title: Development of a 3D Nanofiber Neurocomplex from MSCs-Derived Neuron-like cells for Spinal Cord Injury Regeneration and Functional Recovery

city: Suzhou

first: Hu

last: ya'nan

state: Jiangsu

address: 199 Ren-Ai Road, Suzhou Industrial Park

department: Department of Cell Biology

institute: Medical College of Soochow University

summary: Mesenchymal stem cell (MSC)-derived neurons offer a promising therapeutic approach for the treatment of spinal cord injury (SCI). In this study, we developed a one-step differentiation system utilizing a cocktail of CYSP (CHIR99021, Y27632, SB431542, and Purmorphamine) to convert rat MSCs into neuron-like cells. After 7 days of differentiation, over 80% of the cells were positive for neuronal markers Tubb3 and Map2. Notably, the cells expressed Synapsin-1, a protein associated with functional neuronal synapses, after 14 days of differentiation. In addition, the differentiated cells exhibited characteristics of motor neurons, as evidenced by the presence of Islet1 and CHAT, markers of motor neuron identity. Transcriptomic analysis revealed significant upregulation of genes related to neuronal development, synapse formation, and synapse transmission at day 7 of differentiation, while genes associated with cell proliferation and the cell cycle were downregulated. Notably, the induction process led to the significant inhibition of the Hippo signaling pathway, while activation of the HIF1α, JAK/STAT, and PI3K/AKT signaling pathways was observed. To further enhance therapeutic potential, we developed a biomimetic silk scaffold (BSS) neurocomplex featuring a 3D nanofiber structure, designed to match the compressive modulus of the human spinal cord, by seeding induced neuron-like cells (iNs) onto the scaffold. We demonstrated that this neurocomplex effectively integrates into the host neural circuit, promoting neural regeneration and significantly enhancing functional recovery in rats with SCI. Collectively, our findings suggest that MSC-derived neurons, in combination with the BSS to form the neurocomplex, offer a promising strategy for SCI treatment and provide valuable insights for future regenerative therapies.

overall_design: To investigate the mechanisms underlying CYSP-induced neuronal differentiation of MSCs, we performed RNA sequencing to analyze changes in gene expression at the transcriptional level over a 7-day period. The volcano plot illustrates the number of differentially expressed genes (DEGs) during transdifferentiation, with 1,947 upregulated and 1,919 downregulated genes identified. KEGG enrichment analysis revealed that these DEGs were significantly associated with signaling pathways closely linked to neurogenesis and neuronal differentiation, including MAPK, Hippo, and PI3K/AKT. Further analysis of upregulated and downregulated genes using heatmaps and Gene Ontology (GO) analysis highlighted that DEGs related to nervous system development, neuronal differentiation, synapse formation, and synapse transmission were significantly upregulated, while genes associated with cell proliferation and the cell cycle were notably downregulated. In addition to specifically targeting individual signaling pathways, small molecules also modulate the crosstalk between multiple pathways. Different combinations of these molecules can lead to variations in neuronal subtypes and conversion efficiency. Gene Set Enrichment Analysis (GSEA) revealed that the HIF1α, JAK/STAT, and PI3K/AKT signaling pathways were significantly activated following transdifferentiation, while the Hippo signaling pathway was notably inhibited.

first: Ya'nan

last: Hu

first: Huanxiang

last: Zhang


title: Programming of the Endometrial Immune Milieu by Interferon Gamma during Early Pregnancy in Pigs

status: Public on Jan 08 2026

city: Columbia

first: John

last: Driver

state: MO

address: 1201 Rollins Street

country: USA

institute: University of Missouri

type: Expression profiling by high throughput sequencing

summary: Release of interferon-gamma (IFNG), a pro-inflammatory type II interferon, by the early conceptus is critical for pregnancy establishment in the pig. Yet, the cellular and molecular mechanisms underpinning conceptus-derived IFNG actions in maternal peripheral immune cells and at the embryo–maternal interface remain unclear. Here we show that pregnancy status up-regulates expression of IRF1, an IFNG target-gene, in peripheral blood mononuclear cells on day 15 of pregnancy in the pig. In a second study, loss-of-function IFNG (IFNG–/–) embryos were generated by using CRISPR/Cas9 gene editing and somatic cell nuclear transfer. Single-nuclei RNA sequencing of endometrium from gilts carrying wild-type (Control) or IFNG–/– conceptuses on day 15 of pregnancy revealed cell-type-specific signatures at the embryo–maternal interface in response to conceptus IFNG. Changes in the transcriptome of epithelial and IFNG receptor-expressing immune cells were evident between Control and IFNG–/– samples, along with a downregulation of IFNG target-genes involved with chemotaxis and immune cell differentiation in IFNG–/– recipient endometria. A notable reduction in monocytes and macrophages was observed in IFNG–/– samples, confirmed by immunohistochemistry for AIF1. Differential gene expression (DEG) analysis revealed 391 DEGs in monocytes, implicating IFNG in macrophage polarization, with evidence suggesting a shift toward an M2 phenotype. The study concludes that conceptus IFNG plays an important role in monocyte recruitment and macrophage polarization at the embryo–maternal interface for regulation of inflammation upon conceptus attachment. Insufficient numbers or skewed IFNG-activated macrophages within the endometrium may contribute to pregnancy failure in the IFNG–/– pig model.

overall_design: On day 15 of estrous cycle/pregnancy, recipient (IFNG-/- and IFNG+/+) and bred gilts were euthanized via jugular injection of pentobarbital sodium and phenytoin sodium. The reproductive tracts were excised and transported to the laboratory for immediate processing. Uterine horns were trimmed free of adjacent tissues and processed for sample collection. After flushing and recovery of stage-matched conceptuses to confirm pregnancy, uterine horns were opened longitudinally along the antimesometrial line and endometrial fragments were dissected from the mesometrial side. Tissue samples were snap frozen and stored at −80°C. Prior to flushing, distal parts of each uterine horn near the uterine body were clamped, sectioned transversely, and processed for tissue fixation.


title: Redistribution of RNA localization in early embryos of zebrafish

city: Vestec by Prague

first: Radek

last: Sindelka

address: Průmyslová 595

country: Czech Republic

institute: Institute of Biotechnology, Czech Academy of Science, v.v.i.

summary: This study investigates spatial transcriptomic dynamics during early embryogenesis in Danio rerio (zebrafish). Using TOMO-seq, we profiled RNA localization along the animal–vegetal axis at key embryonic stages for 1 hpf (~4-cell), 2 hpf (~64-cell), and 3 hpf (~1000-cell) embryos. Samples were collected in biological triplicates and sectioned into five defined regions (A–E) along the axis to assess spatial distribution. The data were used to analyze maternal RNA localization, transcript stability, and onset of zygotic transcription.

overall_design: To investigate transcriptomic changes during early embryonic development, TOMO-seq was applied to a series of developmental stages: 1 hpf (~4-cell), 2 hpf (~64-cell), and 3 hpf (~1000-cell) stages. Biological triplicates were used for each condition. Samples were sectioned along the animal–vegetal axis into five distinct regions, labeled A through E, with region A representing the most animal and region E the most vegetal portion. This approach enabled the analysis of both temporal and spatial transcriptomic dynamics to uncover stage-specific transcriptomic changes occurring during the onset of embryogenesis.

first: Katerina

last: Cihakova

first: Ravindra

last: Naraine

first: Viktoriia

last: Hantzsch

first: Roman

last: Franek

first: Martin

last: Psenicka


title: Redistribution of RNA localization in early embryos of trout hybrid (Oncorhynchus mykiss egg fertilized with Salvelinus fontinalis sperm)

summary: This study investigates the spatial transcriptomic dynamics during early embryogenesis in a hybrid trout, where the Oncorhynchus mykiss (rainbow trout) egg was fertilized with the Salvelinus fontinalis sperm. Using TOMO-seq, we profiled RNA localization along the animal–vegetal axis at key embryonic stages, 0 hpf (freshly fertilized egg/zygote), 1 hpf (early cleavage stage), 1 dpf (early blastula stage, ~32-64 cells), and 3 dpf (mid-blastula, ~1000 cells). Samples were collected in biological triplicates and sectioned into two sections (A & B) along the axis to assess spatial distribution. The data were used to analyze for de novo transcription by looking for paternal transcripts. Our results revealed spatially distinct transcriptome changes.

overall_design: To investigate transcriptomic changes during early embryonic development, TOMO-seq was applied to a series of developmental stages: 0 hpf (freshly fertilized egg/zygote), 1 hpf (early cleavage stage), 1 dpf (early blastula stage, ~32-64 cells), and 3 dpf (mid-blastula, ~1000 cells). Biological triplicates were used for each condition. Samples were sectioned along the animal–vegetal axis into two distinct regions, labeled A and B, with region A representing the animal section and region B the vegetal section. This approach enabled the analysis of both temporal and spatial transcriptomic dynamics to uncover stage-specific transcriptomic changes occurring during the onset of embryogenesis with sepecific focus on detecting potential de novo transcriptions.


title: RNA-Seq analysis of Trim28-deleted NPp53 mouse prostate tissue

city: Washington

first: Maho

last: Shibata

state: DC

address: 800 22nd Street, NW SEH 8430

institute: The George Washington University

summary: Tripartite motif-containing 28 (TRIM28/TIF1b/KAP1) is a key transcriptional co-repressor protein that represses ERV expression in many cell types including embryonic stem cells, neural progenitor cells, differentiated adult cells, and cancer cells. In this study, we investigated the effect of Trim28 deletion on the expression of ERVs using an immune competent genetically engineered mouse model for prostate cancer. We found Trim28 deletion in prostate tumors led to the expression of ERVs in prostates from both hormonally intact and castrated mice. ERVs can regulate the expression of neighboring genes, and we detected increased expression of several protein-coding genes near overexpressed ERVs. Our data suggest that Trim28 deletion in prostate tumor epithelial cells may promote an innate immune response. However, Trim28 deletion also led to excessive deposition of tumor extracellular matrix (ECM). Our findings suggest that ECM alterations downstream of ERV derepression could affect immune cells in the tumor microenvironment and may promote tumor progression.

overall_design: RNA-Seq expression profiles from NPp53 (Pten;Tp53 deleted) and NPp53T (Pten;Tp53; Trim28 deleted) mouse prostates

first: Emily

middle: C

last: Williams


title: Fibroblast-derived alarmin promotes oral wound healing by activating Tregs that relay pro_x0002_angiogenic and anti-inflammatory

city: Philadelphia

first: Kang

last: Ko

state: Pennsylvania

address: 240 S. 40th Street

department: Department of Periodontics

institute: University of Pennsylvania

summary: Fibroblasts are abundant structural cells that produce extracellular matrix components and are essential for tissue repair following an injury. Emerging evidence highlights a crucial immunomodulatory role of fibroblasts in health and disease, which is incompletely explored in the wound healing field. Here, we used an oral wound healing model that heals exceptionally fast with minimal scarring and investigated if select fibroblasts are endowed with immune-regulatory functions that can have an impact on optimal healing outcomes. We identified PI16+ oral reticular fibroblasts to be highly enriched in interleukin-33 (IL33), an alarmin cytokine that is rapidly released during the early stages of wound healing. Using mice with lineage-specific, inducible deletion of IL33, we found that baseline expression of IL33 from fibroblasts but not keratinocytes was necessary for proper wound healing in oral mucosa. Singe cell RNA-sequencing (scRNA-seq)analysis revealed that regulatory T cells (Tregs) respond to IL33 and upregulate the expression of a pro-inflammatory cytokine MIF and an anti-inflammatory cytokine TGFB1, which was validated in vivo. Mechanistically, MIF promotes recruitment of angiogenic monocytes to facilitate blood vessel formation in healing wounds, whereas TGFB1 supports an early transition of macrophages to a pro-resolving phenotype. Importantly, we show that human oral mucosa, but not skin, harbors IL33+ PI16+ reticular fibroblasts in deeper aspects of the connective tissue and that Tregs express MIF and TGFB1 in regenerating oral mucosa. Together, our study unveils an essential role of IL33+ oral reticular fibroblasts for the modulation of acute inflammation by engaging Tregs that promote angiogenesis and resolution of inflammation in wound healing.

overall_design: Seven control mice and eight experimental mice with IL33 deletion in fibroblasts were used for scRNA-seq analysis.

first: Zhaoxu

last: Chen

first: Zikeng

last: Huang

first: William

middle: S

last: Kim

first: Rahul

last: Debnath

first: Kawintip

last: Prasongyuenyong

first: Brett

middle: P

last: DerGarabedian

first: Thao

last: Do

first: MacKenzie

middle: A

last: Moore-Kosslow

first: Jonathan

middle: M

last: Korostoff

first: Chiden

first: Yongwon

last: Choi

middle: I


title: Clinical Characteristics and Spatial transcriptome analysis of Early Resistance to Alectinib in ALK-Positive non-small cell lung cancer: A Retrospective OLCSG Study

city: Okayama

first: Shuta

last: Tomida

state: Okayama

address: 2-5-1 Shikata-cho, Kita-ku

department: Center for Comprehensive Genomic Medicine

country: Japan

institute: Okayama University Hospital

summary: In anaplastic lymphoma kinase (ALK) gene rearrangements positive lung cancer, alectinib has shown good efficacy and is used as a first-line drug. However, some cases show early resistance within 3 months, but the characteristics of these cases have not been established. We analyzed patients with unresectable stage III/IV without indications for radical radiotherapy and recurrent ALK-positive lung cancer who received alectinib for primary ALK-TKI. Spatial transcriptome analysis and immunohistochemical staining revealed upregulation of Annexin A1 (ANXA1) in the early resistant group.

overall_design: Six cases with surgically resected samples were analyzed using the NanoString GeoMx instrument. Two patients were in the early resistant group and four were in the responder group. 34 ROIs were selected that were representative of each tumor. Immunofluorescence staining was performed using PanCK, CD45, CD68, and SYTO13. We separately profiled RNA from tumor areas (PanCK+). ANXA1, LCN2, and CLDN4 were upregulated in tumor areas with the early resistance group.

first: Tadahiro

last: Kuribayashi

first: Go

last: Makimoto

first: Kadoaki

last: Ohashi


title: A Multi-omic approach reveals iron availability influences hepatocyte cell fate II

city: Melbourne

first: Kristin

middle: K

last: Brown

state: VIC

address: 305 Grattan St

country: Australia

institute: Peter MacCallum Cancer Centre

summary: Recent evidence has highlighted the importance of employing cell culture media designed to reproduce the physiological metabolic environment in vitro. Here, we utilize the physiological medium Plasmax to examine the impact of nutrient availability on the model human hepatocyte cell line, HepG2. Incubation of HepG2 cells in Plasmax suppressed a transcriptional program driven by Hepatocyte Nuclear Factor 4 (HNF4A), a master regulator of hepatocyte identity. Given that HepG2 cells were originally isolated from a patient with hepatoblastoma, this suggests reversion to the native state in physiological media. Importantly, exclusion of the trace element iron from Plasmax reinstated the HNF4A-driven transcriptional program. Taken together, these studies suggest a relationship between iron availability and regulation of hepatocyte cell fate and highlight the importance of more faithfully recapitulating in vivo metabolite availability in vitro.

overall_design: RNA-Seq profiling of HepG2 cells incubated in EMEM, Plasmax, Plasmax without trace elements (Plasmax-TE), and Plasmax without trace elements and with iron supplementation (Plasmax-TE+Fe) for 96 hours.

first: Athena Jessica

last: Ong

first: Andrew

last: Cox


title: SWAP70 Promotes Atherosclerosis via Endothelial CAV1 Nuclear Translocation [ATAC-seq]

city: Shenzhen

first: Tianyu

last: Gao

address: 1088 Xueyuan Avenue

country: China

institute: Southern University of Science and Technology

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Hemodynamic forces play a pivotal role in modulating endothelial function and contribute to the spatial distribution of atherosclerotic lesions. Here, we identify SWAP70 as a flow-sensitive gene whose chromatin accessibility is dynamically regulated by shear stress. Using ATAC-seq analysis of human endothelial cells exposed to static conditions, laminar shear stress (LSS), or oscillatory shear stress (OSS) for 72 hours, we observed that OSS markedly increased chromatin accessibility at the SWAP70 promoter compared to LSS. This enhanced accessibility under OSS suggests transcriptional activation of SWAP70 in response to disturbed flow. These findings indicate that SWAP70 may serve as a mechanosensitive regulator, epigenetically primed by atheroprone flow patterns to modulate endothelial inflammation.

overall_design: ATAC-seq profiling of HUVECs exposed to static, laminar shear stress (LSS), or oscillatory shear stress (OSS) for 72 hours to assess flow-dependent chromatin accessibility at the SWAP70 promoter.


title: Juvenile hormone degradation enzymes have shared and unique requirements in Drosophila developmental pacing and growth.

city: San Antonio

first: Lacy

middle: J

last: Barton

state: Texas

address: 1 UTSA Circle

department: Neuroscience, Developmental and Regenerative Biology

institute: University of Texas at San Antonio

summary: Development, physiology, and reproduction require the precise control of hormones. Hormone bioavailability is regulated by their synthesis and transport, as well as sequestration, natural turnover, and active degradation. For most hormones, we know far less about active hormone degradation than their synthesis. Here, we use Drosophila melanogaster to investigate the enzymes that degrade the retinoic acid-like Juvenile hormones (JH). While JH titers must decrease to ensure metamorphosis, the developmental requirements of both classes of JH degradation enzymes, JH esterases (JHEs), and JH epoxide hydrolases (JHEHs), have not been determined due to genetic redundancies. To overcome this knowledge gap, we generated double knockout animals lacking both JHEs as well as triple knockout animals lacking all three JHEHs. We found that while neither class of JH degradation enzymes are required for viability, they have unexpectedly distinct requirements in developmental pacing and growth. Animals lacking JHEs pupariate at the expected time but are larger, indicating that JHEs restrain developmental growth but not pacing. In contrast, animals lacking JHEHs are a normal size but are severely delayed in their development, indicating that JHEHs regulate developmental pacing but not growth. To investigate this unexpected separation of requirements among JH degradation enzymes, we analyzed JH-producing glands, performed rescue experiments, and characterized transcriptional changes by bulk RNA-sequencing. Together, our data revealed striking differences in the developmental requirements for JHE and JHEH, yet shared requirements for regulating ecdysone-related genes. By generating these genetic tools, such hypotheses can be explored to shed light on active hormone degradation in development and beyond.

overall_design: RNA-seq profiling of Drosophila melanogaster whole white prepupae from two control genetic backgrounds (white^1118 and Oregon R crossed to white^1118) and two mutants backgrounds (Jhe, JheDup double knockouts and Jheh1,2,3 triple knockouts). White prepupae were separated by sex such that each sample is either male (M) or female (F). Three biological replicates were collected and analyzed, each containing RNA from 5 white prepupae.

first: Harry

last: Siegel

first: Creehan

last: Healy

first: Krystal

last: Goyins

first: Amina

last: Jumamyradova

first: Justina

last: Sanny

first: Alexey

last: Soshnev

first: Rebecca

last: Spokony


title: Single-Cell Exon Deletion Profiling Reveals Splicing Events That Shape Gene Expression and Cell State Dynamics [scRNA-seq]

city: Frederick

first: Thomas

last: Gonatopoulos-Pournatzis

state: MD

address: Building 560

institute: National Cancer Institute

summary: Alternative splicing is a pervasive gene regulatory mechanism critical for diversifying the human proteome. To systematically investigate its role in cell fate determination, we developed scCHyMErA-Seq, a scalable CRISPR-based exon deletion screening platform integrated with 10x Genomics single-cell transcriptomic readouts. This tool enables efficient exon deletion while simultaneously capturing Cas9/Cas12a guides and polyadenylated transcripts at single-cell resolution. Applying scCHyMErA-Seq to high-throughput profiling of alternative cassette exons, we identified numerous exons with strong regulatory effects on gene expression. Analysis of NRF1 alternative exon-7 revealed that this exon modulates NRF1 transcriptional activity by regulating its recruitment to the promoters of target genes. Importantly, gene expression profiles generated using scCHyMErA-Seq accurately recapitulate findings from traditional, labor-intensive orthogonal methods, while offering enhanced scalability and efficiency. Overall, scCHyMErA-Seq represents a robust and versatile platform for systematically unraveling the functional impact of alternative splicing by directly linking specific splicing variants to transcriptional phenotypes.

overall_design: HAP1 cells co-expressing spCas9 and opCas12a were transduced with a hybrid guide RNA (hgRNA) library designed to induce deletions in 224 exons and knockouts in 161 genes at a low multiplicity of infection (MOI = 0.1). Transduced cells underwent selection with puromycin for two days. Four days post-transduction, a total of 413,190 cells were processed using the 10x Genomics Chromium Next GEM Single Cell 3' Reagent Kits v3.1 (Dual Index), with protocol modifications to enable the specific amplification of Cas12a gRNA libraries. For sequencing, libraries corresponding to 1) gene expression, 2) CRISPR perturbations (Cas9 & Cas12a gRNAs using conventional 10x Genomics CRISPR libraries), and 3) Cas12a-specific sequencing (using a custom Cas12 gRNA-specific amplification protocol) were pooled at a 4:1:1 molar ratio. Sequencing was performed on an Illumina NovaSeq platform using a 100-cycle kit, following the standard 10x Genomics protocol: Read 1: 28 bp, Index i7: 10 bp, Index i5: 10 bp, Read 2: 90 bp.

first: Bandana

last: Kumari

first: Arun

last: Damodaran

first: Wilfried

last: Guiblet

first: Mei-Sheng

last: Xiao

first: Amit

last: Behera

first: Tyler

last: On

first: Carl

last: Mcintosh

first: Maxwell

last: Teszler

first: Chelsee

last: Holloway

first: Sandra

last: Le

first: Nikhil

last: Parab

first: Yongmei

last: Zhao

first: Michael

last: Aregger


title: A Multi-omic approach reveals iron availability influences hepatocyte cell fate I

first: Kristin

last: Brown

overall_design: RNA-Seq profiling of HepG2 cells incubated in low-glucose DMEM (LGDMEM), high-glucose DMEM (HGDMEM), EMEM, and Plasmax for 96 hours.

first: Athena Jessica

last: Ong

first: Andrew

last: Cox


title: Paracrine effect of fibroblasts on the proliferation and differentiation of bovine satellite cells in vitro

city: Balice

first: Kacper

last: Zukowski

address: Krakowska 1 Street

country: Poland

institute: National Research Institute of Animal Production

summary: The co-culture of fibroblasts and muscle cells is essential to obtaining cultured meat using in vitro techniques. Recent studies indicate that fibroblasts support the process of myogenesis and regeneration of damaged muscle fibers through cell-cell interactions. However, little research has focused on the fibroblast paracrine effect on myogenesis and transcriptome changes. This study aims to examine the paracrine effect of fibroblasts on the myogenesis process, based mainly on transcriptome study. Studies were conducted at the stage of proliferation and differentiation of muscle cells. RNA-Seq analysis revealed changes in many genes involved in the myogenesis process at the proliferation and differentiation stages – such as upregulation of EGR1, IL6, and SOCS3 and downregulation of ITGA7. The co-culture of muscle satellite cells with fibroblasts at the proliferation stage promotes myogenic differentiation, but at the differentiation stage, the culture conditions set by the type of medium (differentiation medium) have a prevailing effect on the course of myogenesis over the paracrine effect of fibroblasts.

overall_design: RNA Sequencing analysis of bovine muscle satellite cells cultured in co-culture with fibroblasts, compared to muscle satellite cells monoculture - at the 5th day of proliferation and 24h and 72h after the initiation of differentiation.

first: Karolina

last: Zygmunt

last: Żukowski

first: Katarzyna

last: Piórkowska

first: Grzegorz

last: Smołucha

first: Alicja

last: Wierzbicka

first: Wojciech

last: Witarski


title: The effects and mechanisms of exosomal miRNAs derived from TGF-β-induced M2-polarized TAMs in prostate cancer.

city: Guangzhou

first: Xi

last: Ming

state: Guangdong

address: No. 48 Xinhua Road, Xinhua Street, Huadu District, Guangzhou

institute: Guangzhou Huadu District People's Hospital

type: Non-coding RNA profiling by high throughput sequencing

summary: Recent research indicates that exosome-derived miRNAs play a crucial role in disease progression and may serve as potential candidates for therapeutic interventions. Exosomes are associated with M2 polarized macrophages induced by cytokines or proteins secreted by PCa cells. Recent studies have explored the biological role of exosomal miRNAs in PCa progression, but they have not investigated the mechanism by which exosomal miRNAs mediate communication between PCa and M2-polarized macrophages.

overall_design: We analyzed miRNA expression in exosomes from M2-polarized TAMs to assess their role in promoting PCa progression. M2-TAMs were derived from THP-1 monocytes using PMA and TGF-β. Exosomes from macrophages and M2-TAMs were isolated via ultracentrifugation, and miRNAs expression differences were analyzed using small RNA sequencing

first: Rui-feng

last: Deng

first: Lu

last: Cheng

first: Yu-lin

last: Zhou

first: Yuan-ling

last: Liu

first: Wen-cong

last: Jiang

first: Song

last: Wan

first: Min-yao

first: Ming

last: Xi


title: SWAP70 Promotes Atherosclerosis via Endothelial CAV1 Nuclear Translocation

first: Tianyu

last: Gao

summary: Endothelial inflammation is a critical contributor to atherosclerosis and is tightly regulated by mechanical and inflammatory cues. Here, we identify SWAP70 as a key mechanosensitive adaptor protein involved in endothelial inflammatory responses. Using RNA-seq analysis of human umbilical vein endothelial cells (HUVECs) under three conditions—control (KOC), TNF-α stimulation (TKOC), and TNF-α stimulation with SWAP70 knockdown (TKO)—we demonstrate that SWAP70 deficiency profoundly alters the transcriptional landscape induced by TNF-α. SWAP70 knockdown suppresses the expression of key pro-inflammatory mediators such as VCAM1, MCP1, and CXCL8. Functional enrichment analysis reveals that SWAP70 regulates inflammation-related pathways including TNF, NF-κB, and MAPK signaling. These findings suggest that SWAP70 facilitates endothelial inflammation by promoting transcriptional responses to pro-inflammatory stimuli and may serve as a regulatory hub linking disturbed flow and cytokine signaling in atherosclerosis.

overall_design: RNA-seq profiling of HUVECs transduced with control or SWAP70 shRNA under basal and TNF-α-stimulated conditions to investigate SWAP70-mediated inflammatory transcriptional responses.


title: Deregulated megakaryocytic maturation, mitochondrial function and inflammatory signalling in CYCS(c.292T>C)-related thrombocytopenia

city: Athens

first: Eleni

last: Katsantoni

state: Attiki

address: Soranou tou Efesiou 4

department: Basic Research Department

country: Greece

institute: Biomedica Research Foundation Academy of Athens

summary: The human CYCS gene encodes for Cytochrome C, a mitochondrial protein with important cellular functions, including apoptosis and energy production. CYCS variants have been linked to CYCS-related thrombocytopenia, a mild autosomal dominant type of inherited thrombocytopenia. Here we report a novel heterozygous variant of the CYCS gene, c.292T>C, p.(Tyr98His) in a Greek family with thrombocytopenia. The functional role of the novel variant has been examined in several cellular processes to delineate the mechanisms underlying the thrombocytopenic phenotype of the patients. In megakaryocytes, the novel variant has been associated with irregular apoptosis, ATP production, superoxidase activity and maturation. Transcriptomic data have validated the deregulation of these cellular processes and have provided information about the effect of the variant on Tumor Necrosis Factor A (TNFA) signaling. TNFA via Nuclear Factor Kappa B (NFKB) pathway has been positively enriched in megakaryocytes carrying the variant, possibly triggering the observed deregulation of apoptosis and differentiation. This study has provided insights on the novel CYCS variant revealing a connection to the thrombocytopenic phenotype through deregulated apoptosis, energy production, differentiation and TNFA via NFKB signaling in megakaryocytes, providing future opportunities to therapeutically target the deregulated pathways in CYCS-related thrombocytopenias.

overall_design:
To model the effect of the novel CYCS (NM_018947.6):c.292T>C (p.Tyr98His) variant in megakaryocytic the (NM_018947.6):c.292T>C (p.Tyr98His) variant has been inserted in Dami cells through Homology-directed repair using the CRISPR-Cas9 System.
Differential gene expression analysis was performed using data obtained from RNA-seq of 4 homozygous, 5 heterozygous mutant Dami clones and 4 wild type Dami clones (2 separate analyses: a. Homozygous vs Wild type b. Heterozygous vs Wild type)

first: Eirini Sofia

last: Fasouli


title: A high MAPK, low WNT cell state drives metastatic dissemination in colorectal cancer

city: South San Francisco

first: Robert

last: Piskol

state: CA

address: 1 DNA Way

department: gRED Computational Sciences

institute: Genentech Inc.

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

overall_design: Refer to individual Series


title: Lysine lactylation regulates ATF4-mediated stress responses under glucose starvation in canine hemangiosarcoma

city: Sapporo

first: Suzuki

last: Tamami

state: Hokkaido

address: Kita-18-jo, Nishi-9-chome, Kita-ku

department: Department of Clinical Sciences, Faculty of Veterinary

institute: Hokkaido University

summary: Excess lactate is produced in tumor cells by aerobic glycolysis and regulates gene expressions by histone lactylation. However, how histone lactylation functions under glucose-limited conditions remains unknown. Here, we show that lysine lactylation redistributes to transcription start sites (TSSs) during glucose deprivation, thereby altering biological behaviors in canine hemangiosarcoma (HSA) cells. Glucose deprivation significantly decreased global histone lactylation levels, while lactylation peaks were enriched at TSSs of ATF4‑regulated stress‑response, asparagine-synthesis and immune‑related genes. Stress-response gene expressions were upregulated, and ATF4 polyclonal knockout abrogated this activation. [U-13C]glutamine tracing demonstrated that HSA cells synthesized asparagine from glutamine when glucose was scarce, and asparagine supplementation modestly activated cell proliferation. In HSA patient tissues, H3K18la levels were heterogeneous, and M2-like macrophages preferentially infiltrated tumor regions showing low histone lactylation levels. These findings demonstrate that lysine lactylation regulates transcription that supports tumor cell survival and fosters a pro-tumor microenvironment even under glucose-limited conditions.

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first: Tamami

last: Suzuki

first: Keisuke

last: Aoshima


title: Suppression of Notch during efferocytosis prevents macrophages inflammatory polarization [SLAM-seq]

city: Memphis

first: Beisi

last: Xu

state: Tennessee

address: 262 Danny Thomas Pl

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hosipital

summary: We investigated the mechanism of suppression of Notch during efferocytosis. Genetically activation of Notch or ablation of Rubicon in marophages induced pro-inflammatory polarization and enhance anti-tumor effect.

overall_design: We performed slam-seq in the presence or abscence of apoptotic Jurkat cells to study how genes expression is regulated during efferocytosis in different genotypes.

first: Zhenrui

last: Li

first: Douglas

middle: R

last: Green


title: High fidelity detection of endogenous GPCR-G protein activity with a versatile mouse biosensor platform

city: Boston

first: Mikel

last: Garcia-Marcos

state: MA

address: East Concord Street

institute: Boston University

summary: Activation of heterotrimeric G-proteins (Gαβγ) by G-protein-coupled receptors (GPCRs) is a quintessential mechanism of transmembrane signal transduction in eukaryotes with major biomedical implications in therapeutic targeting. We developed a suite of publicly-accessible transgenic mouse lines that, collectively, allow for the conditional expression of biosensors, named BRET sensors with ER/K linker and YFP 3 (BERKY3),  for any class of GPCR-activated G-protein (Gs, Gi/o, Gq/11, or G12/13). These permit detection of endogenous G-protein activation by endogenous GPCRs in diverse contexts, like in different brain cell types or in lung cells under native-like tissue conditions. To address whether the expression of BERKY biosensors in cells isolated from the transgenic mice affected the signaling mechanism under investigation, unbiased transcriptomic analyses were performed, revealing the high fidelity of the biosensor readout. In summary, the experimental platform of genetically-modified mice introduced here provides a versatile resource to reproducibly interrogate biological processes or mechanisms of drug action that operate via GPCR/G-protein signaling under native cellular conditions and across physiologically-relevant systems.

overall_design: RNA-sequencing was performed for cells (astrocytes for Gas*-BERKY3 and lung fibroblasts for Gai*-BERKY3, Gaq*-BERKY3, and Ga13*-BERKY3) isolated from BERKY3 mice. RNA was isolated from agonist (isoproterenol for Gas*-BERKY3 and TRAP-6 for Gai*-BERKY3, Gaq*-BERKY3, and Ga13*-BERKY3) stimulated or unstimulated cells pre-treated with adeno-associated virus (AAV2/1-CMV-Cre; University of Iowa Viral vector Core, cat# VVC-U of Iowa-237) for Cre-recombinase-mediated biosensor expression or a control empty adeno-associated virus (AAV2/1-CMV-empty; University of Iowa Viral vector Core, cat# VVC-U of Iowa-4223). Three replicate samples were taken for each condition.

first: Remi

last: Janicot

first: Sabrina

last: Shoily


title: Gene expression profile at single cell level of skin cells from back skin of control and Piezo1 inducible knock-out mice

city: Chicago

first: Rui

last: Yi

state: IL

address: 303 E. Chicago Ave

institute: Northwestern University

summary: Piezo1 is a mechanoactive calcium ion channel and is expressed in skin cells. We used single cell RNA sequencing (ScRNAseq) to analyze the functions of mechanical sensing by Piezo1 in hair follicle cells.

overall_design: Hair follicle stem cells were sorted from telogen mouse back skin with a regime of K14H2BGFP+/Cd34+/Itga6+/Sca-1-, then Jun Cut-n-Run were performed on the sorted cells.


title: Suppression of Notch during efferocytosis prevents macrophages inflammatory polarization [RNA-seq.Mouse]

overall_design: We performed RNA seq of tumor associated macrophages isolated from wt or notch overactivated mice.


title: Suppression of Notch during efferocytosis prevents macrophages inflammatory polarization


title: Global rewiring of genome organisation during transition to gametogenesis in gonadal germ cells

city: London

first: Tien-Chi

last: Huang

address: Du Cane Road, Hammersmith Hospital Campus

department: Epigenetics

country: United Kingdom

institute: MRC Laboratory of Medical Sciences

summary: Global epigenetic resetting in the gonadal primordial germ cells (PGCs) enables transition to gametogenesis and eventual restoring of totipotency after fertilisation. This reprogramming process involves global DNA demethylation, changes in nuclear morphology as well as remodeling of repressive histone modifications. Here, using combined cytological and Hi-C based methods, we reveal that following the epigenetic reprogramming and their commitment to gametogenesis, pre-meiotic gonadal germ cells are characterised by a novel principle of chromosome and genome architecture. This involves separation of individual chromosomes and anchoring of centromeres at the nuclear periphery, reduction of  inter-chromosome interactions and disentangling of chromosome ends. Furthermore, genome-wide mapping documents striking remodeling of 3D genome architecture across all observable levels including disruption of topological associated domains (TADs), loss of detectable loops and reduced active-active compartment interactions. We further show that the diminished TADs correlate with the reduced levels of CTCF thus providing a unique in vivo physiological model to understand genome folding principles. Last, but not least we show that primordial germ cell like cells (PGCLCs), derived from embryonic stem cells, do not exhibit the same chromatin organisation as embryonic germ cells suggesting that the 3D genome remodeling accompanies acquisition of meiotic competency. Collectively, our findings uncover the existence of a unique chromatin architecture in premeiotic male and female gonadal germ cells and document that alongside global DNA demethylation the germline epigenetic reprogramming involves erasure of memory at the genome architectural level through a complete re-organisation of 3D genome.

overall_design: Hi-C experiments on isolated PGC and somatic cells from female and male E13.5 mouse embryos

first: Maria

last: Rigau

first: Valeriya

last: Malysheva

first: Chad

last: Wildling

first: Stella

last: Siciliani

first: Irina

middle: B

last: Balsells

first: Camille

last: Dion

first: Mikhail

last: Spivakov

first: Juan

last: Vaquerizas

first: Petra

last: Hajkova


title: Single-Cell Exon Deletion Profiling Reveals Splicing Events That Shape Gene Expression and Cell State Dynamics [ChIP-Seq]

first: Thomas

last: Gonatopoulos-Pournatzis

overall_design: ChIP-sequencing was conducted in HEK293 Flp-In cells stably expressing FLAG-tagged full-length (FL) and ∆Exon-7 NRF1 isoforms. Immunoprecipitation was performed using FLAG antibodies, with HEK293 cells expressing FLAG-EGFP serving as a negative control.

first: Bandana

last: Kumari

first: Arun

last: Damodaran

first: Wilfried

last: Guiblet

first: Mei-Sheng

last: Xiao

first: Amit

last: Behera

first: Tyler

last: On

first: Carl

last: Mcintosh

first: Maxwell

last: Teszler

first: Chelsee

last: Holloway

first: Sandra

last: Le

first: Nikhil

last: Parab

first: Yongmei

last: Zhao

first: Michael

last: Aregger


title: Spatial characterization of the transcriptome of the adult healthy and mutant FUS mouse spinal cords [Spatial transcriptomics]

city: Leuven

first: Sandrine

last: Da Cruz

address: Herestraat 49 |

country: Belgium

institute: VIB-KUL Center for Brain & Disease Research

summary: Here we investigated the spatial transcriptome of the aged mouse spinal cord using 10X Genomics Visium platform. We produced local transcriptomes of the full spinal cord with a resolution of 100 um, characterizing ventral and dorsal horn regions, in addition to grey and white matter regions. With these spatial data, it is possible to explore the spatial transcriptome of the aged mouse spinal cord, extrapolating information on the cellular composition of this tissue.

overall_design: Eight 10-um thick sections of spinal cord tissue (4 controls and 4 mutant FUS samples) were layered on the proprietary Visium Spatial Gene Expression Slide (10X Genomics, Cat#PN-2000233) and further processed.

first: Diana

last: Piol

first: Theo

last: Killian

first: Gabriele

last: Partel

first: Nikolai

last: Hecker

first: Sam

last: Kint

first: Katy

last: Vandereyken

first: Thierry

last: Voet

first: Kristofer

last: Davie

first: Stein

last: Aerts

first: Alejandro

last: Sifrim


title: Inflammation Rewires the Enteric Nervous System Through Neurogenic Monocyte Recruitment

city: New York

first: yu

last: liu

state: NY

address: 1428 Madison Ave

institute: Mount Sinai

summary: The proper organization of the enteric nervous system (ENS) is critical for normal gastrointestinal (GI) physiology. Inflammatory bowel disease (IBD) dysregulates GI physiology including bowel movements (motility), but in many IBD patients, GI motility disorders persist in remission through a poorly understood pathological process. Here we uncover that post-inflammatory GI dysmotility (PI-GID) stems from structural ENS remodeling driven by a combination of neuronal loss and neurogenesis. Enteric neurons respond to mucosal inflammation by upregulating CCL2 expression and facilitating the recruitment of CCR2+ monocytes into the neural myenteric plexus of the intestinal muscle followed by the expansion of monocyte-derived macrophages, their migration into the myenteric ganglia and phagocytosis of neurons. However, excessive recruitment of monocytes promotes disproportionate ENS remodeling and PI-GID. Expansion of immune cells in the tissue also promotes tissue hypoxia. We find that enteric neurons are hypoxic upon colitis; hypoxia-induced signaling via HIF1alpha induces an adaptation program in enteric neurons to suppress CCL2 expression and limit monocyte recruitment. We demonstrate that reinforcing HIF1alpha signaling in enteric neurons prevents PI-GID by reducing colitis-associated monocyte recruitment in the myenteric plexus and mitigating ENS remodeling. In summary, our findings unveil PI-GID pathogenesis and identify a regulatory axis for its prevention.

overall_design: the longitudinal muscle/myenteric plexus (LM/MP) tissue of wild type mice GI tract were isolated, processed, and analyzed by scRNAseq

first: Monalee

last: Saha

first: Qian

last: Li

first: Preston

last: White

first: Sushma

last: Nagaraj

first: Ken

last: Liu

first: Subhash

last: Kulkarni

first: Lauren

last: Peters

first: Yu

first: Miliena

last: Bogunovic

first: Pankaj

last: Pasricha


title: Differential Enrichment of MAPK and Wnt Signaling Pathways in metastatic CRC tumors

first: Robert

last: Piskol

summary: Colorectal cancer, a leading cause of cancer-related mortality due to distant metastases, is driven by activating mutations in the Wnt and MAPK pathways. Understanding the interplay between these crucial pathways during metastatic progression is essential for developing effective treatments. Here we developed an immunocompetent mouse model of metastatic colorectal cancer using in vivo orthotopic passaging. We demonstrate that highly metastatic tumor cells show increased MAPK activity, which in turn suppresses Wnt-associated transcriptional programs, including stem cell-associated genes.

overall_design: We have developed an immuno-competent mouse model of metastatic colorectal cancer by sequentially passaging small intestinal organoids with mutations in Apc, Kras, Tp53 and Smad4 in vivo. Organoids from either Passage 1 (P1, m4) or Passage 5 (P5, m484) were orthotopically injected into the colon of C57BL/6N mice. 5 weeks post orthotopic injection colon tumors were harvested, digested into single cells and live Epcam+ cells sorted. P1 tumors: n=4; P5 tumors: n=3

first: Melanie

last: Heinlein

first: Ginny

middle: X


title: Differential chromatin accessibilty at MAPK- and Wnt-dependent transcription factor motifs in metastatic CRC tumors

summary: Colorectal cancer, a leading cause of cancer-related mortality due to distant metastases, is driven by activating mutations in the Wnt and MAPK pathways. Understanding the interplay between these crucial pathways during metastatic progression is essential for developing effective treatments. Here we developed an immunocompetent mouse model of metastatic colorectal cancer using in vivo orthotopic passaging. We demonstrate that highly metastatic tumor cells show increased accessibility of AP-1 TF motifs and less accessibility at TCF/LEF, suggesting higher MAPK and less WNT activity, respectively.

overall_design: We have developed an immuno-competent mouse model of metastatic colorectal cancer by sequentially passaging small intestinal organoids with mutations in Apc, Kras, Tp53 and Smad4 in vivo. Organoids from either Passage 1 (P1, m4) or Passage 5 (P5, m484) were orthotopically injected into the colon of C57BL/6N mice. 5 weeks post orthotopic injection colon tumors were harvested, digested into single cells and live Epcam+ cells sorted. P1 tumors: n=4; P5 tumors: n=4


title: Differential effects on tumor progression by APOBEC3A, APOBEC3B, and APOBEC3H Haplotype I in a breast cancer mouse xenograft model

city: Saskatoon

first: Franco

last: Vizeacoumar

state: Saskatchewan

address: 4D40 Health Sciences Building, 107 Wiggins Road

department: Oncology

country: Canada

institute: University of Saskatchewan

summary: The APOBEC3 (A3) family of cytidine deaminases induce somatic mutations that are highly prevalent in cancers, but the functional consequences are largely unknown. To determine functional consequences we exposed MCF7 tumorigenic breast epithelial cells to APOBEC3A, APOBEC3B or APOBEC3H Haplotype I. Comparative analysis between cells pre and post -APOBEC3 exposure revealed fewer deamination-dependent γH2AX foci post-APOBEC3 exposure, despite maintaining A3 protein expression. In a mouse xenograft model, high expressing, but not low expressing APOBEC3A-exposed cells caused increased tumor progression. In contrast, high expressing, but not low expressing APOBEC3B-exposed cells decreased tumor size. APOBEC3H Haplotype I-exposed cells stochastically increased tumor progression independent of expression levels. Consistent with tumor data, RNA-seq showed upregulation of tumor enhancing pathways only in cells that enhanced tumor progressiongrowth. The results indicate that in a breast cancer xenograft model, APOBEC3A and APOBEC3H Haplotype I are more likely to contribute to enhanced tumor progression than APOBEC3B.

overall_design: MCF7 cells were engineered to express doxycycline inducible APOBEC3A, APOBEC3B, or APOBEC3H Haplotype I (APOBEC3H). Cells were (Induced, I) or were not exposed (Uninduced, U) to doxycycline for 3 weeks in soft agar. Cells were then isolated, RNA extracted and sequenced. Isogenic cells lines were compared in Induced (I) versus Uninduced (U) pairs as follows: APOBEC3A_I4 vs APOBEC3A_U1 (APOBEC3A low expression), APOBEC3A_I5 vs APOBEC3A_U6 (APOBEC3A high expression), APOBEC3B_I2 vs APOBEC3B_U1 (APOBEC3B high expression), APOBEC3B_I5 vs APOBEC3B_U2 (APOBEC3B low expression), APOBEC3H_I4 vs APOBEC3H_U1 (APOBEC3H High 1), APOBEC3H_I1 vs APOBEC3H_U2 (APOBEC3H High 2)

first: Milaid

middle: G

last: Rodríguez

first: Lai

last: Wong

first: Arzhang

last: Shayeganmehr

first: Diogo

last: Pellegrina

first: Frederick

first: Mohamed

last: Helmy

first: Linda

last: Chelico


first: yu

last: liu

overall_design: 8-9 week-old female Cx3Cr1+/GFP Ccr2+/RFP littermates were used to identify and sort different macrophage subsets present in the colonic muscularis during colitis. Mice received sterile 3% dextran sodium sulfate (DSS) in drinking water for 5 consecutive days followed by sterile water till they reached peak of inflammation. Control mice received sterile water throughout the experiment. DSS treated mice were euthanized at the peak of inflammation i.e. D7-8 along with control mice (n=3 to 4, per group). Single cell suspensions prepared from isolated colonic muscularis tissues were pooled to generate 1 replicate per group. In total, 5 such replicates were prepared thus representing 5 independent sorting experiments. BD FACSAria™ Fusion Flow cytometer was used to sort each replicate into the following subsets: CCR2+, CCR2+Ly6c+MHCII+, CCR2+MHCII+, MHCII+ and Ly6c-MHCII- (DN, double negative). Total RNA was isolated from sorted cell populations using Trizol protocol.

first: Krisztina

last: Szabo

first: Sravya

last: Kurapati

first: Azree

middle: Z

last: Ashraf


title: Efficient processing of widespread R-loops through an endo- and exo-cleavage coupling mode prevents genome instability

city: Beijing

first: weibin

last: wang

address: No. 38 Academy Road

institute: Peking University Health Science Center

summary: Excessive accumulation of R-loops is thought to be one of the major causes of genome instability. Endonuclease RNaseH1 acts as a classic, common R-loop resolvase to prevent R-loop accumulation genome-widely, whether there is any exonuclease complementing and teaming up with RNaseH1 to more efficiently resolve genome-wide R-loops is worth investigation. Here we identify an exonuclease REXO4, which collaborates with RNaseH1 endonuclease to more efficiently degrade R-loops in an “endo- and exo-cleavage coupling” manner. Specifically, among many members of DEDDh exonuclease family, REXO4 has the most significant effect on R-loop suppression. REXO4 directly degrades RNA strand in R-loop from the end or internal nick through its 3’-5’ exonuclease activity, and also stimulates RNaseH1 endonuclease activity. The genome-wide R-loop regions regulated by REXO4 highly overlap with those regulated by RNaseH1, and REXO4 overexpression counteracts genome-wide R-loop accumulation caused by RNaseH1 deficiency. Furthermore, REXO4-deficient tumors display elevated R-loop mutation burden, and tumor patient-derived mutations in REXO4 enzymatic region all impair R-loop cleavage activity. Interfering with REXO4 increases the sensitivity of tumor cells to alkylating and G4 stabilizing drugs. Therefore, our study proposes a model for highly efficient processing of genome-wide R-loops by endo- and exo-cleavage, which provides additional insights into understanding the link between R-loop associated genome instability and tumors.

overall_design: To investigate whether REXO4 and RNaseH1 bind to R-loops , we performed ChIP-seq using tet-on stable expression cell lines of nuclease-dead mutant REXO4-D386A or RNaseH1-D210N.

first: Han

last: Yang

first: Chen

last: Nie

first: Jiadong

last: Wang

first: Weibin


title: Transcriptional profiling of adipogenic MSC clones in bovine

city: Roslin

first: F. Xavier

last: Donadeu

address: Easter Bush

institute: University of edinburgh

summary: Understanding the molecular regulation of adipogenesis in farm animals would bring benefits both to animal meat production and to the nascent field of cultivated meat. Adipogenic progenitors are found within heterogenous mesenchymal stem cell (MSC) populations in fat and other animal tissues. Such populations contain only a fraction of bona-fide adipocyte progenitors, resulting in limited and variable fat-forming capacity that is highly dependent on animal of origin. The identification of novel markers of pre-adipocytes in species such as cattle would have signficant potential towards increasing the efficiency and suatainability of both animal meat production and  cultured fat manufacture. Thus, the aim of this study was to compare the transcriptional signatures of MSC clones with a high or low adipogenic capacity in bovine.

overall_design: To investigate the genomic changes in highly adipogenic clones, we performed comparative gene expression analysis on bulk RNA-seq data obtained from 10 non-adipogenic and 10 adipogenic cell clones obtained from 4 different animals.

first: Seungmee

last: Lee

first: Susanna

last: Riley

first: Xavier

first: Esteves

last: Cristina


title: KrasG12D inhibition partially reverts the metastatic transcriptional cell state to a non-metastatic cell state

first: Robert

last: Piskol

summary: Colorectal cancer, a leading cause of cancer-related mortality due to distant metastases, is driven by activating mutations in the Wnt and MAPK pathways. Understanding the interplay between these crucial pathways during metastatic progression is essential for developing effective treatments. Here we developed an immunocompetent mouse model of metastatic colorectal cancer using in vivo orthotopic passaging. We demonstrate that highly metastatic tumor cells exhibit chromosomal amplifications in MAPK pathway genes, leading to increased MAPK activity, which in turn suppresses Wnt-associated transcriptional programs, including stem cell-associated genes. Inhibiting mutant KrasG12D effectively reversed this metastatic transcriptional state, reducing MAPK-driven gene expression and restoring Wnt activity.

overall_design: We have developed an immuno-competent mouse model of metastatic colorectal cancer by sequentially passaging small intestinal organoids with mutations in Apc, Kras, Tp53 and Smad4 in vivo. Passage 5 (m484) organoids harboring mutations in Apc (ko), KrasG12D, P53 (ko), Smad4 (ko) (AKPS) were orthotopically injected into the colon of C57BL/6N mice. 4.5 weeks post orthotopic injection into the colon, mice were treated  with vehicle for 3d (n=4), MRTX1133 for 3d (n=4) and MRTX1133 for 16d (n=4). MRTX1133 treatment: 30mg/kg intraperitoneal injections B.I.D.

first: Melanie

last: Heinlein

first: Ginny

last: Li


title: The cellular balance of NIPBL and PDS5 tunes the rate of cohesin loop extrusion and shapes chromosome organization across scales

city: San Francisco

first: Elphege

last: Nora

address: 555 Mission Bay Boulevard South

department: Cardiovascular Research Institute

institute: University of California San Francisco


title: 10x single cell sequencing for old mouse transcriptomes after sevoflurane exposure

city: shanghai

first: yanyong

last: cheng

address: 639 Zhizaoju Road

department: Department of Anesthesiology

institute: Shanghai Ninth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

summary: Although previous studies have confirmed that sevoflurane treatment has an effect on neurological function of old mouse, the underlying molecular mechanism remain unclear. In the present study, we performed scRNA-Sequencing (scRNA-Seq) analysis in the hippocampus from brain of old mouse . We thus isolated hippocampus from brain of old mouse, with or without sevoflurane exposure, and performed single cell sequencing. Single cell sequencing is a innovative experimental procedures which allows the identification of various subsets of cells in the neverous system after sevoflurane exposure.

overall_design: Six elderly mice were treated with sevoflurane or air.2% concentration for 6 hours. The mouse hippocampus was taken 24 h later for single-cell sequencing

first: Zhang

last: Lei

first: Cheng

last: Yongyan


title: Upstream open reading frame inactivation augments GATA4 translation and cardiomyocyte hypertrophy in mice

city: Rochester

first: feng

last: jiang

state: New York

address: 601 Elmwood Ave box CVRI

department: Biochemistry and Biophysics

institute: University of Rochester

summary: Upstream open reading frames (uORFs) are short peptide-encoding sequences residing in the 5' untranslated region (5' UTR) of mRNAs enabling translational repression of main (m)ORFs. Despite their prevalence, with ~50% of mRNAs harboring at least one uORF in humans, our comprehension of the biological function of these elements remains limited. This study aims to elucidate the role of the uORF in the 5' UTR of the Gata4 (GATA binding protein 4) gene in the context of cardiac biology through inactivation of its start codon (ΔuORF) in the mouse genome. Our investigation reveals that mice with Gata4 uORF inactivation manifest spontaneous cardiac hypertrophy without apparent fibrosis during aging. Leveraging single-nucleus RNA sequencing (snRNA-seq), we unveiled significant transcriptional variations between wild-type (WT) and ΔORF mice. Notably, mRNAs linked to sarcomeric and contractile functions exhibit heightened expression levels, mirroring the hypertrophic phenotype. Functional assessments with isolated primary adult cardiomyocytes validated enhanced hypertrophy and contractility in ΔORF mice. Furthermore, we employed single-nucleus transposase-accessible chromatin (snATAC)-seq to probe alterations in chromatin accessibility. Our results revealed augmented accessibility within specific transcription-regulatory elements associated with amplified gene transcription. These putative cis-regulatory elements (pCREs) are significantly enriched in MEF2 (myocyte enhancer factor 2) binding motifs. In vitro luciferase reporter assays further validated the regulatory potential of three of these pCREs, emphasizing their role in the transcriptional enhancement of three GATA4 target genes that are bound by MEF2 and GATA4. These findings shed light on the role of uORF in regulating GATA4 protein expression and cardiomyocyte hypertrophy.

overall_design: We performed Single-nucleus ATAC-seq (snATAC-seq) and RNA-seq on wildtype and ΔORF mice. Whole hearts were harvested from both mice at an age of 2 month (n = 3), and were fast frozen in liquid nitrogen. Nuclei were isolated from the frozen mouse heart tissue using the 10x Genomics single nuclei isolation kit, adhering to the manufacturer's instructions.

first: Omar

last: Hedaya

first: Feng

last: Jiang

first: Peng

last: Yao


title: The cellular balance of NIPBL and PDS5 tunes the rate of cohesin loop extrusion and shapes chromosome organization across scales [HiC]

summary: Cohesin loop extrusion has emerged as a major contributor to chromosome folding, enabling essential genomic functions from transcriptional regulation to DNA recombination and repair. Despite its requirement for extrusion, the co-factor NIPBL binds cohesin only intermittently. By combining in vivo experimental and in silico modeling approaches, we discovered that limiting NIPBL abundance causes chromosome folding defects that are best explained by reduced extrusion rates. Reduced extrusion rates, but not reduced loading, can counteract an increase in cohesin lifetime brought on by WAPL depletion. Depleting the NIPBL competitors PDS5A and PDS5B increases extrusion rates, in a way that can be shunted by NIPBL-co-depletion. Finally, we observed that extrusion rate and cohesin lifetime, although equally contributing to cohesin processivity, differentially impact genomic compartmentalization. In addition to shedding light on unappreciated roles of NIPBL beyond cohesin loading, in regulating the rate of cohesin loop extrusion, our work provides an experimentally calibrated computational framework to investigate the molecular mechanisms edifying genome architecture and function.

overall_design: Hi-C using in various mouse embryonic stem cell lines with auxin- or dTAG-inducible degrons inserted on endogenous NIPBL, RAD21, WAPL, PDS5A and PDS5B.

first: Shah

last: Rini


title: RNA-Seq analysis of Mapk14 knockout and myogenic differentiation in C2C12 cells

status: Public on Jan 07 2026

city: Shanghai

first: Rong

last: Huang

address: Shanghai Jiao Tong University, Minhang Campus, 800 Dongchuan Road, Minhang District, Shanghai 200240, China

institute: Shanghai Jiao Tong university

summary: This study investigates the role of p38/Mapk14 in myogenic differentiation using C2C12 mouse myoblast cells. Wild-type and Mapk14 knockout cells in the logarithmic growth phase were cultured in growth medium (GM) or differentiation medium (DM) for 5 days. RNA was extracted for sequencing to examine gene expression changes caused by Mapk14 deletion and by differentiation induction. Differential expression analysis identifies genes downregulated in Mapk14 knockout cells compared to wild type and genes upregulated upon differentiation, providing insight into the molecular mechanisms by which p38/Mapk14 regulates myogenesis.

overall_design: RNA-seq profiling of wild-type C2C12 cells and Mapk14 knockout C2C12 cells cultured under growth medium (GM) or differentiation medium (DM) conditions for 5 days.

first: Fangchao

last: Hu

first: Yiyao

first: Qifei

last: Gao

first: Jintao

first: Jiarui

last: Wang

first: Wei

last: Lu

first: Liping

first: Ziyun

last: Wu

first: Keith

last: Blackwell


title: DRIP-seq reveals REXO4 and RNaseH1 work together to process R-loops in the same genomic region across the genome.

first: weibin

last: wang

summary: Endonuclease RNaseH1 acts as a common R-loop resolvase to prevent R-loop accumulation genome-widely, whether there is any exonuclease complementing RNaseH1 to more efficiently resolve R-loops is worth investigation. Here we identify an exonuclease REXO4, which collaborates with RNaseH1 to efficiently degrade R-loops in an “endo- and exo-cleavage coupling” manner.DNA-RNA immunoprecipitation followed by sequencing (DRIP-seq) shows that R-loop regions regulated by REXO4 highly overlap with those regulated by RNaseH1.

overall_design: To investigate whether REXO4 and RNaseH1 work together to process R-loops in the same genomic region, we performed DRIP-seq after knocking down REXO4 and RNaseH1 using siRNA in U2OS cells.

first: Han

last: Yang

first: Chen

last: Nie

first: Jiadong

first: Weibin


title: Histone Lysine Methylation Dynamics Control EGFR DNA Copy-Number Amplification

first: Kashish

last: Chetal

address: 55 Fruit St

department: Molecular biology

institute: MGH

summary: Acquired chromosomal DNA copy gains are a feature of many tumors; however, the mechanisms that underpin oncogene amplifi cation are poorly understood. Recent studies have begun to uncover the importance of epigenetic states and histone lysine methyltrans_x0002_ferases (KMT) and demethylases (KDM) in regulating transient site-specifi c DNA copy-number gains (TSSG). In this study, we reveal a critical interplay between a myriad of lysine methyltransferases and demethylases in modulating H3K4/9/27 methylation balance to control extrachromosomal amplifi ca_x0002_tion of the EGFR oncogene. This study further establishes that cellular signals (hypoxia and EGF) are able to directly promote EGFR amplifi cation through modulation of the enzymes controlling EGFR copy gains. Moreover, we demonstrate that chemical inhibitors targeting specifi c KMTs and KDMs are able to promote or block extrachromosomal EGFR amplifi cation, which identifi es potential therapeu

overall_design: Chromatin Immunoprecipitation DNA-Sequencing (ChIP-seq) for histone modifications H3K4me3 sites in RPE cells upon KDM5A siRNA depletion

first: Johnathan

last: Whetstine

first: Ruslan

last: Sadreyev


title: Assessing the impact of epigenetic inhibitors on reversion of the chromatin landscape from metastatic to non-metastatic organoids

first: Robert

last: Piskol

first: Melanie

last: Heinlein

first: Amanda

last: Moore

first: Ginny

last: Li


title: Transcriptomic Profiling Reveals Thyroid Hormone-Mediated and Compound-Specific Effects of Methimazole and Amitrole on Testis Development

city: Rennes

first: Frédéric

last: Chalmel

state: France

address: 9 avenue du Pr. Léon Bernard

department: Physiology and physiopathology of the urogenital tract

country: France

institute: Inserm U1085-Irset

summary: Thyroid hormones (THs) influence testis development, with early life hypothyroidism resulting in smaller testes in neonates. Developmental exposure to thyroperoxidase (TPO)-inhibiting drugs such as propylthiouracil (PTU) and methimazole (MMI) also impair testis development in rodents by reducing TH levels, leading to smaller testes due to for instance disrupted Sertoli cell proliferation and maturation. Comparable effects are seen for exposure to the TPO-inhibiting pesticide amitrole, one of many environmental chemicals with TH-disrupting properties. Despite this described phenotype, the molecular underpinnings of hypothyroid-induced testis effects are less clear, complicating mechanics-based chemical toxicity testing relying on alternative test methods and omics approaches.

overall_design: Here, we report on transcriptomics profiling of testes from hypothyroid rats induced by chemical exposures. Pregnant Sprague-Dawley rat dams were exposed by oral gavage to two doses of MMI (8 or 16 mg/kg bw/day) or amitrole (25 or 50 mg/kg bw/day) from gestational day (GD) 7 to pup day (PD) 16, with BRB-seq performed for both life stages. Both MMI and amitrole caused significant changes to the testis transcriptome, seen particularly at PD16, with 313 differentially expressed genes (DEGs) defining a shared TH-mediated profile. Additionally, amitrole exposure resulted in a distinct profile of 1,517 DEGs, suggesting compound specific effects beyond TH disruption. Despite some discrepancies between transcriptomic and protein-level data, this study highlights value of establishing comprehensive transcriptomic profiling to improve predictive models in chemical risk assessment.

first: Ida

last: W. Strand

first: Bertrand

last: Evrard

first: Terje

last: Svingen


title: Spatial characterization of the motor and non-motor somal and axonal transcriptome in adult healthy and mutant FUS mice

first: Sandrine

last: Da Cruz

summary: Here we investigated the transcriptome of motor and non-motor axons and cell bodies in the context of mutant FUS-related amyotrophic lateral sclerosis (ALS). We applied Nanostring GeoMX Digital Spatial Profiler platform to profile the transcriptome of subcellular compartments in the lower motor circuitry of a mouse model ricapitulating ALS motor symptoms. This work sheds light for the first time on the transcriptomic alterations in axons and in somas which may contribute to axonal degeneration and neuromuscular junction denervation, early features of ALS.

overall_design: Four 5-um thick spinal cord and sciatic nerve sections derived from control and humanized FUS R521H mice were layered on normal glass microscope slides and sent to Nanostring Technologies facility in dry ice (Seattle, US). Slides were analyzed on the Nanostring GeoMx Digital Spatial Profiler platform using the Whole Mouse Transcriptome Atlas panel (Nanostring). Regions of interest were drawn on spinal cord ventral horns and full sciatic nerve sections, and further segmented into ChAT+ and ChAT- areas of interest.

first: Diana

last: Piol

first: Theo

last: Killian

first: Maria

last: Georgopoulou

first: Alejandro

last: Sifrim


title: A stem cell knockout village reveals lineage rewiring and a non-canonical islet cell fate in monogenic diabetes

city: Washington

first: Bicna

last: Song

state: DC

address: 7144 13th Pl NW

institute: Children's National Hospital

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

overall_design: Refer to individual Series


title: Bulk RNA-sequencing of mesenchymal stem cell clones from pig with high or low adipogenic capacity

first: F. Xavier

last: Donadeu

summary: Understanding the molecular regulation of adipogenesis in farm animals would bring benefits both to animal meat production and to the nascent field of cultivated meat, where adipose tissue provides enhanced flavour and texture profiles of biomanufactured meat products. Adipogenic progenitors are found within heterogenous mesenchymal stem cell (MSC) populations in fat and other animal tissues. Such populations contain only a fraction of bona-fide adipocyte progenitors, resulting in limited and variable fat-forming capacity that is highly dependent on animal of origin. The identification of novel markers of pre-adipocytes in species such as the pig would have significant potential towards increasing the efficiency and sustainability of both animal meat production and  cultured fat manufacture. Thus, the aim of this study was to compare the transcriptional signatures of MSC clones with a high or low adipogenic capacity in pig.

overall_design: Comparative bulk RNA-seq analyses was performed of  MSC clones with high or low adipogenic capacy (12 clones each). Clones had been derived by single cell sorting of MSCs from 4 different piglets, and adipogenic capacity was determined by quantitative Oil Red O staining following culture in adipogenic media for 11 days

first: Thomas

last: Thrower

first: Susanna

middle: E

last: Riley

first: Xavier


title: RNA-seq analysis of low potassium and pmk-1–regulated genes in C. elegans

first: Rong

last: Huang

summary: RNA-seq was performed in C. elegans to identify low potassium–responsive genes and pmk-1–dependent genes. Day 1 adult N2 (wild type) or pmk-1(km25) animals were exposed to 100 mM NaCl or 100 mM KCl for 4 hours, and RNA was extracted. Low potassium genes were identified by comparing N2 under 100 mM NaCl versus 100 mM KCl, and pmk-1–regulated genes were identified by comparing pmk-1(km25) mutants to wild type under 100 mM KCl.

overall_design: RNA-seq profiling of synchronized day 1 adult N2 (wild type) and pmk-1(km25) C. elegans exposed to 100 mM NaCl or 100 mM KCl for 4 hours to identify low potassium–responsive and pmk-1–dependent genes.

first: Fangchao

last: Hu

first: Yiyao

first: Qifei

last: Gao

first: Jintao

first: Jiarui

last: Wang

first: Wei

last: Lu

first: Liping

first: Ziyun

last: Wu

first: Keith

last: Blackwell


title: RNA-seq analysis of wild-type C. elegans under PD (100 mM NaCl) conditions on solid agar plates

summary: This RNA-seq study was designed to identify genes specifically regulated by potassium deficiency (PD) conditions in wild-type Caenorhabditis elegans. Synchronized L4-stage animals were subjected to PD conditions (100 mM NaCl) on solid agar plates and compared with animals grown under 100 mM KCl or standard NGM conditions.

overall_design: For solid agar plate assay, approximately 2,000 synchronized L4-stage wild type (N2) animals were washed twice in either 100 mM NaCl, 100 mM KCl, or NGM solution (51 mM NaCl, 25 mM KPB) and then transferred to agar plates supplemented with 100 mM NaCl, 100 mM KCl, or NGM solution (51 mM NaCl, 25 mM KPB). These plates were seeded with OP50-1 bacteria that had been treated with the corresponding solutions. After 4 hours, the animals were collected and flash-frozen in liquid nitrogen. Genes are upregulated (PD up) or downregulated (PD down) under PD (100 mM NaCl) conditions were identified by comparison with both the 100 mM KCl and NGM conditions in N2 animals (100 mM NaCl vs 100 mM KCl & 100 mM NaCl vs NGM).

last: Li


title: HDI-STARR-seq library profiling of differential accessible chromatin regions (DARs) in livers of male, female and male treated with continuous growth hormone (cGH) mice.

first: David

middle: J.

last: Waxman

address: 5 Cummington Mall

department: Department of Biology and Bioinformatics Program

summary: Massively parallel reporter assays (MPRA) are widely used to discover functional enhancers but have largely been limited to transfected cell models, which are confounded by vector-induced innate immune responses and lack the physiologically relevant cellular and endogenous hormonal context and chromatin environment of complex mammalian tissues. Here, we combine hydrodynamic injection (HDI) with a modified STARR-seq-based MPRA, designated HDI-STARR-seq (PMID:39716078)  to determine condition-specific enhancer activity in mouse liver at scale. Analysis of a synthetic STARR-seq library, comprised of 23,912 reporters regions spanning 1839 ATAC regions enabled functional assessment of mouse liver enhancer activity in vivo across three distinct biological conditions: male iver, feamle liver and continuous growth hormone (GH)-infused male liver, which is substantially feminized with regards to gene expression. HDI-STARR-seq reporters representing 305 ATAC regions showed sex-biased and GH-responsive enhancer activity that mirrored the regulation of their chromatin accessibility in hepatocytes, validating these sites as functional, physiologically regulated enhancers. These enhancers were enriched for activating histone marks (H3K4me1, H3K27ac) and for binding sites for GH-activated transcriptional regulator STAT5 and for the STAT5-dependent, sex-specific repressors BCL6 and CUX2, consistent with a cohesive regulatory network controlling hepatocyte lipid and xenobiotic metabolism. Further, de novo motif analysis identified binding sites for HNF4A and for several novel factors specifically enriched at the regulated enhancers. Importantly, sex-biased and GH-regulated functional enhancers were linked to both MASLD (metabolic dysfunction-associated steatotic liver disease)-enabling and MASLD-protective genes, indicating that GH-dependent chromatin remodeling at these loci is a key determinant of sex-differential liver metabolic disease susceptibility. This integrated in vivo approach defines a validated set of GH-regulated hepatocyte enhancers through which chromatin accessibility and transcription factor binding drive sexual dimorphism in hepatic metabolism and sex-specific MASLD risk.

overall_design: We implemented the synthetic STARR-seq library in control male liver, control female liver and cGH-treated male liver to quantitatively measure intrinsic transcription activity in the corresponding group. A pool of chemically-synthetic DNA fragments in 210 nt length were amplified and delivered to untreated adult male CD-1 mice, untreated adult female CD-1 mice,and 10d cGH-treated male male using osmotic pump. A pooled plasmid library was delivered into mice using hydrodynamic tail vein injection (HDI) for in vivo transfection, preferentially for livers. For a STARR-seq library, three types of sequencing libraries incorporated in this submission (i.e., STARR-seq  plasmid libraries, STARR-seq DNA libraries and STARR-seq RNA libraries) are generated by PCR amplification using  the same PCR condition. The STARR-seq plasmid library, which is the same material injected in HDI livers, represents the abundance of each reporter assaying  DNaseI digested regions in response to sex-specific open chromatin regions or TCPOBOP-responsive open chromatin regions. DNA plasmids extracted from a small piece of  HDI livers  were amplified using DNA reporter-specific primers, and  represented the intake plasmids in livers. The read counts of each reporter were used as denominator to calculate STARR-seq enhancer activity. Poly-adenylated RNA plasmids extracted from HDI livers were reverse-transcribed followed by DNase treatment, and amplified using RNA reporter-specific primers, and represented the self-transcribing activity of the DHS. The read counts of each reporter were used as numerator to calculate STARR-seq enhancer activity.

first: Ting-Ya

last: Chang


title: Decoding the molecular logic of rapidly evolving ZAD zinc finger proteins in Drosophila

city: Bunkyo-ku

first: Raku

last: Saito

state: Tokyo-to

address: 1-1-1 Yayoi

department: Institute for Quantitative Biosciences

institute: The University of Tokyo

summary: The zinc finger-associated domain (ZAD)-containing C2H2 zinc finger proteins (ZAD-ZnFs) represent the most abundant class of transcription factors that emerged during insect evolution, yet their molecular diversity and biological functions remain largely unclear. Here, we established a systematic CRISPR-based protein-tagging approach that enables direct, unambiguous comparison of nuclear localization and genome-wide binding profiles of endogenous ZAD-ZnFs in developing Drosophila embryos. Evidence is provided that a subset of ZAD-ZnFs forms nuclear condensates through the stacking of the N-terminal ZAD dimerization surface. Disruption of condensation activity leads to misregulation of genome-wide binding profiles and lethality, underscoring its functional and physiological significance in development. Importantly, integrative ChIP-seq and Micro-C analyses reveal that many ZAD-ZnFs colocalize with core insulator proteins such as CTCF and CP190 to control the formation of topological boundaries. We suggest that the diverse molecular functions of ZAD-ZnFs have evolutionally arisen from their ancestral role as insulator-binding proteins.

overall_design: ChIP-seq and Micro-C of Drosophila nc14 early embryo, and RNA-seq of Drosophila adult ovaries. All samples include 2 replicates.

first: Yusuke

last: Umemura

first: Shiho

last: Makino

first: Takashi

last: Fukaya


title: Transcriptomic Profiling Reveals Ageing-Related Molecular Signatures in Women with Diminished Ovarian Reserve

city: Nanning

first: Fengxia

last: Liu

address: No. 3 Longyuan Road

institute: Reproductive Hospital of Guangxi Zhuang Autonomous Region, Nanning, Guangxi, China

summary: The increasing incidence of diminished ovarian reserve (DOR) among women undergoing assisted reproductive technology (ART) poses significant challenges, as DOR is associated with lower pregnancy and live birth rates. This study aimed to investigate the molecular signatures related to ageing in women with DOR and their potential implications for understanding the underlying mechanisms of DOR. We collected peripheral blood samples from 20 infertile women under 40 years of age, including 10 patients with DOR and 10 with normal ovarian reserve (NOR). Using DESeq2, we identified differentially expressed genes (DEGs) between the DOR and NOR groups. DOR-related ageing genes were obtained by intersecting DEGs with three senescence-related databases (CellAge, CSGene, SenMayo). Transcriptomic profiling identified 14 ageing-related DEGs, of which E2F2, SYT1, BNIP3L, AREG, FOXO3, CTNNAL1, RBM38, BCL2L1, ALOX15B, MITF, TOP1, TRIM10, and PCGF2 were upregulated, and PROX1 was downregulated, in the DOR group. Functional enrichment analysis indicated a strong association between these DEGs and processes related to oxidative stress, apoptosis, and mitochondrial dysfunction. The findings underscore the systemic molecular ageing abnormalities present in women with DOR, providing insights into potential targets for therapeutic intervention aimed at improving ART outcomes.

overall_design: RNA-seq profiling of peripheral blood samples from infertile women under 40 years of age, including 10 patients with diminished ovarian reserve (DOR) and 10 with normal ovarian reserve (NOR)

first: Zhong

last: Lin

first: Kali


title: RNA-seq of control and sarcoidosis human nasal airway epithelial cell cultures

city: Iowa City

first: Alejandro

middle: A.

last: Pezzulo

state: Iowa

address: 6316 Pappajohn Biomedical Discovery Building

department: Department of Internal Medicine

institute: Universty of Iowa

summary: The goal of this study was to examine differences in gene expression between healthy and sarcoidosis nasal airway epithelia cultures at air-liquid interface (ALI).

overall_design: Nasal epithelial cell cultures were prepared for RNA sequencing via Smart-3SEQ and sequenced on Illumina NovaSeq 6000 system using 101 bp single end SBS chemistry.

first: Miles

middle: D

last: Hagner

first: Andrew

middle: L

last: Thurman


title: Hepatic Hypoxia-Inducible Factor 1α Mediates Ferroptosis via Transferrin Receptor 1 in Acute Liver Injury

first: Jingya

address: 189 Guo Shou Jing Road

institute: Shanghai Institute of Materia Medica

summary: Acute liver injury (ALI) is a potentially life-threatening condition lacking effective clinical drugs. Hypoxia-inducible factor-1α (HIF-1α) is a key regulator of both inflammation and metabolism. In ALI, HIF-1α expressions are upregulated, but the role of HIF-1α in hepatocytes and whether it can be targeted remain unclear. Herein, clinical samples and ALI murine models including lipopolysaccharide/D-galactosamine (LPS/D-GalN), acetaminophen (APAP), and thioacetamide (TAA) revealed an increase in HIF-1α expression and ferroptosis. Using HIF-1α gain and loss of function mouse and hepatocyte culture models, we demonstrated that HIF-1α upregulation exacerbated liver ferroptosis and injury. Mechanistically, HIF-1α/transferrin receptor protein 1 (TFR1) axis drives hepatic iron overload, promoting ferroptotic cell death and liver injury. In addition, TFR1 inhibition reversed HIF-1α-induced ALI. Importantly, pharmacological inhibition of HIF-1α and TFR1 significantly reduced ferroptosis and mitigated liver injury both in vivo and in vitro. Together, our findings demonstrate the pathological role of hepatic HIF-1α, which may serve as a promising target of therapeutic intervention.

overall_design: RNA Seq profiling of hepatic HIF1α overexpression or wild type mouse livers in control gourps and LPS/D-GalN-treated groups.

first: Shichao

last: Cui

first: Jiayu

last: Yang

first: Meicheng

first: Yulan

last: Xia

first: Yinfang

last: Xie

first: Zhu

last: Hu

first: Ni

first: Xinwen

last: Zhang

first: Pengfei

last: Zhu

first: Xu

last: Yu

first: Linshi


title: Beta3-Adrenergic receptor downregulation leads to adipocyte catecholamine resistance in obesity

city: La Jolla

first: Ronald

last: Evans

address: 10010 N Torrey Pines Rd

department: GEL-E

institute: Salk

summary: This project investigates mechanisms underlying catecholamine resistance in obesity. We found that adipocyte Beta3-adrenergic receptor (Adrb3), the dominant isoform mediating lipolysis, undergoes transcriptional downregulation after ligand exposure or inflammatory stimulation, representing homologous and heterologous desensitization, respectively. Both processes are mediated by the EPAC-RAP2A-PI-PLC-TRIB1 signaling axis, which promotes degradation of the transcription factor C/EBP-alpha and suppresses Adrb3 expression. Pharmacologic inhibition of EPAC/RAP restored Beta3-adrenergic responsiveness, enhanced lipolysis, and improved energy expenditure in obese mice. These findings reveal a molecular pathway contributing to catecholamine resistance and impaired energy mobilization in obesity.

overall_design:
RNA-Seq of Mus musculus adipose tissue treated with CL or Vehicle

This study represents a re-analysis of raw data generated for two samples in PRJNA725497.


title: RNA-seq of PRSS23 knockdown in ovarian cancer cell lines JHOC-5 and OVCA420

city: Jacksonville

first: Derek

middle: Charles

last: Radisky

state: Florida

address: 4500 San Pablo Road

department: Cancer Biology

institute: Mayo Clinic

summary: Bulk RNA-seq was performed in ovarian cancer cell lines JHOC-5 and OVCA420 after lentiviral PRSS23 knockdown using two independent shRNAs (shRNA_30 and shRNA_46) or a non-targeting shRNA control. Gene-level read counts for all samples are provided.

overall_design: 2 cell lines (JHOC-5, OVCA420) × 3 conditions (non-targeting control, PRSS23 shRNA_30, PRSS23 shRNA_46) × 2 biological replicates (12 libraries total).


title: Sodium myo-inositol cotransporter-1, SMIT1, promotes cardiac hypertrophy and fibrosis in pressure overloaded mouse hearts

city: Woluwé

first: Jérôme

last: Ambroise

address: Avenue Hippocrate 54

department: Institut de Recherche Expérimentale et Clinique

institute: Université catholique de Louvain

summary: Sodium myo-inositol cotransporter-1 (SMIT1) belongs to the sodium-glucose cotransporter family and accounts for intracellular accumulation of myo-inositol. SMIT1 is expressed in the heart, where its function remains unknown. Here, we demonstrate the contribution of SMIT1 to pathological hypertrophic cardiac remodeling and the progression to heart failure, using a mouse model of pressure overload induced by transverse aortic constriction. We found that aortic banding failed to induce systolic dysfunction, cardiac hypertrophy and fibrosis in mice lacking SMIT1 (Smit1-/-), in contrast to wild type controls. SMIT1 genetic deletion reduced cardiac O-GlcNAcylation, which normally increases following hemodynamic stress, and restored ions homeostasis preventing the resulting pro-hypertrophic transcriptional reprogramming. This work provides important insights into the role of SMIT1 at the onset of heart failure, opening new avenues of potential therapeutic strategy to prevent or treat pathological hypertrophy and heart failure.

overall_design: We subjected five WT and five Smit1-/- mice to transverse aortic contriction (TAC) surgery. After two weeks post TAC, RNA was extracted from mouse hearts for RNA seq, to investigate  what genes are differentially expressed and what potential pathways could be involved in pressure overload. We then performed gene expression profiling analysis using data obtained from RNAseq to compare WT vs SMIT1-/- mice

first: Alice

last: Marino

first: Julien

last: Cumps

first: Laura

last: Guilbert

first: Claire

last: Baufays

first: Audrey

last: Ginion

last: Ferté

first: Sylvain

last: Battault

first: Jerome

first: Bertrand

last: Bearzatto

first: Coert

last: Zuurbier

first: Frank

last: Lezoualch

first: Camille

last: Pestiaux

first: Grzegorz

last: Pyka

first: Donatienne

last: Tyteca

first: Carolin

last: Bouzin

first: Luc

last: Bertrand

first: Sandrine

last: Horman

first: Christophe

last: Beauloye


title: Fishing with Two Lines: A Hybrid Approach to Spatial Transcriptomic Discovery

city: Phoenix

first: Nicholas

last: Banovich

state: AZ

address: 445 North Fifth Street

department: Integrated Cancer Genomics

institute: TGen - Translational Genomics Research Institute

summary: Spatial transcriptomics faces a trade-off between the number of genes assayed and depth of per-gene sensitivity. We developed a 'dual chemistry' method that combines the high sensitivity of a 10X Genomics Xenium V1 custom panel (up to 480 genes) with the broad coverage of the Prime 5K panel (5001 genes) on a single tissue section. This involved co-hybridizing Prime and V1 probes and sequentially running the V1 and Prime decoding chemistries. Applied to a human lung tissue microarray, we observed high concordance between the V1 and Prime chemistries when run independently (on serial sections) and the dual chemistry runs. Overlapping genes (profiled on both V1 and Prime chemistries) showed similar expression patterns in the dual run demonstrating the fidelity of the assay. By combining information from both the V1 and Prime chemistries within the same cell, we retain more cells, gain valuable additional information, and enable both high sensitivity profiling and discovery.

overall_design: 17 samples are included in this study from archived formalin fixed paraffin embedded (FFPE) tissue from human lung. A team with expertise in pediatric lung pathology selected a 3mm x 3mm target location for the region of interest for analysis. A FFPE tissue microarray (TMA) block was designed to fit all samples into the Xenium capture area (10.45mm x 22.45mm) in a 3 x 6 pattern of cores, with the top left core space remaining empty as an orientation marker. Three serial sections were placed onto three Xenium slides and prepped.

first: Arianna

last: Williams-Katek

first: Saahithi

last: Mallapragada

first: Evan

last: Mee

first: Brandon

last: Fischer

first: Laurie

middle: C

last: Eldredge

first: Gail

middle: H

last: Deutsch

first: Jonathan

last: Kropski

first: Jennifer

last: Sucre


title: Development of gene expression signatures for  bone marrow mesenchymal stem cells  with 3D culture in collagen hydrogel

first: Xiao

last: Ru

state: Guangxi Zhuang Autonomous Region

address: 22 Shuangyong Road, Zhongshan Street, Qingxiu District, Nanning City, Guangxi Pr

institute: Guangxi Medical University

summary: To investigate the mechanisms underlying chondrocyte differentiation of bone marrow mesenchymal stem cells during 3D culture, we employed whole genome microarray expression profiling as a discovery platform to identify key genes influencing differentiation. By comparing differentially expressed genes at different time points, we identified  POU5F1  and several autophagy-related genes as potential key players. By using PCR technology and autophagy-related assays, we confirmed that POU5F1 and autophagy pathways influence the chondrogenic differentiation of bone marrow-derived mesenchymal stem cells.

overall_design: Mesenchymal stem cells from bone marrow were cultured  in collagen hydrogel with 3D culture at four time points: 0 day, 7 days, 14 days, and 21 days. Three repeat samples were collected at each time point.

first: Zhongwen

last: Yu

first: Jun

last: Li


title: Transcriptomic profiling of LNCaP/C4-2 cells under stepwise androgen receptor inhibition

city: Toon

first: RYUTA

last: WATANABE

address: 454 Shitsukawa

institute: Ehime University Hospital

summary: This study presents transcriptomic profiling of human prostate cancer cell lines under stepwise androgen receptor (AR) inhibition. LNCaP and C4-2 cells were cultured under untreated conditions, androgen deprivation using charcoal-stripped serum, long-term exposure to the first-generation AR antagonist bicalutamide, or long-term exposure to the second-generation AR antagonist enzalutamide. Drug-resistant cell populations were generated through gradual dose escalation. The neuroendocrine prostate cancer cell line NCI-H660 was included as a reference. Bulk RNA sequencing was performed for three biological replicates per condition. The dataset provides a resource for investigating transcriptional responses to progressive AR suppression and adaptive changes associated with AR-targeted therapies.

overall_design: LNCaP and C4-2 cells were subjected to stepwise androgen receptor inhibition using charcoal-stripped serum, bicalutamide, or enzalutamide. LNCaP/C4-2 cells were subjected to stepwise androgen receptor inhibition using charcoal-stripped serum, bicalutamide, or enzalutamide. Drug concentrations were gradually increased based on cell viability and recovery of proliferation to establish drug-resistant populations. RNA sequencing was performed on untreated, AR-inhibited, and drug-resistant LNCaP cells, with the neuroendocrine prostate cancer cell line NCI-H660 included as a reference. Three independent biological replicates were analyzed for each condition.

first: Ryuta

last: Watanabe

first: Mami

last: Chosei

first: Haruna

last: Arai

first: Noriyoshi

last: Miura

first: Tadahiko

last: Kikugawa

first: Takashi

last: Saika


title: Lysine Pyruvylation Mediated by HAT1/p300-SIRT3 Couples Glycolytic Flux to Epigenetic Regulation [CUT&Tag]

city: HANGZHOU

first: xiaohan

last: song

address: No.1 XIANGSHAN ROAD

institute: University of the Chinese Academy of Sciences Hangzhou Institute for Advanced Study

summary: Post-translational modifications (PTMs) serve as critical regulatory mechanisms connecting metabolism and protein functions. Following our prior discovery of lysine lactylation (Kla), we herein report the identification and characterization of lysine pyruvylation (Kpy), a previously undescribed PTM driven by the central glycolytic hub metabolite pyruvate. Through integrated biochemical and proteomic strategies, we established the existence and specificity of Kpy. Proteomic profiling revealed Kpy sites across both histones and non-histone proteins, implicating its broad physiological significance. Notably, our investigations demonstrated that Kpy abundance fluctuates in respond to alterations in glycolytic flux and pyruvate concentration, providing a direct mechanism by which metabolic alterations influence protein functions. Additionally, we identified Sirtuin 3 (SIRT3) as the "eraser" enzyme for Kpy removal, while Histone acetyltransferase 1 (HAT1) and p300 (EP300) function as "writer" enzymes responsible for Kpy deposition. Initial mechanistic studies suggested Kpy's regulatory role in transcriptional control. Together, the elucidation of Kpy expands our understanding of metabolite-protein crosstalk through PTMs, providing mechanistic insights into pathophysiological processes and facilitating the development of targeted therapeutic interventions for metabolic disorders.

overall_design: RNA-seq profiling of control and 20 mM oxamate-treated HEK293T cells. And CUT&Tag analysis of Kpy in HEK293T cells.

first: Xiaohan

last: Song

first: Panan

last: Peng

first: Haonan

last: Zheng

first: Yanan

first: Qianjing

last: Wang

first: Yu

last: Ge

first: Doudou

last: Tan

first: He

last: Huang


title: Single-Cell Exon Deletion Profiling Reveals Splicing Events That Shape Gene Expression and Cell State Dynamics [RNA-seq_Rescue_exp]

city: Frederick

first: Thomas

last: Gonatopoulos-Pournatzis

state: MD

address: Building 560

institute: National Cancer Institute

summary: Alternative splicing is a pervasive gene regulatory mechanism critical for diversifying the human proteome. To systematically investigate its role in cell fate determination, we developed scCHyMErA-Seq, a scalable CRISPR-based exon deletion screening platform integrated with 10x Genomics single-cell transcriptomic readouts. This tool enables efficient exon deletion while simultaneously capturing Cas9/Cas12a guides and polyadenylated transcripts at single-cell resolution. Applying scCHyMErA-Seq to high-throughput profiling of alternative cassette exons, we identified numerous exons with strong regulatory effects on gene expression. Analysis of NRF1 alternative exon-7 revealed that this exon modulates NRF1 transcriptional activity by regulating its recruitment to the promoters of target genes. Importantly, gene expression profiles generated using scCHyMErA-Seq accurately recapitulate findings from traditional, labor-intensive orthogonal methods, while offering enhanced scalability and efficiency. Overall, scCHyMErA-Seq represents a robust and versatile platform for systematically unraveling the functional impact of alternative splicing by directly linking specific splicing variants to transcriptional phenotypes.

overall_design: RNA-Sequencing was performed in HEK293 Flp-in cells depleted from endogenous NRF1 with RNAi (non-targeting siRNAs were used as control) while expressing either full-length NRF1 (NRF1-FL) or the NRF1 isoform lacking exon-7(NRF1-∆E7) at endogenous levels using dox-inducible HEK293 Flp-In cell lines to systematically explore if NRF1 exon-7 regulates gene expression.

first: Bandana

last: Kumari

first: Arun

middle: P

last: Damodaran

first: Wilfried

last: Guiblet

first: Mei-Sheng

last: Xiao

first: Amit

last: Behera

first: Tyler

last: On

first: Carl

last: Mcintosh

first: Maxwell

last: Teszler

first: Chelsee

last: Holloway

first: Sandra

last: Le

first: Nikhil

last: Parab

first: Yongmei

last: Zhao

first: Michael

last: Aregger


title: Epigenetic plasticity is a driver of heritable pollution tolerance in Atlantic killifish [ONT Long-read sequencing; DNA]

city: Saint Paul

first: Caren

last: Weinhouse

state: Minnesota

address: 1988 Fitch Ave

institute: Oregon H

summary: Heritable epigenetic adaptation to environmental stressors is a compelling but highly contested possibility. Previously, we showed evidence of a generationally heritable epigenetic memory at the cytochrome P450 1A (CYP1A) gene in wild Atlantic killifish (Fundulus heteroclitus) with evolved tolerance to PAH. This memory leads to blunted induction of CYP1A by PAH; this blunting that protects against polycyclic aromatic hydrocarbon (PAH)-induced cancer. Here, using Oxford Nanopore long-read sequencing in PAH-tolerant and sensitive wild-type embryos, we show that genome-wide, PAH-tolerant embryos showed reduced plasticity in DNA methylation response to PAH vs. PAH sensitive embryos that was not due to mutational loss of CpG sites. Notably, we observed population differences in gene methylation in pathways linked to the PAH tolerance phenotype, including AHR and voltage-gated potassium channel signaling, as well as developmental processes and energy metabolism. Specifically, we observed PAH-induced loss of CYP1A gene body methylation in PAH-sensitive (86% CpG methylation in control, decreased to 63% in exposed), but not -tolerant (84% control, 86% exposed), embryos. We observed similar patterns at CYP1B, CYP1C, and the aryl hydrocarbon receptor repressor, AHRR, which show similarly blunted expression. This genic methylation loss was correlated with decreased levels of natural anti-sense RNA transcripts in cis (cis-NATs), which may regulate transcription of these genes. Our data support the existence of stable epigenetic responses to chronic environmental stressors in a natural experimental setting, with broad implications for natural or directed adaptation strategies for other populations.

overall_design: Long-read Oxford Nanopore sequencing and basecalling of genomic sequence and 5mC modifications in four pools of embryos (N=10 embryos/pool): two pools each from PAH-sensitive and PAH-tolerant populations, one control and one challenged with PAH (Elizabeth River sediment extract, ERSE).

first: Mathia

last: Colwell

first: Melissa K.

last: Drown

first: Nicole

last: Flack

first: Carrie

last: Walls

first: Christopher

last: Faulk

first: Samantha

last: Carrothers

first: Emma

last: Weeks