title: Unraveling the Temporal Dynamics of Radiation-Induced Lung Injury

city: Chongqing

first: Dabin

last: Wu

address: No.1 Medical College Road, Yuzhong District, Chongqing

institute: Chongqing medical university

summary: Radiation pneumonitis remains a dose-limiting complication in thoracic radiotherapy, critically impacting treatment efficacy and long-term patient survival. Despite its clinical significance, the dynamic molecular reprogramming underlying radiation-induced lung injury (RILI) progression remains poorly characterized. Utilizing a murine model validated by histopathological analysis, we implemented RNA-seq to systematically map the temporal evolution of RILI at critical phases: acute inflammation, transitional, and fibrotic. Through combining analysis, we identified Ces2e as a pivotal node exhibiting sustained upregulation at both transcriptional and translational levels during early pathogenesis. Functional enrichment revealed time-dependent activation of xenobiotic metabolism and ECM-receptor interaction pathways, with Ces2e overexpression correlating with macrophage polarization and lipid peroxidation accumulation. This temporal multi-omics atlas not only deciphers stage-specific molecular signatures of RILI but also nominates Ces2e as a potential theranostic target for early intervention.

overall_design: RNA-seq profiles of lungs from C57BL/6J mice at 4, 8, and 16 weeks after thoracic radiation.

first: Fei

last: Tang

first: Zhenzhou

last: Yang

first: Zaicheng

last: Xu


title: Genomic Localization of RUNX Proteins in Neonatal Germ Cells.

status: Public on Feb 26 2026

city: Pullman

first: Nathan

middle: C

last: Law

state: WA

address: 100 Dairy Road

department: School of Molecular Biology

country: USA

institute: Washington State University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Prior studies by our group demonstrated the essential role of core-binding factor subunit β (CBFβ) in prepubertal male germline development. CBFβ is a common co-factor to the runt-related family of transcription factors (RUNX), of which RUNX1 and RUNX3 are expressed in prepubertal germ cells. Therefore, to gain insights into the functional roles of CBFβ and RUNX proteins in the male germline, we conducted cleavage under targets & release using nuclease (CUT&RUN) for CBFβ, RUNX1, and RUNX3 within male germ cells. Collectively, our analyses revealed both unique and overlapping genomic localizations of CBFβ and RUNX1/3 in male germ cells.

overall_design: CUT&RUN for genomic localization of CBFβ, RUNX1 and RUNX3 was performed using germ cells isolated from the testes of postnatal day 6 mice via fluorescence-activated cell sorting (FACS).

first: Mustika

last: Rahmawati


title: Characterization of transcriptomic changes across Coccidioides morphologies using RiboMarker-enhanced RNA sequencing

city: Santa Cruz

first: Aidan

middle: Christian

last: Manning

state: CA

address: 2125 Delaware Ave. Suite B

institute: RealSeq Biosciences

type: Non-coding RNA profiling by high throughput sequencing

summary: Coccidioides is a dimorphic, pathogenic fungus responsible for transmission of the mammalian disease colloquially known as “Valley fever”. To better understand the molecular basis of Coccidioides pathogenesis, previous studies have characterized transcriptomes that define transitions between the saprobic and pathogenic life stages of the two species that cause Valley fever - Coccidioides immitis and Coccidioides posadasii. However, none of these studies have focused on small RNA profiles, which have been shown in several pathogenic fungi to play crucial roles in host-pathogen communication, affecting virulence and infectivity. In this study, we analyzed changes in small RNA expression across three major morphologies of C. posadasii: arthroconidia, mycelia, and spherules, from both intracellular and extracellular fractions. Utilizing RiboMarker® small RNA and RNA fragment library preparation, we show enhanced coverage across the transcriptome by increasing incorporation of normally incompatible RNAs into the sequencing pool. Using these data, we observed transcriptomic shifts during the transition of arthroconidia to either mycelia or spherules, marked largely by changes in both protein-coding, tRNA, and unannotated loci. As little is known regarding the mechanisms governing these life stage transitions, these data provide better insight into those small RNA- and fragment-producing genes and loci that may be required for progression between Coccidioides saprobic and parasitic life cycles. Additionally, analysis of fragmentation patterns across all morphologies suggests unique patterns of RNA fragmentation across a cohort of RNA species that correlate with a given ecotype. Finally, we noted evidence of RNA export to the extracellular space, particularly regarding snRNA and tRNA-derived fragments as well as mRNA-derived transcripts, during the transition to either mycelia or spherules, which may play roles in cell-cell, and/or host-pathogen communication. Going forward, this newly established intra- and extracellular Coccidioides sRNA atlas will provide a foundation for potential biomarker discovery and contribute to our understanding of the molecular basis for virulence in Valley fever.

sample_organism:
unidentified
Coccidioides posadasii

platform_organism:
unidentified
Coccidioides posadasii

overall_design: The study investigates how small RNAs change during key life stage transitions in Coccidioides posadasii, the fungus behind Valley fever. A Comparative analysis of intracellular and extracellular small RNA profiles using NGS in three morphologies—arthroconidia, mycelia, and spherules—using a specialized RiboMarker® library preparation to enhance transcriptome coverage.

first: Jonathan

middle: M

last: Howard

first: Rachel

last: Clark

first: Tahirah

last: Williams

first: Clarissa

last: Nobile

first: Sergei

last: Kazakov

first: Sergio

last: Barberan-Soler


title: Transcriptional rewiring by enhancer methylation in CBFA2T3-GLIS2–driven pediatric acute megakaryoblastic leukemia [DNA methylation]

city: Little Rock

first: Akhilesh

last: Kaushal

state: Arkansas

address: One Children’s Way, Slot 512-43

department: Hematology/Oncology

institute: University of Arkansas for Medical Sciences

type: Methylation profiling by genome tiling array

summary: Chemotherapy resistance and relapse remain significant challenges in pediatric acute myeloid leukemia (pAML), particularly in acute megakaryoblastic leukemia (AMKL) driven by the CBFA2T3-GLIS2 (C/G) fusion. To investigate the epigenetic mechanisms underlying these challenges, we employed multi-epigenomic approaches to identify oncogenic enhancers at cis-regulatory elements (CREs) driving aberrant gene expression. This study analyzed DNA methylation profiles in C/G+ AML cell lines (M07e, WSU-AML) compared to non-C/G AML cell lines (KASUMI-1, ME-1, KG-1A). Additionally, we included primary hematopoietic cells, including CD34+ hematopoietic stem progenitor cells (HSCs) and CD41+ megakaryocytic progenitors (MKs). DNA methylation was profiled using the Illumina Infinium HumanMethylation930K BeadChip (MethylationEPICv2.0) across all samples.

overall_design: To explore the epigenetic mechanisms underlying these challenges, we employed multi-epigenomic approaches to identify oncogenic enhancers at cis-regulatory elements (CREs) that drive aberrant gene expression.This study analyzed DNA methylation profiles in the C/G+ AML cell line M07e, where we performed a CRISPR-based functional knockout of DNMT3B, comparing it to the control M07e cell line.

first: Samrat

last: Roy Choudhury

first: Jason

middle: E

last: Farrar


title: MEK/ERK signaling blocks H3K9me3 heterochromatin formation to potentiate human mesoderm and endoderm differentiation. [RNA-Seq]

city: Cincinnati

first: Hee-Woong

last: Lim

state: Ohio

address: 3333 Burnet Ave. MLC 7024

department: Division of Biomedical Informatics

institute: Cincinnati Children's Hospital Medical Center

type: Expression profiling by high throughput sequencing

summary: Pluripotent cells differentiate into the three definitive germ layers – ectoderm, mesoderm, and endoderm, thereby establishing the foundation of the body plan. Mesoderm and endoderm arise through epithelial-to-mesenchymal transition (EMT), a critical process that occurs during gastrulation in early embryogenesis. While these differentiation processes are driven by BMP, WNT, NODAL, and FGF signaling, the functional mechanisms underlying FGF signaling remain the least understood. In this study, we demonstrate that the H3K9me3-marked facultative heterochromatin domains undergo global reorganization during the differentiation of human pluripotent stem cells into mesoderm and endoderm but not ectoderm. We reveal that the MEK/ERK pathway, critical downstream of FGF signaling during gastrulation, mediates this heterochromatin reorganization. Specifically, MEK/ERK blocks the establishment of H3K9me3 domains at EMT- and lineage-specific gene loci necessary for mesoderm and endoderm differentiation. Collectively, our findings uncover the critical role of the MEK/ERK signaling pathway in reshaping the lineage-specific H3K9me3 landscape, addressing a key gap in our knowledge of the interplay between cell singling and epigenetics in cell differentiation.

overall_design: RNA-seq data of human pluripotent stem cell (hPSC)-derived neuroectoderm (NE), paraxial mesoderm (PM), and definitive endoderm (DE), with or without 1 µM MEK/ERK inhibitor (PD0325901) treatment.

first: Satoshi

last: Matsui

first: Makiko

last: Iwafuchi


title: Transcriptomic effects of dietary PUFAs in mouse dendritic cells

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

summary: The immune system is shaped by the balance of n-3 and n-6 polyunsaturated fatty acids (PUFAs), but how these dietary lipids influence dendritic cells (DCs)— key inducers of adaptive immunity—remains largely unexplored. Importantly, whether an excess of n-6 PUFAs, a hallmark of modern diets, could  undermine DC function and immune surveillance remains largely unexplored.  Here, we uncover a striking link between dietary lipids and DC dysfunction. We found that an n-6 PUFA-rich diet promotes ferroptosis in DCs via suppression of the Nrf2 antioxidant pathway, impairing their antigen presenting capacity. Accordingly, interventions with dietary n-3 PUFAs or ferroptosis inhibitors reversed these effects, restoring DC function and enhancing responses to DC-based chemo-immunotherapy in a preclinical model of metastatic ovarian cancer. These findings suggest that dietary lipids are not just passive components of metabolism but active regulators of  DC function and fate. These findings are critical for the creating novel nutritional interventions that improve vaccination and immunotherapy outcomes.

overall_design: Splenic dendritic cells (spDCs) and bone marrow-derived dendritic cells (BMDCs) were isolated from mice fed either an n-6-rich or an n-3-rich diet for 8 weeks for RNAseq profiling

first: Deepika

last: Awasthi

first: Juan

last: Cubillos-Ruiz


title: High-resolution chromatin mapping reveals that CTCF in anchors meiotic loops to the chromosome axis. [Hi-C]

city: Bethesda

first: Florencia

last: Pratto

state: MD

address: 5 Memorial Dr Bg 5 Room 324

department: NIDDK

institute: NIH

summary: When precursor germ cells enter meiosis, chromosomes condense into an array of chromatin loops. Using Hi-C and Micro-C, we explored the trajectory of chromatin reorganization from mouse spermatogonia to spermatocytes at the highest temporal and spatial resolution to date. We show that meiotic chromatin reorganization, characterized by a shift from mitotic-to-meiotic cohesins, precedes the traditionally defined meiotic entry point (meiotic G1/S-phase). We find that large-scale A/B compartments are lost during prophase I, while local sub-compartments and interactions between regulatory elements of gene expression remain. For the first time, we detect distinct looping positions in mammalian meiosis I prophase. These loops are anchored by a subset of CTCF sites at the base of chromatin loops but formed without enriched interactions within the intervening regions, deviating from the typical pattern observed in somatic interphase cells. Our findings allow us to reconcile the current discrepancy in the length of meiotic chromatin loops and support a model where meiotic loops are formed by association of existing loops modulated by CTCF rather than by loop extrusion.

overall_design: Chromosome conformation capture experiments (HiC) done in highly purified substages through mouse meiosis

first: Gang

last: Cheng

first: Kevin

last: Brick

first: Xin

last: Li

first: Benjamin

last: Alleva

first: Mini

last: Huang

first: Kwan-Wood

middle: G

last: Lam

first: Rafael

middle: D

last: Camerini-Otero


title: An InDel Genomic Variant within a Bifunctional Super-Enhancer for LINC00636 and CD47 Regulation in Breast Cancer [RNA-seq]

city: San Francisco

first: Carolina

last: Di Benedetto

address: 2340 Sutter Street, S371

institute: University of California, San Francisco

summary: Highly accessible genomic super-enhancers often upregulate tumor-promoting genes in cancer, yet the role of genomic variation within them remains unclear. We identified a bifunctional super-enhancer that regulates the expression of cancer-promoting genes LINC00636 and CD47 in breast cancer. Our study revealed that a common germline insertion variant within the super-enhancer is associated with better progression-free survival in breast cancer patients and reduced chromatin accessibility at the super-enhancer locus. By deleting the insertion allele in breast cancer cells, we observed increased chromatin accessibility, leading to upregulation of LINC00636 and CD47, delayed cell death, and reduced infiltration of CD80+ pro-inflammatory macrophages—events that promote tumor growth. The absence of the insertion also activated a protumoral transcriptional program through LINC00636 overexpression. Our findings highlight an insertion/deletion variant that fine-tunes the regulatory function of a bifunctional super-enhancer and suggest a protective role for the insertion in breast cancer.

overall_design: Insertion-deleted MCF7 clones: RNA-seq was performed in parental MCF7 cells or in the clones M11 (MCF7Δ#1) and M46 (MCF7Δ#2), in which the germline insertion variant rs58296163 was deleted by CRISPR. This insertion variant is located within a core element of a bifuntional super-enhancer for the regulation of LINC00636 and CD47 gene expression. Two biological replicates per condition were used. LINC00636 overexpression in MCF7: RNA-seq was performed in LINC00636-overexpressing MCF7 cells. LINC00636 overexpression was carried out using CRISPR activation and two different sgRNAs (sgRNA1 or sgRNA2) targeting LINC00636-TSS or scramble sgRNA as control. Three biological replicates per condition were used.

first: Paola

last: Betancur


title: Lactate and histone H3K18 lactylation are associated with metabolic control of gene expression in the retina

first: Matthew

last: Brooks

address: 6 Center Dr Bldg 6, Rm 303

department: NEI

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

overall_design: Refer to individual Series


title: High-resolution chromatin mapping reveals that CTCF in anchors meiotic loops to the chromosome axis. [microC]

overall_design: Chromosome conformation capture experiments at high-resolution (MicroC) done in highly purified substages through mouse meiosis


title: Deconvolution of regulatory T cell heterogeneity identifies cycling precursors as conductors of immune escape during breast carcinoma progression

city: Boston

first: Kornelia

last: Polyak

address: 450 Brookline Ave. S1070

institute: Dana-Farber Cancer Institute

relation:
SuperSeries of: GSE253572
SuperSeries of: GSE253585
SuperSeries of: GSE312050

sample_organism:
Homo sapiens
Rattus norvegicus

platform_organism:
Homo sapiens
Rattus norvegicus


summary: Tumor-immune microenvironment is instrumental in shaping breast cancer tumor evolution. We previously identified an evolutionary bottleneck demarcating ductal carcinoma in situ (DCIS) from invasive ductal carcinoma (IDC). How the microenvironment evolves during such transition remains elusive. We dissected, in parallel, single-cell composition of DCIS and IDC patients and rat tumors that faithfully recapitulate human breast cancer. We discovered T cell diversity distinguishing DCIS and IDC and a novel cycling Treg state occupying the pseudotime bifurcation between DCIS and IDC, preceding more activated Treg subtypes. Multiscale analysis of patient cohorts as part of HTAN Consortium established that cycling Treg predicts recurrence in low-grade DCIS. We proved cycling Treg as Treg progenitors critical for immune escape and demonstrated that OX40 agonism restored immunotherapeutic sensitivity, where responders displayed increased inflammatory CAF subtype heterogeneity. Our study thus established cycling Treg’s importance in preserving immune escape and underscored its prognostic value to stratify future recurrence.

overall_design: Dataset 1: Breast tissues of patients (DCIS, IDC) or healthy individuals (Normal) were subjected to tissue dissociation via collagenase 4/hyaluronidase and FACS sorted for immune, epithelial, myoepithelium, and stroma compartment based on lineage markers and later to droplet-based 10X scRNAseq (3'HTv3)/Illumina NovaSeq6000. Dataset 2: Outbred Sprague Dawley rats were injected with NMU carcinogen (50 mg/kg, twice, 7 days apart, starting at 40 days of age rat) to induce rat mammary tumors. Tissues from mammary glands (MG) of untreated rats or NMU-treated rats and progressing tumors from NMU-treated rats were dissociated by collagenase 4/hyaluronidase, FACS-sorted for immune, epithelium, and stroma fractions, and subjected to droplet based 10X scRNAseq (3'HTv3) pipeline and Illumina NovaSeq6000. Dataset 3: Rats treated with NMU as aboved were subjected to three immunotherapy regimens (+isotype control) right when NMU-tumors became palpable. The rats were treated by anti-OX40 agonist (every 48hr, 2.5 mg/kg, till sacrifice) or anti-PDL1 (every 7 days, 10.0 mg/kg, till sacrifice) or combination of anti-OX40 and anti-PDL1 or isotype (same dosage). Responding versus Non-Responding tumors of each treatment were dissociated by collagenase 4/hyaluronidased and selected for scRNAseq 10X pipeline (5'HTv2)/Illumina NovaSeq6000. Raw reads from dataset 1 were aligned with the human genome hg18 while reads from dataset2/3 were aligned with the Sprague Dawley rat reference genome (Rnor_6). Downstream analyses of Datasets 1-3 include basic filtering and quality control, removal of cell doublets, batch-effect control/integration, cell cluster identification, Milo neighborhood analysis, Trajectory inference by Monocle3, Coexpression hub analysis, GSEA, CellChat, etc.

first: Triet

last: Bui

first: Ernesto

last: Rojas

first: Julieann

last: Puleo

first: Simona

last: Cristea

first: Franziska

last: Michor


title: Ribosome biogenesis and its regulation by the exportin, CSE1L, are selective 4 dependencies in childhood and young adult acute myeloid leukemia

city: Toronto

first: Veronique

last: Voisin

state: ON

address: 101 College St, room 8-353

country: Canada

institute: University Health Network

summary: Nuclear transport receptors, termed importins and exportins, regulate protein transport between the nucleus and cytoplasm through the nuclear pore. Although genetic alterations in the nuclear pore complex are more common in childhood, adolescent and young adult (AYA) AML, nucleocytoplasmic transport has not been studied extensively in childhood/AYA AML. We compared the expression of genes associated with nucleocytoplasmic transport in young and older AML patients and identified enrichment of nucleocytoplasmic transport pathways in childhood/AYA AML. Of the nucleocytoplasmic genes, CSE1L was the top expressed exportin in young AML patients. CSE1L depletion reduced growth, viability and clonogenicity in young (<40 years) AML cell lines and patient samples but spared normal hematopoietic cells. Mechanistically, CSE1L contributed to leukemogenesis by participating in ribosome biogenesis and nuclear export of the pre-ribosomal large subunit (pre-60S). Ribosome biogenesis pathways were the most abundantly expressed gene sets in young AML patients and young primary AML samples demonstrated enhanced rates of ribosome biogenesis and increased sensitivity to ribosome biogenesis inhibitors, compared to older AML samples. Our findings reinforce growing evidence that childhood/AYA AML is a fundamentally different disease to AML in older adults, and is driven by different biologic processes. Through inhibition of CSE1L, or the downstream process it regulates, ribosome biogenesis, we have identified a novel way to target leukemogenesis in childhood/AYA AML.

overall_design:
TEX, an immortalized human acute leukemia cell line, was transduced with lentiviral particles containing a pLKO.1 vector encoding shRNAs targeting the CSE1L gene or a control shRNA. Following transduction, cells were selected using puromycin (2 µg/ml). Total RNA was extracted on days 3 and 7 post-puromycin selection. In total, 18 RNA samples were generated, comprising 3 biological replicates for control cells and for each of the two shRNAs at both day 3 and day 7 time points.

***************************************************************
Raw files for human/patient samples were not submitted to GEO due to concerns about submitting personally identifiable sequence data for open access.
***************************************************************

first: Amit

last: Kumar

first: Grace

last: Egan


title: Characterizing Age-Related Extrachromosomal Circular DNA in Mouse Liver: Potential Biomarker for Liver Aging [ChIP-Seq]

city: changzhi

first: pu

last: wang

address: jiefang road163

country: China

institute: changzhi medical college

summary: Background: Extrachromosomal circular deoxyribonucleic acid (eccDNA) is progressively being recognized as a useful biomarker, however, its presence in the liver remains relatively understudied.  Methods: Through the application of Circle-Seq, this research reports on the identification and subsequent analysis of eccDNAs in both young and aging livers of the house mouse species. As a complement, RNA-Seq tests were conducted, and results subjected to a combined analysis with the initial Circle-Seq findings.  Results: In total, Hundreds of thousands of unique eccDNAs were identified and methodically characterized. The eccDNAs detected were predominantly GC-rich. The majority of eccDNAs were under the size of 10000 base pairs, accumulating predominantly in two distinct peaks. The genomic distribution analysis of the eccDNAs revealed their presence across all chromosomes, concentrating on the 5’UTR and CpG islands. Analysis of the junction sequences infer that microhomology and palindromic repeats may contribute to eccDNA formation. The frequency of eccDNAs in aged mice exceeded that of their youthful counterparts. In addition, there was a noticeable positive correlation between the substantial production of eccDNA and the transcription of its corresponding mRNA, all of which were reported as senescence-related genes.  Conclusions: This research offers the inaugural comprehensive characterisation of aging-related eccDNAs in the liver. It underscores the potential of eccDNA as a valuable biomarker for liver aging.

overall_design: The C57 murine models employed for this investigation were sourced from SPF Biotechnology (Beijing) and were accommodated within SPF-grade animal housing until they attained an age of 24 months. A parallel younger control group was integrated into this research, comprised of a set of 3-month-old C57 mice, which maintained a consistent genetic lineage with the more mature collective. All mice used were male, with 6 mice per group.The mice were euthanized using carbon dioxide anesthesia followed by cervical dislocation, hepatic tissues from mice were collected and subsequently homogenized utilizing a tissue homogenizer. For the sequencing of eccDNA, we pooled the livers from three mice within the same group for the isolation of eccDNA.


title: Cytoplasmic competition between separate parental pronuclei in zygotes

city: Kobe

first: Hirohisa

last: Kyogoku

state: Hyogo

address: 1-1, Rokkodai-chou

department: Agricultural Science

country: Japan

institute: Kobe university

summary: Embryogenesis begins with a zygote, a single cell with two pronuclei that separately enclose maternal and paternal chromosomes. The functional significance of the separation of parental chromosomes into distinct pronuclei remains unexplored, despite the fact that one-pronuclear biparental zygotes are used clinically. Here, using a combination of mouse zygote manipulation, quantitative imaging and theoretical approaches, we show a cytoplasm-mediated competition mechanism between separate parental pronuclei. This mechanism limits pronuclear volume and prevents the loss of epigenetic marks, including maternally inherited trimethylated histones. One-pronuclear biparental zygotes lack this mechanism, resulting in a reduced rate of development to term. This low developmental potential can be rescued by competition-based or drug-based restoration of epigenetic marks. In human zygotes, epigenetic loss correlates with pronuclear volume. This study provides insight into strategies to improve the clinical use of one-pronuclear biparental zygotes.

overall_design: Single two-cell embryos derived from 1PN, 2PN and parthenote were analyzed by RNA-seq.  1PN, 2PN and P1PN zygotes were analyzed by ChIL-seq.

first: Tappei

last: Mishina

first: Tomoya

middle: S

last: Kitajima

first: Akihito

last: Harada

first: Yasuyuki

last: Ohkawa


title: MEK/ERK signaling blocks H3K9me3 heterochromatin formation to potentiate human mesoderm and endoderm differentiation. [ChIP-Seq]

first: Hee-Woong

last: Lim

overall_design: ChIP-seq data of H3K9me3 in human pluripotent stem cells (hPSCs), neuroectoderm (NE), paraxial mesoderm (PM), and definitive endoderm (DE), with or without 1 µM MEK/ERK inhibitor (PD0325901) treatment.

first: Satoshi

last: Matsui

first: Marissa

last: Granitto

first: Makiko

last: Iwafuchi


title: Epigenome analysis of control-siRNA and PHGDH-siRNA treated Human Immortalized Epidermal cells (HaCaT cells)

city: Xi'an

first: Qinqin

last: Meng

state: Shaanxi

address: No.157 Xi Wu Road

department: Department of Dermatology

institute: The Second Affiliated Hospital of Xi’an Jiaotong University

summary: Genome-wide DNA methylation profiling of control-siRNA and PHGDH-siRNA treated HaCaT cells. The Illumina Infinium MethylationEPIC BeadChip was used to obtain DNA methylation profiles across approximately 853000 CpGs in HaCaT cells. Samples included 2 control-treated HaCaT cells and 2 PHGDH-siRNA treated HaCaT cells.

overall_design: The bisulfite modified DNA from the 4 samples were whole-genome amplified, fragmented by an enzymatic process and hybridized to the HumanMethylatio850 BeadChip by the manufacturer

first: Zhengxiao

last: Li


title: Single cell RNA expression data from progenitor cells and myeloid cells of EMT6 tumor bearing Cysltr1 decifient mice

city: Chicago

first: Bin

last: Zhang

state: IL

address: 300 E Superior St, Tarry Building, 4-726

department: Medicine

institute: Northwestern University

summary: In established cancer in mice and humans, “emergency” myelopoiesis usually occurs to facilitate malignancy progression. In particular, neutrophils and immature myeloid cells accumulated in the bone marrow, periphery and tumor are potent mediators of immunosuppression and tumor promotion. However, the molecular pathways regulating tumor-induced emergency myelopoiesis remain largely elusive. Here, we demonstrated that Cysteinyl leukotriene receptor 1 (CysLTR1), a key player for asthma, allergic rhinitis and other inflammatory conditons, was expressed selectively in myeloid cells from tumor-bearing hosts with the most significant expression in infiltrating immature neutrophils. Genetic ablation and pharmacological inhibition of CysLTR1 resulted in diminished tumor growth with enhanced antitumor immunity. The anti-tumor effect of CysLTR1 inhibition was linked with transcriptomic rewiring of granulopoiesis and neutrophil reprogramming toward an anti-tumor immune phenotype; this process required the distinct transcriptional factors to specifically dictate neutrophil progenitor commitment and differentiation in association with controlled degranulation. Furthermore, single-cell RNA sequencing analysis provided a comprehensive transcriptional landscape of neutrophil maturation, function and fate decision in tumor bearers, confirming a CysLTR1-dependent transcriptomic mechanism for fine-tuned regulation of tumor-induced emergency granulopoiesis. CysLTR1-mediated changes in the differentiation and degranulation also occurred in human neutrophils and correlated with the survival and immune checkpoint therapy responsiveness in cancer patients. Consistently, targeting CysLTR1 with clinically available antagonists overcame resistance to immune checkpoint PD-1 inhibitors in several mouse tumor models. These findings thus have important implications for understanding the abnormal myelopoiesis during cancer progression and suggest new therapeutic approaches to improve immune checkpoint blockade.

overall_design: Bone marrow cells, spleen cells and tumor infiltrated cells were isolated from EMT6 tumor bearing Cysltr1 decifient mice and BALB/c WT control. Progenitor cells and CD45+ cells were enriched with immuno-magnetically as indicated. Each sample was derived from a pool of three mice.

first: Hui

last: Tang

first: Ping

last: Xie

first: Jihae

last: Ahn

first: Miran

last: Choi

first: Jie

last: Fan

first: Rachel

last: Orpano


title: Expression data from Cysltr1 deficient bone marrow in vitro induced myeloid cells

overall_design: Bone marrow cells were isolated from BALB/c WT mice and Cysltr1 deficient mice, and cultured in complete RPMI1640 media with GM-CSF (40ng/mL), GM-CSF (40ng/mL) + IL-6 (40ng/mL), or GM-CSF (40ng/mL) + 24h EMT6 conditional media (50% v/v) in vitro to induce myeloid cells. Cells were then gathered for bulk RNA sequence after 4 days. A triplicate of each sample was considered, and  each sample was derived from a pool of three mice.


title: High-resolution chromatin mapping reveals that CTCF in anchors meiotic loops to the chromosome axis.

first: Florencia

last: Pratto

overall_design: ChIP-seq for CTCF done in F1 (B6xCAST) mouse testicular samples with inputs

first: Gang

last: Cheng

first: Kevin

last: Brick

first: Xin

first: Benjamin

last: Alleva

first: Mini

last: Huang

first: Kwan-Wood

last: Lam

first: Rafael

last: Camerini-Otero


title: Testing of a human blood gene signature for quantitative dose reconstruction of radiation dose: dose rate effects

city: New York

first: Shanaz

middle: Adi

last: Ghandhi

state: NY

address: 630, W 168th street

department: Center for Radiological Research

institute: Columbia University Medical Center

overall_design: Comparative gene expression profiling analysis of RNA-seq data for blood cell response to radiation and for identification of survival biomarkers for delayed lung injury

first: Sally

last: Amundson


title: Endothelial PPARγ modulates atherosclerosis by regulating endothelial activation and prostacyclin levels

city: La Jolla

first: Ruth

middle: T

last: Yu

address: 10010 N Torrey Pines Rd

department: Gene Expression Lab

institute: Salk Institute

summary: Systemic activation of the nuclear receptor peroxisome proliferator activated receptor gamma (PPARγ), a key regulator of glucose and lipid homeostasis, has been shown to result in amelioration of atherosclerosis in animal and human studies. However, the pathways and tissues through which this occurs remain unclear. As endothelium is involved in the development of atherosclerosis and expresses PPARγ, we propose a role for endothelial PPARγ in atherogenesis. Using a mouse model of endothelial PPARγ deficiency, we found that these mice developed more severe atherosclerosis in response to dietary challenges and exhibited increased levels of serum and aortic adhesion molecules. Gene expression analyses of primary endothelial cells isolated from mouse hearts revealed that the endothelial cells lacking PPARγ on chow diet displayed an expression profile similar to wild-type endothelial cells on an atherogenic diet, suggesting that PPARγ knockout endothelial cells are already activated prior to diet-induced hypercholesterolemia. In particular, the expression of cytokines, as well as prostacyclin synthases, was altered in PPARγ-deficient endothelial cells. Thus, we propose a mechanism by which endothelial PPARγ exerts an athero-protective role via transcriptional activation of cytokine and prostacyclin synthesis genes during the initiation phase of atherogenesis.

overall_design: RNA from primary mouse cardiac endothelial cells were used in the microarray analyses. Each sample was pooled from five hearts. Two pooled samples from each genotype treated with atherogenic diet for 0 or 2 wks were analyzed.

first: Li

last: Tai

first: Ronald

last: Evans


title: Genome reorganization and its functional impact during breast cancer progression [RNA-Seq]

status: Public on Feb 25 2026

first: Kathleen

middle: Shaindel Metz

last: Reed

address: 41 Medlars Dr, B507

department: Genetics and Molecular Biology

institute: National Cancer Institute, NIH

summary: To explore how chromatin structure and epigenetic parameters of genome architecture changes during cancer progression at a fine scale and genome-wide, we generated high-resolution Micro-C contact maps in non-malignant, pre-cancerous, and metastatic MCF10 breast cancer epithelial cells. We profiled progression-associated reorganization of chromatin compartments, topologically associated domains (TADs), and chromatin loops, and also identified invariable chromatin features. We find large-scale compartmental shifts occur predominantly in early stages of cancer development, with more fine-scale structural changes in TADs and looping accumulating during the later transition to metastasis. We related these structural features to changes in gene expression, histone marks, and potential enhancers and found a large portion of differentially expressed genes physically connected to distal regulatory elements. While changes in chromatin loops were relatively rare during progression, differential loops were enriched for progression-associated genes, including those involved in proliferation, angiogenesis, and differentiation. Changes in either enhancer-promoter contacts or distal enhancer activity were accompanied by differential gene regulation, suggesting that changes in chromatin contacts are not necessary but can be sufficient for gene regulation. Together, our results demonstrate a functionally relevant connection between gene regulation and genome remodeling at many key genes during cancer progression.

overall_design: Paired-end rRNA-depleted RNA-Seq in MCF10A, MCF10AT1, and MCF10CA1a cell lines (3 biological replicates per cell line).

first: Tom

last: Misteli

first: Andrew

last: Fritz

first: Haley

last: Greenyer

first: Seth

last: Frietze

first: Janet

last: Stein

first: Gary


title: Characterization of molecular changes associated with aging in the mouse auditory nerve [re-analysis]

city: Charleston

first: Jeremy

last: Barth

state: SC

address: 173 Ashley Ave, BSB 627

institute: MUSC

summary: Overall goal of the study is to identify key molecular regulators that change in the auditory nerve as a function of aging

relation:
Reanalysis of: GSM4215165
Reanalysis of: GSM4215166
Reanalysis of: GSM4215167
Reanalysis of: GSM4215168
Reanalysis of: GSM4215169
Reanalysis of: GSM4215170

overall_design:
Data from series GSE141865 was reanalyzed using updated tools and reference databases. The study examined differntial gene expression in CBA/CaJ mouse auditory nerve between 2.5 yr and young adult (3 mo) stages. Fastq files from the series (GSM4215165, GSM4215166, GSM4215167, GSM4215168, GSM4215169, GSM4215170) were analyzed using Partek Flow software. Sequencing data was aligned to mm39 using STAR (2.7.8a) and quantified to annotation model (Partek E/M) built from mm39 Ensembl Transcripts release 104. DESeq2 analysis was run to produce normalized count measures.

***************************************************************
The table below lists GEO accessions reused/reanalyzed for this study.
***************************************************************

first: Hainan

last: Lang

middle: L


title: Single cell RNA-seq analysis of Induced Stem-Cell-Derived islets

city: Beijing

first: Jingxiao

last: Cao

state: Beijing

address: No.5 Yiheyuan Road, Yanyuan Street, Haidian District, Beijing

department: Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.

institute: Peking University

summary: The generation of pancreatic islet cells from human pluripotent stem cells (hPSCs) holds promise for cell replacement therapies for diabetes. To further analyse the characteristics of hPSC-islets and compare to primary human islets, we performed single cell RNA-seq analysis of cells sampled from cell preparation prior to transplant.

overall_design: In this study, we induced islets from human pluripotent stem cells. We performed single-cell RNA sequencing analysis to characterize the obtained  iPSC-islets.


title: Genome reorganization and its functional impact during breast cancer progression [ATAC-Seq]

overall_design: OMNI ATAC-Seq in MCF10A, MCF10AT1, and MCF10CA1a cell lines (2 biological replicates per cell line).


title: Deconvolution of regulatory T cell heterogeneity identifies cycling precursors as conductors of immune escape during breast carcinoma progression [Visium]

first: Kornelia

last: Polyak

overall_design:
Dataset 4: Visium of outbred Sprague Dawley rat untreated/NMU-treated mammary glands (MG) and NMU-treated tumors. Frozen sections of MG and rat tissues from rat treated with 50mg/kg NMU (twice, 7 days apart) were cryosectioned serially at 10um thickness. The middle sections with the best morphology was fixed, peremabilized and stained with H&E using standard protocol and processed via the 10X Visium Spatial Gene Expression Reagent Kits (Dual-Index Kit TT, PN-1000184). The sections were mounted onto eight 6.5mm x 6.5mm capture areas surrounding by 8mm x 8mm fiducial frame, enabling at least 2000x2000 pixel portion total and ~5000 gene expression per spot. Image for each sample was captured on a brightfield Zeiss Axio microscope, and these images were used later to map gene expression patterns back onto tissues. Afterward, more permeabilization was performed and capturing was enabled by 30nt poly(dT) probes in the presence of nucleotides, spatial barcodes, and 12nt UMIs  (Read 1). Reverse transcription was allowed to occur in situ on the slide followed by template-switching Oligo via the Second Strand Mix and cDNA was amplified together with the spatial barcodes. Visium spatial library construction was initiated following enzymatic fragmentation and end-repair with P5 and P7 sample indices and TruSeq Read 2, enabling Illumina sequencing via HiSeq.
Note:
Same image set for 4 samples : 1NMFPC, 1RMFPC, 2LMFPC, 1LMFPC
Same image set for 4 samples : 7L, 7R, 5L, 6N
Same image set for 4 samples : 2NMFPC, 3RMFPC, 4LMFPC, 4NMFPC
Same image set for 4 samples : 3LB, 3NC, 4RA, 4RC
Same image set for 4 samples : 5RA, 5NC, 6LD, 6RC

first: Triet

last: Bui

first: Ernesto

last: Rojas

first: Julieann

last: Puleo

first: Aashna

last: Jhaveri

first: Simona

last: Cristea

first: Franziska

last: Michor


title: CATCH-seq analysis of 1PN and 2PN zygotes.

first: Hirohisa

last: Kyogoku

summary: Embryogenesis begins with a zygote, a single cell with two pronuclei that separately enclose maternal and paternal chromosomes. The functional significance of the separation of parental chromosomes into distinct pronuclei remains unexplored, despite the fact that one-pronuclear biparental zygotes are used clinically. Here, using a combination of mouse zygote manipulation, quantitative imaging and theoretical approaches, we show a cytoplasm-mediated competition mechanism between separate parental pronuclei that ensures developmental potential. This mechanism limits pronuclear volume and prevents epigenetic mark dysregulation, including loss of maternal trimethylated histones. One-pronuclear biparental zygotes lack this mechanism, resulting in a reduced rate of development to term. This low developmental potential can be rescued by competition-based or drug-based restoration of epigenetic marks. This study provides a spatial mechanism linking fertilization to the establishment of the full developmental potential for the next generation, highlighting caveats in clinical use of one-pronuclear biparental zygotes.

overall_design: 1PN and 2PN zygotes were analyzed by CATCH-seq for H3K4me3, H3K9me3 and H3K27me3.

first: Tappei

last: Mishina

first: Tomoya

last: Kitajima

first: Masahiro

last: Matsuwaka

first: Mami

last: Kumon

first: Azusa

last: Inoue


title: scRNA‑seq of human intra‑hepatic CD4⁺ T cells reveals unique Treg transcriptional identities and two steady‑state tissue‑adaptation programs across healthy and HCC liver samples

city: London

first: Alberto

last: Sanchez-Fueyo

address: Denmark Hill

department: James Black Centre

country: United Kingdom

institute: Kings College London University

summary: We employed a single‑cell sequencing approach using the 10x Genomics platform, including scRNA‑seq, CITE‑seq, and paired TCR libraries, to investigate the molecular programs of human tissue‑resident regulatory T cells (Tregs). By analyzing CD4⁺ T cells from healthy liver and matched peripheral blood mononuclear cells (PBMCs), as well as hepatocellular carcinoma (HCC) tissue with paired non‑tumoral liver samples, we characterized the transcriptional adaptations of intra‑hepatic Tregs under steady‑state conditions and their reprogramming within the HCC tumor microenvironment.

overall_design: PBMCs were freshly isolated, and liver specimens were enzymatically digested immediately after surgical collection. The resulting single‑cell suspensions were cryopreserved and stored until analysis. Upon thawing, CD4⁺ T cells were enriched using magnetic bead–based negative selection, followed by staining with CITE‑seq antibodies and additional markers for cell sorting. Sorted CD4⁺ populations were then processed for scRNA-seq, including CITE‑seq and TCR library preparations.

first: Elena

last: Perpiñán

first: Nicolas

last: Sompairac

first: Shahram

last: Kordasti

first: Niloufar

last: Safinia


title: Natural constitutive promoters from Actinoplanes siamensis TBRC 4237 enable high-level heterologous gene expression in Streptomyces coelicolor

city: Khlong Luang

first: Wuttichai

last: Mhuantong

state: Pathum Thani

address: National Center for Genetic Engineering and Biotechnology (BIOTEC)

country: Thailand

institute: BIOTEC

summary: Activation of cryptic biosynthetic gene clusters (BGCs) in actinomycetes often requires strong and reliable promoters, yet native promoters from rare actinomycetes remain scarce. Here, we used transcriptome analysis of Actinoplanes siamensis TBRC 4237 to identify highly expressed genes and selected 22 upstream regions as candidate constitutive promoters. Their activities were evaluated in Streptomyces coelicolor M1146 using indigoidine synthetase and latex-clearing protein (LCP) as heterologous reporters. Thirteen promoters drove indigoidine production at levels exceeding those of kasOp* and ermEp*, the widely used strong constitutive promoters in Streptomyces. Several promoters also yielded robust LCP activity, with promoter 650A achieving the highest expression across both reporter systems. Motif analysis showed no clear correlation between predicted -10/-35 elements and promoter strength, indicating additional regulatory features. These natural promoters provide valuable genetic parts for heterologous expression, BGC activation, and pathway refactoring in actinomycetes.

overall_design: RNA of A. siamensis TBRC 4237 was extracted using RiboPure™ RNA Purification Kit, bacteria (Invitrogen, U.S.A.). Cells were harvested from 250–600 microliter cultures in LS2 medium by centrifugation and resuspended with 300 microliter RNAwiz solution. Then, RNA extraction was performed following the kit protocol. RNA eluted from the kit columns were treated with DNaseI. Concentration and quality of RNA was measured by using nanodrop and 0.8% agarose gel electrophoresis, respectively. Approximately 6 microgram RNA of each samples was submitted for RNAseq analysis service at NovogeneAIT Genomics, Singapore. The integrity of RNA samples was analyzed by using Agilent 2100 bioanalyzer. The RNA sequencing was performed on Illumina NovaSeq 6000 with paired end 150 bp and acquired 3 GB data per samples.

first: Suranan

last: Yoolong

first: Jindaporn

last: Kongsee

first: Kitlada

last: Srichomthong

first: Chayaphat

last: Wongsombat

first: Pattanop

last: Kanokratana

first: Chanwit

last: Suriyachadkun

first: Vanicha

last: Vichai

first: Aiyada

last: Aroonsri


title: Teratoma formation by Safe and Allo-Accepted Pluripotent Cells

city: Hong Kong

first: Vivian

last: Tam

address: L3-13, Laboratory Block, 21 Sassoon Rd, Pokfulam

country: Hong Kong

institute: The University of Hong Kong

summary: Pluripotent stem cells are a promising alternative in cell and tissue transplantation as they have the potential to be differentiated into different cell types to treat various diseases. However, two major challenges have hindered their clinical application: concerns associated with risk of allogeneic rejection, in addition to safety issues related to uncontrolled proliferation and tumorigenicity. In this study, we utilised the H1 ESC line that was engineered to possess immune-evading properties to avoid rejection, and equipped with a "SafeCell" kill switch to selectively kill aberrantly proliferating cells. We used a humanised mouse model to demonstrate the successful generation of allogeneic tissues from SafeCell-AlloAccept (SC-AlloAccept) cells transplanted in the immune-active subcutaneous region of immunocompetent humanised mice. These cells formed teratomas and their growth was controlled with pro-drug ganciclovir that activated the kill switch, which successfully eliminated proliferating cells, rendering the remaining tissue dormant. This SC-AlloAccept-derived graft was harvested at 108 days post transplantation, highlighting their potential for long-term engraftment without rejection. We also showed that neither prior rejection of immunogenic parental H1 cells (sensitization) nor the presence of SC-AlloAccept tissue (potential immune compromise) affected the immune response to a subsequent, second transplant. This study validates the application of safe and AlloAccept human cells in transplantation, providing important insights into the immune status of the naive and sensitised human immune system of the host in a mouse model. These findings mark a key step towards the application of stem cells that can be universally accepted, towards cell-based regenerative therapies.

overall_design: Single cell RNA-seq profiling of human SC-AlloAccept cells extracted from a teratoma 108 days post injection

first: Danny

last: Chan


title: CRISPR-based genetic screens to interrogate therapeutic targets on tumor maintenance and heterogeneity in AML patient cells

first: Jacqueline

last: Peng

address: 421 Curie Blvd

institute: University of Pennsylvania

summary: Functional genomics directly in primary tumor cells is warranted to better understand the complexity of the diseases in a context of high clinical relevance. We optimized ex vivo and in vivo CRISPR-based genome/epigenome editing approaches in patient-derived xenograft (PDX) and primary acute myeloid leukemia (AML) cells, including those harboring DNMT3A/FIT3-ITD/NPM1c that predicts a poor clinical outcome and has no model to fully represent. We deployed CRISPR and CRISPRi “drop-out” screenings on patient cells in vivo and prioritized AML-biased gene and cis-element dependencies, including an uncharacterized MYB regulatory element. We further developed a Perturb-seq pipeline for patient cells, where we perturbed known AML therapeutic targets and delineated complex regulatory networks and changes of cell cycle stages and cellular hierarchy in response to perturbations by scRNA-seq. We uncovered an unanticipated role for SETDB1, a suppressor of interferon response, whose depletion caused the emergence of Hematopoietic stem cell (HSC) and progenitor-like population marked with high HOXA expression in a PDX model, and myeloid differentiation were re-induced by DOT1L inhibition, preceding a combinatorial therapy to co-suppress SETDB1 and the HOXA cluster. Our study proposed a strategy to annotate personalized vulnerabilities to predict therapeutic response in AML.

overall_design: mRNA profiles of Cas9 sgRNA-expressing human primary samples and PDX samples

first: Zhendong

last: Cao

first: Jonathan

last: Sussman

first: Jason

last: Xu

first: Changya

last: Chen

first: Kai

last: Tan

first: Junwei

last: Shi


title: Generation of Functionally Competent Testicular Somatic Cells from Pluripotent Stem Cells

city: Yokohama

first: Takahiro

last: Suzuki

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: Center for Integrative Medical Sciences

institute: RIKEN

summary: Cellular interactions between germ cells and gonadal somatic cells are essential for the progression of gametogenesis. Here, we report a culture method for generating fetal testicular somatic cell–like cells (fTeSLCs) from embryonic stem cells. These fTeSLCs exhibit a transcriptomic profile closely resembling that of their in vivo counterparts, including distinct cell populations corresponding to Sertoli cells and interstitial cells. For functional assessment, interstitial cell–like cells (ICLCs) and Sertoli-like cells (SerLCs) were isolated from fTeSLCs. ICLCs differentiated into Leydig cells when cocultured with testes lacking endogenous Leydig cells, thereby restoring androgenic support. SerLCs reconstituted the seminiferous epithelium following selective ablation of endogenous Sertoli cells. Both cell types supported spermatogenesis and generated spermatids reaching the elongating stage. Notably, round spermatids derived from these reconstructed systems produced viable offspring by round spermatid injection. These findings demonstrate that fTeSLCs can generate functional testicular somatic cells, providing a valuable platform for studying testis development and spermatogenesis.

overall_design: in vivo gonadals cells and ES cell-derived gonadal smatic cells  were analyzed using 10X Chromium Single Cell 3' Reagent Kits.

first: Takuya

last: Sato

first: Takashi

last: Yoshino

first: Katsuhiko

last: Hayashi

first: Takehiko

last: Ogawa


title: Lnc-GATS-3:3/MCM7 promotes the proliferation and invasion of cervical squamous cell carcinoma cells by regulating the CDK/Rb/E2F signaling pathway

city: Shanghai

first: Zhang

last: Jun

address: Second Ruijin Road

department: Department of Oncology

institute: Ruijin Hospital

summary: This study investigated the role and mechanism of lnc-GATS-3:3/Mini-chromosome maintenance protein 7 (MCM7) in the proliferation, invasion, migration, and apoptosis of SiHa cervical cancer cells. Whole transcriptome sequencing was conducted on matched pairs of cervical cancer and normal tissue samples, followed by GO and KEGG enrichment analysis. The cis method was utilized to identify lncRNAs and mRNAs associated with the cell cycle. The expression levels of lnc-GATS-3:3 and MCM7 in cervical cancer and normal tissues were measured using qRT-PCR. Subsequently, the CCK-8, TUNEL, Transwell, Western Blot, and flow cytometry experiments were employed to assess the effects of lnc-GATS-3:3 silencing on cervical cancer cell proliferation, apoptosis, migration, and invasion. The impact of lnc-GATS-3:3 downregulation on MCM7 and the CDK/Rb/E2F signaling pathway was confirmed using qRT-PCR and WB analysis. Lastly, tumorigenesis experiments were performed to validate the altered tumor proliferation capacity following lnc-GATS-3:3 silencing. The expression of lnc-GATS-3:3 and MCM7 was significantly elevated in cervical cancer tissues (p < 0.05). Silencing of lnc-GATS-3:3 inhibited the proliferation, migration, and invasion of cervical cancer cells (p < 0.05), promoted cell apoptosis (p < 0.05), and suppressed the expression of MCM7, CDK-4, CDK-6, Rb, and Cyclin D1. Furthermore, silencing lnc-GATS-3:3 inhibited tumor growth in nude mice. In summary, our findings establish that the Lnc-GATS-3:3/MCM7 axis promotes the proliferation, invasion, and migration of cervical cancer cells while inhibiting apoptosis by modulating the CDK/Rb/E2F signaling pathway, thereby identifying it as a key player in cervical cancer progression.

overall_design: In order to explore the mechanism of cervical cancer occurrence, we conducted RNA sequencing on the cancer tissues of 4 cervical cancer patients and the normal cervical tissues of 4 control patients.

first: Fen

last: Li

first: Jinrui

last: Yuan

first: Gulibiya

last: Aizezi

first: A

last: Yinue

first: Yalikun

last: Muhanmode

first: Guqun

last: Shen


title: Effect of PHGDH knockdown on gene expression in human immortalized keratinocytes (HaCaT cells)

first: Qinqin

last: Meng

summary: To investigate the role of PHGDH in the regulation of psoriatic keratinocyte inflammation, we challenged HaCaT cells with PHGDH-siRNA and stimulated with IL-17A, IL-22, IL-1α, OSM and TNFα (mix) coctails. We then performed gene expresssion profiling analysis using data obtained from RNA-seq of 4 groups of samples

overall_design: Overall differential gene expression through RNA sequencing comparing PHGDH-siRNA treated HaCaT cells with control-siRNA treated HaCaT cells with or without mix stimulation

first: Zhengxiao


title: Genome reorganization and its functional impact during breast cancer progression

city: Bethesda

first: Kathleen

last: Reed

summary:
To explore how chromatin structure and epigenetic parameters of genome architecture changes during cancer progression at a fine scale and genome-wide, we generated high-resolution Micro-C contact maps in non-malignant, pre-cancerous, and metastatic MCF10 breast cancer epithelial cells. We profiled progression-associated reorganization of chromatin compartments, topologically associated domains (TADs), and chromatin loops, and also identified invariable chromatin features. We find large-scale compartmental shifts occur predominantly in early stages of cancer development, with more fine-scale structural changes in TADs and looping accumulating during the later transition to metastasis. We related these structural features to changes in gene expression, histone marks, and potential enhancers and found a large portion of differentially expressed genes physically connected to distal regulatory elements. While changes in chromatin loops were relatively rare during progression, differential loops were enriched for progression-associated genes, including those involved in proliferation, angiogenesis, and differentiation. Changes in either enhancer-promoter contacts or distal enhancer activity were accompanied by differential gene regulation, suggesting that changes in chromatin contacts are not necessary but can be sufficient for gene regulation. Together, our results demonstrate a functionally relevant connection between gene regulation and genome remodeling at many key genes during cancer progression.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series

last: Metz Reed

first: Tom

last: Misteli

first: Andrew

last: Fritz

first: Haley

last: Greenyer

first: Seth

last: Frietze

first: Janet

last: Stein

first: Gary


title: The interaction between virus-bound KLF4 and host-bound PARP1 directs the localization of Adeno-Associated Virus Type 2 (wtAAV2) to cellular sites of DNA damage

city: Madison

first: Kinjal

last: Majumder

state: WI

address: 1525 Linden Drive

department: Oncology

institute: University of Wisconsin

summary: Using a modified iteration of a circular chromosome conformation capture to map the location of viral genomes (V3Cseq), we show that the Adeno-Associated Virus genome localizes spatially with cellular sites of DNA damage during treatment with DDR inhibitors or in the presence of a mutated  KLF4 binding site within the wtAAV2 genome.

overall_design: Identification of the cellular interaction site of Adeno-Associated Virus, and the localization of the resultant DNA damage response. Independent replicates of chromosome conformation capture (designated as V3C in the file name) have been performed. For each time-point or treatment, at least two independent replicates of the indicated assays have been performed.

first: Rhiannon

last: Abrahams

first: Clairine

last: Larsen


title: Cellular Survivorship Bias as  a Mechanistic Driver of  Muscle Stem Cell Aging

city: Los Angeles

first: Jengmin

last: Kang

address: 615 Charles E Young Dr S

institute: University of California, Los Angeles

summary: Aging is characterized by a significant impairment in the ability of muscle stem cells (MuSCs) to efficiently contribute to muscle regeneration. Here we uncover a novel cause of this aging-associated stem cell dysfunction - a cell-specific survivorship bias that prioritizes stem cell persistence at the expense of functionality. We show here that, with age, muscle stem cells upregulate a tumor suppressor, NDRG1, which, by blunting the mTOR pathway, increases their long-term survival potential but comes at the cost of their ability to promptly activate and contribute to muscle regeneration. These findings suggest that delayed muscle regeneration with age may be the result of a tradeoff that favors long term stem cell survival over immediate regenerative capacity.

overall_design: In order to determine the extent to which the elevation of NDRG1 might be a causal driver of the impaired activation rate observed in old MuSCs, we generated a MuSC-specific conditional NDRG1 KO mouse model (Pax7CreER/+; NDRG1fl/fl;ROSAeYFP/+ ) to ablate NDRG1 in MuSCs following tamoxifen injection. We next sought to determine the molecular mechanism by which NDRG1 was eliciting its effects in old MuSCs. To this end, we sequenced the transcriptomes of MuSCs from aged WT and NDRG1cKO mice

first: Daniel

middle: I

last: Benjamin


title: Thiolutin Extends Replicative Lifespan by Rewiring Yeast Transcription and Metabolism

city: Rzeszów

first: Mateusz

last: Mołoń

state: Rzeszów

address: Aleksandra Zelwerowicza 4

country: Poland

institute: University of Rzeszów

summary: This study examines the global transcriptomic response of Saccharomyces cerevisiae strain BY4741 to short-term exposure to thiolutin, a transcriptional inhibitor. Exponentially growing cells were treated with 3 µg/mL thiolutin for 3 hours and compared with untreated controls. RNA sequencing was performed using paired-end libraries prepared with the MGIEasy RNA Library Prep Set and sequenced on the BGISEQ-500 platform. Three independent biological replicates were analyzed per condition. Differential expression analysis using DESeq2 (Benjamini–Hochberg false discovery rate < 0.05) revealed extensive transcriptional remodeling affecting pathways related to ribosome biogenesis, oxidative phosphorylation, proteostasis, stress response, and aging-associated processes.

overall_design: Wild-type Saccharomyces cerevisiae BY4741 cells were cultured in YPD medium at 28°C to exponential phase. Cultures were divided into untreated controls and cells treated with 3 µg/mL thiolutin for 3 hours. Total RNA was isolated from three independent biological replicates per condition. Poly(A)-selected RNA libraries were prepared and sequenced using paired-end DNBSeq technology on the BGISEQ-500 platform. Gene-level read counts were generated and analyzed using DESeq2 to identify differentially expressed genes.

first: Patrycja

last: Kielar

first: Zofia

last: Kobylińska

first: Agnieszka

first: Jarosław

last: Winiarski

first: Monika

last: Kula-Maximenko

first: Sabina

last: Galiniak


title: Cellular heterogeneity in hypertrophic burn scars in response to carbon dioxide laser therapy

city: Birmingham

first: Yung-Yi

last: Chen

address: Vincent Drive

institute: University of birmingham

summary: Background: Ablative fractional carbon dioxide (AFCO2) laser therapy is used for treating pathological scarring. However, mechanisms underlying reduction in hypertrophic scarring are poorly understood. Methods: We investigated cellular mechanisms of AFCO2 laser therapy by performing single-cell RNA sequencing (scRNA-seq) on skin biopsies from burn survivors with hypertrophic scars before and after three sessions of AFCO2 therapy. Scar reduction was assessed subjectively and objectively. Results: Those with a good response (GR) to laser therapy have scars less than 6 years from injury, whereas poor responders (PR) have scars over 6 years since injury. ScRNA-seq analysis of skin biopsies reveals that genes enriched in GR are associated with extracellular matrix and structure organisation (COL14A1, POSTN, SPARC); whereas genes enriched in PR are related to enhanced immune inflammatory responses (CXCL14, JUN, TNC). Notably, expression of the pro-fibrotic gene Engrailed-1 (EN1) remains elevated in PR scars compared to GR. The ECM-regulatory gene TIMP-1 (Tissue Inhibitor of Metalloproteinases 1) is also significantly upregulated in PR scars following treatment relative to GR scars, although at the protein level TIMP1 levels decrease in PR but increase in GR after therapy. The regenerative-associated gene, TRPS1 (Transcriptional Repressor GATA Binding 1) expression demonstrates opposing regulation post treatment, with upregulation observed in GR scars but downregulation in PR scars, underscoring distinct transcriptional trajectories associated with differential therapeutic outcomes. Finally, distinct intercellular communication networks and differentiation trajectories are observed after AFCO2, with regenerative mesenchymal fibroblasts predominating in GR but inflammatory fibroblasts associated with PR. Conclusions: We conclude AFCO2 laser therapy is more effective if done early after injury and distinct fibroblast recruitment is associated with a good response, specifically regenerative fibroblasts. Plain English summary: Ablative fractional carbon dioxide (AFCO2) laser therapy is used for reducing scarring. However, results are varied and the factors associated with a good response are poorly understood. We assessed scar reduction after AFCO2 therapy in patients with excessive scarring, taking skin biopsies to determine the cell types present in the treated areas and which genes they expressed. We showed that the therapy was more effective in patients who were less than 6 years from injury, those with a good response had scars containing regenerative fibroblasts and gene expression that was distinct from those with a poor response. We conclude that AFCO2 therapy is most effective if used early after injury and that a more regenerative, less inflammatory cell infiltration is associated with scar reduction.

first: Christopher

last: Mahony

first: Jason

last: Turner

first: Charlotte

last: Smith

first: Abdulrazak

last: Abdulsalam

first: Ezekwe

last: Amirize

first: Amberley

last: Prince

first: Adrian

last: Heagerty

first: Claudia

last: Roberts

first: Adam

last: Croft

first: Yvonne

last: Wilson

first: Naiem

last: Moiemen

last: Lord


title: Discovery of cephalotaxinone enzymes reveals a whole plant model for homoharringtonine biosynthesis

city: Stanford

first: Yaereen

last: Dho

address: 443 Via Ortega, Shriram Center for Biological and Chemical Engineering Room 271

department: Chemistry

institute: Stanford University

summary: Plants produce diverse molecules that inhibit protein translation. A lead example is homoharringtonine (HHT), both a key tool for ribosomal profiling and an FDA-approved treatment for chronic myeloid leukemia. HHT is commercially produced through semi-synthesis by esterifying the alkaloid core cephalotaxine (CET) extracted from endangered Cephalotaxus species. Despite its medicinal significance, a biosynthetic pathway to CET and HHT has not been described. Here, we use paired untargeted metabolomics (stable-isotope labeled precursor feeding) and transcriptomics to elucidate a near-complete biosynthesis to CET without prior knowledge of intermediates and biosynthetic genes. We show that while CET alkaloid core is actively biosynthesized only in growing root tips, both CET and HHT accumulate throughout the plant. We discovered and characterized seven CET pathway intermediates and six novel biosynthetic enzymes that can be used to produce cephalotaxinone, the likely direct precursor of CET. Included are non-canonical cytochrome P450s, an atypical short-chain dehydrogenase, and a 2-oxoglutarate-dependent dioxygenase that together result in carbon excision and pentacyclic backbone formation of HHT alkaloids. This study establishes a metabolic route to the core scaffold of HHT and suggests a whole plant coordination model for biosynthesis of eukaryotic ribosomal toxins in Cephalotaxus, where cephalotaxinone is the last pathway intermediate produced in root tips and distributed throughout the plant for subsequent elaboration to HHT.

overall_design: Various tissues from C. harringtonia var. Fastigiata were excised from the whole plant using ethanol-sterilized scissors in May 2023 for RNA-sequencing. For young inner needles (YIN), actively growing inner young light-green yellowish needles of 0.5-2 cm in length were harvested. Young outer needles (YON) were actively growing outer light-green needles, 1.5-3 cm in length. For young stems (YSt), light-green stems with YIN and YON of 2-3 cm in length from the tip of the stem (meristem) was harvested; all the surrounding needles were removed using a sterile scalpel. Old needles (ON) were mature, dark green needles (≥1-2 years old), 4-7 cm in length. For old stems (OSt), at least 1-2 year-old mature dark green stems (4-5 cm in length) with ON removed were collected. Before harvesting root tips (Rt), they were thoroughly washed with water, quickly rinsed with 30% ethanol, and washed again with water as a final washing step. Then, roots of 5-8 cm in length from the root tip, including the root meristem, were collected. Needles and roots, due to their thin structure, were latitudinally split into equally sized sections for paired metabolomics (feeding experiments) and transcriptomics (RNA-seq). Stems were longitudinally sectioned into equal halves for the same paired analyses. This paired approach ensured that the tissues sequenced for trancriptome analysis contained CET bisoynthetic genes. The processed Illumina sequencing reads were used to quantify each transcript abundance against the processed PacBio Iso-Seq transcriptome.

first: Kevin

first: Elizabeth

last: Sattely


title: Non-cytolytic viral vaccine vectors induce durable effector-memory CD8 T cell immunity by triggering type I interferon

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University of Basel

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


title: Vascular smooth muscle cell state trajectories mediate molecular mechanisms of coronary disease risk [RNA-seq]

first: Thomas

last: Quertermous

state: CA

address: 300 Pasteur Drive

department: Medicine Cardiology

summary: To investigate the genetic basis of SMC cell state trajectories that underlie the SMC component of CAD causality, we developed a dense timecourse single cell transcriptomic and epigenomic mapping of atherosclerosis in a murine disease model with additional high throughput spatial RNA in situ hybridization to localize . We further performed parallel knockout studies with single cell transcriptomics and epigenomics of validated CAD gene Tcf21 to understand its molecular mechanisms in SMC transition. We identified TEAD1 and CEBPB to share significant binding sites with coronary artery disease risk gene TCF21 at enhancer sites across the genome and characterize their genomic relationships through a combination of chromatin immunoprecipitation sequencing for TEAD1, CEBPB, and marker of enhancer activation H3K27ac. We further perform bulk RNAseq to understand the functional effects of TEAD1 knockdown in immortalized smooth muscle cells.

overall_design: For siRNA experiments,SMCs were transfected with siRNAs targeting TEAD1 (Dharmacon ON-TARGETplus SMARTpool siRNA L-012603-00-0005;Horizon Discovery) or Silencer Select negative control siRNA (ThermoFisher 4390844) using Lipofectamine RNAiMax Transfection Reagent (ThermoFisher 13778150) according to manufacturer’s instructions and incubated for 12 hours post-transfection in serum free media followed by an additional 12 hours of recovery in SmBM supplemented media prior to RNA collection.

first: Daniel

middle: Y

last: Li


title: Vascular smooth muscle cell state trajectories mediate molecular mechanisms of coronary disease risk

summary: To investigate the genetic basis of SMC cell state trajectories that underlie the SMC component of CAD causality, we developed a dense timecourse single cell transcriptomic and epigenomic mapping of atherosclerosis in a murine disease model and here present complementary  high throughput spatial RNA in situ hybridization data to map transition cell states within the vascular wall.

overall_design: C57BL/6 mice were treated with tamoxifen at 7 weeks of age and started on high fat diet. This diet was continued for 16 weeks prior to spatial assays. High throughput in situ RNA hybridization assay Xenium 5k was performed using a series of mouse aortic tissue including aortic root, ascending aorta, brachiocephalic artery, peridiaphragmatic descending aorta, peri-renal aorta

first: Matthew

last: Worssam


title: Dissecting FOXA1 pioneering function by acute pharmacological degradation.

first: Lauren

last: Hargis

address: 10650 N Torrey Pines Road, BCC526

institute: Scripps Research Institute

summary: Pioneer factors control transcription by opening chromatin, but a lack of chemical tools has made it difficult to study pioneer activity with kinetic precision. We recently reported covalent chemical probes that remodel the genomic localization of FOXA1, a prototypical pioneer factor essential for the growth of many breast and prostate cancers. Here, we expand the chemical toolbox for FOXA1 by developing a dTAG-based system for small molecule-induced FOXA1 degradation. Coupling pharmacological perturbations to rapid measurements of chromatin structure and function, we find that FOXA1 exclusively initiates chromatin opening at its genomic binding sites, but, interestingly, this unidirectional outcome both activates and represses gene transcription depending on the chromatin environment surrounding FOXA1-binding sites. These effects apply to both androgen receptor (AR) target genes and other FOXA1 targets. Our findings thus uncover regulatory features that translate FOXA1 pioneering activity into both activation and repression of transcriptional programs critical for cancer growth.

overall_design:
ChIP-seq of FOXA1 in the prostate cancer cell line 22Rv1-dTAG-FOXA1 with and without FOXA1 degradation.
ChIP-seq of H3K27ac in the prostate cancer cell line 22Rv1-dTAG-FOXA1 with and without FOXA1 degradation.

first: Paige

middle: A

last: Barta

first: Yuxiang

last: Zhang

first: Rachel

last: Hayward

first: Benjamin

middle: F

last: Cravatt

first: Michael

last: Erb


title: Nutrigenomic Influence of a Curcumin-Supplemented High Glycemic Diet on Hippocampal Microvasculature in Male C57BL/6J Mice

city: Kannapolis

first: Dragan

last: Milenkovic

state: NC

address: 600 Laureate Way

department: Department of Food Bioprocessing & Nutrition Sciences

institute: North Carolina State University

summary:
Curcumin, a dietary polyphenol primarily derived from turmeric, has potent antioxidant and anti-inflammatory capabilities against diet-related chronic diseases. A high glycemic diet (HGD) has been shown to contribute to cognitive decline and dysfunction of murine brain microvasculature. The goal of our study was to elucidate the multi-genomic effects of curcumin on hippocampal microvessels in mice during consumption of a high glycemic diet. The HGD + Curc treatment influenced the differential expression of 1887 genes compared to HGD alone, of which 307 overlapped and were negatively correlated with the fold change expression of the HGD versus LGD comparison. These protein coding and non-coding gene targets modulated by HGD+Curc were involved in pathways related to neurodegeneration, oxidative phosphorylation, cell signaling, and cellular metabolism. The results from this study show that curcumin induces complex nutrigenomic modifications that could elucidate its neuroprotective effect against hippocampal microvascular dysfunction induced by a high glycemic diet.
The gene expression data of the low glycemic diet (LGD, 12% sucrose) and high glycemic diet (HGD, 34% sucrose) can be found in GEO dataset GSE185057

overall_design: Male C57BL/6J mice were fed a high glycemic diet (HGD, 34% sucrose) with 0.2% curcumin (HGD + Curc) for 12 weeks. Global transcriptomic profiles, including protein coding and non-coding genes, of laser-captured endothelial microvessels of the hippocampus (n=3 mice) were analyzed via microarrays. Bioinformatic tools were utilized to uncover networks and functional pathways of differentially expressed genes modulated by curcumin compared to HGD alone as well as interactivity between transcription factors and major curcumin metabolites via in silico docking analysis.

first: Emilio

last: Balbuena

first: Jennifer

last: Rutkowsky

first: Saivageethi

last: Nuthikattu

first: Amparo

last: Villablanca


title: Single-cell profiling of paired nasal brushing and tissue samples reveals distinct cellular landscapes and immune phenotypes

city: Seoul

first: Gyeongyeob

last: Kim

address: 50-1 Yonsei-ro, Seodaemun-gu

department: Otorhinolaryngology

country: South Korea

institute: Yonsei University College of Medicine

summary: Background: Since the COVID-19 pandemic, local immune responses in the nasal mucosa have become an area of growing research interest. In this context, studies using noninvasive nasal brushing (NB) samples have increased markedly. However, it remains unclear whether NB samples accurately reflect the immune landscape of the nasal tissue (NT). Objective: To directly compare the cellular composition and immune cell responses of NB and NT samples. Methods: Paired NB and NT samples were collected from the same anatomical site. The frequency, phenotype, and effector functions of epithelial and immune cells were analyzed using single-cell RNA sequencing and flow cytometry. Results: NB samples contained a significantly higher proportion of epithelial cells than NT samples, while fibroblasts, endothelial cells, and B cells were significantly less abundant. Within the epithelial compartment, NB showed an enrichment of ciliated and secretory cells, whereas basal cells were less frequent and glandular basal/secretory cells were rarely detected. Additionally, CD103+ tissue-resident memory T cells and CD56bright NK cells were more abundant in NB samples than in NT samples. Functional analyses revealed distinct T-cell effector profiles between the two sample types. Notably, SARS-CoV-2–specific T cells were significantly less frequent in NB samples than in NT. Conclusions: NB is well-suited for sampling cells located near the epithelial surface but captures fewer cells from deeper mucosal layers. Additionally, NB samples display distinct T-cell effector profiles and virus-specific T cell frequencies compared to NT. These findings highlight the importance of selecting sampling methods that align with the specific objectives of a study.

overall_design: To collect nasal brushing (NB) samples, flocked swabs (Pap brush; SGS, Daejeon, Korea) were inserted into the nasal cavity of the donors and rotated 10–20 times. The swabs were then placed in tubes containing Dulbecco's Modified Eagle's Medium/F-12 (1:1) (1X) media (Gibco, Grand Island, NY, USA). The tubes were vigorously vortexed to dislodge the cells and pelleted via centrifugation. Nasal tissue (NT) was mechanically dissociated, and single-cell suspensions were prepared using a Tumor Dissociation Kit (Miltenyi Biotec, Auburn, CA, USA) in combination with a gentleMACS dissociator (Miltenyi Biotec) and 70-µm cell strainers (SPL Life Sciences, Gyeonggido, Korea).

first: Sol

last: Lee

first: Min-Seok

last: Koo

first: Sungmin

last: Moon

first: Dachan

first: Hyung-Ju

last: Cho

first: Chang-Hoon

last: Rha


title: Photoacoustic Imaging-Guided Synchronously Targeted Thrombolysis and Neuroprotection of Acute Ischemic Stroke

city: Jinan

first: Donghai

last: Wang

state: Shandong

address: Wenhuaxi Road

institute: Qilu Hospital of Shandong University

summary: Acute ischemic stroke (AIS) is a major cause of disability and mortality worldwide, typically resulting from a thrombus that blocks cerebral blood flow and often leading to severe neurological impairment and irreversible brain damage. Current treatments focus on thrombolysis and neuroprotection, with recombinant tissue plasminogen activator (rt-PA) and edaravone (Eda) as key drugs. However, their therapeutic efficacy is constrained by poor targeting, leading to suboptimal drug delivery to the brain. Herein, we develop a biomimetic delivery system (PLEA) by hybridizing platelet membranes with liposomes, leveraging natural thrombus-targeting ability of platelet membrane to enhance drug delivery efficiency. Eda was encapsulated in the lipid bilayer of PLEA, while rt-PA was loaded into the core. PLEA (platelet membrane-liposome hybrid delivery system encapsulating Eda and rt-PA) effectively targeted thrombus sites, enabling localized drug delivery, synchronously enhancing thrombolysis and providing neuroprotection in a mouse model of AIS. Photoacoustic (PA) imaging was used to monitor clot formation and assess changes in intracranial blood flow and oxygen levels, highlighting its potential for evaluating therapeutic efficacy. These findings indicate that PA imaging-guided PLEA treatment represents a promising approach for precise stroke treatment.

overall_design: RNA-seq profiling of infarct mouse cortex tissues at 3 days after saline or PLEA nanoparticle treatment.

first: Mengtao

last: Han

first: Haoming

last: Zhong

first: Yuling


title: Obeticholic acid accelerates portal vein embolization-induced liver hypertrophy in rabbits by improving bile salt homeostasis

city: Maastricht

first: Frank

middle: G.

last: Schaap

address: Universiteitssingel 50

department: Department of Surgery

country: Netherlands

institute: Maastricht University

summary: Purpose: Obeticholic acid (OCA), an agonist of the bile salt-activated transcription factor farnesoid X receptor (FXR), accelerates liver growth following portal vein embolization (PVE) in rabbits, with largest effect seen on day 3 after PVE (volume gain of 56% vs. 26% in the control group). The aim of this research was to study underlying mechanisms.  Methods: Specimens from rabbits treated by oral gavage with OCA or vehicle (n=6-11/group) and subjected to PVE were analyzed, focusing on aspects of bile salt homeostasis, FXR-regulated gene expression in the ileum and liver, and their correlation with liver growth parameters.  Results: Following PVE, OCA treatment led to earlier normalization of serum total bile salts and reduced bile salt content in the non-embolized liver lobe. Serum levels of the hepatotoxic bile salt lithocholic acid were lower in OCA-treated rabbits on day 1 (p=0.002) and day 3 (p=0.03) post-PVE. Furthermore, serum lithocholic acid showed a strong negative correlation with liver volume gain (ρ=‑0.726, p<0.001) and with the number of proliferating hepatocytes (ρ=-0.718, p=0.009). OCA treatment induced expression of mitotic entry regulator CDC25B in the non-embolized lobe. Untargeted transcript analysis identified candidate signaling factors (C1Qa, BMP3, IHH) as potential mediators of the growth-enhancing effect of OCA in this model.  Conclusion: OCA improved bile salt homeostasis, which was associated with augmented hypertrophy of the non-embolized liver lobe in rabbits subject to PVE. OCA treatment may represent an approach to increase the efficacy of PVE in patients with a small future liver remnant planned for extended partial liver resection.

overall_design: Parallel-group, controlled animal intervention study: Rabbits pre-treated with OCA or vehicle (control) and subjected to PVE.

first: Xinwei

last: Chang

first: Pim

middle: B

last: Olthof

first: Han

last: Jin

first: Steven

last: Chau

first: Zita

last: Soons

first: Hans

last: van Eijk

first: Rowan

last: van Golen

first: Thomas

last: van Gulik

first: Michal

last: Heger

first: Peter

last: Jansen

last: Olde Damink


title: Nasal CD4⁺ tissue-resident memory T cells provide cross-protective immunity to influenza

city: Goteborg

first: Davide

last: Angeletti

address: Medicinaregatan 7a

country: Sweden

institute: University of Gothenburg

summary: CD4 tissue-resident memory T cells (TRM) are crucial adaptive immune components involved in preventing influenza A virus (IAV) infection. Despite their importance, their physiological role in the upper respiratory tract, the first site of contact with IAV, remains unclear. Here, we find that, after IAV infection, antigen-specific CD4 TRM persist in the nasal tissue (NT) compartment after infection and provide protection upon heterosubtypic challenge. Single cell RNA sequencing analysis reveals that NT CD4 TRM are heterogeneous and transcriptionally distinct as compared to their lung counterparts. Mechanistically, we demonstrate that the CXCR6-CXCL16 axis promotes CD4 TRM residency in the NT. Furthermore, we show that the NT of mice and humans contains a high frequency of Th17 CD4 TRM that aid in local viral clearance and in reducing tissue damage. Collectively, our results support a robust physiological role for nasal tissue CD4 TRM in local protection during heterosubtypic IAV infection.

overall_design: Here we have infected mice with IAV-PR8 and sacrificed them at 30 days after infection. For each experiment we collected nasal tissue and lungs and either sorted total CD4 TRM  (CD4+CD44+CD62L-CD69+) or  HA+CD4TRM or NP+CD4TRM cells. Sorted  total CD4 TRM from naive mice used as controls. cells from several mice were pooled. Within each experiment, different groups/organs were hashtagged in order to pool more samples together

first: Nimitha

last: Mathew

first: Romain

last: Gailleton

first: Lydia

last: Scharf

first: Karin

last: Schön

first: Josue

last: Enriquez

first: Hannes

last: Axelsson

first: Anneli

last: Strömberg

first: MatsNils

last: Lycke

first: Mats

last: Bemark

first: Ka-Wei

last: Tang


title: Combination of single-cell and bulk RNA-seq reveals changes in immune landscape in osteomyelitis

city: Changchun

first: zhenhua

last: zhu

address: Xinmin  Street 71#

institute: The First Hospital of Jilin University

summary: Objective: This study profiled the osteomyelitis immune micro-environment in depth, pinpointed driver genes and cell populations that fuel disease progression, and mined the data for actionable drug targets. Methods: We analyzed time-series transcriptomic sequencing data from mouse tibial osteomyelitis samples in dataset GSE168896. Fuzzy c-means clustering was applied to reveal gene sets linked to disease progression. Immune cell infiltration analysis was conducted through online tool ImmuCellAI-mouse. Furthermore, by leveraging single-cell sequencing data, we characterized immune cell subpopulations and pinpointed the key cell subtypes that exhibited in osteomyelitis mouse. Results: We identified six gene clusters exhibiting distinct temporal expression patterns and functional roles in osteomyelitis processes, such as leukocyte and lymphocyte activation, ossification. Single-cell sequencing analysis further revealed 7 distinct cellular subpopulations. Among these, M2-like macrophages demonstrated a significant increase following osteomyelitis. Arg+Sdc4+ Mac and Cxcl1+Ccl4+ Mac were new subpopulations of macrophages that emerged after osteomyelitis, the infiltration of Mif+Cd63+ Mac significantly increased. Besides, Cxcl2-Cxcr2 ligand-receptors contributed mostly in immune cells.

overall_design: Single cell RNA-seq profilling of bone marrow flox mouse, osteomylities flox mouse and Trim59-cKO mouse (flox_ctrl,flox_om,cko_om) two weeks after modeling.

first: Zhenhua

last: Zhu

first: Xiaopeng

last: Jing

first: Jun

last: Chen

first: Jie

last: Tan

first: Ji

last: Zeng

first: Zheng

last: Jin


title: Vascular smooth muscle cell state trajectories mediate molecular mechanisms of coronary disease risk [ChIP-seq]

first: Thomas

last: Quertermous

overall_design: H3K27ac, TEAD1, and CEBPB ChIPseq on immortalized (hTERT) cultured coronary artery smooth muscle cells in serum fed conditions with SmBm smooth muscle media (Lonza).

first: Li

last: Daniel Y

first: Quertermous

last: Thomas


title: Non-cytolytic viral vaccine vectors induce durable effector-memory CD8 T cell immunity by triggering type I interferon [scRNA-Seq]

first: DBM Bioinformatics

last: Core Facility

summary: Replication-deficient viral vector systems hold promise for CD8 T cell-based vaccination, but the molecular mechanisms accounting for platform-specific differences in immunogenicity remain ill-defined. Here we compared lymphocytic choriomeningitis virus- (rLCMV) and vesicular stomatitis virus-based (rVSV) single-cycle vectors to explore vector-specific features determining long-lived effector-memory CD8 T cell induction. rLCMV, a non-cytolytic vector, elicited more durable CD8 T cell responses and a higher proportion of effector-memory CD8 T cells than cytolytic rVSV. When rVSV was re-engineered to be non-cytolytic (rVSVMq), also this vector induced durable and effector-differentiated CD8 T cell memory, reminiscent of rLCMV-induced responses, and it afforded superior protection against Listeria challenge than rVSV. Improved CD8 T cell responses of non-cytolytic rVSVMq depended on an elevated type I interferon (IFN-I) response and its direct sensing by vaccination-induced CD8 T cells. Many rVSVMq-infected cells in the splenic marginal zone that were in contact with antigen-specific CD8 T cells expressed not only vectorized antigen but also IFN-I, suggesting that non-cytolytic viral vectors promote the integration of peptide-MHC and IFN-I signals during T cell activation. These mechanistic insights should help to refine vaccines aimed at eliciting durable and protective effector-memory CD8 T cell immunity.

overall_design: Single-cell RNA sequencing was performed on antigen-specific CD8 T cells isolated from C57BL/6 mice vaccinated with replication-deficient viral vectors. Mice received either rVSV-S1, rVSVMq-S1, or rLCMV-S1 vectors, and SARS-CoV-2 spike S1 epitope-specific CD8 T cells were sorted using MHC class I tetramers at day 7 and day 14 post-immunization. Each condition included 3 biological replicates which were labelled with hashtag oligos (HTOs) before being pooled prior to GEM generation. Experimental variables include vector type (rVSV, rVSVMq, rLCMV) and time point (day 7 vs. day 14).

first: Matias

last: Ciancaglini

first: Robin

last: Avanthay

first: Anna-Friederike

last: Marx

first: Tiago

last: Abreu-Mota

first: Davide

last: Finozzi

first: Jonas

last: Fixemer

first: Florian

last: Geier

first: Dominik

last: Burri

first: Ingrid

last: Wagner

first: Ilena

last: Vincenti

first: Mario

last: Kreuzfeld

first: Doron

last: Merkler

first: Gert

last: Zimmer

first: Daniel

last: Pinschewer


title: Non-cytolytic viral vaccine vectors induce durable effector-memory CD8 T cell immunity by triggering type I interferon [TCR-Seq]

overall_design: Single-cell RNA and TCR sequencing was performed on antigen-specific CD8 T cells isolated from C57BL/6 mice vaccinated with replication-deficient viral vectors. Mice received either rVSV-S1, rVSVMq-S1, or rLCMV-S1 vectors, and SARS-CoV-2 spike S1 epitope-specific CD8 T cells were sorted using MHC class I tetramers at day 7 and day 14 post-immunization. Each condition included 3 biological replicates which were labelled with hashtag oligos (HTOs) before being pooled prior to GEM generation. Experimental variables include vector type (rVSV, rVSVMq, rLCMV) and time point (day 7 vs. day 14).


title: A role for ETV1 and endothelial cell-derived extracellular vesicle microRNAs in priming fibroblast response to vesicle-bound FGF2

city: Chicago

first: Heidi

last: Yuan

address: 801 S Paulina St

institute: University of Illinois Chicago

summary: Communication between various cell types following wounding is paramount for proper healing and regeneration of injured tissue. Endothelial cells and fibroblasts are critical cellular players involved in cutaneous wound repair, yet their communication mechanisms are not well understood. It has previously been shown that extracellular vesicles derived from endothelial cells (ECEVs) induce dermal fibroblasts to express a gene signature correlated with FGF2-mediated cancer associated fibroblast (CAF) activation, under the control of transcription factor ETV1. In this report, we utilize loss-of-function studies to define the mechanistic role of ETV1 in conferring this ECEV-induced transcriptomic shift and functional change in fibroblasts. Additionally, we identify highly expressed ECEV microRNAs and examine their potential contribution to the ECEV mechanism through downstream gene modulation. In summary, we describe a plausible mechanism by which both ETV1 and top ECEV microRNAs promote a genotypic and phenotypic shift in dermal fibroblasts that have taken up ECEVs.

overall_design: Small RNA sequencing of extracellular vesicles isolated from primary human dermal microvascular endothelial cells (ECEVs) using a PEG-based isolation reagent.

first: Chen

last: Han

first: Lin

last: Chen

first: Sriram

last: Ravindran

first: Luisa

last: DiPietro


title: Therapeutic optimization of LIPA targeting to induce endoplasmic reticulum stress and cell death in Ovarian Cancer

city: San Antonio

first: Yidong

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

summary: Ovarian cancer (OCa) remains the most lethal gynecologic malignancy in the United States, with a five-year survival rate below 20%. Elevated basal levels of endoplasmic reticulum stress (ERS) have recently emerged as a therapeutic vulnerability in OCa. We have previously shown that the tris-benzamide ERX-41 can induce ERS and cancer cell death in OCa by targeting LIPA. In this study, using iterative structure–activity relationship–guided studies to enhance activity in OCa, we identified a more potent ERX-41 derived analogue, ERX-208. Importantly, ERX-208 consistently and significantly reduced cell viability in 23 OCa cell lines spanning five major histological OCa subtypes, with IC₅₀ values ranging from 50–100 nM, compared to ∼500 nM for ERX-41. Notably, ERX-208 showed minimal cytotoxicity toward normal ovarian surface epithelial cells, indicating selectivity. Mechanistic studies using RNA sequencing, Western blotting, RT-qPCR, transmission electron microscopy, and immunohistochemistry validated robust activation of ERS pathways upon ERX-208 treatment. Through in silico molecular docking simulation and confirmatory detailed site-directed mutagenesis, we identified that ERX-208 binds to LIPA over a broader interaction surface than ERX-41. ERX-208 induced apoptosis and suppressed colony formation in vitro in OCa cells. At the 10mg/kg dose, ERX-208 demonstrated favorable biodistribution, no observable toxicity and potent antitumor efficacy in vivo against established cell line derived xenograft (CDX), patient-derived xenograft (PDX), and patient-derived explant (PDE) models. Immunohistochemical analysis of treated tumors demonstrated changes in expression of proliferative marker (ki67, decreased) and the ERS marker (GRP78, increased). These findings support the clinical advancement of ERX-208 for the treatment of patients with OCa.

overall_design: RNA-seq profiling of SKOV3 cells treated with vehicle, and ERX-208 (1000 nM) for 48 hours

first: Suryavathi

last: Viswanadhapalli

first: Ratna

middle: K

last: Vadlamudi

first: Zhao

last: Lai


title: Developmental and transcriptional programs that define the initiation of the forelimb

city: Austin

first: Vighnesh

last: Ghatpande

address: 2500 Speedway

department: Molecular Biosciences

institute: University of Texas at Austin

summary: The vertebrate forelimb initiates as a localized swelling in the somatic lateral plate mesoderm (somatic LPM) in response to Tbx5-dependent transcription. The molecular pathways driving limb morphogenesis have been extensively studied but the steps directly preceding limb bud formation remain poorly characterized. To address this, we defined the temporal onset of forelimb initiation in mouse embryos using sequencing based high-throughput approaches (RNA-seq, scRNA-seq, ChIP-seq, and Ribo-ITP) benchmarked to known features in forelimb development, identifying four distinct stages. Using scRNA-seq at the onset of forelimb-specific transcription, we determined the transcriptional profile of the somatic LPM and identified signature genes that distinguish the nascent forelimb from other cell types. This group includes multiple genes involved in neural projection as well as cell adhesion. Interestingly, these genes are highly enriched for TBX5 binding sites, suggesting they are candidate early transcriptional targets of  TBX5. As TBX5 is essential for forelimb outgrowth, the identification of these genes suggests new mechanistic models for TBX5-driven limb initiation.

overall_design: Two 15 somite-stage Fgf10+/+ and two 16 somite-stage Fgf10-/- embryos (E8.75) were dissected in cold 1X DPBS . The heart and tissues anterior to somite 7 and posterior to somite 13 were dissected away. The resulting core of embryonic tissue included the forelimb field as well as other embryonic tissues present at this axial level. Single embryos were trypsinized and then filtered through a cell strainer, transferred into a 1% BSA coated tube and centrifuged for 10 minutes at 500g at 4°C. Cells were fixed as described using (Tran et al., 2022) and ~58-73k cells per embryo were stored in -80℃. scRNASeq libraries were prepared using the Parse Evercode WT Mini v2 kit according to the manufacturers protocol. The libraries were sequenced on an Illumina NovaSeq X Plus.

first: Can

last: Cenik

first: Steven

last: Vokes


title: Cancer Susceptibility to Stapled Oncolytic Peptides is Dictated by Membrane Cholesterol and Inflammatory Signaling

city: Boston

first: Michael

middle: James

last: Schmidt

state: MA

address: 360 Longwood Ave

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

summary: Relapsed and refractory cancers effectively overcome diverse modalities of cancer treatment, whose principal targets are nucleic acids and proteins. The plasma membranes of cancer cells represent an alternative and underutilized target, with the potential for membrane lysis to induce a rapid, pro-inflammatory cell death that circumvents the challenges of intratumor heterogeneity and immune evasion. Here, we repurposed StAMP51.2, a stapled Magainin II peptide previously optimized for selective membrane lysis of gram-negative bacteria, to target cancer cell membranes. Using PRISM, a high throughput cancer cytotoxicity screen, we identified cancer cells most vulnerable to StAMP51.2 and biomarkers of susceptibility, specifically reduced cholesteryl esters and elevated triacylglycerols. We validated this signature in a pair of sensitive (OCI-AML3) and resistant (K562) leukemia cell lines, correlating their differential responses to distinct lipidomic profiles. Susceptibility of OCI-AML3 cells in culture extended to the in vivo context, where StAMP51.2 suppressed leukemic growth in orthotopic and intraperitoneal models. To further characterize the mechanism of action, we undertook the challenge of generating StAMP51.2-resistant OCI-AML3 cells, which required four months of low-level exposure. Strikingly, drug-resistant OCI-AML3 cells recapitulated the lipidomic phenotype of naturally-resistant K562 cells. Transcriptomic analyses further revealed that lipid reprogramming was accompanied by pervasive downregulation of inflammatory signaling. Thus, in advancing StAMP51.2 as an oncolytic prototype, we uncovered an immune regulatory axis that links membrane integrity to inflammatory signaling.

overall_design: 3x10^6 OCI-AML3 sensitive and resistant cells, as well as K562 cells, were harvested by centrifugation and washed once with 1x PBS. Supernatants were discarded, and total RNA was isolated using the Qiagen RNeasy Mini Kit, following the manufacturer’s protocol. Purified RNA samples were sent to the Molecular Biology Core Facility (MBCF) at Dana-Farber Cancer Institute for library preparation and sequencing. Libraries were generated from 200 ng of total RNA using the Roche Kapa mRNA HyperPrep strand-specific kit according to the manufacturer’s guidelines, automated on a Beckman Coulter Biomek i7. Double-stranded DNA libraries were quantified using a Qubit fluorometer and Agilent TapeStation 4200. Dual-indexed libraries were pooled in equimolar amounts and initially shallow-sequenced on an Illumina MiSeq to assess library concentration and pooling accuracy. The final library pool was sequenced on an Illumina NovaSeq6000 with a target of 40 million 100 bp paired-end reads per sample. Sequencing reads were aligned to the hg38 human genome, and gene expression counts were obtained. Differential expression analysis was conducted using DESeq2 v1.22.1 (Love et al., 2014). The entire RNA-seq data analysis workflow was executed using the VIPER Snakemake pipeline (Cornwell et al., 2018).

first: Utsarga

last: Adhikary

first: Bethany

last: Tesar

first: Loren

last: Walensky