title: Centromeres are hotspots of DNA methylation epimutations that are transmitted and occur at high rates in a filamentous fungus

city: Colorado Springs

first: Andrew

middle: David

last: Klocko

state: Colorado

address: 278 Centennial Hall, 1420 Austin Bluffs Pkwy

department: Chemistry and Biochemistry

institute: University of Colorado Colorado Springs

summary: Epimutations are changes in chromatin modifications, such as DNA methylation or histone modifications. Some of these epigenetic changes can be inherited for several generations, and thus could contribute to evolutionary processes. Estimates of epimutation rates now exists in a few species, but epigenetic mechanism are not conserved across all life, and epigenetic marks funtion differently in different species. To understand the properties of epimutations in fungi, we performed a mutation accumulation experiment with the filamentous fungus Neurospora crassa and investigated spontaneous DNA methylation and trimethylation of lysine 9 on histone H3 (H3K9me3) changes in the mutation accumulation lines. We observed that centromeric regions are hotspots of spontaneous DNA methylation changes in N. crassa. In these hotspot regions, DNA methylation changes were transmitted across mitoses, but changes occurring in euchromatin were not maintained. The rate of DNA methylation changes was more than 10 000-fold faster than the genetic mutation rate. We did not observe spontaneous changes in H3K9me3 that were transmitted across mitoses. Our results show that while spontaneous epimutations occur in this species, they occur predominantly in gene poor heterochromatic regions, so their impact for evolutionary adaptation may be limited.

overall_design: Chromatin Immunoprecipitation-sequencing (ChIP-seq) of the trimethylation of lysine 9 on histone H3 (H3K9me3) of the filamentous fungus Neurospora crassa subject to a Mutant Accumulation experiment of single colony transfers followed by asexual growth

first: Mariana

last: Villalba de la Peña

first: Clayton

last: Hull-Crew

first: Taylor

last: Hutter

first: Cynthia

middle: A

last: Vino

last: Sarkies

first: Maria

last: Colomé-Tatché

first: Frank

last: Johannes

middle: D

first: Ilkka

last: Kronholm


title: Deletion of miR-130b/301b cluster promotes macrophage efferocytosis and resolution of adipose tissue inflammation

status: Public on Mar 02 2026

city: New Haven

first: Shaoning

last: Jiang

state: CT

address: 310 Cedar Street, BML142

country: USA

institute: Yale University

type: Expression profiling by high throughput sequencing

summary: Macrophage efferocytosis, the clearance of apoptotic cells, is essential for tissue homeostasis and preventing inflammation. Impaired efferocytosis contributes to chronic inflammatory conditions, including obesity. However, its key regulators remain unclear. MicroRNA-130b (miR-130b) is increased in adipose tissue macrophages of individuals with obesity. Here, we found that miR-130b was enriched in bone marrow of mice, and its expression in bone marrow-derived macrophages was suppressed by IL-4 and by apoptotic cell uptake. Deletion of the miR-130b and its cluster member miR-301b enhanced macrophage efferocytosis in vitro and apoptotic cell clearance in vivo, accompanied by increased mitochondrial respiration and anti-inflammatory polarization. In high-fat diet-fed mice, global deletion of miR-130b/301b reduced inflammatory gene expression in adipose tissues. Mechanistically, miR-130b suppressed PPARγ and PGC-1α, regulators of mitochondrial metabolism and inflammation, and miR-130b/301b deletion increased CX3CR1, a receptor for apoptotic cell “find me” signals. Together, miR-130b/301b deletion promotes macrophage efferocytosis and resolves adipose tissue inflammation.

overall_design: Bone marrow derived macrophages (BMDMs) from WT and miR-130b/301b KO mice were collected, and total RNA was extracted for RNA sequencing.

first: Yang

last: Lei

first: Abuduyimiti

last: Tuerdiguli

first: Xi

last: Tibo

first: Coppola

last: Gianfilippo

first: Liu

last: Chen

first: Jiang

last: shaoning


title: Advanced dual-payload antibody-drug conjugates (DualADCs) for targeted cancer chemo-immunotherapy

city: COLUMBUS

first: Zhuoxin

last: Zhou

state: OH

address: Gateway Lofts Columbus, 2211 Dublin Rd

institute: Ohio State University

summary: Antibody–drug conjugates (ADCs) are a powerful class of targeted cancer therapeutics that combine the specificity of monoclonal antibodies with the potency of cytotoxic payloads. In this study, we developed novel dual-payload ADC (DualADC) platforms that enable co-delivery of a chemotherapeutic agent for direct tumor cell killing and a toll-like receptor agonist to stimulate antitumor immunity. Using triple-negative breast cancer (TNBC) as a model, we established advanced cysteine/lysine co-conjugation strategies optimized for antibody–drug ratio (ADR) and drug–drug ratio (DDR). These refinements minimized hydrophobicity-induced precipitation, enhanced conjugation efficiency, and improved formulation stability. In vivo evaluations in two xenograft mouse models demonstrated strong antitumor efficacy, highlighting the therapeutic potential of DualADCs as a next-generation approach for synergistic chemo-immunotherapy.

overall_design: TNBC tumors were collected from syngeneic mouse models at the study endpoint. Total RNA was extracted using the RNeasy Plus Mini Kit following the manufacturer’s protocol. cDNA library preparation and bulk RNA sequencing were conducted by Novogene America (Sacramento, CA, USA) using the Illumina HiSeq™ X Ten platform.


title: Molecular basis of target RNA cleavage by Cas13 II

city: Hong Kong

first: Joe

last: Lam

address: 21 Sassoon road

department: School of Biomedical Sciences

country: Hong Kong

institute: The University of Hong Kong

summary: RNA-targeting CRISPR-Cas13 enzymes are robust RNA knockdown tools with both on-target and collateral cleavage activities. However, to this date, the in vivo RNA cleavage mechanisms remain poorly understood. Here, we combine in vitro and in vivo methods to elucidate the exact cleavage sites of Cas13. We reveal that some subtypes of Cas13, including Cas13b and Cas13bt, cleave the target RNA in predominant positions, and rational engineering of Cas13 further improves the precision. Building on this fact, we developed RNA segment editing (RSE), a targeted RNA cleavage and repair method, to restore dysfunctional RNA in cells. We anticipate that RSE will enable precision RNA engineering for therapeutics and basic research.

overall_design: Cleavage site analysis of Cas13 proteins and other RNA cleavage samples using different methods (5' RACE and in vivo adaptor ligation)

first: SC

last: Kwon


title: scRNAseq analysis of hepatocytes from liver cirrhosis patient

city: Minato City, Tokyo

first: Teh-Wei

last: Wang

address: 4 Chome-6-1 Shirokanedai

country: Japan

institute: IMSUT

summary: We used the Flex single-cell RNA sequencing platform (10x Genomics) to investigate the transcriptomic differences of hepatocytes between healthy and liver cirrhosis liver samples obtained from resected tissues (non-tumorous regions) of patients with colorectal cancer liver metastases and patients with hepatocellular carcinoma accompanied by liver cirrhosis.

overall_design: In this experiment, we obtained liver surgical specimens from patients with colorectal cancer liver metastasis (representing healthy liver tissue) and from patients with hepatocellular carcinoma accompanied by cirrhosis (representing cirrhotic liver tissue). Following tissue fixation, samples were dissociated into single-cell suspensions using the gentleMACS Dissociator in combination with Liberase. Hepatocytes were then processed for cDNA library construction and subsequent transcriptomic analysis.

first: Koji

last: Nishikawa

first: Makoto

last: Nakanishi


title: scRNAseq analysis of hepatocytes from p16-Tom mice following CCl4 treatment

summary: We used the Flex single-cell RNA sequencing platform (10x Genomics) to investigate the transcriptomic differences between p16high (Tom+) and p16low (Tom-) hepatocytes from p16-CreERT2/R26-LSL-tdTomato mice following 4 weeks of CCl4 treatment.

overall_design: In this experiment, we obtained liver from p16-Tom mice following 4 weeks of CCl4 treatment. After tissue fixation, samples were dissociated into single-cell suspensions using the gentleMACS Dissociator in combination with Liberase. Hepatocytes were FACSorted through MitoBrilliant 646 and Hoechst staining then processed for cDNA library construction and subsequent transcriptomic analysis.

first: Satoshi

last: Kawakami


title: scRNAseq analysis of hepatic stellate cells in CCl4-induced liver fibrosis with eliminating p16high hepatocytes

summary: Using scRNA-seq, we investigated the mechanism by which the removal of p16-high hepatocytes leads to the amelioration of CCl₄-induced liver fibrosis. Because liver fibrosis is primarily driven by hepatic stellate cells, we utilized a cell isolation protocol optimized for the efficient recovery of stellate cells.

overall_design: In this experiment, we obtained liver from p16-CreERT2/ Alb-DreERT2/ R26-CAG-LSL-RSR-tdTomato-2A-DTR (p16-Alb-LRTD) and p16-CreERT2/ R26-CAG-LSL-RSR-tdTomato-2A-DTR (p16-LRTD) mice following 4 weeks of CCl4, tamoxifen, and diphtheria toxin treatments. After perfusion, stellate cells were dissociated into single-cell suspensions using the pronase/ collagenase solution. Hepatic stellate cells were isolated by density gradient separation using Nycodenz solution and subsequent transcriptomic analysis.


title: Reactivation of the silenced BASP1 gene suppresses oncogenic WNT signaling in human colorectal cancer cells

city: Innsbruck

first: Markus

last: Hartl

state: Tyrol

address: Innrain 80-82

department: Institute of Biochemistry

country: Austria

institute: University of Innsbruck

summary: Starting from human colon cancer cells showing aberrant WNT/β-catenin/TCF4 signaling, hyperactivated MYC and silenced BASP1, we generated stable cell lines overexpressing BASP1, either ectopically, or by reactivating the dormant BASP1 promoter using a lentiviral CRISPR-based system. BASP1 encodes a neuronal signaling protein and transcriptional co-repressor, from which a tumor-suppressive function has been described in avian cell systems and in multiple human cancer cell types. Proteome and transcriptome analyses revealed activation of several tumor and metastasis suppressors in BASP1-expressing cells, which also show strong repression of the transformed phenotype in terms of contact inhibition, anchorage-independent growth, and tumorigenesis. Cells with reactivated BASP1 display a flat and differentiated morphology with enhanced migratory potential, accompanied by expression of multiple genes implicated in actin polymerization, focal adhesion, and neuronal migration. Furthermore, MYC protein expression is substantially repressed due to BASP1-mediated transcriptional MYC downregulation involving BASP1 interaction with β-catenin and binding to the MYC promoter. Upon BASP1 activation, multiple key proteins of the canonical WNT signaling pathway become suppressed. One of these BASP1 targets is the protein kinase TNIK catalyzing phosphorylation of TCF4, the latter required for transcriptional MYC activation. Results obtained with a preclinical TNIK inhibitor in human colorectal cancer cells show efficient abrogation of MYC expression and consequently impaired dimerization with its interaction partner MAX. The antagonistic BASP1 effect on MYC and the MYC dependency on TNIK could enhance the development of strategies to interfere with oncogenic functions of the cancer driver MYC.

overall_design: RNA-seq profiling of SW480 colon cancer cells and comparison with SW480 expressing ectopic BASP1 and SW480 with CRISPR-activated endogenous BASP1.

first: Weber

last: Leonie

first: Hartl

last: Markus


title: Genetic analysis of polyadenylation patterns reveals distinct classes of yeast genes and local chromatin effects on Pol II elongation

city: Boston

first: Zarmik

last: Moqtaderi

state: MA

address: 240 Longwood Avenue C2-355

department: BCMP

institute: Harvard Medical School

summary: The poly(A) profile of a typical yeast gene comprises approximately 50 poly(A) sites corresponding to distinct 3’ mRNA isoforms.  Poly(A) profiles are shifted upstream in strains with slow RNA polymerase II (Pol II) elongation rates resulting from Pol II mutations or to depletion of histone chaperones FACT or Spt6.  Conversely, downstream-shifted poly(A) profiles occur in strains with fast Pol II elongation rates caused by Pol II mutations or by depletion of histones.  Downstream-shifted poly(A) profiles also arise when components of the cleavage/polyadenylation machinery are depleted.  Here we examine poly(A) profiles in 45 yeast strains with mutations that affect a wide variety of DNA- or RNA-based processes.  Typically, altered poly(A) profiles occur in only a subset of genes, and some strains show both upstream and downstream poly(A) shifts depending on the gene.  Hierarchical clustering of the poly(A) profiles reveals 6 classes of genes that behave similarly over the genetic conditions tested and have different RNA sequence preferences in their 3’ untranslated regions.  Many chromatin-modifying or chromatin-associated proteins affect poly(A) profiles, indicating that they affect the rate of transcriptional elongation.  Chromatin-modifying activities, but not cleavage/polyadenylation factors, often have non-uniform effects on 3’ mRNA isoform levels of the same gene, suggesting that chromatin differentially affects Pol II dwell time at individual sites during transcriptional elongation.

overall_design: 3' READS analysis of polyadenylated RNA samples to determine polyadenylation profiles of strains with deletions or anchor-away depletions affecting a variety of gene regulatory pathways.  The study involves two biological replicates for each strain and uses cells cultured to mid-log phase in YPD medium.

first: Joseph

middle: V

last: Geisberg

first: Kevin

last: Struhl


title: Chromatin accessibility profiling of IMR-90 SV40-T cells expressing wild-type and mutant H2B

city: La Jolla

first: Xue

last: Lei

state: CA

address: 10901 N Torrey Pines Rd

institute: SBP medical discovery institute

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Nucleosomes are the minimal repeating units of chromatin. Their dynamic assembly and disassembly underpins chromatin organization and genome regulation. However, how intrinsic nucleosome stability contributes to higher-level yet fundamental cellular and organismal properties—such as preservation of cell identity, lineage specification, stress resilience and healthy aging—remains unclear. To address this, we tested the impact of intrinsic nucleosome instability across multiple cell, tissue and organismal models by introducing histone mutants that weaken histone–histone interactions. Despite no overt effects on global chromatin accessibility, DNA damage, steady-state proliferation or cell viability, nucleosome instability impaired lineage-specific gene expression programs, altered lineage specification and activated intrinsic inflammatory and stress pathways in a manner reminiscent of aging in mouse tissues and human cells. Consistently, in Caenorhabditis elegans and Drosophila melanogaster, nucleosome instability accelerated the onset of age-associated transcriptional alterations and functional decline in Caenorhabditis elegans and Drosophila melanogaster, and . At the cellular level, nucleosome instability also heightened cellular sensitivity vulnerability to exogenous perturbations—including environmental, epigenetic and mitotic stress—in human cells and Saccharomyces cerevisiaeyeast.  These cross-species findings identify nucleosome stability as an evolutionarily conserved epigenetic safeguard that preserves cell identity and stress resilience, sustaining organismal function and longevity.

overall_design: IMR-90 SV40-T immortalized human fibroblasts were transduced with lentiviral vectors expressing wild-type or mutant H2B construct. ATAC-seq libraries were prepared using the Active Motif ATAC-seq Kit and sequenced on NovaSeq 6000. Peaks were called using MACS2, quantified with featureCounts and analyzed for differential accessibility using DESeq2.

first: Hiroshi

last: Tanaka

first: Peter

last: Adams


title: Single-cell transcriptomic profileing of IMR-90 SV40-T cells expressing wild-type, E76K or E76R H2B

overall_design: IMR-90 SV40-T immortalized human fibroblasts were transduced with lentiviruses expressing wild-type or mutant H2B constructs (E76K, E76R). Single-cell suspensions were processed using the Chromium platform at the UC San Diego Center for Epigenomics. Libraries were sequenced and analyzed to identify gene expression changes and cluster-specific marker genes.


title: Reconstitution of human fetal ovaries reveals niche requirements for primordial germ cell-like cell progression

city: Leiden

first: Susana

last: Chuva de Sousa Lopes

address: Einthovenweg 20

department: Anatomy and Embryology

country: Netherlands

institute: Leiden University Medical Center

summary: Human primordial germ cell-like cells (hPGCLCs) can be specified from human induced pluripotent stem cells (hiPSCs), offering a valuable model for human germ cell development. However, further maturation steps of hPGCLCs rely on mouse feeders, or co-culture with mouse gonadal somatic cells. Exposure of hPGCLCs to human embryonic niche has not been attempted. Here, we co-cultured female hPGCLCs in two distinct somatic compartments. In reconstituted ovary (rOv) culture, human fetal germ cells proliferate and initiate meiosis, while hPGCLCs upregulate gonadal germ cell markers such as DDX4. Additionally, hPGCLCs can be supported in 3D culture by the amnion-like cells (AMLC) generated during PGCLC differentiation. Compared to rOV, hPGCLCs are less prone to dedifferentiation in PGCLC/AMLC aggregates. Finally, we demonstrated that SCF is crucial for the survival of hPGCLCs but not second trimester fetal germ cells. Together, this work highlights a shift in niche is required in human germ cell development.

overall_design: One hiPSC line was used for differentiation to hPGCLC and was used for single cell cluster analysis (Day 0, Day 5, Day 22)

middle: M

first: Ioannis

last: Moustakas

first: Arend

last: Overeem

first: Yolanda

middle: W

last: Chang


title: P300/CBP inhibition with gilteritinib and venetoclax targets leukemia stem cells in epigenetic mutant AML [ChIP-Seq]

city: Philadelphia

first: Sara

middle: E

last: Meyer

state: PA

department: Cancer Biology

institute: Thomas Jefferson University

summary: Acute myeloid leukemia (AML) is a fatal blood cancer with cytotoxic chemotherapy offering at best 25% 5-year survival. While targeted BCL2 and FLT3 inhibitors venetoclax and gilteritinib are used upfront in the treatment of a subset of adult AML patients and help to extend the survival of some patients, a curative treatment combination with minimal side effects has yet to be discovered. We find that use of the dual histone acetyltransferase p300/CBP bromodomain inhibitor CCS1477 (Inobrodib), together with venetoclax and gilteritinib, virtually eliminates leukemia stem cells in an aggressive preclinical model of DNMT3A/FLT3-mutant AML by impairing pro-oncogenic survival and proliferation factors to effectively block leukemogenesis. This work identifies potential clinical utility of a novel, targeted, triplet combination therapy for treatment of AML.

overall_design: H3K27ac ChIP-seq profiling of Dnmt3a/Flt3 and Tet2/Flt3 mutant murine AML cells after 1 hours of in vitro p300/CBP inhibitor treatment with CCS1477.

first: Melanie

middle: L

last: Goetz

first: Jennifer

middle: S

last: Romer-Seibert

first: Amanda

last: Versace

first: Scott

last: Kogan

first: Robert

last: Bowman

first: Nigel

last: Brooks

first: Kis

last: Frese


title: SLAM-seq profiling of IMR-90 SV40-T Cells expressing wild-type and mutant H2B

overall_design: IMR-90 SV40-T cells expressing WT or mutant H2B were labeled with 100 µM 4sU for 6 hours. RNA was extracted and alkylated with iodoacetamide (IAA). Libraries were prepared using Lexogen QuantSeq kits and sequenced on NovaSeq 6000. Reads were trimmed with Trimmomatic, aligned to GRCh38 and analyzed using SLAM-DUNK for mutation calling and quantification. DESeq2 was used to identify transcriptionally regulated transcripts based on T>C conversion rates.


title: Single-cell multimodal profiling of pan-cancer cell lines uncovers gene regulatory principles underlying intrinsic cell states and environmental features

city: New York

first: Aileen

last: Ugurbil

state: NY

address: 87 Bedford St, Apt 4

institute: The Rockefeller University

summary: Cancer arises from somatic mutations whose effects are executed through dysregulated gene-regulatory programs that reshape chromatin, transcription, and malignant phenotypes. To uncover gene regulatory principles underlying heterogeneous cancer cell states and their linked environmental features, here we present a pan-cancer single-cell, multi-omic atlas of human cancer cell lines, including a compendium of 240,957 transcriptomes and 223,347 chromatin-accessibility profiles from primary cancers spanning 20 tumor types. We revealed extensive pan-cancer cell-state heterogeneity, core gene-regulatory networks, and consensus epithelial–mesenchymal transition (EMT) trajectories that transcend tissue of origin and are governed by conserved epigenomic and transcriptomic features. In addition, our copy-number variation analysis implicated transcription factor amplification, followed by hyperactive downstream regulation, as a major driver of malignant states. Further focused analysis of acral versus cutaneous melanoma cell lines uncovers a universal inflammation-suppressive program in acral melanoma versus an inflamed regulatory landscape in cutaneous melanoma, highlighting the JAK–STAT axis as a key discriminator. Finally, by integrating single-cell and bulk datasets across models and patient cohorts, we revealed tumor–microenvironment co-adaptation in vivo, and this was associated with immunotherapy responsiveness.

overall_design:
Easy-Sci ATAC Seq and Easy-Sci RNA seq profiling of 60 pooled cancer cell lines across 20 cancer types

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The table below lists SRA accessions for raw data already submitted to SRA under PRJNA1354039.
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first: Zihan

last: Xu

first: Joshua

last: Kwan

first: Chloe

last: Schaefer

first: Abdulraouf

last: Abdulraouf

first: Ziyu

last: Lu

first: Wei

last: Zhou

first: Junyue

last: Cao


title: P300/CBP inhibition with gilteritinib and venetoclax targets leukemia stem cells in epigenetic mutant AML [RNA-Seq]

overall_design: RNA-seq profiling of Dnmt3a/Flt3 and Tet2/Flt3 mutant murine AML cells after 6 hours of in vitro p300/CBP inhibitor treatment with CCS1477.


title: Adipocyte exosomal-derived microRNA30a-3p exacerbates liver steatosis in obese mice

city: Anshun

first: Longkun

last: Hu

state: Guizhou

address: Machang Town, Yunmanhu Campus of Guizhou Medical University

country: China

institute: Guizhou Medical University

summary: Adipose tissue dysfunction results in hepatic lipid overload, driving the progression of liver steatosis and non-alcoholic steatohepatitis. The involvement of adipose tissue-derived small extracellular vesicles (sEVs) in initiating and propagating nonalcoholic fatty liver disease (NAFLD) remains unexplored. Herein, we unveiled that transplanting adipose tissue from high-fat diet (HFD)-fed mice exacerbated insulin resistance and liver steatosis in lean mice, and Sirt3 expression was markedly reduced in adipose tissue from both NAFLD patients and murine NAFLD models. Interestingly, fat-specific Sirt3 overexpression (Sirt3AKI) mice enhanced insulin sensitivity and improved liver steatosis under HFD feeding. Furthermore, adipose tissue-derived sEVs were found to regulate hepatic lipid metabolism in Sirt3AKI mice. In vitro studies demonstrated that Sirt3 overexpressing adipocytes (Sirt3OE) released sEVs to ameliorate lipid accumulation in palmitic acid/oleic acid (P/O)-stimulated hepatocytes. Conversely, sEVs derived from NAFLD patients exacerbated hepatic lipid accumulation in HFD-fed Sirt3AKI mice. MicroRNA sequencing further identified a significant decrease in miR-30a-3p levels in sEVs derived from Sirt3OE adipocytes. Fat-specific miR-30a-3p overexpression worsened hepatic steatosis in HFD-fed Sirt3AKI mice. In contrast, engineered sEVs loaded with miR-30a-3p antagonist or miR-30a-3p inhibition robustly enhanced insulin sensitivity and mitigated hepatic accumulation in HFD-fed mice. Mechanistically, CHIP-qPCR and CHIP-sequencing analyses revealed that Sirt3 suppressed miR-30a-3p transcription through H3K56 acetylation. Dual-luciferase reporter assays validated Beclin1 as a bona fide target mRNA of miR-30a-3p. Taken together, these findings highlight the critical role of exosomal microRNAs in mediating adipocyte-hepatocyte crosstalk, provide novel insights into the mechanisms underlying lipotoxicity in hepatocytes, and suggest miR-30a-3p inhibitor could be a therapeutic agent for NAFLD.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for Histone Acetyl H3K56  (H3K56ac) in 3T3-L1 cells.

first: Tian

last: Zhang

first: Diao

last: Chen

first: Yongxin

first: Fei

first: Ruohan

last: lou

first: Yuxia


title: Bulk mRNA-seq analysis of Caenorhabditis elegans expressing wild-type and mutant H2B

first: Xue

last: Lei

overall_design: Worms expressing either wild-type or E73R mutant H2B (his-41) were collected at three time points post-adulthood (day 1, day 3, and day 10). Total RNA was isolated, sequenced and analyzed to identify gene expression changes associated with the H2B mutation and aging.

first: Hiroshi

last: Tanaka

first: Michael

last: Petrascheck

first: Peter

last: Adams


title: Knockdown of RNA editing proteins reshapes the HepaRG transcriptome and pharmacogene expression

city: Gainesville

first: Danxin

last: Wang

state: FL

address: 1345 Center Drive MSB PG-05B

department: Pharmacotherapy and Translational Research

institute: University of Florida

summary: The RNA-editing proteins, ADAR and ADARB1, regulate gene expression through editing-dependent and editing-independent mechanisms. Both proteins have been shown to have essential functions in the liver, including regulating the expression of drug-metabolizing enzymes. Here, using RNA-Seq, we profiled widespread changes to the hepatic transcriptome after knockdown (KD) of either ADAR or ADARB1 in HepaRG cells. Nearly a thousand pharmacogenes had altered expression or alternative splicing across both KDs, with splice isoform switches occurring for both HNF4A and CYP2C9. The two ADAR proteins largely affected different sets of genes, with KD of ADAR having more widespread effects than KD of ADARB1. Subsequent analyses of differential editing indicated that most transcriptomic alterations were independent of RNA editing. As KD of ADAR stimulates a type I interferon response; we compared changes to gene expression between siADAR and IFNα treatment. While both conditions triggered interferon signaling, their transcriptional fingerprints differed substantially; nevertheless, 70% of the genes dysregulated by ADAR KD were restored by BX795, an inhibitor of the type I response, supporting that many of the effects of siADAR were related to the induction of an immune pathway. Overall, our results suggest that the ADARs play key roles in maintaining liver homeostasis and the expression of many pharmacogenes, especially those involved in drug metabolism and disposition.

overall_design: RNASeq analysis of HepaRG hepatic cell lines treated with siADAR, siADARB1, siNC, IFNa, BX795, and siADAR1/BX795

first: Joseph

last: Collins


title: Bulk mRNA-seq analysis of IMR-90 SV40-T cells expressing wild-type and mutant H2B

overall_design: IMR-90 SV40-T immortalized human fibroblasts were transduced with lentiviruses expressing wild-type or mutant H2B constructs. Total RNA was isolated, sequenced and analyzed to identify gene expression changes.


title: Bulk mRNA-seq analysis of mouse skeletal muscle, heart and liver expressing wild-type and mutant H2B

overall_design: Mouse skeletal muscle, heart and liver were transduced with AAV9 vector expressing wild-type or mutant H2B. After four weeks, tissues were collected. Total RNA was isolated, sequenced and analyzed to identify gene expression changes.


title: Bulk RNA-seq analysis of primary human dermal fibroblasts from young and aged donors

first: Jingting

last: Yu

address: 10010 N Torrey Pines Rd

institute: Salk Institute for Biological Studies

summary: Primary human dermal fibroblasts were obtained from four young donors (ages 23–33) and five aged donors (ages 64–72) through the San Diego Nathan Shock Center (SD-NSC) Human Cell Models of Aging Core. Cells were cultured under standard conditions and subjected to bulk RNA sequencing to investigate age-associated transcriptional changes. Libraries were prepared using polyA selection and sequenced on the Illumina NovaSeq 6000 platform. Differential gene expression analysis was performed using the HOMER pipeline.

overall_design: Dermal fibroblasts from young and aged human donors were cultured in DMEM supplemented with 10% FBS, non-essential amino acids, and GlutaMAX. After 48 hours of culture, total RNA was extracted using the RNeasy Mini Kit with on-column DNase digestion. PolyA RNA libraries were prepared at the Salk Institute Genomics Core and sequenced using the NovaSeq 6000 SP platform. Reads were aligned to the hg19 reference genome using STAR (v2.5.3a), and differential expression analysis was performed using HOMER (v4.11.1).

first: Tatiana

last: Moreno

first: Caroline

last: Kumsta


title: Molecular Signatures of Peripheral and Central Dental Pulp Subpopulations in Response to Streptococcus mutans: A Bulk RNA-Seq Analysis

city: Regensburg

first: Sandra

last: Pohl

address: Franz-Josef-Strauß-Allee 11

department: Department of Conservative Dentistry and Periodontology

country: Germany

institute: University Hospital Regensburg

summary: Pulp cells play a central role in the defence against cariogenic microorganisms, orchestrating key immunological processes. Peripheral pulp cells, located adjacent to dentin, encounter bacteria and toxins earlier than central cells. To understand the specific signalling pathways between pulp cells and their interplay with immune cells, this study aimed to analyse the transcriptomic profiles of two distinct pulp cell subpopulations - dentin-adherent cells (DACs) and central dental pulp cells (DPCs) - in coculture with Streptococcus mutans. Primary cultures of both DACs and DPCs were obtained from healthy third molars of three female and three male donors aged 17 to 18. Cells were cocultured with viable S. mutans (2 × 10⁸ CFU/mL) for 6 hours (n = 6). Controls included γ-inactivated bacteria and unexposed cells. RNA was isolated, subjected to library preparation (Illumina® Stranded mRNA Prep) and transcriptome profiling was performed via paired-end RNA sequencing (Illumina NextSeq2000). Bioinformatic analysis included differential gene expression (DESeq2), gene set enrichment analysis (GSEA), and protein-protein interaction (PPI) network construction using STRING and Cytoscape. Batch effects were corrected, and significantly regulated genes (|log₂FC| > 1.5, padj < 0.05) were identified. Validation of DEGs was performed via reverse transcription quantitative polymerase chain reaction (RT-qPCR). RNA-Seq revealed a dynamic shift in the transcriptome of DACs and DPCs stimulated with S. mutans, while cells exposed to γ-inactivated or no bacteria did not. Although DACs and DPCs shared common DEGs (33 up, 8 down), several regulations were exclusive to DACs (22 up, 9 down) and DPCs (9 up, 25 down) highlighting a donor-independent functional specificity of the pulp subpopulations. Functional enrichment analysis revealed a strong and comparable activation of hypoxia-related pathways in both DPCs and DACs. However, DACs additionally showed enrichment in extracellular matrix organization and cytokine signaling, while DPCs were characterized by intracellular stress responses and protein folding pathways. Additionally, protein-protein-interaction analysis identified IL-6 as a key hub gene in DACs, while ANGPTL4 played a primary role in DPCs. Following exposure to S. mutans, mechanically isolated DACs and DPCs displayed distinct transcriptomic profiles, indicating functional heterogeneity in the pulpal immune response. DACs engaged immunomodulatory pathways, while DPCs were marked by cellular stress responses, suggesting divergent contributions to tissue defense and homeostasis.

overall_design: RNA-Seq profiling of dental pulp cells from six donors upon exposure with Streptococcus mutans (live or gamma-irradiated) for 6 hours

first: Matthias

last: Widbiller


title: Spatial Transcriptomics of Lung Squamous Cell Carcinoma Assosciated with Idiopathic Pulmonary Fibrosis

city: Okayama

first: Atsushi

last: Matsuoka

state: Okayama

address: 2-5-1 SHIKATA-CHO, KITAKU, OKAYAMA 700-8558 JAPAN

institute: Okayama University

summary: Spatial transcriptomic profiling was performed using the GeoMx Digital Spatial Profiler (NanoString Technologies) on FFPE lung specimens from six patients with lung squamous cell carcinoma (LUSC), including tumors arising within or outside idiopathic pulmonary fibrosis (IPF)-associated usual interstitial pneumonia (UIP) regions. Tissue sections were hybridized with the Human Whole Transcriptome Atlas (WTA) to measure protein-coding transcript expression.

overall_design: FFPE tissue sections from six LUSC patients were analyzed. A total of 52 ROIs were profiled, including core tumor regions, adjacent fibrotic or normal alveolar tissue, and tumor–stroma interfaces. ROI selection included both segmented (PanCK⁺ tumor vs. PanCK⁻ stroma) and unsegmented (full ROI) regions.

first: Kazuhiko

last: Shien

first: Shuta

last: Tomida

first: Masayoshi

last: Ohki


title: Bulk mRNA-seq analysis of mouse hematopoietic stem and progenitor cells expressing wild-type and mutant H2B during myeloid and megakaryocyte/erythroid differentiation

overall_design: Mouse hematopoietic stem and progenitor cells (HSPCs) were transduced with MSCV retroviral vector expressing wild-type or mutant H2B. The cells were subjected to differentiation into myeloid and megakaryocyte/erythroid lineages using MethoCult GF M3434 supplemented with 20 ng/ml mouse FLT3L and 50 ng/ml mouse TPO. After 9 days, cells were collected, and total RNA was isolated, sequenced and analyzed to identify gene expression changes.


title: Biological processes in hind paws, dorsal root ganglia and spinal cord after PTX treatment (the short model)

city: SAN ANTONIO

first: YI

last: ZOU

state: TX

address: 8403 Floyd Curl Drive

institute: UTHSA-GCCRI

summary: We investigated biological processes in hind paw, dorsal root ganglion (DRG) and spinal cord (SC) associated with chemotherapy treatment.

overall_design: Chemotherapy treatment was implemented by systemic (intraperitoneal (i.p.)) injection of Paclitaxel (PTX). The treatment protocol was two injections of PTX (2mg/kg) separated by one day. Paw skin samples from both sides were isolated 2, 7, 22 and 35 days after the last PTX injection. L3-L5 from both sides DRG samples were isolated 2, 7, 22 and 35 days after the last PTX injection. Spinal cord samples were isolated 2, 7, 22 and 35 days after the last PTX injection. There were two controls: the paw, DRG and spinal cord samples isolated 1 and 7 days after vehicle injections.

first: Alexei

last: Tumanov

first: Jennifer

last: Mecklenburg

first: Sergei

last: Belugin

first: George

middle: T

last: Naratadam

first: Priscilla

last: Barba-Escobedo

first: Ekaterina

last: Koroleva

first: Anahit

middle: H

last: Hovhannisyan

last: Shein

first: Koji

last: Tamada

last: Croft

first: Yi

last: Zou

first: Zhao

last: Lai

first: Armen

middle: N

last: Akopian


title: Biological processes in hind paws and dorsal root ganglia in males and females after PTX treatment (the intermediate model)

summary: We investigated biological processes in hind paw and dorsal root ganglion (DRG) of male and female mice associated with chemotherapy treatment

overall_design: Chemotherapy treatment was implemented by systemic (intraperitoneal (i.p.)) injection of Paclitaxel (PTX). The treatment protocol was two injections of PTX (3mg/kg) separated by one day. Paw skin samples (both sides) from male mice were isolated 2, 6 and 15 days after the last PTX injection. Paw skin samples (both sides) from female mice were isolated 2, 6, 16 and 26 days after the last PTX injection. L3-L5 DRG samples (both sides) from male mice were isolated 2 and 6 after the last PTX injection. L3-L5 DRG samples (both sides) from female mice were isolated 2 and 6 after the last PTX injection. Controls for male and female mice: the paw and DRG samples were isolated 1 day after vehicle injections

first: Michael


title: A Bioorthogonal Nanoconcentrisome System for Epigenetic and Immunometabolic Reprogramming in Osteoporotic Bone Repair

city: hangzhou

last: lan

state: Zhejiang Province

address: Dinglan Street

institute: Hangzhou Traditional Chinese Medicine Hospital

summary: Despite the promising potential of stem cell–based therapies in regenerative medicine, their therapeutic instability remains a major challenge, often resulting in inconsistent clinical outcomes. Achieving robust tissue regeneration requires precise control over the behavior of key cellular mediators—such as macrophages and progenitor cells—particularly at the epigenetic level, which remains an unmet need. Here, by applying single-cell RNA sequencing to systematically profile cellular heterogeneity during tissue regeneration, we identified a pronounced depletion of S-adenosylmethionine (SAM), a central epigenetic metabolite, in impaired bone tissues. We hypothesize that SAM depletion contributes to inadequate modulation of the regenerative microenvironment and associated epigenetic dysregulation. To address this, we developed a compartmentalized, fusogenic nanovesicle system (SMNV), termed the “nanoconcentrisome,” composed of SAM-loaded fusogenic liposomes encapsulating mesenchymal stem cell–derived nanovesicles (MNVs) via bio-orthogonal click chemistry. This dual-compartment architecture enables spatiotemporally controlled cellular modulation through membrane fusion. Upon fusion with macrophages, cytoplasmic delivery of SAM suppresses inflammation, followed by MNV-mediated enhancement of efferocytosis and metabolic reprogramming to establish a pro-regenerative immune niche. Concurrently, fusion with senescent stem cells restores epigenetic integrity via SAM-mediated heterochromatin reinforcement, while MNVs rejuvenate mitochondrial function and promote osteogenic differentiation. This synergistic, cell type–specific modulation significantly enhanced tissue regeneration and effectively repaired bone defects in osteoporotic rats. Collectively, our study presents a precision nanomedicine platform that integrates epigenetic and regenerative reprogramming to counteract aging-associated regenerative decline, with broad translational potential for complex multicellular diseases driven by metabolic dysfunction.

overall_design: RNA-seq profiling of Doxorubicin-induced rMSCs and SMNV intervention in senescence of rMSCs

first: Lan

last: Zhao

first: Kaiyu

last: Liang


title: SOX9 is part of a combinatorial marker that reveals early development and embryological origins of the mouse brown adipose tissue depots

last: Mansfield

address: 3009 Broadway

department: Biology

institute: Barnard College

summary: Brown adipose tissue (BAT) is a mammalian thermogenic tissue that helps to maintain body temperature and provides other important metabolic functions. Most brown adipocytes are located in structures called depots including the interscapular (iBAT), scapular (sBAT), and cervical (cBAT) depots. BAT depots arise from embryonic structures called somites, but their development is incompletely understood. Here, scRNA-seq was applied to whole-trunk tissue from axial levels where the three major BAT depots are located in order to profile the transcriptome of brown adipocyte progenitors as well as other lineages derived from somites and lateral plate mesoderm. The range of timepoints was chosen to profile brown adipocyte progenitors from early lineage segregation, as observed by a combination of markers including Sox9 at E11.5, to E13.5 when depots are morphologically identifiable and brown pre-adipocyte markers are expressed.

overall_design: Whole trunk tissues from mouse embryos were manually dissected to include C3-T2, or the third cervical to the second thoracic segments at three different embryonic stages (E11.5, E12.5, E13.5). Three littermate replicates were pooled together for each sample.  Briefly, trunks were excised at the axial levels indicated and the thoracic organs and forelimbs were removed.  Remaining tissue includes the trunk (both somite and lateral plate mesoderm derivatives) and neural tube.

first: Ava

last: Brent

first: Rika

last: Chan

first: Vaishnavi

last: Sirkay

first: Brian

middle: R

last: Morton


title: Nascent glial precursors in human bone marrow allow rapid induction of functional oligodendrocyte precursors for therapy

city: Cambridge

first: Kenneth Lap Kei

last: Wu

state: Cambridgeshire

address: Cambridge Biomedical Campus, Francis Crick Avenue

country: United Kingdom

institute: MRC LMB

summary: Loss of myelinating oligodendrocytes and myelin in white matter diseases impacts motor and cognitive functions, and even life expectancy. Transplantation of autologous oligodendrocyte precursors (OPCs) hold promise for treatment of such diseases, but a protocol for rapid generation of human OPCs from safe, ethical and accessible cell source remains unfound. We pursued strategies whereby rat bone marrow stromal cells (BMSCs) could be differentiated into myelinating glia of both the central and peripheral nervous system (1). By source, it remains unknown clinically collected human BMSCs (hBMSCs) could differentiate into OPCs, with good purity and yield. Furthermore, whether the multipotency of BMSCs resulted from diverse progenitors pre-existing in the bone marrow or from a single multipotent progenitor population remained unaddressed. hBMSCs collected from 3 healthy individuals were sequenced at single cell level and featured a transcriptomically distinct population of CD90hiEGFR+PDGFRA+ pre-oligodendrocyte precursors cells (pre-OPCs). To achieve targeted expansion of this population a two-step, virus-free and supporting cell-free induction protocol was designed and implemented. This was sufficient to derive immature-OPCs from hBMSCs. Transcriptomes of these immature-OPCs were characterized by single cell sequencing and their marker expression was examined by immunostaining.  Transplantation into myelin-deficient shiverer mice was used to demonstrate that our derived cells were capable of myelinating naked axons. Immature-OPCs were derived from hBMSCs in eight days using a simple two-step protocol. Resulting cells were positive for OPC markers and capable of myelinating naked axons when transplanted into the corpus callosum of myelin-deficient Shiverer mice. Our results provide evidence that hBMSCs harbour multipotent pre-OPCs, that features inherent diversity in lineage-restricted progenitors pre-existing in the bone marrow. We show that one such progenitor pool can be selectively enriched and maturated harnessing protocols to yield highly pure fate-committed oligodendrocytes. This could address myelin deficiency due to autoimmune, degenerative and traumatic conditions of the central nervous system.

overall_design: BMSCs from 3 patients were collected and derived into pre-OPCs using the protocol described in the study. Cells from each patient were sequenced at 3 key stages throughout the derivation process, namely, BSC stage, post-GIM stage and at the fate committed OPC stage using 10X Chromium single cell RNA sequencing pipeline. Cells from all patients were run together using CellPlex multiplexing.

first: Guy

last: Lam

first: Alex Yat-Ping

last: Tsui

first: Kin-Wai

last: Tam

first: Maximilian Tak Sui

last: Li

first: Alfred Ho Lai

last: Pao

first: Zora Chui Kuen

first: Chun Hei

last: Kwok

first: Yvonne Cheuk-Yin

last: Wong

first: Graham Ka Hon

last: Shea

first: Daisy Kwok-Yan

last: Shum

first: Ying-Shing


title: Biological processes in hind paws, dorsal root ganglia and spinal cord of PTX (the short model) and lymphotoxin-beta receptor (LTβR) antagonist treated mice

first: YI

last: ZOU

summary: We investigated biological processes in hind paw, dorsal root ganglion (DRG) and spinal cord (SC) associated with lymphotoxin-beta receptor (LTβR) antagonist treatment of chemotherapy modeled mice.

overall_design: Chemotherapy treatment was implemented by systemic (intraperitoneal (i.p.)) injection of Paclitaxel (PTX). The treatment protocol was two injections of PTX (2mg/kg) separated by one day. These mice were injected with a LTβR antagonist between PTX treatments and 1 day after PTX treatment. LTβR antagonist (15μg each) was injected simultaneously into hind paw (intraplantar (i.pl.)) and spinal cord (intrathecal (i.t.)). The controls were i.pl. + i.t. IgG (10μg each) injected mice. For the experiment, paw skin samples from both sides were isolated 6 days after the last PTX injection. For the experiment, L3-L5 from both sides DRG samples were isolated 6 days after the last PTX injection. For the experiment, spinal cord samples were isolated 6 days after the last PTX injection. For control, paw, DRG and SC samples were isolated 1 and 7 days after last PTX injection.

first: Alexei

last: Tumanov

first: Jennifer

last: Mecklenburg

first: Sergei

last: Belugin

first: George

last: Naratadam

first: Priscilla

last: Barba-Escobedo

first: Ekaterina

last: Koroleva

first: Anahit

last: Hovhannisyan

last: Shein

first: Koji

last: Tamada

first: Michael

last: Croft

first: Yi

last: Zou

first: Zhao

last: Lai

first: Armen

last: Akopian


title: Biological processes in Nav1.8-posistive DRG neurons after PTX treatment (the long model) in control (LTβR-fl/fl) and Na1.8-cre/LRβR-fl/fl mice

summary: We investigated biological processes in Nav1.8-posistive DRG neurons associated with chemotherapy treatment and LTβR sensory neuronal ablation.

overall_design: Chemotherapy treatment was implemented by systemic (intraperitoneal (i.p.)) injection of Paclitaxel (PTX). The treatment protocol was three injections of PTX (6mg/kg) separated by two day. All mice were injected with WGA-488 into paw 16 days after the last PTX injection. L3-L5 DRG samples from both sides were isolated 18 days after the last vehicle or PTX injection into LTβR-fl/fl and Na1.8-cre/LRβR-fl/fl male mice. DRG samples were converted into single-cell suspension. WGA-488-positive DRG neurons were FACS sorted and isolated for RNA isolation and RNA-seq. Overall, four groups (n=3 each) were: vehicle-treated LTβR-fl/fl and Na1.8-cre/LRβR-fl/fl male mice, and PTX-treated LTβR-fl/fl and Na1.8-cre/LRβR-fl/fl male mice.


title: Biological processes in hind paw skin fibroblasts, keratinocytes and immune cells after PTX treatment (the short model)

summary: We investigated biological processes in hind paw skin fibroblasts, keratinocytes and immune cells associated with chemotherapy treatment.

overall_design: Chemotherapy treatment was implemented by systemic (intraperitoneal (i.p.)) injection of Paclitaxel (PTX). The treatment protocol was two injections of PTX (2mg/kg) separated by one day. Paw skin samples from both sides were isolated 6 days after the last PTX injection into wild-type (WT), Col1a2-cre-ER/tdTom or K5-cre-ER/tdTom male mice. Control skin samples were from vehicle treated male and female mice. Paw skin samples were converted into single-cell suspension. CD45-postive cells (immune cells) were isolated from vehicle-treated WT male and female mice, and 6 days post-PTX-treated WT male mice. Col1a2-postive cells (fibroblasts) were isolated from vehicle-treated Col1a2-cre-ER/tdTom male and female mice, and 6 days post-PTX-treated Col1a2-cre-ER/tdTom male mice. K5-postive cells (keratinocytes) were isolated from vehicle-treated K5-cre-ER/tdTom male and female mice, and 6 days post-PTX-treated K5-cre-ER/tdTom male mice.


title: Single-cell RNA sequencing of Lung Squamous Cell Carcinoma Assosciated with Idiopathic Pulmonary Fibrosis

first: Atsushi

last: Matsuoka

summary: This dataset contains single-cell RNA sequencing (scRNA-seq) data from two patients with lung squamous cell carcinoma (LUSC) associated with idiopathic pulmonary fibrosis (IPF). Tumor and adjacent lung tissues (within and outside UIP lesions) from two patients were snap-frozen, fixed, and processed using the 10x Genomics Chromium Fixed RNA Profiling workflow. Libraries were sequenced on an Illumina NovaSeq 6000 platform and processed using Cell Ranger (10x Genomics).

overall_design: Fresh-frozen tumor and adjacent lung tissues were obtained from two patients with LUSC and CT-confirmed usual interstitial pneumonia (UIP). Tissue samples were processed for single-cell RNA sequencing using the Chromium Fixed RNA Profiling pipeline (10x Genomics).

first: Kazuhiko

last: Shien

first: Shuta

last: Tomida


title: Biological processes in hind paws, dorsal root ganglia and spinal cord of lymphotoxin-beta receptor (LTβR) agonist treated mice

last: ZOU

summary: We investigated biological processes in hind paw, dorsal root ganglion (DRG) and spinal cord (SC) associated with lymphotoxin-beta receptor (LTβR) agonist treatment.

overall_design: The treatment protocol was two hind paw (intraplantar (i.pl.)) injections LTβR agonistic antibodies (10μg each) separated by one day. The controls were i.pl. IgG (10μg each) injected mice. For the experiment, paw skin samples from ipsilateral sides were isolated 1 day after first LTβR agonistic antibody injection, and 6 days after two LTβR agonistic antibody injections. For the experiment, L3-L5 DRG samples from ipsilateral sides were isolated 1 day after first LTβR agonistic antibody injection, and 6 days after two LTβR agonistic antibody injections. For the experiment, lumbar portion of spinal cord samples were isolated 1 day after first LTβR agonistic antibody injection, and 6 days after two LTβR agonistic antibody injections. For control, paw, DRG and spinal cord samples were isolated 1 day after IgG injection.


title: HAND1 controls the lineage divergence between amnion and trophoblast from human pluripotent stem cells

city: Guangzhou

first: Qifeng

last: Yang

state: Guangdong

address: Jingxi Subdistrict

institute: Southern Medical University

summary: Trophoblasts and amnion, as extra-embryonic lineages, can be differentiated from human pluripotent stem cells (PSCs) under defined culture conditions, but the regulatory mechanisms that coordinate the cell fate decisions between these lineages during PSC differentiation remain poorly defined. In this study, leveraging CRISPR/Cas9-mediated targeted screening and lineage reporter pluripotent stem cells (PSCs), we identified the transcription factor HAND1 as a critical determinant governing the divergence of trophoblast and amnion lineages in PSCs. Genetic ablation of HAND1 effectively suppressed the amnion differentiation capacity of EPSCs while enhancing their trophoblast differentiation potential. Conversely, ectopic overexpression of HAND1 have adverse effects. Notably, forced expression of HAND1 activated amnionic transcription program in human trophoblast stem cells (TSCs), demonstrating its lineage-reprogramming capability. Mechanistic analyses revealed that HAND1 cooperates with Wnt signaling pathway co-factors TCF/b-catenin to form a transcriptional complex that antagonistically regulates trophoblast- and amnion-associated gene networks. Collectively, our findings establish HAND1 as a pivotal regulator that orchestrates the fate choice between amnionic and trophoblast lineages during human PSC differentiation, providing insights into the molecular logic of extra-embryonic lineage specification.

overall_design: To investigate the role of transcription factor HAND1 in the differentiation of stem cells into trophoblast stem cells (TSCs).

first: Xuefei

last: Gao

first: Changmiao

last: Pang


title: Multi-timescale analysis of whole-genome gene expression across the life cycle of wild Arabidopsis thaliana accessions in a natural environment

city: Seville

first: Francisco

middle: José

last: Romero-Campero

address: Americo Vespucio 49

department: Institute for Plant Biochemistry and Photosynthesis

country: Spain

institute: University of Sevilla

summary: Discerning the genes, regulatory networks, and environmental cues involved in plant development represents a major goal in the plant sciences. However, genes and regulatory networks have not evolved in controlled environmental conditions, which means that conducting experiments in natural settings is of paramount importance to dissect the underlying mechanisms of plant development realistically. We undertook common garden experiments in a natural environment to quantify whole-genome gene expression patterns over diurnal, seasonal, and annual timescales over the life-cycle phenology of the annual mustard Arabidopsis thaliana with wild Iberian accessions. Importantly, study accessions were locally adapted to their environments by adjusting key life-history traits across an altitudinal gradient in southern Spain. We found that diurnal (between morning and afternoon) and seasonal (across developmental stages) comparisons chiefly structured whole-genome gene expression in A. thaliana accessions. The most important difference between years, which differed in the precipitation regime, was in the number of over-represented genes detected across diurnal and seasonal timescales. Furthermore, we detected most of the differentially expressed genes from various biological functions as shared among all accessions. Nevertheless, the two accessions more similar in flowering time without an obligate flowering requirement also exhibited more similar gene expression patterns. Finally, we detected several flowering time genes from all known regulatory pathways across timescales, particularly from the photoperiod and circadian clock pathways. Overall, our results paved the way for more ambitious gene expression analyses in natural settings, whilst stressing the remarkable plasticity in both life-cycle phenology and gene expression in A. thaliana.

overall_design: RNA-seq profiling of different Arabidopsis thaliana ecotypes in a natural environment at different moments during the day and different developmental stages.

first: Picó

last: F. Xavier

first: Romero-Campero

last: Francisco J.


title: A549 cells with glucocorticoid treatment

city: Illkirch/Strasbourg

first: Wolfgang

last: Raffelsberger

address: 1 rue Laurent Fries

department: DBGS

country: France

institute: IGBMC

summary: Processing bodies (P-bodies) are cytoplasmic, membraneless organelles that play a key role in regulating RNA translation. To identify new pathways controlling their formation, we conducted a Food and Drug Administration (FDA)-approved drug screen. We found that glucocorticoids, among the most prescribed medicines, significantly increase P-body numbers across diverse epithelial cell types. This effect was fully reversible after glucocorticoid withdrawal, illustrating the adaptive dynamics of P-bodies. Using genetic invalidation and rescue approaches, we demonstrated that this accumulation requires the Glucocorticoid Receptor alpha isoform. P-body accumulation was associated with selective post-transcriptional regulation of P-body-associated mRNAs rather than global inhibition of translation. This selectivity was driven by intrinsic transcript features, including nucleotide composition and codon usage: AU-rich transcripts with low Codon Adaptation Index (CAI) were preferentially accumulated and translationally repressed, whereas GC-rich transcripts with higher CAI displayed enhanced protein output under glucocorticoid treatment. Furthermore, we associated the decrease of LSM14B, a negative regulator of P-bodies, under glucocorticoid treatment to P-body reshaping. Our results reveal that, beyond their known transcriptional activity, prolonged exposure to glucocorticoids influences mRNA post-transcription and translation through a nucleotide composition-based mechanism.

overall_design: A549 cells (human lung adenocarcinoma epithelial cell line, ATCC CCL-185 were cultured Dulbecco's modified eagle medium (DMEM). Cells were treated with or without dexamethasone (n= 4 wells) for 48 h at 1 µM concentration. Identical sets of samples were prepared in parallel for RNA-seq and proteomics analysis.  For RNAseq, total RNA was extracted using TRIzol reagent (Thermo Fisher), purified on Direct-zol RNA miniprep kit (Zymo Research). Libraries were prepared using after ribosomal RNA depletion (Ribo-Zero Gold rRNA Removal Kit, Illumina), fragmentated and first-strand cDNA synthesized using random hexamer primers, second-strand cDNA synthesized and remaining overhangs were converted into blunt ends. Adapoters were ligated to after adenylation of 3' ends and cDNA fragments of preferentially 370-420 bp length were purified with AMPure XP system. After PCR and quality assessment libraries were sequenced using a Illumina NovaSeq 6000 platform in 150 bp paired-end configuration to a depth of 40-50 million read pairs per sample. Raw reads were quality-checked using FastQC (v0.11.9), adapter sequences were trimmed using Cutadapt (v3.4), and resulting reads were aligned to the human reference genome (GRCh38) using STAR aligner (v2.7.9a). Gene expression was quantified with featureCounts (Subread package v2.0.3) and differential expression analysis was performed using DESeq2 (v1.32.0)

first: Victoria

middle: J

last: Nicolini

first: Mathilde

last: Dupart

first: Olivia

last: Vidal-Cruchez

first: Tifenn

last: Rete

first: Karine

last: Jacquet

first: Frédéric

last: Brau

first: Sophie

last: Abelanet

first: Marie

last: Irondelle

first: Antonin

last: Bourdin

first: Jérôme

last: Durivault

first: Célia

last: Gotorbe

first: Adeline

last: Knittel

first: Bruno

last: Didier

first: Pascal

last: Villa

first: Christophe

last: DiGorgio

first: Baharia

last: Mograbi

first: Arnaud

last: Hubstenberger

first: Paul

last: Hofman

first: Patrick

last: Brest


title: Lactose-Derived Carbohydrates Induce Sexually Dimorphic Nutritional Programming Effects on Lifespan in Drosophila melanogaster

city: Wageningen

first: Evert

middle: M.

last: van Schothorst

address: De Elst 1

institute: Wageningen University

summary: Galactose, the monosaccharide that gives together with glucose the milksugar lactose, plays a critical role in early-life nutrition and may exert long-lasting effects on later-life health. We tested whether early-life consumption of glucose and galactose (GLUGAL; as in hydorlysed lactose) shapes later-life metabolic health in the Drosophila melanogaster model. In the early life, GLUGAL versus glucose consumption alone (GLU) significantly extended the developmental time of larvae, increased the pupal volume, decreased pupal oxygen consumption, and reduced the pupal mitochondrial mass. These early-life effects were translated into sextually dimorphic effects on adult lifespan: the survival of adult male flies was reduced but the adult females lifespan was particularly extended by early-life GLUGAL consumption. Transcriptomics and lipidomics analyses in adult females revealed that early-life GLUGAL consumption systematically reduced glycerophospholipids saturation under a later-life high-carbohydrate obesogenic diet, which is characterized by decreased abundance of monounsaturated fatty acid-containing glycerophospholipids and increased abundance of polyunsaturated fatty acid-containing glycerophospholipids. This was accompanied with higher transcription levels of genes involved in hydrocarbon biosynthesis, a pathway that preferentially consumes saturated and monounsaturated fatty acids. Conclusively, early-life galactose and glucose co-consumption shortened adult males lifespan, but extended the lifespan and remodelled lipid metabolism in adult females.

overall_design: Drosophila were fed glucose (GLU) or glucose+galactose (GLUGAL) diets in early-life (the larval period) and a high-glucose diet (HGLU) in later life (the adult period after eclosion).

first: Peixin

last: Sun

first: Jaap

last: Keijer


first: Chao

last: Li

overall_design: Performing in situ ChIP-seq on HAND1 to specifically study the HAND1 binding regions.

first: Xuefei

last: Gao

first: Shanshan

last: Ai

first: Yulong

last: Zhong


title: RAG1-Independent Atypical B Cell Development in Chickens: Redefining the Role of RAG1 in Avian Immunology

city: University Park

first: Tae Hyun

last: Kim

address: 317 AVBS Building

institute: Penn State University

summary: The importance of RAG1 in avian B cell development has been a topic of significant debate, as chickens exhibit limited antibody diversity through RAG1-mediated V(D)J recombination compared to mammals. In chickens, antibody diversity is predominantly achieved through gene conversion in the bursa of Fabricius. However, the absence of RAG1 disrupts gene conversion and impairs B cell signaling pathways, underscoring its importance. In this study, we utilized a RAG1-deficient chicken model to uncover a classical RAG1-dependent and an alternative RAG1-independent B cell developmental pathway unique to avians. Unlike mammals, where RAG1-induced double-strand breaks (DSBs) activate ATM-dependent DNA damage responses (DDR) for B cell development, we found that ATR mediates this process in chickens. In RAG1-deficient chicken bursa, normal development of B cells is halted due to the absence of V(D)J recombination and reduced ATR-mediated B cell development signals. Although the absence of RAG1 significantly reduced B cell numbers, a small number of B cell subset was still observed. These atypical B cells (ABCs), which developed in the bursa, exhibited reduced ATR-mediated signaling but elevated expression of inflammatory and migration-related genes, allowing them to migrate into the bursa. ABCs were also specifically observed in peripheral organ (spleen) of RAG1-deficient chicken and expressed IgM with only harboring J and C segments. Additionally, ABCs displayed autoimmune-like phenotypes, including lysosome, TLR signaling activation, autophagy, and inflammation. This study highlights avian-specific alternative RAG1-independent B cell development and provides insights into autoantibody-independent mechanisms of autoimmune diseases, contributing to comparative immunology and therapeutic development.

overall_design: Bulk RNAseq of embryonic day 18 bursa from wildtype and RAG1 knock out chickens, three biological replicates each

first: Seung Je

last: Woo

first: Kyung Youn

last: Lee

first: Jin Lee

first: Jin-Kyoo

first: Jae Yong

last: Han


title: Super-enhancer-driven MAB21L2 promotes neuroblastoma progression

city: suzhou

first: yang

last: yang

address: zhongnan road

institute: soochow university

summary: Neuroblastoma (NB) is a prevalent pediatric tumor, accounting for over 15% of cancer-related fatalities in children. Super-enhancers (SEs), as pivotal cis-regulatory elements known for driving oncogene expression across various tumors, may serve as an innovative strategy for deciphering NB pathogenesis. Here, we meticulously analyzed epigenomic and transcriptomic data to delineate the distinct SE landscape in NB. Our study identified a NB-specific and NB-common SE at the MAB21L2 locus. Functional analyses further underlined MAB21L2’s oncogenic role in NB, linking its high expression to poor patient outcomes. MAB21L2 knockdown strikingly inhibited the growth of NB tumor cells in vitro and reduced their proliferation in vivo. Notably, through RNA-seq analysis and experimental verification, we demonstrated that MAB21L2 substantially enhanced the migratory capacity of NB cells. Collectively, these findings underscore the indispensable role of MAB21L2, an SE-driven gene, in the oncogenesis and progression of NB, indicating its potential as a promising therapeutic target for the treatment of this aggressive malignancy.

overall_design: mRNA profiles of SK-N-BE(2) cells treated with short hairpin RNAs (shRNAs) targeting MAB21L2 or negative control (shNC) were generated by RNA sequencing, in double, using Illumina NovaSeq6000.

first: Yang

last: Yang


title: c-Rel drives pancreatic cancer metastasis through fibronectin-integrin signaling- induced isolation stress resistance and EMT

first: BiNGS

last: Core

address: 3 E 101st St

institute: Icahn School of Medicine at Mount Sinai

summary: Pancreatic ductal adenocarcinoma (PDAC) remains one of the deadliest malignancies, with limited treatment options and a high recurrence rate. Recurrence happens often with metastasis, for which cancer cells must adapt to isolation stress to successfully colonize distant organs. While the fibronectin-integrin axis has been implicated in this adaptation, its regulatory mechanisms require further elaboration. Here, we identify c-Rel as an oncogenic driver in PDAC, promoting epithelial-to-mesenchymal transition (EMT) plasticity, extracellular matrix (ECM) remodeling, and resistance to isolation stress. c-Rel directly regulates fibronectin (Fn1) and CD61 (itgb3) transcription, enhancing cellular plasticity and survival under anchorage-independent conditions. Fibronectin is not essential for EMT, but its absence significantly impairs metastatic colonization. These findings establish c-Rel as a key regulator of PDAC metastasis by controlling cellular niche and survival under isolation stress. Overall, targeting the c-Rel–fibronectin–integrin axis could provide new therapeutic strategies to mitigate disease progression and recurrence.

overall_design: RNA-Seq profiling of pancreatic cell lines with wildtype Rel (CKP) and Rel knockout and overexpression derivatives (CCKP and GCKP)

first: Derya

last: Bakırdöğen

first: Kıvanç

last: Görgülü

first: Xin

last: Jiaqi

first: Sonia

last: Alcalá

first: Laura

last: Ruiz-Cañas

first: Katrin

last: Frank

last: Wu

first: Kalliope

last: Diakopoulos

first: Chenyue

last: Dai

first: Harun

last: Ozturk

first: Deniz

last: Demircioglu

first: Katja

last: Peschke

first: Raphela

last: Ranjan

first: Federico

last: Fusco

first: Javier

last: Martinez-Useros

first: Maria

last: Fernandez-Aceñero

first: Nirav

middle: F

last: Chhabra

first: Juan

middle: C

last: López-Gil

first: Jiaoyu

first: Dietrich

last: Ruess

first: Ezgi

last: Kaya-Aksoy

last: Steiger

first: Fränze

last: Schmidt

first: Larissa

last: Kohlmann

first: Alexandra

last: Berninger

first: Roland

last: Schmid

first: Maximillian

last: Reichert

first: Mazhar

last: Adli

first: Marina

last: Lesina

first: Bruno

last: Sainz Jr

first: Hana

last: Algül


title: RNA-seq Analysis of Entamoeba histolytica KERP2 Knockdown Strain

city: Tokyo

first: Ruofan

last: Peng

state: Tokyo

address: 7-3-1 Hongo, Bunkyo-ku

department: International Health

institute: University of Tokyo

summary: This dataset contains RNA-seq data from Entamoeba histolytica strains, including a KERP2-knockdown strain (psAP-KERP2gs) and a control strain (psAP-mock). To investigate the functional role of KERP2 (EHI_065630), the knockdown strain was generated using small interfering RNAs with the psAP-2-Gunma plasmid. RNA-Seq analysis revealed distinct transcriptional profiles between KERP2gs and psAP-mock strains. GO and KEGG pathway enrichment analyses identified upregulation of genes involved in proteolysis regulation, sulfur amino acid metabolism, and amoebiasis in the KERP2-knockdown strain. Notably, cysteine synthases (EHI_024230, EHI_160930), methionine γ-lyase (EHI_057550), cysteine protease (EHI_010850), and pore-forming peptides (EHI_169350, EHI_194540, EHI_15940) were significantly upregulated. These findings suggest a potential role for KERP2 in regulating parasitic activities, possibly through chromatin binding. This dataset provides a valuable resource for studying KERP2-associated gene expression changes in E. histolytica.

overall_design: RNA-seq profiling of KERP2 knockdown strain and the control psAP-mock strain.

first: Herbert

last: Santos

first: Tomoyoshi

last: Nozaki


title: Lactate and histone H3K18 lactylation are associated with metabolic control of gene expression in the retina [explant_RNA-seq]

city: Bethesda

first: Matthew

last: Brooks

state: MD

address: 6 Center Dr Bldg 6, Rm 303

department: NEI

institute: NIH

summary: High aerobic glycolysis in retinal photoreceptors, as in cancer cells, is implicated in mitigating energy and metabolic demands. Lactate, a key product of glycolysis, is implicated in epigenetic regulation through histone lactylation in cancer. Here, we demonstrate that increased ATP production during retinal development is achieved primarily through augmented glycolysis. Histone lactylation, especially H3K18La, parallels enhanced glycolysis and its product, lactate, in developing retina and in retinal explants. Multi-omics analyses, combined with confocal imaging, reveal the localization of H3K18La near H3K27Ac in euchromatin at promoters of active retinal, especially photoreceptor, genes. H3K18La and gene expression also correspond to glucose metabolism in retinal explants. Evaluation of accessible chromatin at H3K18La promoters uncovers an enrichment of GC-rich motifs for transcription factors of SP, KMT and KLF families, among others, indicating specificity of H3K18La-mediated gene regulation. Our results highlight glycolysis/lactate/H3K18La as a regulatory axis in fine-tuning gene expression in developing and mature retina.

overall_design: Biologically replicated RNA-seq was performed on retinal explant cultures. The dissected retinas were incubated in Neurobasal-A media supplemented with 5 mM glucose/25 mM glucose. Gene-level differential expression analysis was performed using RNA-seq data.

first: Mohita

last: Gaur

first: Xulong

last: Liang

first: Milton

last: English

first: Laura

last: Campello

first: Claire

last: Marchal

first: Anand

last: Swaroop


title: Chromatin Immunoprecipitation of GFP-HA-KERP2 expressing Entamoeba histolytica

summary: Approximately 1 x 10^8 GFP-HA-KERP2 expressing Entamoeba histolytica cells were cross-linked in 0.5% formaldehyde (in PBS) for 10 minutes at room temperature. Cross-linking was quenched with 125 mM glycine for 5 minutes. Cells were washed once with PBS and subjected to nuclear fractionation using nuclei isolation buffer (10 mM Hepes-KOH pH 7.9, 1.5 mM MgCl2, 10 mM KCl, 2% NP-40, 1 uM E-64, 0.5 mM PMSF, and 1x cOmplete protease inhibitor cocktail). Nuclear pellets were resuspended in sonication buffer (50 mM Tris-HCl pH 8.0, 140 mM NaCl2, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 5 mM DTT, 1 uM E-64, 0.5 mM PMSF, 1x cOmplete) and sonicated using a Covaris instrument. Sonicated samples were centrifuged at 16000 x g for 20 minutes. A 200 uL aliquot of supernatant was transferred to a 1.5 mL Protein LoBind tube. Remaining sample was stored as input control. For immunoprecipitation, 1 mL of ChIP dilution buffer (16.7 mM Tris-HCl pH 8.0, 0.01% SDS, 1% Triton X-100, 1.2 mM EDTA, 167 mM NaCl, 0.5% BSA, 1x cOmplete) containing 50 uL of GFP(ab290)-antibody conjugated Dynabeads was added and rotated at 4 C for 12 hours. Beads were washed five times with low-salt wash buffer (20 mM Tris-HCl pH 8.0, 0.1% SDS, 1% Triton X-100, 2 mM EDTA, 150 mM NaCl), followed by two washes with high-salt wash buffer (same as above, but 500 mM NaCl). DNA-protein complexes were eluted with 200 uL of ChIP elution buffer (10 mM Tris-HCl pH 8.0, 1% SDS, 5 mM EDTA, 300 mM NaCl) at room temperature for 20 minutes. Input samples were thawed and diluted with 190 uL of elution buffer. All samples were incubated at 65 C for 8 hours to reverse cross-links, followed by RNase A treatment (1 uL) at 37 C for 1 hour and Proteinase K digestion (5 uL) at 55 C for 2 hours. DNA was purified by phenol/chloroform extraction with 1 uL glycogen as carrier, followed by ethanol precipitation overnight at -30 C. DNA pellets were washed with 80% ethanol, air-dried, and resuspended in 20 uL TE (ChIP) or 40 uL TE (input). DNA concentrations were quantified using a Qubit dsDNA High Sensitivity Assay Kit (Thermo Fisher Scientific). Purified DNA was submitted to Rhelixa for ChIP-seq.

overall_design: ChIP-seq of GFP-HA-KERP2 expressing E. histolytica pulled down by anti-GFP, together with input samples without antibody pull-down.


title: Transcriptomic Analysis of Caco-2 Cells Co-cultured with KERP2-related Entamoeba histolytica Strains

summary: KERP2 is a secreted parasitic factor in Entamoeba histolytica that interacts with host colon epithelial cells, potentially contributing to pathogenesis. To investigate its influence on host gene expression, RNA-seq was performed on Caco-2 cells co-cultured with HA-KERP2-overexpressing E. histolytica (HA-KERP2), psAP-KERP2gs (partial KERP2 knockdown), or wild-type G3 strains, alongside untreated controls. Differential expression analysis identified upregulation of key pro-inflammatory mediators (IL1B, IL36G), signaling adapters (SLA), and heme-related genes (HRG) in HA-KERP2-treated cells, while cytoskeletal regulators (CYTIP, MYOCD), stress-response factor (NUPR1), and solute transporters (SLC15A3) were downregulated. In contrast, psAP-KERP2gs-treated cells exhibited increased expression of extracellular matrix components (TNC), contractility regulators (MYL7), and metabolic enzymes (CYP4B1), while genes involved in cilia function (CFAP43), solute transport (SLC2A12), and the pentose phosphate pathway (TKTL1) were downregulated.

overall_design: RNA-seq profiling of Caco-2 cells co-cultured with Entamoeba histolytica strains with differential KERP2 Expression


title: Lactate and histone H3K18 lactylation are associated with metabolic control of gene expression in the retina [timecourse_CUT&Tag]

overall_design: Biologically replicated CUT&Tag assays for H3K18La were performed on postnatal mouse retinal at ages P4, P10 and P28. Consensus peaks were determined and quantitative binding was performed.


title: Lactate and histone H3K18 lactylation are associated with metabolic control of gene expression in the retina [explant_CUT&Tag]

overall_design: Biologically replicated CUT&Tag assays for H3K18La and H3K27Ac were performed on retinal explant cultures. The dissected retinas were incubated in Neurobasal-A media supplemented with 5 mM glucose/25 mM glucose. Concensus peaks were determined and quantitative binding was performed. Gene-level differential expression analysis was performed using RNA-seq data.


title: Alterations in single-cell transcriptomic levels and cellular localisation of hnRNP proteins in Frontotemporal Lobar Degeneration

city: London

first: Yazead

last: Buhidma

state: London

address: 1 Wakefield Street

department: Department of Neurodegenerative Diseases

institute: University College London

summary: Frontotemporal dementia (FTD) is a neurodegenerative disorder with a strong heritable component. Frontotemporal lobar degeneration (FTLD) refers to the pathological changes seen in FTD, characterised by atrophy of the frontal and temporal lobes and the presence of abnormal protein inclusions. In the case of FTLD with hyperphosphorylated TDP-43 positive inclusions (FTLD-TDP), five pathological  subtypes (A, B, C, D, and E) are observed based on the types and distribution of inclusions found in the brain. In all subtypes, there tends to be a large variability in the amount of pathological inclusions observed between cases, with limited correlation to clinical manifestations. TDP-43 is an RNA binding protein belonging to the heterogeneous nuclear ribonucleoprotein (hnRNP) family which along with other hnRNPs modulates multiple aspects of RNA processing. HnRNPs other than TDP-43 have been implicated in several neurological diseases, including ALS, FTLD-TDP, FTLD-FUS and Alzheimer's disease. Multiple hnRNPs have been found in pathological inclusions in specific subtypes of FTLD-TDP, suggesting potential roles in the disease process. The role of the hnRNP network in FTLD disease pathogenesis has not yet been investigated. This study aimed to comprehensively evaluate the presence and expression of hnRNP proteins in two pathological subtypes of sporadic FTLD-TDP (A and C) as well as the genetic form FTLD-TDP A C9orf72 using immunohistochemistry and gene expression analysis by single cell RNA-sequencing. We sought to determine whether hnRNPs exhibited aberrant expression at the protein and transcript level in FTLD cases with TDP-43 pathology.

overall_design: Nuclei were isolated from frozen frontal cortex grey matter from 3 FTLD-TDPA, 3 TDPA-C9, and 5 TDPC, and 5 healthy controls. Tissue was transferred directly onto ice-cold sucrose buffer and homogenised by hand. The homogenate was layered on top of a sucrose cushion and nuclei were recovered after centrifugation. Nuclei were resuspended in PBS containing BSA (to prevent clumping) and RNase inhibitors, counted and diluted to 1,000 nuclei/μl. Sequencing libraries were prepared using the “single cell 3’ library kit v3” with the Chromium instrument (10X Genomics). Aiming to obtain libraries for ~5,000 independent nuclei per sample. Libraries were sequenced on an Illumina NovaSeq6000 instrument (UCL Genomics), to an average of at least 100,000 reads/nucleus. Raw sequencing data were processed through the software CellRanger (10X Genomics) to assign each transcript read to its respective nucleus, we performed alignment to the transcriptome, counting reads, and processing of the unique molecular identifier tag to reduce PCR bias. The resulting gene count table was analysed using the Seurat package (version 4.4). Quality control was performed to remove low-quality cells based on the number of detected genes and unique molecular identifiers (UMIs). Cells with an unusually high number of UMIs, suggesting potential doublet events, were also excluded using scDblFinder. Using SCTransform, gene expression data were normalised to adjust for differences in sequencing depth between cells and scaled to correct for cell-to-cell variation in total UMI count. Data were also normalised to remove confounding sources of variation such as mitochondrial mapping percentage, post-mortem delay, age of death, and batch number.

first: Tammaryn

last: Lashley

first: Ariana

last: Gatt


title: Genomic Analysis of T cell Receptors Provides Novel Insights of Cancer Immunology in Lynch Syndrome Carriers

city: Houston

first: Eduardo

last: Vilar-Sanchez

address: 1515 Holcombe Blvd

institute: The University of Texas MD Anderson Cancer Center

summary: Lynch Syndrome (LS) provides the perfect context to understand DNA mismatch repair deficient (MMRd) carcinogenesis. LS carriers develop MMRd tumors with high neoantigen loads, which are shared by different LS tumors and recognized by T-cell receptors (TCRs) to trigger adaptive immunity.  However, the TCR landscape in LS remains unexplored. Therefore, we performed TCR-sequencing in 277 blood samples from 102 LS cancer survivors, 130 LS previvors, and 45 controls, as well as three LS colorectal cancers, and 11 pre-cancers. For the first time, we found that up to 41% of the most expanded TCRβs from colorectal cancers and pre-cancers are detectable in the blood of several LS carriers, whereas these TCRs have minimal or no expansion in the blood of controls. Additionally, we developed a classification model that distinguishes LS carriers from controls with excellent performance using a set of 1,114 TCRβs that associates with all LS carriers, regardless of MMRd cancer history, and a set of 2231TCRβs that associates with LS previvors who have never developed cancer. This study is the first to describe circulating TCRβs that recognize neoantigens derived from colorectal cancers and pre-cancers in LS carriers, moving the field towards the identification of a blood based TCRβ cancer biomarker.

overall_design: We used this RNF43_3 peptide in conjunction with a dextramer to stimulate PBMCs from a LS patient, thereby obtaining RNF43-specific CD3+ T-cells. Subsequently, we performed single-cell RNA and single-cell TCR sequencing on these RNF43-dextramer-specific CD3+ T-cells. We then compared the TCRβ sequences obtained from these cells to our Lynch-associated signature TCRβs and separately to our LS-survivor-associated signature TCRβs to assess overlap and validate the neoAg specificity of the identified TCRβ signature sequences.


title: Identification of immunogenic outer membrane vesicle vaccine antigen components using a meningococcal protein microarray

city: Manchester

first: Fidel

last: Ramirez Bencomo

state: England

address: Michael Smith Building

department: FBMH/SBS/EIGen

institute: The University of Manchester

summary: Outer membrane vesicle (OMV)-based vaccines have been employed worldwide in response to epidemic meningococcal disease outbreaks caused by Neisseria meningitidis. The complex composition of OMVs raises challenges in the identification of antigens which contribute to a protective immune response. Here, we measured total IgG antibody binding profiles to a dedicated antigen microarray using human sera from an open-label Phase II trial (NCT00962624) of 4CMenB (Bexsero), a licensed vaccine containing an OMV component. Significant IgG responses were observed against specific Outer Membrane Proteins (OMPs) from OMV antigens, including FetA, PorB, BamA and PorA. Partial Least Squares Regression was used to correlate IgG antibody reactivity profiles with the human complement-dependent killing of meningococci. We show that this approach is a powerful method to identify the potential contributions of OMV antigens - notably OpcA, FetA, PorA and PorB- towards serum bactericidal activity in human vaccinee serum against indicator strains, a recognised correlate of protection against invasive meningococcal disease

overall_design: A panel of recombinant meningococcal proteins were printed in 4 replicates on a non-commercial protein microarray. Selected proteins from the proteome of the meningococcal strains H44/76 and NZ98/254 included transmembrane beta-barrel outer membrane proteins and proteins of non-cytoplasmic origin containing a signal peptide at their N-termini. All proteins were expressed in E. coli as His-tagged proteins. Proteins with transmembrane sections were purified from inclusion bodies and the rest were purified from cytoplasmic fraction as soluble forms. Positive controls consisted of 8 serial 2-fold dilutions of mouse, human, rat, and rabbit IgG (from 0.5 mg/mL to 0.004 mg/mL in 40% glycerol). Negative controls were the different protein buffers + 40% glycerol. Sera were profiled for anti-human IgG-specific analysis of reactivity to the spotted proteins.

first: Jeremy

last: Derrick

last: RamirezBencomo

first: Viola

last: Viviani

first: Angela

last: Thistlethwaite


title: Patients based and Knock-in-mouse analysis reveals I536T variant of RBM20 is not contributory to myopathy

city: Nishinomiya

first: Takuma

last: Yamamoto

address: 1-1 Mukogawa-Cho

institute: Hyogo Medical University

summary: Introduction: RBM20 regulates pre-mRNA splicing, and its mutations cause dilated cardiomyopathy by disrupting cardiac RNA splicing, particularly of the TTN gene. While RBM20 is known to affect TTN splicing in the heart, its role in skeletal muscle remains unclear. This study investigated the effects of an RBM20 variant using an Rbm20 I538T knock-in mouse model, performing pathological and RNA-seq analyses to assess its impact on skeletal muscle. Methods: We used Rbm20 I538T knock-in mouse and performed pathological and RNA-seq analyses to evaluate the effect of the variant on skeletal muscle. Results and Discussion: Histopathological examination revealed no skeletal muscle abnormalities in any genotype. Although potential splicing effects on Ttn and Ldb3 were considered, no abnormal splicing was detected. Differentially expressed gene analysis showed no differences among genotypes. Therefore, we conclude that the Rbm20 I538T variant does not affect the splicing of skeletal structural proteins or lead to a skeletal muscle phenotype.

overall_design: Using the CRISPR/Cas system, we generated KI mice harboring the c.T1613C (p.I538T) point mutation in the mouse Rbm20 gene, which corresponded to human c.T1607C (p.I536T).


title: Detect the expression of PIWI‐interacting RNAs (piRNAs) in High glucose and palmitate treated cardiomyocytes

first: Yuehong

last: Wang

address: 160 Pujian Road

institute: Harbin medical university

summary: To further explore the function of piRNA in regulating pyroptosis in DCM by combining piRNAs microarray expression analysis and transcriptome sequencing technology (RNA-seq),

overall_design: According to the experimental protocol, cardiomyocytes were exposed to high glucose (HG, 40 mM) combined with palmitate (Palm, 300 mM). Then collected the cardiomyocytes for Mouse piRNA microarray

first: ANDE

last: JIAO

first: LU

last: FU


title: The myeloid SRC family kinase HCK regulates breast cancer growth by activating tumor associated macrophage-led invasion and inhibiting cytotoxic T cell activity

city: Perth

first: Michael

middle: William

last: Murrey

state: WA

address: 35 Stirling Hwy, Crawley

department: Biomedical Sciences

country: Australia

institute: University of Western Australia

summary:
The normal developmental and homeostatic roles of tissue resident macrophages are subverted in tumor-associated macrophages to promote tumor progression. Pro-tumoral macrophage activities include immune suppression and promotion of invasion and metastasis.
We used the Py8119 mouse mammary tumor model to investigate the role of Hck activity in tumor growth through therapeutic inhibition and genetic modification. Single cell RNA sequencing and immunohistochemistry approaches were used to investigate changes to the immune compartment.
Loss of HCK activity reduced the growth of Py8119 mammary tumors by 70-80% while excessive HCK activity increased growth four-fold. Consistent with a role for HCK in macrophage invasiveness, plasma membrane-associated Src family kinase activity at the tumor margins was lost in the absence of HCK. Regarding immune evasion, HCK-deficient tumors contained increased CD8+ T cell numbers and, while CD8+ T cell depletion reduced survival in all mouse cohorts, CD8+ T cell-depleted HCK-deficient mice survived much longer than CD8+ T cell-replete control mice. Characterisation of the tumour microenvironment by single cell sequencing showed 5 major subtypes of TAMs (immunoregulatory (Folr2high ), inflammatory (MHC-IIhigh ), interferon-primed, angiogenic and tissue resident), which together made up 40% of cells in the tumour. While Hck activity did not affect the recruitment of TAMs or their subtype composition, pathway analysis showed that its loss decreased TAM motility and increased their interferon signalling and reduced EMT pathways in the Py8119 tumor cells.
This study provides evidence that HCK activity in TAMs enhances tumour growth via promotion of invasive behaviour as well as suppression of anti-tumor immunity. These findings highlight HCK as a promising therapeutic target to limit tumor progression.

overall_design: Single cell RNA sequencing was used to characterise orthotopic Py8119 mammary tumors in C57BL/6 mice across several experiments. 1: Treatment with RK20449 or vehicle control (Captisol) (3 replicates per condition), 2: Untreated tumors at two timepoints, early (day 10) and late (day 14) 3: Tumors grown on HckKO mice with matched WT controls (3 replicates per condition), 4: Tumors grown on Hck CA mice with matched WT controls (2 replicates per condition)

first: Ashleigh

last: Poh

first: James

last: Steer

first: Catherine

last: Rinaldi

first: Kellie

middle: A

last: Mouchemore

first: Amy

last: Dwyer

first: Elena

last: Denisenko

first: Irina

last: Kuznetsova

first: Yen

last: Yeow

first: Matthew

last: Jones

first: Khaing

middle: P

last: Hmon

first: Dáithí

last: Ó Muirí

first: Ya-Yu

last: Liu

first: Weitao

last: Lin

first: Alistair

last: Forrest

first: Lesley

middle: G

last: Ellies

first: David

last: Joyce

first: Matthias

last: Ernst

first: Fiona

last: Pixley


title: Cardiomyocyte βII Spectrin Plays a Critical Role in Maintaining Cardiac Function via Regulating Mitochondrial Respiratory Function

city: Xi’an

first: Rongjin

last: Yang

address: 169 Changle West Road

department: Department of Cardiology

institute: Air Force Medical University

summary:
To investigate the Cardiomyocyte βII Spectrin in the regulation of mitochondrial respiratory function, we established mouse neonatal cardiomyocytes (NCMs) in which SPTBN1 has been knocked down by shRNA.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 2 different cells at the same point.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for mouse neonatal cardiomyocytes (NCMs) and its βII spectrin overexpression.

first: Shan

last: Wang


title: Exosomal Transfer of Mitochondria Reprograms T Helper Cell Function In Chronic Airway Inflammation

city: Birmingham

first: Jessy

last: Deshane

state: AL

address: 1900 University Boulevard

institute: University of Alabama at Birmingham

summary: Cell-to-cell communication in complex multicellular organisms is mediated by soluble factors and extracellular vesicles that include exosomes. Myeloid-derived regulatory cells (MDRCs) are regulators of CD4+ T cell responses in asthma. Here, we demonstrate that airway MDRC-derived exosomes from asthmatics mediate T cell receptor engagement and mitochondrial transfer that promote antigen-specific activation and polarization of Th17 and Th2 cells, drivers of chronic airway inflammation in asthma. Exosomal mitochondria are internalized by CD4+ T cells predominantly by membrane fusion, although their activation is internalization-independent. Additionally, blocking mitochondrial oxidant signaling in MDRC-derived exosomes mitigates T cell activation.  In asthmatics, a Drp1-dependent mitochondrial fission process in pro-inflammatory MDRCs generates exosomal mitochondria. Importantly, internalized exosomal mitochondria co-localize with polarized cytoskeleton and mitochondrial networks suggesting a role in organization of the immune synapse in recipient T cells. These results indicate an unrecognized role for mitochondrial fission and exosomal transfer in immunological cross-talk in chronic airway inflammation.

overall_design: 14 samples were analyzed (6 samples for asthma and 8 samples for healthy).  Healthy samples with no exosomes were used as a control for within sample conditions and cross-sample groups. TUBB and RPL19 were used as housekeeping genes.

first: Kenneth

last: Hough

first: Jennifer

last: Trevor

first: Balu

middle: K

last: Chacko

first: John

last: Strenkowski

first: Yong

first: Kayla

last: Goliwas

first: Nathaniel

middle: B

last: Bone

first: Shia

last: Vang

first: Sandeep

last: Bodduluri

first: Young-il

last: Kim

first: Renita

last: Holmes

first: Sultan

last: Tousif

first: Veena

last: Antony

first: Jay

last: Chin

first: Mohammad

last: Athar

first: Diptiman

last: Chanda

first: Jaroslaw

last: Zmijewski

first: Jianhua

last: Zhang

first: Kasturi

last: Mitra

first: Steven

last: Duncan

first: Victor

last: Thannickal

first: Susanne

last: Gabrielsson

middle: M

last: Darley-Usmar


title: Aldh1a3 accelerates lung metastasis of PDAC via enhancing tumor cells - lung epithelial cells cross talk through Sema4d-Plxnb1 and Sema3a-Nrp1 signaling

city: Nanjing

first: Xuetian

last: Qian

state: Jiangsu

address: No. 68 Changle Road, Nanjing, China

institute: Nanjing First Hospital Affiliated to Nanjing Medical University

summary: In previous studies, we found that high expression of aldehyde dehydrogenase 1 family member A3 (ALDH1A3) was associated with more lymph node metastases in pancreatic ductal adenocarcinoma (PDAC). We here report in PDAC Aldh1a3 promotes lung colonization, while is dispensable in liver colonization or proliferation. Aldh1a3 upregulates the transcription of Plxnb1 and Nrp1 via accelerating acetylation at histone H3 lysine in the promoter regions of Plxnb1 and Nrp1. The enhancing signaling of Sema4d-Plxnb1 and Sema3a-Nrp1 between pancreatic cancer cells and lung epithelial cells facilitate tumor cells to colonize in the lung. Our studies have uncovered Aldh1a3 as a key regulator of semaphorin signaling. Sema4d-Plxnb1 and Sema3a-Nrp1 signaling is important for lung metastatic organotropism of PDAC, but is dispensable in liver metastasis.

overall_design: To investigate the effect of Aldh1a3 on the metastatic ability of PDAC and its potential regulatory mechanism, we generated stable overexpressing murine PDAC cell lines by initially transfecting them with an Aldh1a3 cDNA ORF clone, followed by monoclonal selection. Subsequently, we conducted gene expression profiling analysis using data derived from RNA-seq of murine PDAC cells overexpressing Aldh1a3 and control cells. We conducted a comparative gene expression profiling analysis of RNA-seq data and performed functional enrichment analyses on differentially expressed genes.

first: Hongzhen

last: Li


title: Transcriptome sequencing of E14.5 fetal liver erythroblast stage 1 cells in WT and LDB1 conditional KO mice

city: Seoul

first: Si-Won

last: Park

address: Anam-ro

country: South Korea

institute: Korea University

summary: This study investigated the role of LDB1 in early erythroid development by comparing gene expression patterns between WT and LDB1 cKO embryo. These data may provide better knowledge about the exact mechanisms underlying the role of LDB1 in erythropoiesis at distinct differentiation stage.

overall_design: Erythroblast stage 1 cells from E14.5 WT and cKO fetal livers were sorted as Ter119⁻CD71⁺ cells, and RNA extracted from these populations was used for transcriptome analysis.


title: Genes differentially regulated by knockdown of miR-30e-3p and miR-34b-5p in human primary trophoblast

first: Bernadette

middle: Carolyn

last: Baker

state: Lancashire

address: Oxford Road

department: Maternal and Fetal Health Research Centre

institute: University of Manchester

summary:
Maternal folate deficiency during pregnancy results in adverse outcomes. We have found miR-30e-3p and 34b-5p to be directly downregulated by folate deficiency in placental trophoblast cells and wanted to determine cell functions/pathways affected by these miRNAs.
Using microarrays we identified a number of functional pathways for further analysis that could contribute to placental dysfunction in folate deficient women.

overall_design: Isolated primary cytotrophoblast from term placentas were transfected with inhibitors of miR-30e-3p or 34b-5p and 48hrs later total RNA isolated and analysed by microarray.

first: Karen

last: Forbes


title: Identification of a human hematopoietic stem cell subset that retains memory of inflammatory stress

city: Toronto

first: Alexander

middle: James

last: Murison

state: Ontario

address: 101 College Street, TMDT room 11-706

country: Canada

institute: University Health Network

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

overall_design: Refer to individual Series


title: Intrinsically disordered regions restrain genomic targeting of RNA and histone demethylases in mammals and plants

city: Chicago

first: Long

last: Zhao

state: Il

address: 929 E 57th Street

department: Department of Chemistry

institute: University of Chicago

type: Methylation profiling by high throughput sequencing

sample_organism:
Arabidopsis thaliana
Mus musculus

platform_organism:
Arabidopsis thaliana
Mus musculus


title: H3K27me3 spreading organizes canonical PRC1 chromatin architecture to regulate developmental programs

city: Montreal

first: Jacek

last: Majewski

state: Quebec

address: 740 Dr. Penfield

department: Human Genetics

institute: McGill University

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Temperature and developmental stage govern intestinal susceptibility to human coronavirus 229E.

status: Public on Mar 01 2026

city: Wrocław

first: Heng-Chang

last: Chen

address: Stablowicka 147

country: Poland

institute: Łukasiewicz Research Network – PORT Polish Center for Technology Development

summary: Transcriptional profiling of fetal, pediatric, and adult human intestinal enteroids following Human Coronavirus 229E infection at 32C and 37C.

overall_design: 6 different human intestinal enteroids (2 fetal donors, 2 pediatric donors, and 2 adult donors) were generated, differentiated, and subsequently infected for 48h with clinical strain of  human coronavirus 229E at either 32C or 37C. Controls included mock-infected enteroids.

first: Aleksandra

last: Synowiec

first: Katarzyna

last: Owczarek

first: Maciej

last: Borowiec

first: Michal

last: Pietrusinski

first: Izabela

last: Drozdz

first: Agnieszka

last: Robaszkiewicz

first: Krzysztof

last: Pyrc


title: Gene expression from laser capture microdissected epithelium and stroma during pancreatic carcinogenesis

city: Munich

first: Hans

middle: Carlo

last: Maurer

state: Bavaria

address: Ismaninger Str. 22

department: II. Medizinische Klinik

institute: Klinikum rechts der Isar

summary: This study used laser capture microdissection to obtain highly purified epithelial and stromal RNA samples from frozen sections of human pancreatic ductal adenocarcinoma (PDA), low-grade pancreatic intraepithelial neoplasias (PanIN) and low-grade intraductal papillary mucinous neoplasms (IPMN). Libraries were prepared using the Nugen Ovation RNA-Seq System V2 and sequenced to a depth of 30 million 100bp single-end reads. These data were used to reconstruct both an epithelial and stromal gene regulatory network of malignant pancreatic disease using the ARACNE algorithm and elucidate regulatory proteins whose dysregulation drives progression and dedifferentiation in PDA.

overall_design:
Epithelial gene expression data are presented for 197 human PDA, 26 low-grade PanIN and 19 low-grade IPMN epithelia, respectively. Stromal gene expression was profiled for 124 human PDA.

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Raw files for human/patient samples will be made available in dbGaP for controlled access to the personally identifiable sequence data.
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first: H

first: Kenneth

last: Olive