of TFIIB D207G editing in clonal Jurkat lines during 6 h TRAIL treatment

state: California

department: PMB

country: USA

overall_design: Using Jurkat T cells, which are sensitive to apoptotic stimuli, two different sgRNAs targeting the TFIIB D207 locus were validated (D207G-#1 and D207G-#2; also referred to as sgRNA1 and sgRNA2). A control dinucleotide base edit was made in the AAVS1 locus (Control/sgRNA3). Clonal lines for each guide were established with single cell dilution cloning, and pristine editing at each target locus were validated by PCR amplicon sequencing. 1-2 representitive clonal lines per sgRNA were submitted to SLAM-sequencing (protein-level impacts were confirmed in parallel by western blotting). Cells were treated with SUPERKILLER TRAIL (Enzo) for 6 h and 4sU was pulsed on to label nascent RNA in the last 3 hours of this treatment. This was followed by RNA extraction, alkylation, library preparation, RNA-sequencing, and differential gene expression analysis.

middle: A


title: Extracellular Matrix Origin Directs Morphogenesis and Gene Regulation in Bioengineered Human Skin

city: Napoli

first: Paolo

middle: Antonio

last: Netti

address: Istituto Italiano di Tecnologia (IIT), Largo Barsanti e Matteucci 53

department: IIT - Center for Advanced Biomaterials for Healthcare

country: Italy

institute: IIT

summary: The cellular microenvironment plays a pivotal role in directing tissue development, repair, and homeostasis through a complex interplay of biochemical and mechanical cues. The extracellular matrix (ECM) serves as a key instructive component, guiding transcriptional programs that determine cell fate, function, and identity. In this study, we investigated the impact of microenvironmental context on the biofabrication of human skin equivalents, comparing constructs based on endogenous versus exogenous ECMs. Our RNA sequencing analyses reveal that ECM origin profoundly influences transcriptional trajectories, highlighting the importance of a native-like microenvironment in supporting appropriate gene expression profiles and morphogenetic processes. Notably, skin equivalents featuring endogenously produced ECMs exhibit physiologically relevant architecture, including a well-organized dermo-epidermal junction (DEJ), whereas constructs based on exogenous matrices—such as animal-derived collagen—display abnormal epithelial expansion and fail to replicate key structural features. These findings underscore the necessity of recapitulating the native ECM to achieve functional tissue constructs in vitro and raise critical considerations regarding scaffold choice in regenerative medicine and tissue engineering applications. We also discuss the implications of these findings for the development of organ-on-chip systems, where the accurate recapitulation of native tissue architecture and function is essential for modeling physiological and pathological conditions in human-relevant experimental assays.

overall_design: Morphological characterization (collagen and elastin quantification) and RNA-Seq profiling (differential gene expression analysis and enrichment analysis) of endogenous and exogenous human skin equivalents to highlight the role of the ECM in guiding the correct production of relevant 3D skin model.

first: Francesco

last: Galardo

first: Giorgia

last: Imparato

first: Costatino

last: Casale

last: Urciuolo

first: Luca

last: Mannino

first: Antonio

last: Federico

first: Dario

last: Greco


title: 3D chromatin contacts via HiChIP - Multimodal epigenetic and enhancer network remodeling shape the transcriptional landscape of beige adipocytes

city: Oslo

first: Philippe

last: Collas

address: PO Box 1112 Blindern

department: Institute of Basic Medical Sciences

country: Norway

institute: University of Oslo

summary: Epigenetic regulation is a key determinant of adipocyte fate and function, conferring phenotypic plasticity to adipose tissue in response to metabolic and thermal challenges. To understand the spatiotemporal regulation of chromatin during the establishment of a beige thermogenic adipocyte phenotype, we analyzed the transcriptomic, epigenetic, and enhancer connectome dynamics during white and beige adipogenesis. Using a machine learning approach, we find that the white-specific transcriptional program is associated with promoter modulations of H3K2ac levels and chromatin accessibility. In contrast, beige-specific mitochondrial gene expression correlates with promoter changes in H3K4me3 levels. Adipocyte beiging is also mediated by a remodeling of the 3D genome involving the recruitment of short range enhancers targeting fatty acid oxidation and thermogenic genes. These increased promoter-enhancer contacts correlate with increased chromatin opening at sites enriched for C/EBP transcription factor motifs. We notably identify the C/EBP transcription factor NFIL3 as differentially bound between white and beige adipocytes at enhancers regulating PDK4, a key metabolic switch promoting fatty acid oxidation. Our results highlight a multimodal, pathway-specific regulation of the transcriptional program underlying the beige adipocyte phenotype.

overall_design: Primary human adipocyte stem cells from a single subject were differentiated for 15 days into both beige and white adipocytes in the presence or absence of rosiglitazone, respectively, and short range chromatin contacts at loci with H3K27ac were assessed using Hi- Chromatin Immunoprecipation and sequencing (Hi-ChIP-Seq).  Two differentiations were seqeuenced as a bioloigcal duplicate.

first: Sarah

last: Hazell Pickering

first: Mohamed

last: Abdelhalim

first: Natalia

middle: M

last: Galigniana

first: Anita

middle: L

last: Sørensen

first: Manuela

last: Zucknick

first: Nolwenn

last: Briand


title: ATAC-seq - Multimodal epigenetic and enhancer network remodeling shape the transcriptional landscape of beige adipocytes

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: Primary human adipocyte stem cells from a single subject were differentiated into both beige and white adipocytes in the presence or absence of rosiglitazone, respectively, and harvested for Chromatin Immunoprecipation and sequencing (ChIP-Seq). Six histone post translational modifications (H3K27ac, H3K4me3, H3K4me1, H3K27me3, H3K36me3 and H3K9me3) were assayed before differentiation (day0) and 1, 3 and 15 days after induction of differentiation.  Four marks (H3K27ac, H3K4me3, H3K4me1, and H3K27me3) at day15 were previously published under accession GSE256260.


title: Analysis of human macrophages exposed to marennine

city: Paris

first: Elodie

last: Segura

address: 156 rue de Vaugirard

department: INSERM U1151

country: France

institute: INSERM

summary: Human monocyte-derived macrophages were exposed to marennine or vehicle for 8h. We found that marennine induces an inflammatory response in human macrophages.

overall_design: Human monocyte-derived macrophages were exposed to marennine or vehicle for 8h. Transcriptomic analysis was performed by RNA-sequencing.


title: Targeting of a novel interplay between MET Tyrosine Kinase and NRF2 enhances sensitivity to Paclitaxel in Triple Negative Breast Cancer

city: Rome

first: Daniela

last: Barilà

address: Via Cracovia, 90

department: Department of Biology

institute: Università Tor Vergata

summary:
Triple-negative breast cancer (TNBC) is a very aggressive and heterogeneous cancer. The lack of effective targeted therapies and frequency of relapse point to the urgent need for identifying molecular vulnerabilities to overcome resistance to chemotherapy.
Nuclear Factor Erythroid 2-related factor 2 (NRF2) is a transcription factor that plays a central role in response to oxidative stress. Its hyperactivation contributes to metabolic rewiring and resistance to therapy in several tumors including TNBC. Unfortunately, efficient pharmacological approaches that block NRF2 functions are still missing. Protein Tyrosine kinases (PTKs), often overactivated in cancer and influencing several signalling pathways, are promising candidates to explore for their potential impact on NRF2.
The link between Receptor Tyrosine Kinases and NRF2 expression and its impact on the survival probability of TNBC and non-TNBC patients were investigated by bioinformatic analyses using TCGA and GEO databases. MET-NRF2 connection was further confirmed by immunoblotting, immunofluorescence, qRT-PCR and RNAseq experiments through the combinatorial use of murine and human TNBC cellular models. The efficacy of combination treatments with Paclitaxel and specific inhibitors of MET-NRF2 signalling was assessed by viability assays and flow-cytometry analyses on TNBC cellular models as well as on TNBC patient-derived organoids.
Here, we identify a novel interplay between MET and SRC kinases with NRF2 expression and activity and demonstrate that its targeting enhances the sensitivity to the standard Paclitaxel treatment of TNBC cells and patient-derived organoids.
Our study shows that RTKs regulate NRF2 expression and activation in TNBC providing a proof of principle for the ability of Tyrosine Kinase Inhibitors (TKIs) to impinge on NRF2 signalling. Our findings also uncover the value of the MET-SRC-NRF2 axis as exploitable vulnerability in NRF2-hyperactivated TNBC, paving the way for the repositioning of TKIs as modulators of NRF2 signalling.

overall_design: Gene expression profiling through RNA-seq for each biological replicate of MGT-13 cell line with and without PHA-665752 and with and without siNRF2

first: Irene

last: Taddei

first: Claudia

last: Cirotti

first: Fabienne

last: Lamballe

first: Oliver

last: Castellanet

first: Flavio

last: Maina

first: Fabrizio

last: Fierro

first: Francesca

last: De Nicola

first: Maurizio

last: Fanciulli

first: Eleonora

last: Cesari

first: Vanessa

last: Medici

first: Claudio

last: Sette


title: Transcriptome Sequencing of Cecum Tissues Form Septic Rats Treated With or Without Tongfu Pingchuan Decoction

city: Shanghai

first: Limeng

last: Yang

address: No. 358 Datong Road, Pudong New Area

department: Department of Internal Medicine

country: China

institute: Shanghai Pudong New Area Hospital of Traditional Chinese Medicine

summary: This study aimed to investigate the protective mechanisms of the Traditional Chinese Medicine Tongfu Pingchuan decoction (TFP) in the cecum of septic rats. Thirty rats were randomly divided into three groups: Sham, Model (sepsis induced by cecal ligation and puncture), and TFP (sepsis treated with TFP). Rats received 1 mL/kg TFP or PBS via gavage twice daily for one week, after which whole blood and cecum tissues were collected. Transcriptome sequencing was conducted on six cecum tissues per group. Bioinformatics analyses predicted the potential mechanisms of TFP, which were subsequently validated in cecum tissues and RAW264.7 cell cultures. We found that Pathways such as TNF signaling, complement and coagulation cascades, fatty acid metabolism, and PPAR signaling were activated, while cholinergic synapse, ECM-receptor interaction, and VSMC contraction were inhibited in the Model group compared to Sham. These changes were largely reversed in the TFP group. Chrm4 and Pygm were identified as potential TFP targets, as they were overlapping differentially expressed genes (DEGs) in the predicted TFP targets and an identified WGCNA module of interest. Chrm4 was downregulated in the Model group and restored by TFP treatment. In the Model group, M1 macrophages were induced, while M2 macrophages were suppressed. TFP inhibited M1 macrophages and further enhanced M2 macrophages. These effects were corroborated in LPS-stimulated RAW264.7 cells, where TFP also modulated cytokine levels (IL-6, IL-10, TNF-α). The effects of TFP were negated by Boc-2 (a PCTR1 inhibitor) or Chrm4 silencing. Additionally, TFP suppressed IL1RN, p-ERK2/ERK2, and p-AKT/AKT levels in LPS-treated RAW264.7 cells, but these effects were abolished upon Chrm4 silencing. Collectively, we show that TFP alleviates sepsis by promoting Chrm4/IL1RN-regulated macrophage polarization and facilitating inflammation resolution.

overall_design: The sequencing data involves rat cecum tissues form sham (S1-S6), sepsis (M1-M6), and sepsis+TFP (D1-D6) groups, 6 replicates.

first: Jialong

last: Qi

first: Jun

last: Wang

first: Jingjing

last: Gu

first: Jiayuan

last: Bai

first: Ruimin

last: Xu

first: Yalan

last: Zhang

first: Wei

last: Sun

first: Dan

last: Hu


title: Single-cell transcriptomics reveals alveolar macrophages-specific responses in single-hit ozone exposure model in mice

city: Raleigh,

first: Yogesh

last: Saini

state: NC

address: 1060 William Moore Drive

department: Population Health and Pathobiology

institute: NCSU

summary: Ozone (O3) is known to cause lung injury, which can influence the health and function of resident immune and non-immune cells of the respiratory tract. Alveolar macrophages (AMs), a highly plastic lung resident cell population, are among the first responders to the inhaled O3 and ozonized products. However, the complete understanding of how AMs respond to O3, particularly to different concentrations, remains elusive. Through single cell RNA sequencing (scRNA-seq), we aimed to profile AM transcriptome from O3-exposed mice and understand the relevance of these transcriptomic changes to the population and functional heterogeneity. Accordingly, we exposed C57BL/6J male mice to filtered air (FA), 1 ppm O3, or 1.5 ppm O3 for 3 hours. After 24h of exposure, bronchoalveolar lavage (BAL) was performed to harvest immune cells, which were subjected to ScRNA-seq. As compared to FA-exposed mice, O3-exposed mice exhibited increased alveolar macrophages and neutrophils in the lung airspaces, consistent with the elevated levels of macrophage and neutrophil chemokines, i.e., MIP-2, MCP-3, MCP-5. The ScRNA-Seq data analyses were performed to identify distinct and annotate distinct cellular clusters. AM clusters were analyzed for the alterations in gene expression and associated enrichment of biological pathways. Although the O3 exposure did not result in the appearance of a distinct cellular cluster, there was a significant difference in the number of differentially expressed genes (DEGs) between AMs from mice exposed to 1 ppm and 1.5 ppm O3, relative to those exposed to FA. As compared to AMs from FA-exposed group, AMs from 1 ppm and 1.5 ppm O3-exposed groups displayed enrichment of pathways including oxidative phosphorylation, EIF2 signaling, and non-canonical NF-kB signaling. Furthermore, AMs from 1 ppm O3-exposed mice were uniquely activated in IL-10 signaling pathway. On the other hand, AMs from 1.5 ppm O3-exposed mice were uniquely enriched in pathways including DNA damage bypass and repair pathways. Interestingly, UMAP analyses on annotated AMs resulted in five distinct subclusters. DEGs and IP analyses for each subcluster revealed O3 concentration-dependent enrichment of pathways relevant to protein translation, cholesterol biosynthesis and mitochondrial biogenesis. Further analyses revealed that O3 exposure results in cluster-specific alterations to the expression of gene signatures associated with macrophage activation. Finally, AMs from 1.5 ppm O3-exposed mice displayed elevated expression of proliferation associated gene signatures. Taken together, this study identified O3 concentration-dependent alterations in AMs transcriptomes and associated functional modulations at single cell resolution.

overall_design: 12-week-old C57BL/6J mice were exposed to either Filtered Air (FA), 1 ppm ozone (O3) or 1.5 ppm O3 for 3 hours. Necropsy was performed 22-24 hours after the end of exposure and the bronchoalveolar lavage (BAL) immune cells were collected and submitted for scRNA-sequencing


title: Single-cell mitochondrial genotyping of exonuclease-deficient DNA polymerase γ (POLGD274A) knock-in HEK293 cell lines

city: Berlin

first: Leif

last: Ludwig

address: Hannoversche Str. 28

country: Germany

institute: Berlin Institute for Medical Systems Biology

summary: Exonuclease-deficient DNA polymerase γ (POLGD274A) lead to an hypermutated mitochondrial genomes and cause OXPHOS defect. Exonuclease-deficient DNA polymerase γ (POLGD274A) lead to an elevated mutational rate and hypermutated mitochondrial genomes, which cause OXPHOS defect. Here, leverage mitochondrial single-cell ATAC-seq (mtscATAC-seq) to estimate genome-wide mtDNA mutational burden in HEK293 cell lines with POLGD274A knock-in. Our method sensitively detects up to a a median of 472 variants per cell, corresponding to a 50-fold increase comared to control, with a predominance of replication-driven C>T transitions. We further examined how POLGD274A knock-in cells adapt to OXPHOS-enforcing metabolic stress in galactose. After 1 and 3 days in glucose or galactose, CTRL and KI36 were subjected to mtscATAC-seq to examine the mtDNA variants heteroplasmy dynamic. We found that pseudo-bulk heteroplasmy, single-cell VAF distributions, and mtDNA mutational burden were unchanged. Instead, mtDNA copy number rose, and subclone DAGs highlighted stress/inflammatory programs and increasing accessibility at GDF15, suggesting population-wide metabolic rewiring.

overall_design: POLGD274A knock-in HEK293 cell lines, with (Knock-in clone A2, KIA2) or without (Knock-in clone 36, KI36) the introduction of a tetracycline-inducible mitochondrial restriction exonuclease mitoEagI, were previously described (PMID: 29712893). Cryopreserved cells were thawed cultured for a maximum of 2 weeks before single-cell sequencing to limit the accumulation of additional mtDNA mutations. For the Galactose treatment experiment, control and POLGD274A  knock-in clone 36 HEK293 cell lines were cuturled in glucose-free DMEM supplemented with 1 mM sodium pyruvate and with either 10 mM glucose (3 days) or 10 mM galactose (1 day or 3 days). Each cell line–treatment combination was labeled with dedicated TotalSeq-B hashtag antibodies, washed, and pooled at equal ratios. The pooled cells were subsequently processed using the mtscATAC-seq protocol.

first: Yu-Hsin

last: Hsieh

first: Janet

last: Liebold

middle: S


title: The Absence of Claudin-10 In the Enamel Organ Alters Its Integrity

city: Montrouge

first: Caroline

last: Andrique

address: 1 rue Maurice Arnoux

department: UFR Odontologie

institute: Université Paris Cité

summary: Enamel, the hardest structure in the body, is affected throughout life by chronic or rare diseases. The study of the underlying pathological mechanisms has revealed new players in enamel formation. Among them, the disorders related to tight junction (TJ) proteins and kidney have been associated with impaired ameloblast function. Pathogenic variants of CLDN10, encoding claudin-10b, a cation transport channel, cause the autosomal recessive HELIX syndrome (Hypohidrosis, Electrolyte imbalance, hypoLacrymia, Ichthyosis, Xerostomia) in which patients experience disabling enamel wear. This study explored whether this premature enamel wear is due to intrinsic enamel fragility or xerostomia. In this purpose, we analyzed amelogenesis and enamel in several constitutive or conditional Cldn10 knockout (KO) murine models and human teeth. Our data show that claudin-10 was present in the cell membranes of the stratum intermedium, but not TJs, and that its absence disrupted signaling pathways related to ion transport and pH control. Although the ameloblasts still formed enamel, higher levels of aluminum were found in transplanted Cldn10 KO molars and in human HELIX enamel. These findings suggest that while xerostomia is the main cause of enamel wear, claudin-10 plays a key role in amelogenesis by regulating pH, and its deficiency leads to a loss of enamel organ integrity.

overall_design: Microdissected ameloblasts (WT or KO claudin 10) and Microdissected Stratum intermedium cells (WT or KO claudin 10)

first: The Nghia

last: Nguyen

first: Sandy

last: Ribes

first: Benjamin

last: Saint Pierre

first: Céline

last: Gaucher

first: Tilman

last: Breiderhoff

first: Catherine

last: Chaussain


title: Effect of FAM83H-AS1 knockdown in MDA-MB-468 cells [cellseq]

city: Guangzhou

first: Zhimei

last: Liang

state: Guangdong

address: No. 107, Yanjiang West Road, Yuexiu District

department: Medical Research Center

institute: Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University

summary: To investigate the role of lncRNA FAM83H-AS1 in breast cancer, we used shRNA to silence FAM83H-AS1 in MDA-MB-468 cells and performed RNA-seq analysis.

overall_design: Two shRNAs were used to silenc FAM83H-AS1 (shFAM83H-AS1_1, shFAM83H-AS1_2). Triplicate experiments were performed for the RNA-seq analysis.

first: Zhi-Mei

first: Man-Li

last: Luo


title: Analysis and ceRNA network construction of differentially expressed lncRNAs and mRNAs in human osteoarthritis cartilage

city: Harbin

first: Yong

last: Zhou

address: 37 Yiyuan Street

institute: The Fourth Affiliated Hospital of Harbin Medical University

type: Non-coding RNA profiling by high throughput sequencing

summary: This study aimed to identify differentially expressed long non-coding RNAs (lncRNAs) and messenger RNAs (mRNAs) in damaged cartilage (DC) and un-damaged cartilage (UDC) from osteoarthritis (OA) patients. RNA sequencing was performed on cartilage samples from five OA patients undergoing total knee arthroplasty. Bioinformatics analysis, including Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment, and competing endogenous RNA (ceRNA) network construction, was conducted.

overall_design: Cartilage samples were obtained from osteoarthritis (OA) patients undergoing total knee arthroplasty (TKA). For each patient, both damaged cartilage (DC) from the lesion area and un-damaged cartilage (UDC) from the relatively preserved area were collected. RNA was extracted from these samples, and long non-coding RNA (lncRNA) sequencing was performed to identify differentially expressed lncRNAs and mRNAs.

first: Yishu

last: Liu

first: Xi


title: Baseline tumor features and peripheral blood immune dynamics that underlie efficacy in MSS metastatic colorectal cancer treated with regorafenib, ipilimumab, and nivolumab [Blood]

city: Duarte

first: Jian

last: Ye

state: CA

address: 1500 E Duarte Rd

department: Department of Medical Oncology and Therapeutics Research

institute: City of Hope National Medical Center

summary: Microsatellite-stable metastatic colorectal cancer (MSS mCRC) remains resistant to conventional immunotherapies, yet in a phase I trial the combination of regorafenib, ipilimumab, and nivolumab (RIN) demonstrated a 27.6% overall response rate and a median overall survival of 20 months, particularly benefiting patients without liver metastases. Correlative studies of tumor biopsies from eight patients and peripheral blood samples from 29 patients revealed that good responders had a more immunogenic tumor microenvironment (TME) at baseline, with enhanced cellular proliferation, active DNA repair pathways, and elevated STING pathway expression, along with a Th1-skewed cytokine profile in peripheral blood. Poor responders exhibited dysregulated inflammation, vascular remodeling, and T cells showing pathogen-response gene signatures indicative of chronic inflammation; in those with liver metastases, T cells showed immune senescence and metabolic hyperactivation. After RIN therapy, good responders displayed increased TME immune cell infiltration, upregulation of immune-related genes, marked expansion of previously low-frequency TCR clones in CD8 T cells, heightened naive T cell proliferation, and activation of immune and metabolic pathways. Poor responders initially showed transient increases in bulk CD8 T cells, NK cells, Th1 cytokine production, and reduced exhaustion markers but did not sustain meaningful TCR repertoire expansion. These findings underscore the potential of RIN to reshape the immunological landscape of MSS mCRC by modulating both TME and systemic immunity, highlighting the importance of predictive biomarkers to guide personalized therapeutic strategies, particularly for overcoming resistance in liver metastases.

overall_design: RNA-seq profiling was performed on FACS-sorted non-naive CD4 and CD8 T cells from PBMCs collected at baseline and after 1 and 2 cycles of RIN treatment (4 and 8 weeks).

first: Chongkai

last: Wang

first: Colt

last: Egelson

first: Weihua

last: Guo

first: Peter

middle: P

last: Lee

first: Marwan

middle: G

last: Fakih


title: Glutamine metabolism suppresses neutrophil recruitment via epigenetic regulation to control inflammatory resolution and skin repair [Multiomic]

city: NEW HAVEN

first: Yiting

last: Xu

state: CT

address: 111 Park St., Apt 9s

institute: Yale University

summary: Tissue repair requires the resolution of inflammation. However, the molecular mechanisms that attenuate inflammation in vivo are not fully understood. Here, we identify that glutamine metabolism suppresses neutrophil recruitment to abrogate inflammation and drive tissue repair. Integrated metabolomic and transcriptional profiling identified glutamine metabolism as a key feature of macrophages during inflammatory resolution. Dietary depletion studies and conditional deletion of glutaminase (Gls), the essential enzyme involved in glutamine metabolism, in innate immune cells in mice reveals an essential role for glutamine metabolism in suppressing inflammation and promoting tissue repair. Genes involved in neutrophil recruitment are upregulated in macrophages lacking Gls and in foot ulcers of diabetic patients. Multimodal single cell transcriptomics and epigenomics reveals that Gls is required for chromatin remodeling of neutrophil recruitment genes in innate immune cells during resolution of inflammation. These findings highlight the role of glutamine metabolism in controlling cellular communication during tissue repair and suppressing neutrophil recruitment to advance inflammation resolution.

overall_design: scMulti-omics profiling of macrophages isolated from wildtype and Gls cko mouse wounds  day 3 post injury.

first: Maria

last: Forni

first: Diane

last: King

first: Qiushi

last: Sun

first: Stephen

last: Siebel

first: Van Anh

last: Tran

first: Richard

last: Kibbey

first: Kathryn

last: Miller-Jensen

first: Valerie

last: Horsley


title: Glutamine metabolism suppresses neutrophil recruitment via epigenetic regulation to control inflammatory resolution and skin repair [CUT&Tag]

overall_design: CUT&Tag of H3K4me3 profiling of macrophages isolated from wildtype and Gls_cko mouse wounds day 3 post injury.


title: Glutamine metabolism suppresses neutrophil recruitment via epigenetic regulation to control inflammatory resolution and skin repair [D1D3 RNAseq]

overall_design: RNA-seq profiling of macrophages isolated from mouse wounds day 1 and day 3 post injury.


title: Glutamine metabolism suppresses neutrophil recruitment via epigenetic regulation to control inflammatory resolution and skin repair [CtrlGls_RNAseq]

overall_design: RNA-seq profiling of macrophages isolated from wildtype and Gls_cko mouse wounds day 3 post injury.


title: Aging-Associated Modulation of UFMylation Hampers Proteostasis in C. elegans

city: Jerusalem

first: Inbar

last: Plaschkes

address: The Hebrew University of Jerusalem - Ein Kerem

department: The Faculty of Medicine - Ein Kerem

country: Israel

institute: HUJI

summary: The attachment of Post-Translational Modifications (PTMs) to proteins plays key roles in the regulation of the activity and stability of various proteins. Here we utilized the nematode Caenorhabditis elegans to test whether UFMylation, a PTM that was found to be essential for key biological functions, is involved in the regulation of aging and protein homeostasis (proteostasis). Our results indicate that reduced rate of UFMylation extends lifespan and mitigates the toxicity of aggregative proteins that underlie the development of neurodegenerative disorders in humans. Mass spectrometric analysis unveiled that UFMylation of aging-regulating proteins, including components of the nucleolar FIB-1-NOL-56 complex and the germline resident proteins CAR-1 and CGH-1, governs proteostasis across tissues. Functional analyses indicate that the proteostasis-regulating transcription factors DAF-16 and SKN-1 are crucial for the counter proteotoxic effect of reduced UFMylation which is mediated by reduced rate of aggregation and enhanced protein degradation. These insights highlight the important roles of PTMs in the regulation of proteostasis and point at research directions for the development of new therapies for neurodegenerative disorders.

overall_design: 2 synchronized groups of CL2006  worms were included in the experiment. These worms express Aβ in thier body wall muscle causing a progressive  proteotoxic challegein the worm population. The worms were grown for two generations on EV bacteria or on bacteria that expressed ufm-1 RNAi at 20C.  Four independent sets of the experiment were collected (for instance EV1, EV2, EV3 and EV4). Total RNA was extracted from 6 days old worms and sent for RNA-sequencing.

first: Ehud

last: Cohen

first: Reut

last: Bruk-Haimson

first: Hana

last: boocholez

first: Huadong

last: Zhu

first: Adam

last: Zaretsky

first: Irit

first: Xiaofeng

last: Feng

first: Meng

last: Qiu Dong


title: ALKBH1-mediated DNA N6-methyladenine Modification Regulates H3K9me3-dependent Heterochromatin in Neural Tube Development II

city: beijing

first: shan

last: wang

address: 2yabao road

institute: Capital Institute of Pediatrics

summary: Neural Tube Defects (NTDs) are a class of severe congenital developmental defects caused by abnormal closure of the neural tube during early embryonic development, including conditions such as anencephaly, spina bifida, and encephalocele. Currently, NTDs are considered to result from the combined effects of genetic and environmental factors, particularly maternal folate intake during pregnancy, leading to widespread epigenetic dysregulation. However, the role of N6-methyladenine (N6-mA) in embryonic neural development remains largely unknown. Here, we found significant upregulation of Alkbh1 and concomitant significant downregulation of overall 6mA in brain tissue of a mouse model of NTDs. Further investigation through MeDIP, CUT&TAG, and single-cell sequencing revealed crosstalk between N6-mA and H3K9me3-marked heterochromatin, primarily impacting the involvement of embryonic glial cells in the formation of the hindbrain during embryonic neural tube development. These findings collectively suggest a potential epigenetic role of N6-mA in mammalian brain development, potentially exhibiting cell type specificity.

overall_design: Establishment of NTD Mouse Model: MTX is a folate antagonist. Under conditions of low folate diet in pregnant mice, we intraperitoneally injected MTX (1.5 mg/kg) at gestational day 7.5. We began observing the closure status of the neural tube in fetal mice during the neural tube closure window at E9.5-10.5. Normal mice appeared plump and round, with fully closed neural tubes, and were categorized into the normal group. Embryos from mice on low folate diet and injected with MTX exhibited varying degrees of developmental delay, smaller embryos, and primarily showed phenotypes of hindbrain malformations and spina bifida, and were categorized into the NTD group. 6mA MeDIP was performed on normal and NTD fetal brains to investigate the genomic localization of DNA 6mA and identify genomic regions enriched with DNA 6mA.

first: Xuejia

last: He

first: Jinying

last: Shen

first: Shan

last: Wang


title: Screening CRC-specific lncRNA

city: weifang

first: Jiaqiu

last: Li

address: Baotong west street No.7166

institute: shandong second medical university

summary: CRC-specific lncRNAs were identified by lncRNA microarray. The differentially expressed lncRNAs were determined between HCT116 and FHC cell (p value <0.05 and |log2FC|≥1.0).

overall_design: We detected the lncRNAs in colorectal cancer cell HCT116 and normal colon epithelial cell FHC by lncRNA microarray. We compared the lncRNA expression levels between them and got the differentially expressed lncRNAs.


title: A pathogenic alpha synuclein variant exacerabtes disease progression in a neuron-specific Gba KO mouse

city: Bethesda

first: Hannah

middle: B. D.

last: Duffy

state: MD

address: 10 Center Drive

institute: National Institutes of Health

summary: GBA variants are among the most significant genetic risk factors for synucleinopathies including Parkinson’s disease and dementia with Lewy bodies. The GBA gene encodes the lysosomal enzyme glucocerebrosidase (GBA), which is essential for glycosphingolipid catabolism. There is a reciprocal relationship between GBA and 𝛼-synuclein (𝛼-syn), in which reduced GBA levels lead to elevated 𝛼-syn. To explore this relationship specifically within neurons in vivo, we have introduced a human pathogenic variant of 𝛼-syn, A53T, into a neuron-specific Gba-KO mouse. This double variant mouse exhibited a reduced lifespan relative to the neuron-specific Gba-KO mouse and more pronounced weight loss, demonstrating a faster disease course and more severe phenotype than neuron-specific Gba-KO mice.  Additionally, their brains showed elevated levels of glucosylceramide (GlcCer) and phosphorylated 𝛼-syn compared to the single-variant mice.   Surprisingly, glucosylsphingosine (GlcSph) levels were comparable between double-variant and neuron-specific Gba-KO mice, suggesting impaired GlcSph generation. A small number of genes were significantly different between double variant and neuron-specific Gba-KO mice. These findings suggest that GlcCer accumulation, due to GBA loss, interacts with 𝛼-syn in neurons, driving increased pathogenic 𝛼-syn levels and modulating GlcCer metabolism.

overall_design: The purpose of the experiment was to better understand the combined effects of a neuron-specific GBA deficiency and a human variant of alpha synuclein (A53T) in a mouse model. Brain tissue was collected from control (GbaFlox, hSNCAA53T, Gba-nKO, and Gba-nKO/hSNCAA53T mice at approximately 13-14 weeks. Gba-nKO mice were developed using a tamoxifen-inducible Cre system. All mice were therefore fed a tamoxifen diet for 5 weeks from weaning. Bulk RNA sequencing was performed on total RNA extracted from mouse brain tissue (one hemisphere, including the cerebellum and brainstem).

first: Colleen

last: Byrnes

first: Samantha

last: Olmsted

first: Galina

last: Tuymetova

first: Sydney

middle: N

last: Pettit

first: Frances

last: Platt

first: Richard

last: Proia


title: Baseline tumor features and peripheral blood immune dynamics that underlie efficacy in MSS metastatic colorectal cancer treated with regorafenib, ipilimumab, and nivolumab

first: Jian

last: Ye

overall_design: RNA-seq profiling was performed on snap-frozen tumor biopsies collected at baseline and after 1 cycle of RIN treatment (4 weeks).

first: Chongkai

first: Colt

last: Egelson

first: Weihua

last: Guo

first: Peter

last: Lee

first: Marwan

last: Fakih


title: Disruption of ligand binding domain of the Epidermal Growth Factor Receptor by sequential knock in CRISPR/Cas9 genome editing alters its subcellular localization and phosphorylation in cervical cancer cells

city: Chicago

first: Jelena

last: Popovic

state: IL

address: 300 E Superior St. Tarry 4-770

department: Radiation Oncology

institute: Northwestern University

summary: Upregulation of Epidermal Growth Factor Receptor is evident in most cases of cervical cancer and is usually associated with a poor prognosis. At the same time, therapies directed against EGFR are generally not successful in this type of cancer, which suggests that therapeutic inactivation of EGFR can be easily overcome. In order to evaluate mechanisms by which cervical cancers with alterations in EGFR signaling thrive, we have generated several EGFR mutant clones by CRISPR/Cas9 genome editing. This work details the approach used to generate EGFR mutant cells and describes changes in cell characteristics associated with decreased quantity and altered subcellular distribution of EGFR.

overall_design: We performed CRISPR/Cas9 experiments with the intention to introduce amino acid substitutions into EGF binding region of EGFR gene in cervical cancer cell line ME180 genome. We porformed Whole genome sequencing in order to get full insight into CRISPR/Cas9 results in 5 single cell isolated clones  The aim of this approach was to precisely evaluate the variants of EGFR across the entire EGFR gene region and to compare the entire genomes between the clones and wild type cells.

first: Anna

last: Hahut

first: Tatjana

last: Paunesku

first: Gayle

last: Woloschak


title: RNase H1-dependent R-loop Clearance is a Prerequisite for Genome Silencing in Mouse Oogenesis [Stacc-seq]

city: Nanning

first: liu

last: shaoyuan

address: Guangxi province of china

institute: Guangxi university

summary: The raw Stacc_seq data

overall_design: The Stacc-seq was based on the published research with some modifications. Firstly, oocytes at different stages were microinjected with NLS-3xHBD-HA mRNA and then incubated in M2 medium with 2 M milrinone for 6 hours.

first: Qianqian

last: Sha

first: Shaoyuan

last: Liu


title: Granulocyte Derived Resistin Induces Classical Monocyte Repartition and Immune Suppression in CMML

city: Manchester

first: Kiran

last: Batta

address: The University of Manchester

country: United Kingdom

institute: University of Manchester

summary: Chronic myelomonocytic leukemia (CMML) is a clonal malignancy characterized by overlapping myeloid dysplasia and proliferation with persisting monocytosis. Characteristic repartitioning of classical monocytes is now a supporting diagnostic criterion (WHO5), though its mechanistic basis remains unknown. While monocytes are the cardinal malignant cell type in CMML, as a stem cell neoplasm the disease clone comprises most lineages and differentiation stages including granulocytes.  To investigate the pathogenic contribution of granulocytes in CMML maintenance and progression, we have performed molecular and functional characterization of CMML granulocytes. Compared with healthy age-matched controls, CMML granulocytes exhibited defective maturation with reduced granularity and phagocytic capacity. Transcriptome analysis revealed activation of pathways linked to proliferation, Myc activity and inflammation. Notably, RETN, which encodes inflammatory mediator Resistin, was upregulated 100-fold in CMML granulocytes; but not differentially expressed in CMML PBMNCs, sorted monocytes, or stem and progenitor cells compared to their healthy counterparts. Accordingly, Resistin protein levels were 10-fold higher in plasma from CMML patients and higher plasma Resistin levels correlate with poor overall survival. Remarkably, exposure of healthy monocytes to exogenous recombinant Resistin induced classical monocyte repartition, recapitulating the pattern seen in CMML, and inhibited macrophage differentiation. Transcriptome analysis of Resistin treated monocytes revealed that Resistin induces gene signatures related to immune suppression and myeloid-derived suppressor cell phenotype. We found SEMA4A to be a downstream target of Resisin and is overexpressed in CMML monocytes.  Consistent with known roles for SEMA4A, CMML patients displayed higher percentage of T-regs and elevated Th2/Th1 ratio compared with healthy controls, apparently corresponding with associated Resistin levels. Furthermore, we demonstrated that Resistin directly induces the T-reg expansion and skews the Th2/Th1 ratio by binding to monocytes. In conclusion, we showed that immature granulocytes in CMML produce high levels of Resistin, which contributes to classical monocytosis phenotype and immune suppression.

overall_design: CD14 positive monocytes were sorted from healthy PBMCs using MACS separation and seeded into 12 well plates at 5 x 105 cells/ml and subjected to either GFP, resistin or LPS for 6 or 24 hours. Following treatment cells were subjected to RNA isolation and RNA-seq.

first: Nathan

last: Hull

first: Kristian

last: Gurashi


title: Therapeutic circRNA aptamer alleviates PKR-associated osteoarthritis

first: Li

last: Yang

address: 131 Dong-An Road

department: Institutes of Biological Sciences

institute: Fudan University

summary: Osteoarthritis(OA) is characterized as an inflammation-related disease. Recent studies have identified pattern recognition receptors (PRRs) as key regulators in auto-inflammatory diseases. Protein kinase R (PKR) is a key member of PRRs in vertebrates that recognizes long double-stranded RNAs (dsRNAs) produced from viruses or aberrant cellular dsRNAs. We found out that a general consistency with previous reports that aberrant PKR activation was associated with the OA pathogenesis upon dsRNA stress rather than other stimulations[12], but the role of PKR in the mouse model of OA has not been specified. we selected chondrocytes as the primary target cells to examine the potential application of ds-cRNA(circCAMSAP1 and EPIC) aptamers in OA.And ds-cRNAs delivery showed minimized inflammatory response, high efficacy, safety and beneficial effects on OA phenotypes.

overall_design: To make sure IVT circCAMSAP1 contain short dsRNA region, we perform circSHAPE-MaP of IVT circCAMSAP1.

first: Si-Kun

first: Fang

first: Ling-Ling

last: Chen


title: Interrupting T cell memory ameliorates exaggerated metabolic response to weight cycling

city: Nashville

first: Matthew

last: Cottam

state: TN

address: 2301 Vanderbilt Place

department: Surgical Sciences

institute: Vanderbilt University Medical Center

summary: People frequently go through cycles of weight gain and loss. This weight cycling has been demonstrated, in humans and animal models, to increase cardiometabolic disease and disrupt glucose homeostasis. Obesity itself — and to an even greater extent weight regain — causes adipose tissue inflammation, resulting in metabolic dysfunction. Studies show that even after weight loss, increased numbers of lipid associated macrophages and memory T cells persist in adipose tissue and become more inflammatory upon weight regain. These findings suggest that the immune system retains a "memory" of obesity, which may contribute to the elevated inflammation and metabolic dysfunction associated with weight cycling. Here, we show that blocking the CD70-CD27 axis, responsible for immunological memory, decreases the number of memory T cells and reduces T cell clonality within adipose tissue after weight loss and weight cycling. Furthermore, while mice with impaired ability to create obesogenic immune memory have similar metabolic responses as wildtype mice to stable obesity, they are protected from the worsened glucose tolerance associated with weight cycling. Our data are the first to target metabolic consequences of weight cycling through an immunomodulatory mechanism. Thus, we propose a new avenue of therapeutic intervention by which targeting memory T cells can be leveraged to minimize the adverse consequences of weight cycling. These findings are particularly timely given the increasing use of efficacious weight loss drugs, which will likely lead to more instances of human weight cycling.

overall_design: Immune cells from mouse epididymal adipose tissue were isolated by FACS according to the presence or absence of CD45+ and CD4/8+ and analyzed by scRNAseq.

first: Jamie

last: Garcia

middle: C

last: Winn

first: Alec

last: Rodriguez

first: Anwar

middle: F

last: Hussein Agha

first: Alyssa

middle: H

last: Hasty


title: Streptococcus parasanguinis Transcriptomics Data with and without Exogenous Nitrite

city: Birmingham

first: Sara

middle: Elizabeth

last: Edmonds

state: AL

address: 1720 2nd Ave South, BBRB 744

department: Microbiology

institute: University of Alabama at Birmingham

summary: Oral commensal streptococci play a large role in mediating microbial homeostasis. Our published findings have demonstrated that hydrogen peroxide (H2O2) produced by oral commensal streptococci can react with salivary nitrite (NO2) and generate peroxynitrite (ONOO-), a potent antimicrobial. We have shown that the combinatorial antimicrobial effects of NO2 and H2O2 produced from the commensal Streptococcus parasanguinis, inhibit the colonization and pathogenesis of oral pathogens to promote homeostasis. Remarkably, S. parasanguinis is highly resistant to the NO2 and ONOO-. However, it remains unclear how S. parasanguinis copes in the presence of nitrosative stress. The goal of this study was to identify mechanisms used by S. parasanguinis to resist NO2-mediated nitrosative stress using a transcriptomics approach. Transcriptomic analysis showed that the competence response regulator, comE, is upregulated in the presence of NO2. Loss of comE resulted in a decrease in biofilm development, H2O2 production, increased acid tolerance and sensitivity to ONOO- compared to wild-type S. parasanguinis. Our data show that ComE is critical for key aspects of S. parasanguinis physiology and potentially impacts this commensal's ability to colonize and modulate homeostasis in the oral cavity.

overall_design: Wild-type Streptococcus parasanguinis were grown in the presence of 2 mM of Nitrite in Todd-Hewitt Broth to late-exponential phase and RNA was harvested for RNA-sequencing analysis.

first: Hernan

last: Grenett

first: Jessica

last: Scoffield


title: RNase H1-dependent R-loop Clearance is a Prerequisite for Genome Silencing in Mouse Oogenesis

first: liu

last: shaoyuan

summary: The raw ATAC_seq data

overall_design: Each sample contains 50 oocytes collected from mated female mice at 44 hours after PMSG injection. Oocytes were washed with DNase/RNase-free 0.01% BSA and collected in DNA-lowing binding tubes. Lysis buffer (0.05% digitonin, 0.5% NP-40, and 0.5% Tween20) were added immediately after sample collection.

first: Qianqian


title: Metabolic reprogramming and ferroptosis occurring in granulosa cells from patients with diminished ovarian reserve

city: Shanghai

first: Jiani

last: Lu

address: No.85 Wujin Rd.

institute: Shanghai General Hospital

summary: Granulosa cell (GC) dysfunction contributes to diminished ovarian reserve (DOR). We collected GC and follicular fluid samples from the patients of normal ovarian reserve (NOR) and DOR. RNA-seq of GCs showed that cholesterol/sterol metabolism and biosynthesis and extracellular matrix organization were enriched in the DOR group. Metabolomics of follicular fluid revealed enrichment in steroid hormone biosynthesis, tryptophan metabolism, and fatty acid β-oxidation in DOR. The apoptosis rate was increased, whereas the proliferative rate was decreased in GCs of DOR. The Prussian blue staining rate was increased whilst GPX4 and SLC7A11 expression were downregulated in GCs of DOR. Mitochondrial morphology displayed the features of ferroptosis in GCs of DOR. FSHR, CYP19A1, NR5A1, and phosphorylated CREB levels were substantially downregulated in GCs, accompanied by increased androgen levels in follicular fluids in DOR. The key factors linked to the mevalonate pathway, HMGCR, SQLE, and SREBF2, were robustly increased in DOR. FSHR and NR5A1 levels were correlated with CYP19A1 levels, whilst CYP19A1 levels were positively correlated with GPX4 and SLC7A11 levels. Our findings indicate ferroptosis and dysregulation of cholesterol/sterol metabolism and biosynthesis occurrence in GCs of DOR, which might be associated with reduced FSHR signaling and decreased conversion of androgen to estrogen.

overall_design: RNA-seq profiling of the granulosa cells of the ovarian follicles from the patients with diminished ovarian reserve and normal ovarian reserve

first: Yan

last: Huang

first: Yang

last: Yu

first: Yalin

last: Shan

first: Zhengshan

last: Tang

first: Mingyang

last: Li

first: Xinyu

last: Guo

first: Xin

last: Ni


title: BCAA Metabolism Promotes Tumorigenesis of Lung Cancer through Cholesterol Synthesis Modification

city: Nanjing

first: Huimin

last: Ma

address: 101 Longmian Avenue, Jiangning District, Nanjing City

department: School of Public Health

institute: nanjin medical university

summary: To investigate the downstream gene expression characteristics regulated by AUH in A549 cells, we generated AUH knockdown A549 cells and analyzed the transcriptome changes through double ended RNA-seq.

overall_design: RNA-seq sequencing analysis of A549 cells compared to AUH knockdown A549 cells (si-NC and si-AUH)

first: Erbao

last: Zhang


title: Mitochondrial Protein Import Stress Causes Lysosomal Damage and Tissue Atrophy

city: Syracuse

first: Nicholas

last: Brennan

state: New York

address: 766 Irving Ave

department: Biochemistry and Molecular Biology

institute: SUNY Upstate Medical University

summary: Mitochondrial abnormalities are commonly associated with aging-related degenerative disease and the atrophy of tissues including muscle and brain. Whether bioenergetic defect is the sole pathogenic factor has been long questioned. Lysosomal damage is another hallmark of degenerative disease. However, it is unknown whether these two pathogenic pathways affect tissue homeostasis independently, convergently or epistatically. Here, we show that mitochondrial protein import stress, which can be induced by many forms of mitochondrial injuries, causes structural and functional damage to the yeast vacuole and its mouse counterpart, the lysosome. This effect is independent of bioenergetic defects and the production of reactive oxygen species. We found that unimported mitochondrial proteins are targeted to the vacuole for degradation in yeast. Overloading by these proteins causes V-ATPase disassembly, and vacuolar deacidification, fragmentation and membrane permeabilization. In a mouse model of mitochondrial protein import stress and muscle atrophy induced by overloading of the mitochondrial protein ANT1, genes involved in amino acid uptake/biosynthesis, one-carbon metabolism, nucleotide biosynthesis, lysosomal biogenesis and iron homeostasis are activated. These signatures are recapitulated in yeast mutants of severe vacuolar damage. Supporting lysosomal dysfunction, the Ant1-transgenic muscles accumulate glycogens, lipofuscins and poorly processed multiple vesicle bodies. Multiple lysosomal repair and lysophagic pathways are activated. Luminal proteolytic enzymes including cathepsins are released into the cytosol, which likely contributes to imbalanced cellular proteostasis, reduced myofiber size and progressive muscle atrophy. In summary, we show an evolutionarily conserved pathway wherein mitochondrial defect can epistatically cause proteostatic damage to the lysosome thereby leading to tissue atrophy. This finding could help the better understanding of how the mitochondrial and lysosomal pathways of pathogenesis interact to cause degenerative disease.

sample_organism:
Saccharomyces cerevisiae
Mus musculus

platform_organism:
Saccharomyces cerevisiae
Mus musculus

overall_design:
Quadricep skeletal muscle mRNA profiles of 2-month-old wild type (WT) and Ant1-transgenic overexpressing female mice were generated by stranded paired-end RNA sequencing, in quadruplicate, using Illumina NextSeq500.
Yeast cells were grown in YP+2% galactose+ 2% raffinose to mid-log phase of OD600 around 1.0. mRNA profiles of wildtype, vma13, GAL10-AAC2 and vma13_GAL10-AAC2 were generated by stranded paired-end RNA sequencing, in triplicate, using Illumina NextSeq2000.

first: Xiaowen

last: Wang

first: Arnav

last: Rana

first: Sanaea

last: Bhagwagar

first: Jason

last: Horton

first: Patricia

last: Kane

first: Xin Jie

last: Chen


title: RNase H1-dependent R-loop Clearance is a Prerequisite for Genome Silencing in Mouse Oogenesis [RNA-Seq]

first: liu

last: shaoyuan

summary: The raw RNA_seq data

overall_design: Oocytes were collected from the indicated genotypes (10 oocytes per sample). Each sample was lysed directly using 4 μL lysis buffer (0.2% Triton X-100, RNase inhibitor, dNTPs, oligo-dT primers, and 100 pg ERCC mRNA spike-in) and immediately used for cDNA synthesis using the Smart-seq2 method as previously described.

first: Qianqian

last: Sha

first: Shaoyuan

last: Liu


title: An IL-33–LMO4 axis instructs type 2 myelopoiesis via GATA factor re-allocation (BMT LMO4 RNA-Seq)

city: Oxford

first: Claus

last: Nerlov

address: John Radcliffe Hospital, University of Oxford

department: MRC Molecular Haematology Unit

institute: Weatheral Institute of Molecular Medicine

summary: In this study we examine the role of LMO4 and it regulation by helminth infection in type 2 myelopoiesis. The effect of LMO4 on type 2 myeloid progenitors is examined by RNAseq and ATACseq, as well as functional readouts, to establish the mechanism by which LMO4 carries out its lineage instructive effect.

overall_design: LMO4 was introduced into murine HSPCs by lentiviral transduction and cells transplanted into recipient mice. After engraftment, progenitor cell populations were isolated by cell sorting and subjected to bulk RNAseq.

first: Alexandre

last: Fagnan

first: Cristina

last: Di Genua

first: Roy

last: Drissen

first: Zishan

first: Yiran

last: Meng

first: Fränze

last: Progatzky


title: An IL-33–LMO4 axis instructs type 2 myelopoiesis via GATA factor re-allocation (IL33 RNA-Seq)

overall_design: Progenitor cell populations were isolated by cell sorting from control mice and mice injected with IL-33, respectively, and subjected to bulk RNAseq.

last: Zhang


title: An IL-33–LMO4 axis instructs type 2 myelopoiesis via GATA factor re-allocation (G320D RNA-Seq)

overall_design: HSPCs from control and Gata2 G320D mutant mice were transplanted into recipient mice. After engraftment, progenitor cell populations were isolated by cell sorting and subjected to bulk RNAseq.


title: An IL-33–LMO4 axis instructs type 2 myelopoiesis via GATA factor re-allocation (BMT LMO4 ATAC-Seq)

overall_design: LMO4 was introduced into murine HSPCs by lentiviral transduction and cells transplanted into recipient mice. After engraftment, progenitor cell populations were isolated by cell sorting and subjected to bulk ATACseq.


title: An IL-33–LMO4 axis instructs type 2 myelopoiesis via GATA factor re-allocation

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: An IL-33–LMO4 axis instructs type 2 myelopoiesis via GATA factor re-allocation (G320D ATAC-Seq)

overall_design: HSPCs from control and Gata2 G320D mutant mice were transplanted into recipient mice. After engraftment, progenitor cell populations were isolated by cell sorting and subjected to bulk ATACseq.


title: Real-time visualization of spliceosome assembly reveals basic principles of splice site selection

first: Daniel

middle: R

last: Larson

address: 41 Medlar Dr.

institute: NIH

summary: The spliceosome is a megadalton protein-RNA complex which removes introns from pre-mRNA, yet the dynamic early assembly steps have not been structurally resolved. Specifically, how the spliceosome selects the correct 3’ splice site (3’SS) amongst highly similar non-functional sites is not known. Here, we develop a kinetic model of splice site selection based on single-molecule U2AF heterodimer imaging in vitro and in vivo. The model successfully predicts alternative splicing patterns and indicates that 3’SS selection occurs while U2AF is in complex with the spliceosome, not during initial binding. This finding indicates the spliceosome operates in a ‘partial’ kinetic proofreading regime, catalyzed in part by the helicase DDX42, which increases selectivity to the underlying U2AF binding site while still allowing for efficient forward progression.

overall_design:
To investigate the relationship betwen relative binding site strength and 3' splice site selection, we performed RNA sequencing in human bronchial epithial cells (HBECs) under two conditions (a) transfection with control siRNA and (b) transfection with DDX42 siRNA.
We then performed transcript quantification and alternative splicing analysis using data obtained from RNA-seq of siControl and siDDX42 samples.

first: Benjamin

middle: T

last: Donovan

first: Bixuan


title: An IL-33–LMO4 axis instructs type 2 myelopoiesis via GATA factor re-allocation (H. polygyrus RNA-Seq)

overall_design: Progenitor cell populations were isolated by cell sorting from control mice and mice infected with H Polygyrus for 4 and 11 days, respectively, and subjected to bulk RNAseq.


title: Single cell transcriptome sequencing analysis of gene expression in blood PBMCs of patients with systemic lupus treated with belimumab

city: Weifang

first: Wenchang

last: Sun

state: Shandong

address: No.151，Guangwen street

institute: The First Affiliated Hospital of Weifang Medical University

summary: Single cell transcriptome sequencing to detect genes in PBMC of patients with systemic lupus erythematosus treated with belimumab.

overall_design: This study included three confirmed SLE patients treated with belimumab (SLE_BAFF). According to the 2019 European Union Against Rheumatology (EULAR) and American Society of Rheumatology (ACR) EULAR/ACR criteria, patients diagnosed with systemic lupus erythematosus (SLE) are classified. Patients with immune diseases such as malignant tumors or rheumatoid arthritis were excluded from the study. This study was approved by the Medical Ethics Committee of the First Affiliated Hospital of Shandong Second Medical University. Prior to the test, all participants provided written informed consent and the study complied with the ethical guidelines outlined in the Helsinki Declaration. Collect peripheral blood samples from patients and separate peripheral blood mononuclear cells (PBMCs) using Ficoll Paque gradient centrifugation. Mix three freshly isolated PBMCs and resuspend them in fetal bovine serum with 10% dimethyl sulfoxide. Freeze at -80 ° C for at least 4 hours, store them in liquid nitrogen, and then use them for single-cell transcriptome sequencing (scRNA seq).


title: Depot-Specific Differences and heterogeneity of Adipose-Derived Stem Cells in Diet-Induced Obesity

city: Jinan

first: Honglin

last: Guo

address: No. 324, Jingwu Road

department: Department of Pathology, Department of Endocrinology

institute: Shandong University, Shandong Provincial Hospital

summary: Obesity is a global health concern. Studying the heterogeneity of ADSCs play pivotal roles in understanding metabolic disorders such as obesity. Using Mass cytometry, we discerned the spatial heterogeneity of ADSCs and their alterations at the single cell level in a diet-induced-obesity (DIO) model treated with Liraglutide. We characterized the relationship of ADSCs markers and found that CD26 and CD142 are capable of identifying the most representative heterogeneous ADSCs in Subcutaneous Adipose Tissue (SAT) and Visceral Adipose Tissue (VAT). Specifically, CD26+CD142- and CD26+CD142+ADSCs were exclusive to SAT and VAT, respectively, while CD26-CD142+ADSCs were present in both.  To acquire more robust examination of the expression variances for a range of functional markers within these depot-specific heterogeneous subpopulations, transcriptomic sequencing was performed on the Fluorescence-activated cell sorting (FACS) sorted CD26+CD142-, CD26+CD142+ and CD26-CD142+ ADSCs from SAT and VAT of chow diet mice. In the VAT of DIO mice, we observed significant down-regulation of CD26+CD142+ ADSCs and up-regulation of CD26-CD142+ ADSCs, both of which could be mitigated by Liraglutide. Our research illuminates the spatial heterogeneity of ADSCs and their alterations under DIO, which can be potentially reversed by Liraglutide treatment. This study contributes new insights for identifying more specific ADSCs subgroups to explore the etiology for metabolic-related diseases.

overall_design: FACS was performed on SVFs from SAT and VAT of 30 chow diet mice (12-14 weeks old) to obtain ADSCs subclusters with different expression pattern of CD26 and CD142. A total of 5 samples were obtained from FACS sorting, which included a single sample for SAT_CD142+, SAT_CD26+CD142-, VAT_CD26+CD142+ ADSCs, and two samples for VAT_CD142+ ADSCs.  Transcriptomic sequencing was performed on these FACS sorted ADSCs subpopulations.

first: Xu

last: Hou

first: Ailing

last: Sheng


title: Single cell profiling reveals three endothelial to hematopoietic transitions with divergent isoform expression landscapes

first: Georges

last: Lacaud

state: England

address: Wilmslow Raod

department: Stem Cell Biology

institute: Cancer Research UK Manchester Institute

summary: Hemogenic endothelium (HE) is recognized as the origin of all definitive blood cells including hematopoietic stem cells (HSC). However, the mechanisms governing the hematopoietic progenitor versus HSC fate choice within the HE remains unknown. To explore this, we combined differentiation assays with full-length single-cell transcriptome data for extra-embryonic yolk sac (YS) and intra-embryonic aorta–gonad–mesonephros (AGM) region HE populations. We identified and localized three differentiation trajectories, each containing a distinct HE subset and potential: erythro-myeloid progenitor-primed HE in the YS plexus, lympho-myeloid progenitor-primed HE in large YS arteries, and HSC-primed HE in the AGM. Chromatin modifiers and spliceosome components were enriched AGM HE. Nanopore long-read sequencing identified AGM specific, functionally unique, splice variants of stemness-associated factors Runx1, Mecom, and Dnmt3b. Our data indicate that isoform expression changes are associated with HSC generation and provide a unique resource for studying cell fate decisions in HE.

overall_design: Long Read single cell RNA-seq of cells undergoing hemogenic to endothelial transition in AGM at E9.5 and E10.5 and Yolk Sac (YS) at E9, E9.5, E10.5.  To study the HE populations present at different anatomical locations and time points during the mouse development, we used transgenic reporter mouse lines GFI1-GFP and RUNX1B-RFP and performed Oxford Nanopore Long Read Sequencing (single cell RNA seq) on FACS isolated E9.5 and E10.5 AGM HE cells (RUNX1+, KIT-,CDH5+, GFI1+/-, CD41-, CD45-), and E9, E9.5, E10.5 YS HE cells (RUNX1+, KIT+, GFI1+/-, CD31+, CD41-, CD45-). Total 27 cells were used. We selected 9 cells from the middle of AGM_3 and AGM_4 cluster for AGM HE (HE-HSC),  9 cells from the middle of YS_m1 and YS_m2 as YSm HE (HE-LMP) and 9 cells from the middle of YS_b2 and YS_b3 as YSb HE (HE-EMP).

first: Wen

last: Neo

first: Muhammad

last: Zaki Hidayatullah Fadlullah

first: Harshangda

last: Bhatnagar

first: Cristiana

last: Barone

first: Giulia

last: Quattrini

first: Filipa

last: Timóteo-Ferreira

first: Joana

last: Carrelha

first: Gianluca

last: Sala

first: John

last: Weightman

first: Wolfgang

last: Breitwieser

first: Natalia

last: Moncaut

first: Roshana

last: Thambyrajah

first: Sten

middle: E

last: Jacobsen

first: Mudassar

last: Iqbal

first: Syed

last: Baker

first: Emanuele

last: Azzoni

first: Michael

last: Lie-A-Ling


title: Single-cell transcriptomics identifies altered neutrophil dynamics and accentuated T-cell cytotoxicity in tobacco -flavored e-cigarette -exposed mouse lungs

city: Rochester

first: Gagandeep

last: Kaur

address: 601 Elmwood Ave

department: Environmental Medicine

institute: University of Rochester Medical Center

summary: E-cigarettes (e-cigs) are a public health concern for young adults due to evidence for increased oxidative stress, lipid dysfunction, and inflammation. Yet an extensive study defining the cell-specific alterations on exposure to flavored e-cigs remains elusive. To understand the immunological lung landscape upon exposure to flavored e-cig (mango-, menthol- or tobacco-flavor) aerosols we performed single cell RNA sequencing (scRNA seq).

overall_design: C57BL/6J mice were exposed to 5-day nose-only exposure to air, propylene glycol: vegetable glycerin (PG:VG), mango-, menthol- and tobacco-flavored e-cig aerosols. Following exposure the mouse lungs were perfused, harvested and digested to obtain single cell suspension. scRNA seq was performed on the thus obtained single cell suspension.

first: Thomas

last: Lamb

first: Ariel

last: Tjitropranoto

first: Irfan

last: Rahman


title: Royal Jelly Acid in Ulcerative Colitis Treatment: Modulating miR-210-3P/Gbp3 Pathway and Pyroptosis via miRNA Expression and NLRP3 Inflammasome (miRNA-Seq)

city: Changchun

first: Mingchuan

last: Wang

state: Jilin

address: No. 126, Xiantai Street

department: Department of Gastrointestinal Colorectal and Anal Surgery

institute: China-Japan Union Hospital of  Jilin University

summary: This study investigates the therapeutic effects of RJA (purity 99.42%) on DSS-induced colitis in male C57BL/6J mice. Using high-throughput miRNA sequencing, we analyzed the miRNA expression profiles in mouse colon samples. The study revealed significant changes in miRNA expression in response to DSS and RJA treatments, identifying potential molecular mechanisms behind RJA's protective effects against DSS-induced colitis.

overall_design: Study Type: High-throughput sequencing of miRNA. Organism: Mus musculus (C57BL/6J mice). Total Number of Samples: 9 Groups/Conditions: Control group (normal diet and water). DSS-treated group (2.5% DSS in drinking water). RJA group (2.5% DSS in drinking water + RJA treatment). Sample Source: colon samples from mice. Specific Focus: miRNA sequencing to analyze differential gene expression in response to DSS and RJA treatment.

first: Mengyuan

first: Xinyi

last: Gao

first: Yang

last: Jiang


title: Transcriptomic effects of caspase cleavage at TFIIB residue D207 during apoptosis and KSHV infection [TFIIB(D207A)]

city: Berkeley

first: Britt

last: Glaunsinger

address: RM 565, 1951 Oxford St

department: PMB

institute: University of California, Berkeley

summary: Cellular stressors often cause widespread repression of RNA polymerase II (RNAP II) activity, which is thought to facilitate a focused transcriptional output towards stress resolution. In many cases, however, the underlying regulatory mechanisms remain unknown. Here, we demonstrate that stress-induced downregulation of the general transcription factor TFIIB tempers expression of specific stimulus response genes. Following a variety of stressors, TFIIB is proteolytically cleaved between its cyclin folds at conserved aspartic acid residue D207 by caspases- 3 and 7. Cleavage in this portion of the protein significantly reduces the ability of TFIIB to form a TBP-TFIIB-DNA promoter complex in vitro. Using both overexpression and endogenous base-editing, we find that B and T cells that are unable to cleave TFIIB upregulate expression of a select gene set during apoptosis. These TFIIB-sensitive genes are primarily short, stimulus-responsive and proto-oncogenic loci, and cleavage of TFIIB temporally restricts their expression. Failure to cleave TFIIB during stress leads to aberrant lymphocyte proliferation during chemical perturbation. Hence, caspase targeting of TFIIB destabilizes transcription to tune gene expression, allowing for proper stress resolution.

overall_design: The effects of caspase-driven TFIIB depletion on gene expression during apoptosis and lytic KSHV infection were assessed by comparing cells exogenously overexpressing TFIIB-2xStrep ("WT") or caspase-resistant TFIIB(D207A)-2xStrep ("D207A"). Cells were mock treated, treated with the extrinsic apoptosis inducer TRAIL, or treated with doxycycline ("DOX") to initiate lytic viral infection for 24 or 48 hours. This was followed by RNA-seq and differential gene expression analysis.

first: Leah

last: Gulyas


title: PRC2 primes bivalent target genes for transcription induction independent of histone methyltransferase activity [ChIP-seq]

city: Tianjin

first: xuejiao

last: lv

state: Tianjin

address: No.22 Qixiangtai Rd

institute: Tianjin Medical University

summary: The loss of PRC2 results in decelerated kinetics of transcription induction of its target genes. Mechanistically, PRC2 deletion rather than its inactivation impairs ERK activity, and therefore leads to loss of phosphorylated RNA polymerase II (RNAPII) at serine-5, which is critical for rapid induction of bivalent genes. To further support these findings, ectopic expression of constitutively active ERK in PRC2-null embryonic stem cells partially restores transcription induction kinetics. Therefore, these findings propose a priming function of PRC2 in maintaining poised RNAPII and differentiation potential, extending its role beyond preserving cellular identity.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for the histone modification H3K27me3 and ERK2, RNAPII in WT and EZH2 KO ESCs.

first: Meihan

last: Gong

first: Ye

last: Yuan

first: Zhongye

last: Dai

first: Xuejiao

last: LV


title: The BMAL1/HIF2A heterodimer modulates circadian variations of myocardial injury (human)

city: Houston

first: Holger

middle: K.

last: Eltzschig

state: TX

department: Department of Anesthesiology

institute: The University of Texas Health Science Center at Houston

summary: Cardiac injury following myocardial infarction exhibits a circadian pattern, yet the underlying mechanism remains unclear. To elucidate genes governing circadian variation of myocardial injury, we conducted transcriptomic profiling of left-ventricular tissues from mice or humans experiencing myocardial injury at different daytimes. Through comprehensive analyses, including transgenic mouse models and functional studies, we identified BMAL1 as a pivotal transcription factor modulating diurnal variation of myocardial injury. Remarkably, we discovered that BMAL1 regulates circadian-dependent cardiac injury by forming a transcriptionally active heterodimer with HIF2A. Substantiating this finding, we determined the cryo-EM structure of the BMAL1/HIF2F/DNA complex, revealing a previously unknown capacity for structural rearrangement within BMAL1. Furthermore, we confirmed amphiregulin (AREG) as a transcriptional target of the BMAL1/HIF2A heterodimer, critical for modulating circadian variation of myocardial injury. Finally, targeting the BMAL1/HIF2A-AREG pathway via timed AREG administration or enhancing circadian rhythm pharmacologically offered significant cardioprotection, implicating this pathway in treating ischemic heart disease.

overall_design:
We examined samples from a prospective study of myocardial injury in humans during cardiac surgery (clinicaltrials.gov: NCT00281164). The study population consisted of consecutive patients (aged ≥20 years) with aortic stenosis referred to our cardiovascular surgery department at Brigham and Women's Hospital (MA, USA) for aortic valve replacement (with or without coronary artery bypass graft) between Jan 1, 2009, and Dec 31, 2014. Patients enrolled in a concurrent drug or device trial were excluded. This ongoing study involved 56 patients in the morning (samples collected between 8:00 am-12:00 pm, median time 10:32 am) and 17 patients who underwent the same procedure in the afternoon (samples collected between 3:00-9:00 pm, median time 5:15 pm). Patients whose surgery fell between our outside of these time periods were excluded from the analysis. The ethics committee of our institution approved the protocol, and written informed consent was obtained from all patients.
Patients underwent aortic valve replacement either in the morning or in the afternoon by the same senior surgeon. Anesthesia, cardiopulmonary bypass, cardioplegia, and surgical procedures were done according to standard guidelines. Anesthesia was induced with intravenous fentanyl or sufentanil and propofol (0.5-1.5 mg/kg) and maintained with isoflurane. Surgery was done using normothermic cardiopulmonary bypass and repeated antegrade and retrograde cold blood cardioplegia. Left ventricular biopsy samples from the morning and afternoon patient cohorts were obtained after approximately 80 minutes of aortic cross-clamping at the site of the routinely placed left ventricular vent.

first: Wei

last: Ruan

first: Tao

last: Li

first: Jaewoong

last: Lee

first: In

last: Bang

first: Wankun

last: Deng

first: Xinxin

last: Ma

first: Seung-Hee

last: Yoo

first: Boyun

last: Kim

first: Jiwen

first: Xiaoyi

first: Yu

last: An

first: Yin-Ying

first: Yafen

last: Liang

first: Matthew

last: Deberge

first: Dongze

last: Zhang

first: Zhen

last: Zhou

first: Yanyu

first: Josh

last: Gorham

first: Jonathan

last: Seidman

first: Christine

first: Sary

last: Aranki

first: Ragini

last: Nair

first: Lei

first: Jagat

last: Narula

first: Zhongming

last: Zhao

first: Jochen

middle: D

last: Muehlschlegel

first: Kuang-Lei

last: Tsai

middle: K


title: PRC2 primes bivalent target genes for transcription induction independent of histone methyltransferase activity [RNA-seq]

first: xuejiao

last: lv

overall_design: Ezh2f/f and Ezh2-/- ESCs were treatment by retinoic acid (RA) for 0,3,6h, and then extract RNA for sequencing.

first: Meihan

last: Gong

first: Ye

last: Yuan

first: Zhongye

last: Dai

first: Xuejiao

last: LV


title: Multimodal remodeling of epigenetic and enhancer networks shapes the transcriptional landscape of beige adipocytes

city: Oslo

first: Philippe

last: Collas

address: PO Box 1112 Blindern

department: Institute of Basic Medical Sciences

institute: University of Oslo


title: Transcriptomics-based analysis of sex-differentiated mechanisms of hepatotoxicity of long-term exposure to bisphenol AF in adult zebrafish (Danio rerio)

first: Xiaoyu

state: Shanghai

address: Shangda Road, no.99, Shanghai University

department: School of Environmental and Chemical Engineering

institute: Shanghai University

summary: Bisphenol AF (BPAF) is an emerging contaminant prevalent in the environment as one of the main substitutes for bisphenol A. And gender is an important factor in the study of biological toxicity of endocrine disruptors, but the mechanism remains unclear. Four-month-old male and female zebrafish were exposed to 10 μg/L BPAF for 28 days, separately. Sex differences in liver injury and toxicity were predicted by transcriptional changes assessed by the enriched Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Ingenuity Pathway Analysis (IPA). More differentially expressed genes were detected in males (811) than in females (195), spermatogenesis was the top GO term in males, circadian regulation of gene expression was most abundant in females, and qRT-PCR results verified the expression of related genes. Consistent with the effects predicted by transcriptional changes, the pathological analysis showed that male livers exhibited significant vacuolization, which did not occur in female tissues, suggesting that BPAF may have a greater effect on male livers than females. In addition, upstream regulatory molecules of BPAF toxicity in male and female fish were also predicted respectively, contributing to a more in-depth mechanistic study. Overall, BPAF affects liver metabolism in different ways in zebrafish of different sexes.

overall_design: Causal analysis of mathematical differences in RNA-seq of male and female zebrafish liver tissues.

first: Yuanyuan

first: Ming

last: Yang


title: Royal Jelly Acid in Ulcerative Colitis Treatment: Modulating miR-210-3P/Gbp3 Pathway and Pyroptosis via miRNA Expression and NLRP3 Inflammasome

first: Mingchuan

last: Wang

summary: This study focuses on the mRNA sequencing analysis of DSS-induced colitis in mice and examines the therapeutic effects of RJA.  We conducted high-throughput mRNA sequencing to explore gene expression changes and the molecular mechanisms by which RJA mitigates colitis symptoms in DSS-treated mice.

overall_design: Study Type: High-throughput sequencing of mRNA. Organism: Mus musculus (C57BL/6J mice). Total Number of Samples: 9 Groups/Conditions: Control group (normal diet and water). DSS-treated group (2.5% DSS in drinking water). RJA group (2.5% DSS in drinking water + RJA treatment). Sample Source: colon samples from mice. Specific Focus: mRNA sequencing to analyze differential gene expression in response to DSS and RJA treatment.

first: Mengyuan

first: Xinyi

last: Gao

first: Yang

last: Jiang


title: TPX2 as key downstream target of the eIF4A controlled translational program in MYCN driven neuroblastoma

city: Ghent

first: Sarah-Lee

last: Bekaert

state: No state

address: Corneel Heymanslaan 10

country: Belgium

institute: UGent


title: TPX2 as key downstream target of the eIF4A controlled translational program in MYCN driven neuroblastoma[RNA-Seq]

summary: Current therapies for neuroblastoma are often ineffective and survivors suffer from severe long-term therapy related side-effects, underscoring the need for identification of novel drugging strategies. We performed an in-depth evaluation of phenotypic and molecular responses following exposure of neuroblastoma cells to the rocaglate CR-1-31-B, scrutinizing its mode-of-action through integrative ribosome footprinting and shotgun proteome profiling. We could show that CR-1-31-B significantly reduces tumor growth in vivo without apparent toxicity. By means of combined ribosome footprint and transcriptome analysis we could show that CR-1-31-B treatment induces downregulates factors involved in the G2/M checkpoint, while upregulated targets are enriched for oxidative phosphorylation pathway components and DNA repair. At the proteome level, CR-1-31-B revealed downregulation of a FOXM1 driven gene signature, with TPX2 as prominent marker. Knockdown of TPX2 leads to reduced neuroblastoma cell confluence and elevated levels of DNA damage. In conclusion, our data support CR-1-31-B as a potent novel therapeutic agent in neuroblastoma.

overall_design: Neuroblastoma cell line (IMR32) upon TPX2 knockdown using three different siRNAs and four biological replicates.

first: Carolina

last: Nunes

first: Iris

last: Nelen

first: Fien

last: Martens

first: Sara

last: T’sas

first: Peihua

first: Fanny

last: De Vloed

first: Aline

last: Eggermont

first: Steven

last: Goosssens

first: Anna

last: Sablina

first: Hans-Guido

last: Wende

first: Kaat

last: Durinck


title: Comparison of differential gene expression in blood PBMCs from healthy controls, patients with rheumatoid arthritis,and  patients with lupus using single-cell transcriptome sequencing analysis.

first: Wenchang

last: Sun

summary: Single-cell transcriptome sequencing was used to detect and compare differentially expressed genes in PBMCs from healthy controls in patients with rheumatoid arthritis, systemic lupus erythematosus patients.

overall_design: The study included three healthy controls (NC group), three patients with rheumatoid arthritis, three newly diagnosed and untreated patients with systemic lupus erythematosus (SLE group). Inclusion criteria for rheumatoid arthritis patients required seropositivity for antibodies to cyclic citrullinated peptide (CCP) and strict adherence to the American College of Rheumatology (ACR) 2010 classification criteria for rheumatoid arthritis, with the absence of any other rheumatic diseases. Patients diagnosed with systemic lupus erythematosus (SLE) were classified according to the 2019 European League Against Rheumatism (EULAR) and American College of Rheumatology (ACR) EULAR/ACR criteria. Patients with concurrent immunological conditions such as malignancy or rheumatoid arthritis were excluded from the study. Healthy controls consisted of individuals undergoing medical examinations during the same timeframe. Approval for this study was obtained from the Medical Ethics Committee of the First Affiliated Hospital of Shandong Second Medical University. Prior to testing, all participants provided written informed consent and the studies adhered to the ethical guidelines outlined in the Declaration of Helsinki. Peripheral blood samples were collected from patients, and peripheral blood mononuclear cells (PBMCs) were isolated using Ficoll-Paque gradient centrifugation. The freshly isolated PBMCs were resuspended in fetal bovine serum with 10% dimethyl sulfoxide, frozen at -80°C for at least 4 hours, stored in liquid nitrogen, and subsequently utilized for single-cell transcriptome sequencing (scRNA-seq).


summary: Current therapies for neuroblastoma, a pediatric tumor arising from immature sympathoblast progenitors of the peripheral sympathetic nervous system, are often ineffective and most survivors suffer from severe long-term therapy related side-effects, underscoring the need for identification of novel drugging strategies with limited toxicity. We performed for the first time an in-depth phenotypic and molecular evaluation of pharmacological eIF4A inhibition in neuroblastoma using the rocaglate CR31B, scrutinizing its mode-of-action through a comprehensive and integrated shotgun proteome profiling and combined ribosome/RNA-seq footprinting approach. Short-term treatment of neuroblastoma cells with CR31B significantly affected viability within the very low nanomolar concentration range. Notably, ribosome footprinting following short-term CR31B exposure (6 hours) revealed amongst others strong enrichment for transcripts encoding proteins involved in N-glycan biosynthesis amongst the downregulated hits, while upregulated targets are enriched for oxidative phosphorylation pathway components. Shotgun proteome profiles during long-term (24h-48h-72h) CR31B exposure revealed a strong enrichment of a FOXM1 driven signature amongst the downregulated hits, a key regulator implicated in cell cycle control and DNA damage response in neuroblastoma. Last, we could show that CR31B significantly reduces tumor growth in vivo without apparent toxicity in a neuroblastoma PDX model. In conclusion, we present CR31B as a potent novel potent therapeutic agent in neuroblastoma.

overall_design: Neuroblastoma cell line (IMR32) upon CR31B treatment and DMSO (0.1%). Four biological replicates.

first: Muhammad

last: Rishfi

last: Zhao


title: Cellular milieu of the neural retina informs complement immune regulation [Hs]

city: Philadelphia

first: Dwight

middle: Edward

last: Stambolian

state: PA

address: 422 Curie Blvd.

department: Opthalmalogy

institute: University of Pennsylvania

summary:
Purpose: We present a comprehensive map of the human retinal complement expression at a single-cell resolution, spanning 11 cell types.
Methods: Retinal mRNA profiles from were generated by scRNA sequencing (10x Genomics) from a healthy human donor immediately within 4 hours of death. The data was normalized using Seurat.
Results: Using an optimized data analysis workflow, we found novel patterns of complement expression in the retina
Conclusions: Our landmark atlas provides crucial mechanistic insights in complement immunology

overall_design:
Retinal cell mRNA data from a healthy human donor, separated into Macula (mac) and Peripheral (per) retina.
11 cell types:  Amacrine Cells, Cone BCs, Cone Photoreceptors, Endothelial Cells, Horizontal Cells, Microglia, Muller Glia, Pericytes, Retinal Ganglion Cells, Rod BCs, Rod Photoreceptors.

first: Nicholas

last: Dana


title: Csep1P protein from Campylobacter concisus induces a chemokine-dominant inflammatory state in macrophages and enhances proinflammatory response to gut bacteria

city: Sydney

first: Li

last: Zhang

state: NSW

address: Botany Street

department: School of Biotechnology and Biomolecular Sciences

country: Australia

institute: University of New South Wales

summary: The THP-1 macrophage gene responses to csep1 protein and the pathogenic mechanisms were investigated by comparative differential expression analysis

overall_design: Comparative gene expression profiling analysis of RNA-seq data for THP-1 macrophage cells with and without csep1 protein treatment


title: A Longitudinal, Multi-omic Atlas Reveals the Emergence of a Spatially Organized Immunosuppressive Ecosystem in Resistant Melanoma [nCounter RNA]

status: Public on Jan 31 2026

city: Hong Kong

first: hongbin

last: lan

address: 34 Hospital Road, Sai Ying Pun, Hong Kong

country: Hong Kong

institute: The University of Hong Kong

summary: This study employed the NanoString nCounter platform to perform targeted, quantitative molecular profiling of longitudinally collected FFPE tumor samples to elucidate molecular mechanisms underlying resistance to anti–PD-1 therapy.  nCounter® Vantage 3D™ Single Nucleotide Variant assay was integrated using a solid tumor panel to screen 104 driver variants across 25 genes frequently mutated in solid tumors. We quantified the expression of 770 cancer-related mRNA transcripts to identify persistently activated oncogenic pathway signatures in non-responders, which were further complemented by quantitative profiling of 27 total and phosphoproteins using antibody–oligonucleotide conjugates for functional validation of pathway activity. To characterize the tumor microenvironment spatially, GeoMx Digital Spatial Profiler analysis was utilized to assess the distribution of 38 proteins across distinct histological regions, revealing an immunosuppressive spatial architecture associated with treatment resistance.

overall_design: We applied the nCounter® Vantage 3D™ RNA:Protein Solid Tumor Assay to a longitudinal cohort of 34 metastatic melanoma tumor samples obtained from 7 patients. To ensure data robustness, technical replicates were performed for expression profiling, yielding a total of 46 analyzable data points, including two tumor samples analyzed in triplicate, eight tumor samples analyzed in duplicate, and the remaining samples analyzed as single measurements.

first: Gao


title: PoxTMA7 has essential impacts on translation landscape in Penicillium oxalicum

city: Nanning

first: Di

last: Tian

address: DaXue east road

institute: College of Life Science and Technology,GuangXi university

summary: PoxTMA7 containing a highly conserved domain TMA7 (Translation machainary associated protein 7). The deletion of PoxTMA7 significanlty reduced the cellulase production by 70% in P. oxalicum, but the underlying translation regulatory mechanism remain unclear.  In order to inveatigating the mechanism of PoxTMA7 in translation regulation. We performed ribosome profiling sequencing (Ribo-seq) of WT and detaPoxTMA7 to explaining the landscape of PoxTMA7 in translation regulation.

overall_design: Mycelia of P. oxalicum strains WT and detaPoxTMA7 were collected after cultured in medium containing 1% Avicel, and then powdered in liquid nitrogen. Powdered mycelia were mixed with cold polysome extraction buffer, and lysed on ice for 25 min. The ribosome protected frames were extracted by Trizol method after RNase I digested. he Ribo-seq library construction of P. oxalicum was measured by QEZ-seq 1.0 kit.

first: Shuai


title: A Longitudinal, Multi-omic Atlas Reveals the Emergence of a Spatially Organized Immunosuppressive Ecosystem in Resistant Melanoma [SNV]

overall_design: To detect somatic mutations in metastatic melanomas, we performed nCounter® Vantage 3D™ Single Nucleotide Variant assay in 10 longitudinal tumor specimens from two patients (MP13_674 and G001). The solid tumor panel contains 104 driver variants from 25 genes that are frequently mutated in solid tumors, including Single Nucleotide Variant (SNV), Multi-Nucleotide Variant (MNV), and Insertions or Deletions (InDels).


title: A Longitudinal, Multi-omic Atlas Reveals the Emergence of a Spatially Organized Immunosuppressive Ecosystem in Resistant Melanoma [nCounter protein]

overall_design: We applied the nCounter® Vantage 3D™ RNA:Protein Solid Tumor Assay to a longitudinal cohort of 34 metastatic melanoma tumor samples from 7 patients. To ensure robustness of the protein expression data, technical replicates were included, yielding a total of 46 protein measurements for analysis, comprising two tumor samples analyzed in triplicate, eleven analyzed in duplicate, and the remaining samples analyzed as single measurements.


title: TPX2 as key downstream target of the eIF4A controlled translational program in MYCN driven neuroblastoma [MYCN_CutAndRun]

first: Sarah-Lee

last: Bekaert

overall_design: Identification of MYCN bindingsites through CUT&RUN sequencing in the neuroblastoma cell line IMR-32.

first: Iris

last: Nelen

first: Fien

first: Sara


title: In perennial Arabis alpina CONSTANS and FLOWERING LOCUS T have common and distinct effects on flowering and inflorescence architecture

city: Cologne

first: Niharika

last: Sashidhar

address: carl von linne weg 10

department: George Coupland

institute: Max Planck Instite for Plant breeding

summary:
Flowering of perennial Arabis alpina, is differentially regulated on primary and axillary shoots. Although contributions of vernalization and aging pathways have been analyzed, those of photoperiodic flowering genes CONSTANS (CO), FLOWERING LOCUS T (FT), and TWIN-SISTER OF FT (TSF) remain unexplored.
CRISPR-Cas9 mutations in AaCO and AaFT/TWIN SISTER OF FT-LIKE (TSFL) were recovered. Aaco and Aaft/tsfl mutants in pep1 background were scored for flowering time, inflorescence branching and floral phenotypes under long (LD) or short days (SD) and after vernalization. RNAseq data on primary and axillary branches were compared.
AaCO activates AaFT/TSFL transcription in leaves, and Aaco and Aaft tsfl mutations delay flowering under LDs. Axillary branches flowered in Aaco mutants but not in Aaft tsfl mutants. Both lacked inflorescence branches and flowers on the primary shoot under LDs. However, Aaft tsfl mutants produced some flowers after vernalization, and Aaco a few in SDs. RNAseq identified genes responsive to AaFT, TSFL and AaCO on the primary shoot and in axillary branches.
Therefore, AaCO-AaFT promote flowering of A. alpina under LDs, but with distinct roles in axillary branch flowering. Both genes are required for inflorescence branching and flower formation on the primary shoot. The complex role of the CO-FT module in inflorescence architecture may underlie the polycarpic, perennial life history of A. alpina.

overall_design: CRISPR-Cas9 mutants were generated in pep1 mutant background for CO and FT and phenoytping was performed with and without vernlization and RNA seq was done to understand the molecular basis

first: George

last: Coupland


title: Expression data from MDA-MB-231 breast cancer cells treated by exosomes derived from M2 macrophage

city: hangzhou

first: wei

last: pan

address: 杭州医学院滨康路587号

institute: hangzhou medical college

summary:
The tumor-associated macrophage (TAM) plays important roles in modulating the favorable tumor microenvironment. M2 macrophages facilitate tumor progression by promoting migration, angiogenesis and invasion. The exosome from M2  macrophage mediated crosstalk between tumor cells and macrophages in breast cancer. The miRNA expression changes play an important role  in the breast cancer development.
The miRNA regulate the target genes in EMT-associated signaling pathways, and influence tumor cell invasion and metastasis.

overall_design: Exosomes from M2 macrophage treat the breast cancer cells.Total RNA and miRNA were extracted by trozol. The miRNA expression profiles were examined by the affymetrix microarray chip to identify the differential expressed miRNA.

first: Yu

last: Liu

first: Chaoqun

last: Wang

first: Jiangzheng

last: Zeng

first: Bingyu

last: Gao

first: Fangfang

first: Bin

last: Chen


title: Micro-bulk RNA-seq of trilaminar omphalopleure of Monodelphis domestica to investigate placental cytokine signaling

city: New Haven

first: Gunter

last: Wagner

address: 165 Prospect Street

department: Ecology & Evolutionary Biology

institute: Yale University

summary: The brief placental attachment of the gray short-tailed opossum Monodelphis domestica spans only the final two days of the 14-day pregnancy. During this time the fetus grows rapidly and a pronounced spike in inflammatory signaling occurs. It was recently discovered that these cytokines are produced primarily by fetal cells, the syncytial knots which develop at the end stage of placentation after day 13 of gestation. To investigate this further, we conducted laser microdissection on placental membranes (omphalopleure) at 13.5 days post copulation to compare to published transcriptomes at 12.5 days post copulation. Analysis revealed indeed a pronounced expression of inflammatory cytokines in the 13.5 samples. We hypothesized that placental cytokines act as solicitation signals benefitting the fetus by effects on maternal nutrient transfer. To test this, we administered anti-inflammatory drugs to pregnant opossums during the attachment phase targeted at three arms of this response: IL1A via the receptor inhibitor anakinra, IL6 via the receptor inhibitor tocilizumab, and prostaglandin E2 via the PTGS2 synthetase inhibitor meloxicam. Inhibition of IL-1 and IL-6 signaling resulted in significant increases in fetal biomass, suggesting that they impose a cost to biomass acquisition by offspring rather than acting in direct solicitation. However, in the case of anakinra, saline-treated control individuals showed a greater mean surviving litter size compared to IL-1-inhibited animals. Together, our results suggest that marsupial end-pregnancy inflammation has acquired a novel function modulating both fetal growth and survival during pregnancy.

overall_design: Opossums were mated (no drug treatment or other intervention) and pregnant uteri were collected at 13.5 days post copulation. Placental tissues, which normally appose maternal uterine lining, were isolated by laser microdissection and subjected to RNA sequencing.

first: Daniel

middle: J

last: Stadtmauer


title: Transcriptome of Anthurium andraeanum under high temperature

city: Ji'nan

first: Chunxia

last: Wu

address: No.1,University Road,Science Park,Changqing District

department: Life Sciences

institute: Shandong Provincial Key Laboratory of Plant Stress

summary: The transcriptome of two Anthurium cultivars of MH and Ken under high tempearture were sequenced. The differences between the control and the high tempearture treatment samples were analyzed and numerous differentially expressed genes that exhibited distinct expression patterns were identified.

overall_design: Gene expression profiling analysis of RNA-seq data  for the full-flowering MH and Ken under high tempearature