title: Robust T cell activation kills tumors regardless of T cell specificity

first: Tyler

last: Dao

address: 45 Carleton St

institute: Massachusetts Institute of Technology

summary: Immunotherapies putatively depend upon tumor-specific T cells. Here, we show how T cells can eliminate tumors without tumor-specificity via paracrine signaling. Activating unexhausted bystander non-tumor-specific T cells within tumors resulted in tumor elimination without conventional recognition-dependent mechanisms and in the absence of any tumor-specific TCRαâ T cell. Robust T cell activation recruited immune cells, utilized innate leukocytes, and triggered a tumoricidal combination of effector molecules and panoptotic pathways. Mechanistically, IFN-γ, TNF, and NO induced caspase-dependent death, recapitulating melanoma clearance in mice or human melanoma cell death in vitro. Gene expression signatures associated with this response in mice predicted survival among human melanoma patients. Thus, triggering productive T cell activation within tumors can be sufficient for immunotherapy, without needing to induce or rescue cancer-specific responses.

overall_design: B16.F10 tumors were seeded into OT-I chimeras (C57BL/6J CD45.2 mice with CD45.1 OT-I CD8+ T cells transferred in) and treated with relevant or irrelevant viral peptide, innate agonist and/or checkpoint blockade. Before treatment, 24 hours and 48 hours after treatment, tumors were harvested and procesed for scRNAseq via the 10x 3’ pipeline.

last: Ghirardelli Smith

first: Noah

middle: V

last: Gavil

first: Stephen

middle: D

last: O'Flanagan

first: Adam

middle: J

last: Rubin

first: Son

last: Nguyen

first: Matthew

middle: B

last: Watowich

first: Nuo

last: Liu

first: Eyob

last: Weyu

first: Clare

middle: F

last: Quarnstrom

first: Andrew

last: Soerens

first: Vineet

last: Goag

first: Pamela

last: Rosato

last: Krummel

first: Melissa

last: Geller

first: Jeffrey

last: Miller

first: Alessio

last: Giubellino

first: Vaiva

last: Vezys

first: Alex

last: Shalek

first: David

last: Masopust


title: ZFP90 deficiency exacerbates high fat diet-induced hepatic transcriptomic remodeling.

status: Public on Aug 05 2026

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

type: Expression profiling by high throughput sequencing

summary: RNA-seq identified 1,038 upregulated and 263 downregulated genes (fold-change > 2) in ZFP90 KO livers compared to those in WT livers. Pathway enrichment analysis revealed that ZFP90 deficiency upregulated programs involved in immunity, inflammatory responses, and lipid metabolism-specific cytokine-cytokine receptor interactions, NF-κB, and chemokine signaling. To explore the  mechanisms underlying ZFP90 deficiency-induced hepatic steatosis, we assessed hepatic gene expression based on RNA-seq data. ZFP90 deficiency increased mRNA levels of genes related to fatty acid uptake, inflammation, and fibrosis, indicating that ZFP90 loss accelerates MASLD progression through integrated inflammatory and metabolic pathways.

overall_design: To investigate the hepatic molecular changes, RNA-seq profiling was performed on liver tissues from  WT and ZFP90 knockout mice fed a  high-fat diet for 20 weeks.

last: Okuzaki


title: CD47 Blockade Reprograms the Monocyte-Macrophage Axis to Promote Inflammation Resolution in Atherosclerosis

city: Heidelberg

first: Murat

last: Kirtay

address: Im Neuenheimer Feld 410

department: Department of Cardiology, Angiology, and Pneumology

country: Germany

institute: Heidelberg University Hospital

summary: Targeting the CD47-SIRPα axis, a dominant “don’t-eat-me” signal, via innate immune checkpoint inhibition limits atherosclerosis in preclinical models and early clinical studies. However, how this pro-efferocytic intervention reshapes the immune landscape of atherosclerotic lesions remains incompletely understood. Using single-cell transcriptomics, we comprehensively characterized the transcriptomic profile of mouse CD45+ aortic leukocytes by CD47 blockade.

overall_design: We performed single-cell RNA sequencing of FACS sorted viable, aortic CD45+ leukocytes from the anti-CD47 or isotype control treated (6 weeks or 12 weeks) atherosclerotic (14 or 12 weeks of high-fat diet) low-density lipoprotein receptor-deficient (Ldlr-/-) mice.

first: Kai-Uwe

last: Jarr


title: Circulating miRNAs released by mammals with high and low mammary cancer incidence as indicators of human breast cancer risk

city: Bar Harbor

first: James

middle: Leonard

state: ME

address: 600 Main Street

country: USA

institute: The Jackson Laboratory

summary: Accurate assessment of breast cancer (BC) risk is critical to improve early detection strategies and patient prognosis. Our research group takes a comparative species approach to study BC risk by capitalizing on data from species with inherently low or high incidence of mammary cancer to supplement rare human samples. Circulating microRNAs (c-miRNAs) are a promising class of molecules that have the potential to serve as biomarkers for BC risk. The expression of these non-coding RNAs controls numerous cellular processes and their dysregulation is associated with various pathological conditions, including cancer. To explore whether c-miRNA expression profiles can identify individuals at high risk for BC, we conducted a multi-species pilot study. We analyzed biofluid samples (i.e., saliva, serum, and plasma) from patients with early-stage BC and patients with no prior history of cancer and mammosphere-derived epithelial cells (MDECs) from dogs (canines) and horses (equines), species with a relatively high and low incidence of mammary cancer, respectively. We identified 16 c-miRNAs that were upregulated in saliva from patients in the early-stage BC group when compared to the control patient group. Notably, 6 of these c-miRNAs (i.e., miR-361, miR-148b, miR-205, miR-186, miR-223, and miR-197) were also found to be secreted at higher levels by canine MDECs when compared to equine MDECs. Although assessment of these 6 c-miRNAs in a larger human cohort did not yield statistically significant results to confirm their use as BC risk indicators, our findings introduce a novel comparative framework in which species-to-species variation in cancer susceptibility may inform candidate biomarkers for human disease.

overall_design: In this study, we isolated RNA from biofluids (plasma, serum, and saliva) obtained from patients (N = 6) with breast cancer (n = 3) and without breast cancer (n = 3) and analyzed circulating miRNAs (c-miRNAs) present within the three biofluids types obtained from each patient using NanoString nCounter. The differentially expressed c-miRNAs were then compared with miRNAs released by primary mammary cells from mammalian species that intrinsically exhibit low or high incidences of mammary cancer. This comparison aimed to determine whether miRNA expression patterns associated with inherent mammary cancer risk across species correlate with those observed in patients at higher risk of developing breast cancer.

middle: L

first: Gerlinde

middle: R

last: Van de Walle

first: Mariza

last: DaCosta

first: Kimaya

middle: M

last: Bakhle

first: Lisa

last: Lai

first: Dawn

middle: E

last: Post

first: Rebecca

last: Harman


title: Landscape of plastid DNA breaks in Arabidopsis during development and environmental stimulus.

city: Hefei

first: Wenjie

last: Wang

state: Anhui

address: No. 130, Changjiang West Road

country: China

institute: Anhui Agricultrual University

summary: Exposure to external and internal environmental factors can lead to the genomic DNA modifications and even DNA breaks. While the landscapes of DNA break in eukaryotic nuclear genomes have been extensively studied, the frequencies and genomic loci of DNA breaks in endosymbiotic organelle remain poorly understood. Here, we employ DEtail-seq, a deep sequencing-based assay, to profile the DNA breaks in the Arabidopsis plastid genome. We find that plastid DNAs (ptDNA) in cotyledons and true leaves remains relatively stable during the juvenile stage but undergoes extensive breaks in older tissues. The break levels in seeds are significantly lower than those in leaves. Notably, rDNA regions experience more breaks, with a preference for the template strands. Additionally, we examine variations in ptDNA break patterns between the wild-type (Col-0) and mutants defective in DNA repair, replication, and transcription under varying environmental conditions, including light, temperature, and photoperiod. While wild-type plants maintain genome integrity under most tested conditions, the ptDNA damage repair and replication mutants why1/3/reca1, why1/3/polIb, and atrnh1c do not. Additionally, shortening the photoperiod alleviates ptDNA breaks in Col-0, with an even more pronounced effect in atrnh1c. This study provides a comprehensive and detailed view of ptDNA breaks, advancing our understanding of endosymbiotic organellar genome damage and repair mechanisms.

overall_design: First, the chloroplasts were isolated from tissues and embedded in an agarose plug, and lysed. Then, the ssDNA adaptor was ligated to the 3’ overhangs of DSBs in situ. After denaturation and sonication, the DEtail-seq library was prepared following an ssDNA library protocol.

first: Chengxia

last: Zheng

first: Kuan

last: Li

first: Qianwen

last: Sun


title: Loss of Sox10 prevents tumor initiation in vivo and induces luminal-to-basal reprogramming in Neu+ tumor cells

city: Ottawa

first: Luc

last: Sabourin

state: Ontario

address: 501 Smyth Rd

department: Cancer Research

country: Canada

institute: Ottawa Hospital Research Institute

summary: The SRY-HMG-Box transcription factor SOX10 plays a critical role in neural crest development, but its function in epithelial tumorigenesis remains unclear. Here, we identify SOX10 as a key regulator of tumor-initiating activity in Neu-driven mammary cancers. Genetic ablation of Sox10 in the luminal compartment of MMTV-Neu (NIC) mice resulted in delayed but normal mammary gland development. Sox10 deletion conferred a dose-dependent delay in tumor onset, with a complete loss of tumor initiation in Sox10-deficient luminal cells. CRISPR/Cas9-mediated Sox10 inactivation in Neu-transformed tumor cells led to reduced 3D invasion and diminished self-renewal in mammosphere assays. Established Sox10-null cell lines exhibited markedly impaired growth in orthotopic transplant models and failed to colonize lung tissue following tail vein injection, suggesting a loss of tumor-initiating capacity. Transcriptomic profiling revealed that Sox10-deficiency in Neu+ tumor cells induces a luminal-to-basal/stem-like shift and the downregulation of several genes associated with genetic networks regulating stemness. Collectively, these findings demonstrate that Sox10 is required for a permissive cell progenitor state for Neu-driven tumor initiation and that it is critical to sustain the invasive and self-renewing traits that drive tumor progression and metastasis.

overall_design: Bulk RNA-sequencing was performed on MMTV-Neu-IRES-Cre (MMTV-NIC) tumor derived cell lines. Mammary epithelial cells were isolated from endpoint tumors and knockout clones were expanded from a bulk CRISPR knockout population using guide RNAs targeting the Sox10 ORF in exon 3.

first: Samuel

last: Delisle

first: Brennan

last: Garland


title: RNA epigenetic and mitochondrial signatures of azacitidine response in higher-risk myelodysplastic syndromes

city: Patras

first: Argyro

last: Sgourou

address: Parodos Aristotelous 18

country: Greece

institute: Hellenic Open University

type: Non-coding RNA profiling by high throughput sequencing

summary: Azacytidine (AZA) treatment for higher-risk myelodysplastic syndromes (HR-MDS) has been extensively used in the clinic but its role goes beyond the DNA de-methylation and reactivation of critical genes silenced by DNA methylation. Among other mechanisms implicated to AZA mechanism of action, the documented partial restoration of chromatin structure and the recombinational repair, mainly attributed to the enhanced expression of long-noncoding RNAs highlight more stimulated epigenetic signatures. We present novel AZA effects in the epigenome that discriminate Responders from Non-Responders. Specific miRNA families significantly suppressed or upregulated, which promote the restoration of several critical cell pathways as a consequence; prostaglandin synthesis and regulation, ribosomal protein synthesis and function, glycolysis as well as response to starvation regression, offering overall unique benefits to MDS clinical phenotype of AZA Responders. Also, a trend for reduction of 2'-O-Methylguanosine (Gm) RNA modification in AZA Responders and differentiated expression patterns of other kinds of chemical modifications studied, such as methyladenosine (m6A), 5-Methylcytidine (5mC) and N1-Methyladenosine (m1A), between Responders and Non-Responders. Finally, AZA treatment significantly reduced copies of mitochondrial DNA (mtDNA) in both HR-MDS patient groups. Liquid chromatography combined with mass spectrometry (LC-MS/MS) was employed for the accurate assessment of various RNA modifications, mapping of AZA treatment-responsive regulatory pathways was performed by miRNA-NGS followed by a multi-layered bioinformatic pipeline integrating miRNA differential expression, gene set enrichment and network analysis. The precise number of mtDNA copies was evaluated by digital PCR assays. Our results support epigenetic and mitochondrial mechanisms of re-directing MDS neoplastic hematopoietic stem and progenitor cells (HSPCs) upon hypomethylating agents’ (HMA) therapy.  In patients who respond to AZA, HSPCs adapt by shifting toward glycolytic metabolism and restoring ribosomal activity while reducing mtDNA content and oxidative phosphorylation (OXPHOS) dependence, supporting survival and suppression of malignant progression. Non-Responders, however, despite experiencing mtDNA depletion, seem unable to coordinate metabolic reprogramming and consequently remain metabolically disadvantaged and less responsive to AZA-therapy.

overall_design: miRNA-seq of bone marrow mesenchymal cells of seven (n=7) matched pre and post Azacytidine treatment higher-risk myelodysplastic syndrome (HR-MDS) patients, categorized as Responders (n=3) or Non-Responders (n=4).

first: Theodoros

last: Nikolopoulos

first: Irene

last: Dereki

first: Vasiliki

last: Chondrou

first: Argyri

last: Chroni

first: Theodora

last: Alexiou

first: Katerina

last: Athanasopoulou

first: Eleftherios

last: Bochalis

last: Chatzilygeroudi

first: John

last: Zafeiropoulos

first: Ilias

last: Georgakopoulos-Soares

first: Kyriakos

last: Bourikas

first: Argiris

last: Symeonidis


title: Fluvastatin plus dipyridamole suppresses canine hemangiosarcoma growth in patient-derived xenograft models through lactate dehydrogenase-associated cholesterol/lipid metabolism

city: Sapporo

first: Keisuke

last: Aoshima

state: Hokkaido

address: Kita 18 Nishi 9

department: Faculty of Veterinary Medicine

institute: Hokkaido University

summary: Tumor cells exhibit distinct metabolic features such as the Warburg effect, consuming abundant glucose and producing large amounts of lactate even under aerobic conditions. Lactate dehydrogenase (LDH) plays a central role in regulating the intracellular lactate levels. Canine hemangiosarcoma (HSA) is a highly aggressive malignant tumor arising from vascular endothelial cells, and no effective targeted therapies have been established due to limited understanding of its molecular pathogenesis. The endothelial cells also rely on glycolysis for energy sources, although the involvement of lactate and LDH in HSA remains unknown. In this study, we investigated the role of lactate metabolism and LDH in HSA. The dual LDHA/LDHB inhibitor (R)-GNE-140 significantly suppressed HSA cell proliferation in vitro and reduced the expression of cholesterol-related genes. Knockout experiments showed that loss of LDHA, but not LDHB, was associated with decreased expression of cholesterol-related genes and reduced lipid droplet formation in HSA cells. Based on the association, we tested fluvastatin with or without dipyridamole to evaluate their anti-tumor efficacy using PDX models. While fluvastatin monotherapy had limited effect, the combined treatment significantly inhibited tumor growth. These findings suggest that LDH may link to cholesterol metabolism and that cholesterol pathway inhibition could offer a therapeutic opportunity in HSA.

overall_design: RNA-seq in a canine hemangiosaroma cell line treated with or without (R)-GNE-140

first: Tamami

last: Suzuki

first: Suzune

last: Tanaka


title: TOX sustains the longevity and multipotency of CD4 Tprog cells during chronic LCMV infection

city: Philadelphia

first: E

middle: JOHN

last: WHERRY

state: PA

address: 421 Curie Blvd,354 BRB II/III

department: Systems Pharmacology       and Translational Therapeutics,Institute for Immunology

institute: University of Pennsylvania

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Progenitor CD4 T cells (Tprog) develop during chronic viral infection and cancer and retain developmental plasticity to replenish Tfh and Th1 populations over time. Although considerable attention has been given to progenitor CD8 T cells, the distinct biological roles and multiple fates of CD4 T cells raise questions about the molecular circuitry controlling CD4 Tprog in settings of chronic stimulation. Here, we interrogated the impact of the HMG-box transcription factor (TF) TOX on the developmental flexibility of virus-specific CD4 T cells and the role of this TF in coordinating the transcriptional and epigenetic program of CD4 Tprog during chronic infection. These studies revealed key elements of CD4 Tprog biology that are central to sustaining T cell responses to persistent infection. First, TOX was dispensable for CD4 Tprog development but required for maintenance and function of these cells over time. Second, TOX promoted CD4 Tprog maintenance and survival by regulating expression of BIM and BCL-2. Third, loss of TOX in CD4 Tprog resulted in transcriptional and epigenetic dysregulation, highlighted by loss of TCF-1 pathway activity and gain of NFAT, NFkB, and RUNX-coordinated transcriptional circuitry. Finally, functional interrogation revealed a key role for TOX in the multipotent potential of CD4 Tprog to differentiate into Th1-like or Tfh-like cells during chronic viral infection. These data reveal a TOX-driven molecular network that sustains the core function of CD4 Tprog, highlighting a role for this TF not just in terminal exhaustion, but also in stem-like CD4 T cells that support development of downstream CD4 T cell subsets during persisting antigen stimulation.

overall_design: TOX KO and Ctrl NIP cells were co-transferred into congenically distinct recipient mice and  infected with LCMV (cl13 or Arm). Splenocytes were pooled, CD4 enriched, stained with surface antibodies, and Ctrl and KO NIP cells FACS sorted separately.   Sorted NIP cells were subjected to nuclei isolation and further processing for scRNA/ATAC-seq using the 10x Multiome protocol.

first: Stefan

last: Lundh

first: Josephine

last: Giles

first: Christopher

middle: H

last: Holliday

first: Amy

last: Baxter

first: Sasikanth

last: Manne

first: Katherine

middle: A

last: Dalton

first: Warren

middle: S

last: Pear

first: Martha

last: Jordan

last: Wherry


title: Cell-Specific DNA Methylation Markers in Plasma cfDNA Reveal Diagnostic Potential for Head and Neck Cancer

city: Shanghai

first: Tianci

last: Wang

address: NO. 800 Dongchuan Road

department: School of Biomedical Engineering

institute: Shanghai Jiao Tong University

type: Methylation profiling by high throughput sequencing

summary: Head and neck cancer is the seventh most common type of cancer worldwide. This study screened cell-specific methylation sites using WGBS data of healthy tissues (GSE186458), identifying 1,157 sites, including 146 hypermethylated and 1,011 hypo-methylated sites. By clustering adjacent sites within 150 bp, 11 composite methylation markers were obtained, showing strong cell type specificity. Validation in plasma cfDNA revealed marker fragments in cancer patients but not in healthy individuals, supporting their diagnostic potential.

overall_design: Targeted Bisulfite Sequencing of plasma cfDNA from head and neck cancer patients using selected methylation marker regions.

first: Fei

last: Han

first: Yuxuan

last: She

first: Mengju

last: He

first: Yicen

last: Ding

first: Qi

last: Mei

first: Yani

last: Kang


title: High resolution mapping of human skin chronic wound tissues biofilm infected using integrated single-cell, spatial and in situ analysis [Xenium]

city: Pittsburgh

first: Fabio

last: Muniz De Oliveira

address: 450 Technology Drive

institute: University of Pittsburgh

summary: Wound-edge skin section of patients with low or high-biofilm infections defined based on the biofilmQ analysis were evaluated using Xenium spatial transcriptomes custom 470-gene expression panel that included built-in human-, mouse-, and bacteria-specific probes, as well as positive and negative controls.

overall_design: Two formalin-fixed & paraffin-embedded (FFPE) 5µm section from patients biofilm chronic wound infected. Sections were mounted on Xenium-v1 slides and processed per the manufacturer’s FFPE workflow (deparaffinization, antigen retrieval/permeabilization). The probe hybridization, ligation, and rolling circle amplification were performed accordingly to the manufacturer’s protocol (CG000749 Rev B, 10x Genomics). Single-cell segmentation was performed using the Xenium Cell Segmentation Staining workflow, combining DAPI (nuclei), membrane protein markers, and intracellular RNA to identify cell boundaries; background autofluorescence was chemically quenched per protocol (CG000749 Rev B, 10x Genomics). Imaging and signal decoding were done using the Xenium Analyzer instrument (10x Genomics).

first: Pradipta

last: Banerjee

first: Piya

last: Das Ghatak

first: Surabhi

last: Singh

first: Subhadip

last: Ghatak

first: Chandan

last: K Sen

first: Sashwati

last: Roy


title: Spatial transcriptomics dataset of non-human primates

city: Richardson

first: Marisol

last: Mancilla Moreno

address: 800 w. Campbell Road

department: Neuroscience

institute: University of Texas at Dallas

summary: 10X genomics Visium spatial RNA sequencing was performed on 18 non-human primate dorsal root ganglia (16 Macaca fascicularis, 1 Macaca mulatta, Papio anubis)

sample_organism:
Macaca fascicularis
Macaca mulatta
Papio anubis

overall_design: Fresh frozen dorsal root ganglia from non-human primates were recovered from organ donors and tissue samples were processed with 10X VISIUM. Raw seq files were run with 10X SpaceRanger to determine gene counts per barcode.  Seurat was used for clustering.

first: Jayden

last: O’Brien

first: Nishka

last: Kuttanna

first: Khadijah

last: Mazhar

first: Asta

last: Arendt-Tranholm

first: Joseph

last: Lesnak

first: Michael

last: Wilde

first: Rainer

last: Haberberger

first: Jane

last: Brandon

first: Katherin

last: Gabriel

first: Seph

last: Palomino

first: Theodore

last: Price


title: Cardiac contractions shape endocardial identity by repressing veno-lymphatic fate.

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

institute: MPI for heart and lung research

summary: The heart responds to mechanical cues generated by its own contractions and by blood flow. Multiple cardiac features are shaped by these mechanical forces, including epicardial coverage, trabeculation, and valves. To further investigate the role of cardiac contractions during cardiac development, we developed a specific marker for endocardial cells that also labels the sinus venosus in zebrafish. We show that cardiac contractions are necessary to maintain endocardial identity during development by restricting venous fate to the sinus venosus and the lower atrium. Furthermore, we found that the ventricular endocardium, which expresses arterial markers, is also defined by mechanical forces. We identify Notch signaling as a key regulator of venous fate in the endocardium, via the repression of the transcription factors mafb and nr2f1a. In a therapeutic context, we show that cardiac contractions, not blood flow, are required to repress venous fate in the endocardium. We observe that myocardial infarction patients display a similar effect in regions with impaired contractility. Altogether, these results indicate that cardiac contractions regulate endocardial heterogeneity by repressing venous fate in developmental and pathological contexts, thereby advancing our understanding of the consequences of heart failure.

overall_design: Single-cell RNA sequencing was performed on kdrl:EGFP-positive cells FACS-sorted from pools of 48 hours post-fertilization (hpf) zebrafish embryos. Embryos were obtained from an incross of tnnt2a tc300b heterozygous animals. The tnnt2a mutants displayed a non-beating heart, while the wild-type and heterozygous siblings retained a beating heart and remained pooled. Single-cell libraries were prepared using a 10x Genomics Chromium single-cell 3′ gene expression protocol and sequenced on an Illumina NextSeq 2000.

first: Thomas

last: Juan


title: Intestinal BMP SMADs impart the mid-villus pattern via direct targeting of villus zonation genes and by controlling a transcription factor hierarchy [CUT&Run]

city: Piscataway

first: Alexandra

last: Logerfo

state: New Jersey

address: 145 Bevier Road

institute: Rutgers University

summary: Intestinal villus enterocytes exist in spatially restricted cell states, called zones, and continuously transdifferentiate as they migrate toward the villus tip. Bone morphogenetic protein (BMP) signaling through the BMPR1A receptor is required for zonation of enterocytes; however, the molecular mechanisms and transcriptional regulators downstream of BMP ligands/receptors are unclear. Using compound genetic mouse models and epigenomic techniques, we find that SMAD1 and SMAD5 are necessary for activation of middle villus zone genes via direct binding and control of a transcription factor hierarchy. Spatial transcriptomics reveal a homeotic-like shift in the villus pattern of SMAD1/SMAD5 double mutants, with the villus bottom and tip domains expanding at the expense of the middle. Surprisingly, SMAD1 and SMAD5 are not required for regulation of villus tip identity, which is dependent on SMAD4. Epigenomics approaches identify a mechanism for villus patterning in which SMAD1/5 directly activate some mid-villus genes and control others via a transcription factor hierarchy, including a SMAD-regulated transcription factor, TBX3, as a downstream effector of villus zonation.

overall_design: CUT&RUN of SMAD1 or SMAD4 in murine proximal small intestine villus epithelium. CUT&RUN of IgG in equivalent villus epitheum was used as a control for each library.

first: Jahangir

last: Iqbal

first: Rachel

last: Ofer

first: Sneha

last: Kandalgaonkar

first: Rahma

last: Rizly

first: Kiranmayi

last: Vemuri

first: Lei

last: Chen

first: Martin

last: Matzuk

middle: P

last: Verzi


title: Intestinal BMP SMADs impart the mid-villus pattern via direct targeting of villus zonation genes and by controlling a transcription factor hierarchy [ATAC-seq]

overall_design: Intestinal organoids were grown in 0H, 24H, 48H, or 72H of BMP2 and collected for ATAC-seq to assess chromatin accessibility changes across timepoints of BMP exposure.


title: Intestinal BMP SMADs impart the mid-villus pattern via direct targeting of villus zonation genes and by controlling a transcription factor hierarchy [Spatial Transcriptomics]

overall_design: Spatial transcriptomic analysis of control and SMAD1/5 iDKO intestine (jejunum) tissues was performed using Visium HD.


title: Intestinal BMP SMADs impart the mid-villus pattern via direct targeting of villus zonation genes and by controlling a transcription factor hierarchy [RNA-seq]

overall_design: RNAseq: differential gene expression analyses using proximal small intestinal epithelium tissue from SMAD and TBX3 mutants vs control; four separate experiments were conducted: SMAD1/5 iDKO vs control (n=3 per genotype), SMAD1/4/5 vs SMAD1/5 vs control (n=2-5 per genotype), SMAD4 KO vs control (n=2 per genotype), and TBX3 KO vs control (n=3 per genotype).


title: Under Pressure: A unique mechanoresponsive mechanism of body site-specific keratin regulation in palmoplantar epidermis

city: Ann Arbor

first: Michigan

middle: CDB

last: Bioinformatics

state: MI

address: 109 Zina Pitcher Pl

department: Cell & Developmental Biology

institute: University of Michigan

summary: The palmoplantar epidermis, in adapting to the exceptional mechanical strain it bears during locomotion, is molecularly and histologically distinct from other body sites. However, the mechanisms specifying and maintaining its distinct identity remain incompletely defined. Here, we identify the type 1 keratin 9 (KRT9/K9), a protein uniquely expressed in the palmoplantar epidermis, as a key modulator of mechanosensitive YAP1 signaling in response to postnatal mechanical compression. K9 loss-of-function variants, as observed in human KRT9 palmoplantar epidermal differentiation disorder (KRT9-pEDD), results in aberrant YAP1 subcellular partitioning and elevated levels of the stress-induced keratin 16 (KRT16/K16). Krt9 null mice recapitulate these molecular phenotypes as early as postnatal day 3 (P3). We further identify dynamic, YAP1-dependent regulation of Krt9/K9 and Krt16/K16 during early postnatal development and in response to ex vivo mechanical compression, highlighting the role of mechanical stress in epidermal specification. Mechanistically, K9 interacts with the YAP1 binding protein 14-3-3σ and sequesters YAP1 in the cytoplasm, inhibiting its transcriptional activity; these functions are disrupted by KRT9-pEDD-causing variants in K9. Notably, genetic or pharmacological inhibition of YAP1 ameliorates palmoplantar keratoderma in Krt9 null mice. These findings provide insight into the influence of mechanical force in specification and maintenance of palmoplantar skin and suggest new therapeutic interventions for inherited palmoplantar epidermal differentiation disorders (pEDDs).

overall_design: RNA-seq expression profiling of Krt9-/- and WT mouse paws at postnatal day 0 and day 3

first: Sarah

middle: N

last: Steiner

first: Pierre

last: Coulombe

first: Craig

last: Johnson


title: Pertussis toxin-induced lymphocytosis enhances anti-tumor immune environments and improves the anti-PD1 treatment response in a squamous cell carcinoma model.

city: Suwon

first: Truc

middle: Do Thanh

last: Nguyen

state: All

address: 2066 Seobu-ro, Jangan-gu

country: South Korea

institute: Sungkyunkwan University School of Medicine

summary: Elevation of the neutrophil-to-lymphocyte ratio (NLR) in cancer patients predicts a worse prognosis, and NLR is a good discriminator in response to anti-tumor immune checkpoint inhibitors. However, the therapeutic potential of NLR normalization to enhance the efficacy of anti-tumor immunotherapy has not been investigated. In this study, we chose pertussis toxin (PTX) as an agent to induce lymphocytosis and lower NLR. PTX decreased NLR in squamous cell carcinoma (SCC)-tumor-bearing mice and shifted the tumors from low to high immune scores. PTX-induced elevation of CXCL9 led to lymphocytosis and increased immune cell infiltration in tumor tissues. The combination treatment with PTX and anti-PD1 antibody significantly suppressed in vivo SCC tumor growth, compared to anti-PD1 treatment alone. The combination treatment induced a larger proportion of T cells in the tumor microenvironment, and these findings were associated with an increase in terminally differentiated CD8 T cells and their augmented Ki-67 expression. In addition, tumor-specific IFN-γ production was augmented in animals treated with anti-PD1 antibody and combination treatments, but not with PTX alone. In summary, PTX can induce high lymphocyte infiltration into tumor tissue, leading to the NLR normalization and a favorable immune environment for immune checkpoint inhibitors.

overall_design: Tumor tissues and draining lymph nodes were collected from mice at a defined tumor volume, dissociated into single cells using Liberase, and processed through the 10x Genomics Chromium Next GEM Single Cell 3′ v3.1 workflow. Libraries were sequenced on an Illumina NovaSeq 6000, and data were analyzed using Cell Ranger (v5.0.0) and Seurat (v5.3.0) to profile cellular heterogeneity and gene expression changes.

first: Jae-Keun

last: Cho

first: Kyungmin

last: Lee

first: Da-Yong

last: Shin

first: Woong-Yang

last: Park

first: Se jin

last: Im

first: Han-Sin

last: Jeong


title: Cohesin loop extrusion tethers DNA replication forks to drive their slowing and reversal II

city: Madrid

first: Daniel

last: Gimenez

address: Calle de Melchor Fernández Almagro, 3

country: Spain

institute: CNIO

summary: DNA replication forks challenged by genotoxic agents have a high degree of plasticity to ensure their stability, DNA damage tolerance and complete genome duplication. How genome architectural factors influence this response is poorly understood. Here, we investigated the role of cohesin and its different functions by the use of auxin-inducible degrons (AID) and separation of function mutants. With a newly-developed Micro-C based technique to capture chromatin contacts at nascent DNA (Repli-C), we describe that loop-extruding cohesin helps tethering replication forks in proximal chromosomal regions, including those departed from adjacent replication origins. Replication stress strengthens these contacts by promoting cohesin stabilization at forks. This process promotes replication fork reversal and active fork slowing, by preventing PRIMPOL action on ssDNA. These findings reveal how cohesin loop extrusion, mainly implicated in genome organization, is employed upon replication stress to restrict fork progression, mediating fork plasticity and protecting genome stability.

overall_design: Repli-C analysis to map chromatin contacts at replicating DNA regions in HCT116 cells. Repli-C is a Micro-C-based methodology that captures genomic contacts specifically at nascent DNA by pulldown of EdU-labeled replicating DNA followed by MNase digestion and proximity ligation. Cells were labeled with EdU for 15 minutes, treated with auxin-inducible degron (AID) system to deplete cohesin subunits (SMC1) and re-expression of separation-of-function SMC1 mutants (SMC1-WT and SMC1-4E loop extrusion-deficient mutant), and exposed to replication stress (2 mM hydroxyurea for 2 hours).

first: Gonzalez-Acosta

last: Daniel

first: Giménez-Llorente

first: Rodrigues

last: Melani

first: Aouami

last: Moses

first: Barroso-Gomila

last: Orhi

first: Muñoz

last: Javier

first: Cuadrado

last: Ana

first: Losada

first: Lopes

last: Massimo


title: Cohesin loop extrusion tethers DNA replication forks to drive their slowing and reversal

overall_design:
Micro-C analysis to investigate chromatin organization and loop extrusion dynamics mediated by cohesin in HCT116 cells. Cells were treated with auxin-inducible degron (AID) system to deplete cohesin subunits (SMC1, NIPBL) and re-expression of separation-of-function SMC1 mutants (SMC1-WT and SMC1-4E loop extrusion-deficient mutant) following endogenous SMC1 depletion

Micro-C analysis was used to investigate chromatin organization and cohesin-mediated loop extrusion dynamics in HCT116 cells. Cells were treated using the auxin-inducible degron (AID) system to deplete WAPAL and Sororin. Additionally, cells were treated with HU in the presence or absence of cohesin.

last: Gonzalez-Acosta

last: Giménez-Llorente

first: Melani

last: Rodrigues

first: Moses

last: Aouami

first: Orhi

last: Barroso-Gomila

first: Javier

last: Muñoz

first: Ana

last: Cuadrado

last: Losada

first: Massimo

last: Lopes


title: Targeting GL-Lect driven endocytosis to suppress cell plasticity in breast cancer

city: Milan

first: Sara

last: Sigismund

address: via adamello 16

country: Italy

institute: European Institute of Oncology

summary: To gain molecular insights into the hyperbranching phenotype mediated by EPN3 overexpression, we performed scRNA-seq on viable EpCAM-positive cells isolated from pooled  mammary glands of 18-week-old EPN3-KI and control mice

overall_design: Following mammary gland digestion, epithelial cells were cleaned from non-epithelial contaminants and FACS-sorted for EpCAM positivity, in presence of a viability dye (live/dead viability stain, BV-510).

first: Amir

last: Fardin

first: Chiara

last: Tordonato


title: Peripheral glia drive the initiation of cutaneous squamous cell carcinoma

city: Zurich

first: Adrian

last: Salas-Bastos

address: Winterthurerstrasse 190

department: Institute of Anatomy

country: Switzerland

institute: University of Zurich

summary: Although tumor innervation is known to promote cancer progression, underlying mechanisms remain poorly understood and have mostly been linked to axonal signaling. Here, we identify peripheral glia as critical drivers of cutaneous squamous cell carcinoma (cSCC), the second most common skin cancer in humans. Tumor-associated glial cells (TAGs) resemble embryonic Schwann cell lineage stages, are abundant in the stroma of premalignant lesions and established murine and human cSCC, and are essential for tumor formation. TAG activation in premalignant lesions is triggered by UV-induced anti-inflammatory macrophages, which in turn are polarized by TAGs into pro-tumorigenic FcεRIα⁺ macrophages, key components of the cSCC microenvironment. Consequently, TAG depletion reduces FcεRIα⁺ macrophages, cancer-associated fibroblasts, and epithelial-mesenchymal transition in keratinocytes, thereby impairing cSCC initiation by disrupting intercellular communication required for tumor development. As most solid tumors are innervated and harbor peripheral glia, our findings reveal TAGs as previously unrecognized regulators of tumor initiation with relevance beyond skin cancer.

overall_design: 2cmX2cm tissue of day-5 irradiated skin from a wild type mouse was collected and digested to obtain a single cell suspension, which was then analysed using scRNA-seq BD Rhapsody Platform

first: Lukas

last: Sommer

first: Sofia

last: Micheli


title: MAFF as a Key Transcriptional Regulator of Ferroptosis via Iron Homeostasis and Fatty Acid Synthesis

city: Headington

first: Eui Jung

last: Moon

address: Old Road Campus Research Building, Roosevelt Drive

department: Department of Oncology

country: United Kingdom

institute: University of Oxford

summary: Ferroptosis is an iron-dependent form of regulated cell death driven by lipid peroxidation. In this study, we identify the transcription factor v-maf musculoaponeurotic fibrosarcoma oncogene homolog F (MAFF) as a key regulator that promotes breast cancer progression while simultaneously sensitizing tumor cells to ferroptosis. Integrated RNA-sequencing and chromatin immunoprecipitation (ChIP)-sequencing revealed that MAFF directly regulates genes involved in iron and fatty acid metabolism. MAFF enhances intracellular iron availability by transactivating SLC11A2 and NCOA4, expanding the labile iron pool essential for ferroptotic signaling. In parallel, MAFF represses CPT2, FASN, and SCD1, reprogramming lipid metabolism to favor the accumulation of polyunsaturated fatty acids (PUFAs) over monounsaturated fatty acids (MUFAs), thereby increasing lipid peroxidation susceptibility. T

overall_design: RNA from MDA-MB-231 with MAFF knockdown was collected by using Rneasy kit (Qiagen). RNA samples were sent to Novogene (Cambridge, UK) for library preparation and sequencing. Sequencing was performed by Novoseq 6000.

first: Nuria

last: Vilaplana Lopera

first: Jiyoung

last: Kim


title: Impeding two p53-pathways fosters HCC initiation via MTHFD1L-RNA m6A-elicited autonomous cell growth and immune evasion

city: Indianapolis

first: Gang

last: Peng

state: IN

address: 635 Barnhill Dr

department: Medical & Molecular Genetics

institute: Indiana University

summary: Background and Aims: HCC develop from mature hepatocytes in chronic liver injuries, during which dynamic regulation of p53 activity is crucial for ensuring normal liver regeneration while preventing HCC initiation. Yet, it remains unaddressed if and how impairing p53 response might trigger HCC initiation. Two p53 regulatory pathways, ribosomal proteins (RPs)-MDM2 and 14-3-3-MDMX, are shown to activate p53 in response to multiple stresses. We investigated the role of the p53-pathways in HCC initiaition, and determined how dynamic p53 activation is required for preventing HCC initiation. Approach and Results: We generated double knock-in (DKI) mice harboring impaired RPs-MDM2- and 14-3-3-MDMX- p53 pathways, and employed DEN and NASH-induced HCC mouse models. Correlation between the p53-pathways and HCC prevention in human cirrhosis was also assessed. We demonstrated that carcinogen- or unhealthy diet-induced HCC initiation is accelerated in DKI mice, and the p53- pathways are activated in human cirrhotic livers. We futher identified a one-carbon metabolism (1CM) enzyme methylenetetrahydrofolate dehydrogenase 1 like (MTHFD1L) as the p53-suppressed player in HCC initiation. MTHFD1L promotes HCC initiation by enhancing autonomous cell growth and immune evasion of HCC progenitor cells (HcPCs). With Nanopore RNA sequencing, we unveiled that MTHFD1L fulfills these bi-functions by fueling methionine cycle that produces methyl groups to maintain mRNA m6A of cell growth mediators Prickle1 and Snail, and B2m, a light chain of MHC-I critical for antigen presentation. Conclusions: Stress-MDM2/MDMX-p53-MTHFD1L-RNA m6A pathways are crucial for preventing HCC initiation by reversing 1CM reprogramming-boosted cell autonomous growth and immune evasion.

overall_design: Knock-in mice with weakned p53 pathways, plus human liver samples, to test how loss of p53 control promotes early liver cancer.


title: GeoMx GeoMx-DSP Toxic Lipid-induced Epigenetic Activation of ICAM1 in Liver Sinusoidal Endothelium Regulates Myeloid-Driven Fibro-inflammatory Response in MASH

city: Rochester

first: Alexandra

last: Krivonos

state: MN

address: 200 1st St SW

department: Quantitative Health Sciences

institute: Mayo Clinic

summary: Background: Liver sinusoidal endothelial cells (LSECs) acquire a proinflammatory phenotype in metabolic dysfunction-associated steatohepatitis (MASH), characterized by elevated adhesion molecules and inflammatory mediators—a process termed lipotoxic endotheliopathy. However, the molecular drivers of this transformation remain incompletely defined. Methods: We employed complementary models of lipotoxicity and MASH, including palmitate-treated primary human LSECs (in vitro), cultured precision-cut liver slices from normal human and mice liver with MASH-inducing media as well as MASH mice (ex vivo), and diet-induced MASH models (in vivo). Results: GeoMx digital spatial profiling of human MASH livers revealed enriched proinflammatory and fibrogenic signaling between LSECs and myeloid cells. Among the top upregulated genes and ligand-receptor pairs was ICAM1, whose expression correlated with disease severity and was increased in human MASH by immunostaining. ATAC-seq on primary mouse LSECs showed enhanced chromatin accessibility at the Icam1 promoter in MASH. Chromatin immunoprecipitation confirmed enrichment of the active epigenetic mark H3K27ac and BRD4 binding at the ICAM1 promoter in human LSECs under lipotoxic stress. Mechanistically, we identified the GSK3β/c-Jun/BRD4 axis as a key regulator of ICAM1 induction in LSECs. In vivo, ICAM1-neutralizing antibody or endothelial-specific epigenetic suppression reduced hepatic inflammation, injury, and fibrosis in MASH mice. Conclusion: ICAM1 is epigenetically upregulated in LSECs during lipotoxic stress and promotes myeloid cell recruitment in MASH. Targeting the epigenetic regulation of ICAM1 may offer a novel therapeutic strategy for treating human MASH.

overall_design: FFPE slides from patients with healthy donor, steatosis or MASH were labeled with von Willebrand Factor (VWF)for LSEC marker, CD68 for macrophage marker and Elastase/ELA2 for neutrophil marker. SYTO83 orange fluorescent (Thermo Fisher, S11364) was used for nucleic acid staining. Regions of interest (ROI) were selected, and segmentation was performed based on cell positivity for CD68, VWF, ELA2, or areas within the ROI negative for all three markers which was labeled as “else.” Each of the segments were also denoted as portal/periportal area for zone 1, central/pericentral area as zone 3, and between periportal and pericentral area as zone 2.

first: Qianqian

last: Guo

first: Nantawat

last: Satthawiwat

first: Akitoshi

last: Sano

first: Chady

last: Meroueh

first: Asma

last: Hamdi

first: Xin

last: Dai

first: Khaled

last: Warasnhe

first: Alexander

last: Washington

first: Patrick

last: Starlinger

first: Alex

first: Sheng

last: Cao

first: Enis

last: Kostallari

first: Johan

middle: W

last: Jonker

first: Bart

last: van de Sluis

first: Feda

last: Hamdan

first: Samar

last: Ibahim


title: Integrative tissue analysis of men with prostate cancer VIII

city: Bethesda

first: Adam

middle: G.

last: Sowalsky

state: MD

address: 37 Convent Drive Building 37 Room 1062B

department: Genitourinary Malignancies Branch

institute: National Cancer Institute

summary: Prostate cancer is readily curable if detected early. The overall goal of this study is to conduct integrative profiling of tumor genomics and transcriptomics.

overall_design:
Whole transcriptome sequencing of longidinally collected and laser capture microdissected prostate tissues and buffy coat samples from patients with newly-diagnosed prostate cancer.

***************************************************************
Raw files for human/patient samples are being made available in dbGaP (https://www.ncbi.nlm.nih.gov/gap/) (accession ID phs001813) for controlled access to the personally identifiable sequence data.
***************************************************************

middle: G


title: In vivo screen for osteoclast derived osteogenic factors using non-resorptive osteoclasts in zebrafish bone

city: Atlanta

first: Katrin

last: Henke

state: GA

address: 21 Ortho Lane

department: Orthopaedics

institute: Emory University

summary: Bone homeostasis requires the balanced action of bone forming osteoblasts and bone resorbing osteoclasts and is maintained through local as well as systemic factors. Loss of osteoclast resorptive activity leads to development of osteopetrosis with increased bone volume but reduced skeletal integrity. Work on osteopetrotic mouse models has identified a role for osteoclast released factors in the regulation of bone anabolism, but further analysis of these factors is hampered by the general essential function of osteopetrosis genes in development and the inability to isolate primary osteoclasts in sufficient numbers. Here we generated a zebrafish osteopetrosis model through CRISPR mediated knockout of chloride voltage-gated channel 7 (clcn7) which is adult viable and shows increased vertebral bone thickness. Isolation of primary osteoclasts from wildtype and clcn7 mutants by FACS followed by transcriptional profiling, identified upregulation of genes involved in chemotaxis and cytokine signaling in clcn7 deficient osteoclasts. Global transgenic overexpression of a subset of the upregulated genes further identified distinct, but positive effects of the cytokines csf3b, cxcl19 and the glycosylated peptide progranulin 1 (grn1) on skeletal parameters, while the cytokine ccl35.1 negatively impacted bone volume. Our findings suggest that the concerted function of these cytokines plays an important role in the regulation of bone homeostasis and that individual cytokines affect regional areas and distinct parameters of vertebral bone form and differentiation.

overall_design:
RNA-seq profiling of dsRed positive cells isolated via FACS from 10wpf ctsk:dsRed transgenic clcn7-/- mutants and WT siblings (zebrafish).

Grant ID: R21 AR077768
Grant title: Talking Back: leveraging dysfunctional osteoclasts to identify novel pathways of osteoclast-osteoblast communication
PI: Julia F. Charles
Funding source: NIAMS, NIH

first: Julia

last: Charles


title: Landscape of plastid DNA breaks in Arabidopsis during development and environmental stimulus II

city: Hefei

first: Wenjie

last: Wang

address: No. 130, Changjiang West Road

institute: Anhui Agricultrual University

summary: Exposure to external and internal environmental factors can lead to the genomic DNA modifications and even DNA breaks. While the landscapes of DNA break in eukaryotic nuclear genomes have been extensively studied, the frequencies and genomic loci of DNA breaks in endosymbiotic organelle remain poorly understood. Here, we employ DEtail-seq, a deep sequencing-based assay, to profile the DNA breaks in the Arabidopsis plastid genome. We find that plastid DNAs (ptDNA) in cotyledons and true leaves remains relatively stable during the juvenile stage but undergoes extensive breaks in older tissues. The break levels in seeds are significantly lower than those in leaves. Notably, rDNA regions experience more breaks, with a preference for the template strands. Additionally, we examine variations in ptDNA break patterns between the wild-type (Col-0) and mutants defective in DNA repair, replication, and transcription under varying environmental conditions, including light, temperature, and photoperiod. While wild-type plants maintain genome integrity under most tested conditions, the ptDNA damage repair and replication mutants why1/3/reca1, why1/3/polIb, and atrnh1c do not. Additionally, shortening the photoperiod alleviates ptDNA breaks in Col-0, with an even more pronounced effect in atrnh1c. This study provides a comprehensive and detailed view of ptDNA breaks, advancing our understanding of endosymbiotic organellar genome damage and repair mechanisms.

overall_design: First, the chloroplasts were isolated from tissues and embedded in an agarose plug, and lysed. Then, the ssDNA adaptor was ligated to the 3’ overhangs of DSBs in situ. After denaturation and sonication, the DEtail-seq library was prepared following an ssDNA library protocol.

first: Chengxia

last: Zheng

first: Kuan

last: Li

first: Qianwen

last: Sun


title: Landscape of plastid DNA breaks in Arabidopsis during development and environmental stimulus [2]


title: Landscape of plastid DNA breaks in Arabidopsis during development and environmental stimulus


title: Transcriptional reprogramming in immune cells of HTLV-1 asymptomatic carriers and HAM/TSP patients following antiretroviral therapy

city: Newark

last: Lemenze

address: 185 South Orange Ave

institute: Rutgers

summary: Human T-cell lymphotropic virus type 1 (HTLV-1) causes HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP), a chronic, immune-mediated spinal cord disease in which peripheral immune activation is thought to fuel central neuroinflammation. To delineate cell type-specific programs linked to disease, we performed single-cell RNA sequencing on the peripheral blood mononuclear cells (PBMCs) of the HTLV-1 infected asymptomatic carrier (AC) and HAM/TSP patient. Differential expression and pathway analyses localized that the most pronounced transcriptional divergence to the monocyte compartment, revealing coordinated remodeling of macrophage classical (M1-like) activation, IL-10-regulatory signaling, leukocyte adhesion/diapedesis, and trans-endothelial migration pathway, and cytokine storm-related modules. Ingenuity Pathway Analysis highlighted overlap with multiple sclerosis-associated signaling, consistent with myeloid-driven neuroinflammation and potential blood-spinal cord barrier involvement. In an independent validation phase, we assayed the selected subsets of up- and down-regulated monocyte genes in AC and HAM/TSP participants enrolled in a randomized, open-label pilot trial in Brazil. Expression of several inflammatory markers was higher at baseline in HAM/TSP and decreased during dolutegravir (DTG) therapy, paralleling reductions in HTLV-1 proviral load (PVL) in the DTG arm. Collectively, these data suggest that antiviral strategies may modulate immune cell transcriptional programs that help reduce HTLV-1 PVL.

overall_design: PBMCs were thawed, washed, and resuspended in PBS + 1% BSA. Cells were counted on a Countess 3 (Thermo Fisher). Two 96-well round-bottom plates were prepared with 1.25 × 10^5 cells/well. One plate was incubated with exosomes (30 µg/well) and the other left untreated for 18 h at 37 °C. After incubation, ~20,000 cells from each condition were loaded into HIVE CLX collectors per manufacturer’s instructions (Honeycomb Bio) and stored at -80 °C until processing.

first: Herrera

last: Bobby Brooke

first: Jain

last: Pooja


title: ALDH2 inhibition reprograms tubular epithelial cell metabolism and promotes renal injury susceptibility

city: Ji Nan

first: Guo

last: jialin

address: 107 Wenhua Xilu, Jinan, Shandong, China

institute: Shandong University

summary: Tubular epithelial cells (TECs), viewed as the initiating factor in renal fibrosis, undergo a transition from re-absorptive to pro-fibrotic phenotype during chronic kidney disease (CKD) progression. Serving as a critical energy source, Free fatty acid (FFA) metabolism disruption results in injured TECs. Nevertheless, mechanisms underlying pathological FFA metabolism in injured TECs remain unclear. We observed an inverse correlation between ALDH2 expression in TECs and lipid deposition in the renal tissues from CKD patients. To determine whether ALDH2 protects against fibrosis via regulating FFA metabolism, we generated TEC–specific ALDH2 knockout (Aldh2TEC-KO) mice, and observed exacerbated fibrosis and lipid deposition in the renal tissues of Aldh2TEC-KO mice in two different CKD models. Mechanically, we verified that ALDH2 facilitated the formation of PPARα/RXRα heterodimer via nuclear translocation, while ALDH2 deficiency hindered that process, suppressed PPARα/RXRα complex activation, and disrupted fatty acid oxidation. Notably, Fenofibrate, the PPARα-specific agonist, failed to alleviate fibrosis or lipid deposition in the renal tissues from Aldh2TEC-KO mice, indicating that ALDH2 deficiency attenuated Fenofibrate's efficacy. Furthermore, the ALDH2 E487K mutation similarly impaired FFA metabolism and promoted fibrotic phenotype. Together, this work uncovers ALDH2 as a novel FAO regulator and an influencing factor of Fenofibrate therapeutic efficacy in CKD.

overall_design: Primary tubular epithelial cells (TECs) were isolated from Aldh2Ctrl mice and Aldh2TEC-KO mice.

first: Jialin

last: Guo

first: Fengyang

last: Xu

first: Jiaxin

last: Ma

first: Tonghui


title: Single-cell atlas of rhesus monkey testis reveals aging- and season-dependent regulation of spermatogenesis and microenvironment homeostasis [RNA-Seq]

city: yunnan

first: wang

middle: yi

last: chao

address: Jingming South Road, Chenggong District, Kunming City, Yunnan Province

institute: Kunming University of Science and Technology

summary: Spermatogenesis is a highly orchestrated process that depends on precise coordination between germ cells and the testicular microenvironment. However, how aging and seasonal shifts jointly regulate this process in nonhuman primates remains largely unexplored. Here, we generated a comprehensive single-cell transcriptomic atlas of the rhesus monkey testis across different ages and reproductive seasons. Our analyses reveal that Sertoli cells actively regulate the blood–testis barrier (BTB) by dynamically remodeling tight and adherens junctions, thereby mediating seasonal fluctuations in meiotic germ cells. We further identified a previously uncharacterized SSC subpopulation (U3) enriched in the non-breeding season, defined by PDGF pathway activation. By integrating this pathway into a three-dimensional collagen–PDGF scaffold, we successfully established an in vitro rhesus SSC culture system with enhanced clonogenicity and long-term propagation. In parallel, testicular immunosenescence emerged as a key determinant of age-related reproductive decline. We provide the first evidence that double-negative T cells (DNTs) markedly accumulate in aged testes, while pro-inflammatory macrophages (Mφ_SPAG16, M1-like) aberrantly expand during the non-breeding season, together disrupting immune homeostasis and niche support. Collectively, this study delineates the age- and season-dependent regulation of spermatogenesis in rhesus monkeys by integrating Sertoli–BTB dynamics, SSC niche signaling, and immune remodeling, thereby providing new mechanistic insights into testicular aging and reproductive homeostasis. experimental design：Following the manufacturer's protocol, cells were isolated from rhesus monkey testicular tissue for single-cell RNA sequencing, with results validated via immunocytochemistry and qPCR.


title: Single-cell atlas of rhesus monkey testis reveals aging- and season-dependent regulation of spermatogenesis and microenvironment homeostasis [scRNA-Seq]

overall_design: Following the manufacturer's protocol, cells were isolated from rhesus monkey testicular tissue for single-cell RNA sequencing, with results validated via immunocytochemistry and qPCR.


title: The Mechanism of PEDV-Induced Exosomes from Intestinal Epithelial Cells Inhibiting Macrophage Migration and Phagocytic Function_mRNAseq

city: nanjing

first: qiu

last: zhong

address: No. 1 Weigang, Xuanwu District

department: College of Veterinary Medicine

institute: Nanjing Agricultural University

summary: Virus-induced inflammation has long served as a canonical hallmark of host immune activation. Paradoxically, the same pathogen can sculpt an immunosuppressive milieu that accelerates its own dissemination.

overall_design: Here we show that, although porcine epidemic diarrhea virus (PEDV) rapidly triggers intestinal epithelial cells to secrete pro-inflammatory cytokines and chemokines—thereby amplifying epithelial–macrophage crosstalk and engaging RIG-I and Toll-like receptor signaling in macrophages—the cells’ phagocytic, endocytic, and lysosomal effector pathways are markedly repressed. Mechanistic dissection revealed that PEDV-infected epithelial cells release exosomes that potently inhibit macrophage migration and phagocytosis. Exosomal miR-190a, induced by PEDV, targets tropomodulin-3 (TMOD3), disrupting actin capping, reducing cellular stiffness and adhesion, and consequently impairing macrophage motility. Concomitantly, PEDV-induced exosomal lncRNA TS-2083 binds ANXA2, facilitating its ubiquitin-dependent degradation and disrupting phagocytic-cup formation, thereby attenuating macrophage engulfment. Notably, after oral PEDV challenge, piglet serum contains circulating exosomes enriched in miR-190a and lncRNA TS-2083 that recapitulate the same inhibitory effects on macrophage migration and phagocytosis. Our findings reposition PEDV immune evasion from “interferon antagonism” to “cross-cell communication reprogramming,” providing a new theoretical framework and translational roadmap for dissecting pathogenesis and designing host-directed interventions against porcine coronaviruses and other mucosa-tropic viruses.

first: Qiu

last: Zhong


title: Bulk RNAseq in control and LACTB KD human THP1 macrophages

city: New York City

first: Carmen

last: Romero Molina

state: NY

address: 1 Gustave L. Levy Pl

department: Genetics and Genomic Science

institute: Icahn School of Medicine at Mount Sinai

summary: Our mendelian randomization analysis showed that lower expression of LACTB in myeloid cells might be protective for Alzheimer's Disease. We evaluated how the reduced levels of LACTB, using small-interfering RNA, might lead to transcriptional changes in human THP1 macrophages.

overall_design: Control (scrambled, SCR) and LACTB KD THP1 macrophages. Five independent macrophages differentiations per gentoype.

last: Romero-Molina

first: Alison

last: Goate

first: Edoardo

last: Marcora


title: Bulk RNAseq in control and LACTB KO iPSC-derived microglia

summary: Our mendelian randomization analysis showed that lower expression of LACTB in myeloid cells might be protective for Alzheimer's Disease. We evaluated how the LACTB knock-out might lead to transcriptional changes in human induced pluripotent stem cells (iPSC)-microglia.

overall_design: RNA-seq profiling of mature iPSC-derived microglia (iMGLs) lacking Lactamase B (LACTB) and wild-type (WT) (labeled as SCR, scrambled) controls.

first: Wen Yi

last: See


title: The Mechanism of PEDV-Induced Exosomes from Intestinal Epithelial Cells Inhibiting Macrophage Migration and Phagocytic Function_total_RNAseq


title: Effect of cpa1 and cpa5 duoble konckout in zebrafish.

city: Guangzhou

first: yan

middle: Zi

last: Wu

address: xiaoguwei

institute: South China university of technology

summary: RNA-seq profiling of 3 dpf Wild type and cpa1 and cpa5 double konck out zebrafish. We reported that Cpa1 can compensate for Cpa5 deficiency, but we don't know cpa5 function. So we eliminated this genetic compensation, in order to investigate what effects CPA5 has on mast cells or neutrophils.

overall_design: We collect 3 dpf embryo from cpa1 & cpa5 double knockout zebrafish and set it's siblings as control. We guarantee that these young fish were produced by the same pair of parents, which can minimize the influence of the background. After that, we cut off the heads of these fish. The head tissues were used for genotype identification, while the tail tissues were used for extracting RNA and were stored in Trizol. The RNA that meets the standards will be sent to the sequencing company for further processing.

first: Ziyan

first: Songen

first: Wei

last: Liu

first: Wenqing

last: Zhang


title: Fibroblast Growth Factor Receptor Signaling in Maturing Osteoblasts Controls Cell-Matrix Interactions Critical for Osteocyte Survival

city: St Louis

first: Tiandao

last: Li

state: MO

address: 4444 Forest Park Ave

institute: Washington University

summary: Inactivation of fibroblast growth factor receptor 1 (FGFR1) in the mature osteoblast lineage using DMP1-CreER to target a floxed allele of Fgfr1 (FGFR1-CKO) results in extensive osteocyte death. To identify changes in gene expression in response to inactivation of Fgfr1 in vivo, femoral diaphyseal bone was harvested from 16-week-old Control (Fgfr1f/f) and FGFR1-CKO mice following 4 weeks exposure to Tamoxifen and subjected to bulk mRNA sequencing. RNA sequencing demonstrated reduced expression of extracellular matrix (ECM) genes and neuronal regulatory genes, and differential expression of apoptosis regulatory genes. These data demonstrate that signaling through FGF receptor may be directly required for ECM remodeling and osteocyte projection formation, and loss of FGFR signaling causes retention of an osteoblast-like gene expression signature and apoptosis of bone-embedded cells.

overall_design: To identify changes in gene expression in response to inactivation of Fgfr1 in vivo, femoral diaphyseal bone was harvested from 16-week-old Control (Fgfr1f/f) and FGFR1-CKO mice following 4 weeks exposure to Tamoxifen, flushed with PBS and subjected to bulk mRNA sequencing. Because of variability in tissue homogeneity and efficiency of gene inactivation, of the 6 Control (Fgfr1f/f) and 7 FGFR1-CKO samples sequenced, 4 Control samples with the highest Fgfr1 expression were compared to 4 CKO samples with the lowest Fgfr1 expression. With an adjusted P-value threshold set at <0.05 and a Log2FC threshold set at ≥0.5 or £-0.5, 1994 differentially expressed genes (DEG) were identified, with 1265 DEG lower and 729 DEG higher in FGFR1-CKO samples.

first: David

last: Ornitz

first: Debabrata

last: Patra

first: Craig

last: Smith


title: Characterization of DENV E-dimer-Binding Memory B cells and Antibodies

city: Phnom Penh

first: Sivyi

last: Chhay

address: Monivong 5

department: BAIA

country: Cambodia

institute: Institut Pasteur du Cambodge

summary: We investigated sE-dimer-binding memory B-cell responses in a well-characterized cohort of patients with hospitalized dengue and their subclinical household contacts. Using sE-dimer-binding B-cell staining, single-cell RNA sequencing, and ex vivo single-B-cell cultures, we defined persistence, repertoire features, and antibody functionality of sE-dimer binding MBC

overall_design: sE-dimer-binding B cells were sorted by fluorescence-activated cell sorting (FACS) and analysed using 10X Genomics scRNA-seq, paired with B cell repertoire profiling

first: Candice

last: Bohaud

first: Mary

last: Chhim

first: Giorgio

last: Gonnella

first: Sokchea

last: Lay

first: Lien

last: De Caluwé

first: Alice

last: Dejoux

first: Francois

last: Huetz

first: Sotheary

last: Sann

first: Emanuele

last: Gioacchino

first: Sopheak

last: Sorn

first: Sreymom

last: Ken

first: Pierre

last: Bruhns

first: Sowath

last: Ly

first: Felix

last: Rey

first: Anavaj

last: Sakuntabhai

first: Veasna

last: Duong

first: Giovanna

last: Barba-Spaeth

first: Tineke

last: Cantaert


city: Boston

first: Courtney

last: Mazur

state: MA

address: 50 Blossom Street

department: Endocrine Unit

institute: Massachusetts General Hospital

summary: Osteocyte loss is a hallmark of bone aging and fragility, yet the mechanisms regulating osteocyte formation and survival are poorly understood. This study measured the effect of FGF receptor (FGFR) inhibition on osteocytes and on bone integrity. FGFR inhibition in Ocy454 cells regulated cell morphology and regulated gene programs involved in osteoblast-osteocyte development, axon guidance, and bone ECM organization. These findings establish FGFR signaling as a critical regulator of osteocyte differentiation and bone homeostasis.

overall_design: We compared the transcriptome of Ocy454 cells treated for 48 hours with FGF2 or control, with or without treatment with the pan-FGFR inhibitor BGJ398.

first: Marc

last: Wein

first: David

last: Ornitz


title: Regulatory T cells inhibit CD8+ TRM-like cells during the early stages of tumor immune escape

first: Jason

last: Williams

address: 77 Ave Louis Pasteur, Building HIM Room 660

department: Dermatology

institute: Brigham and Women's Hospital

summary: Tissue-resident memory T (TRM) cells are increasingly recognized as crucial components and potential targets in cancer immunotherapy. However, studying TRM cells within the tumor microenvironment (TME) has been challenging due to limitations in existing tumor models. Traditional cell lines injected subcutaneously fail to replicate the biological cues of dermal and epidermal tumors, and many genetically engineered mouse models (GEMMs) lack a specific tumor antigen for tracking immune responses. Here, using the autochthonous Braf/PTEN model of melanoma, modified to express OVA as a tumor-specific antigen, we show that CD103+ TRM-like cells orchestrate the initial antitumor immune response, which is hindered by infiltration of regulatory T (Treg) cells.  By longitudinal CyCIF and flow cytometry analysis we found that TRM-like cells rapidly filled a stable niche in the tumor. TRM-like cells were phenotypically and transcriptionally distinct, expressing low levels of PD-1 and Tim-3, but uniquely expressed CD101 and GzmB.  Depletion of Treg cells led to augmentation of the OVA-specific antitumor immune response, activation of TRM-like CD8+ TILs, substantial CD8+ and CD4+ T cell infiltration, and a decrease in tumor growth.  Deletion of CD8+ T cells prior to Treg depletion blunted T cell recruitment to the tumor. Together, these data suggest early tumor immune escape is mediated by Tregs suppressing TRM immunosurveillance and T cell recruitment.

overall_design: Bulk RNASeq on CD8+ T cells expressing CD103, CD69 or both from Braf/PTEN/OVA autochthonous tumors

first: Williams

last: Jason

first: Kupper

last: Thomas


title: DNA Hypomethylation is Not Cell Intrinsically Toxic to Polycomb Repressive Complex 2 Deficient Malignant Peripheral Nerve Sheath Tumors

city: Minneapolis

last: Largaespada

address: 515 Delaware St SE

department: Department of Pediatrics

institute: University of Minnesota

summary: Malignant peripheral nerve sheath tumors (MPNSTs) are aggressive soft tissue sarcomas and the most common cause of disease-associated death for Neurofibromatosis Type 1 (NF1) patients. In the context of NF1, MPNSTs develop from benign premalignant precursors. In the majority of cases, the transition to malignancy is accompanied by loss of the Polycomb repressive complex 2 (PRC2), which results in aberrant upregulation of over 1200 genes due to global depletion of histone H3 lysine 27 trimethylation (H3K27me3). Studies have suggested that cells compensate for the loss of this repressive histone mark by increasing DNA methylation throughout the genome. This study used a Nanopore-based genome skimming method to analyze genome-wide DNA methylation and the transcriptome in MPNST cell lines and isogenic PRC2-deficient and -proficient CRISPR-engineered immortalized human Schwann cells. In addition to effects of PRC2 status, we also measured the effects of two DNA methyltransferase inhibitors (DNMTi), decitabine and azacitidine. We found that PRC2 status does not affect global DNA methylation state and that decitabine and azacitidine have differential effects on MPNSTs. While both DNMTis greatly decrease global DNA methylation, they upregulate different targets. Azacitidine upregulates genes involved in RNA processing pathways and can kill MPNST cells directly, while decitabine upregulates genes involved in the immune response and is only able to reduce tumor growth via indirect effects on the tumor microenvironment in vivo. We show that DNA hypomethylation alone is insufficient to kill MPNST cells, regardless of PRC2 status. However, DNMTi could be useful in combination with other therapies for MPNST patients.

overall_design: RNA-Seq of MPNST cell lines (PRC2-deficient and -proficient) treated with azacitidine and decitabine (DNMTi) for 4 days.

first: Madilyn

last: Stahl


title: Spatial Transcriptomics of Pulmonary Tuberculosis lesions in a Mouse Model

city: Mountain View

first: Lester

last: Kobzik

state: California

address: 320 Logue Avenue

institute: Cellecta, Inc

summary: To characterize gene expression in tuberculosis lung lesions (paucibacillary and multibacillary) , we performed spatial transcriptomics analysis using the NanostringGeoMX Digital Spatial Profiler (DSP) system.

overall_design: Based on routine hematoxylin and eosin histopathology and labeling of tuberculous bacilli, we selected lungs from mice with paucibacillary (controlled) lesions and mice with (uncontrolled) multibacillary lesions with necrotic areas. Additional FFPE sections were stained with fluorescent antibodies to CD45, Iba (macrophage marker), or cytokeratin (CK), as well the nuclear stain DAPI. Diseased regions of interest (ROI) were selected to focus on myeloid-rich areas avoiding necrosis and tertiary lymphoid tissue . Multiple ROI each of paucibacillary and multibacillarylesions (respectively) were studied. The profiling used the Mouse Whole Transcriptome Atlas (WTA) panel which targets ~21,000+ transcripts for mouse protein coding genes

first: Igor

last: Kramnik


title: Core clock pharmacological control in the mouse hepatic stellate cell (HSC) EMS404

city: Lille

first: Lefebvre

last: Philippe

state: Nord

address: Blvd Pr. J.Leclerc

country: France

institute: Inserm

summary: The impact of REVERBalpha agonism and of CLOCK:BMAL1 blockade on HSC activation was studied in the presence or not of the profibrotic stimulus TGFb

overall_design: Triplicate biological RNA samples from EMS404 cells treated with vehicle, TGFb, the TGFb receptor inhibitor SB431542, the REVERBalpha agonist SR9011, or  the CLOCK:BMAL1 dimer disruptor CLK8 or the indicated combination thereof were analyzed by RNA sequencing.  Cells were treated for 24 hours with compounds prior to an additional incubation in the presence of 10ng/mL TGFb

first: Johanns

last: Manuel


title: Identifying broad spectrum stress-responsive genes in Trametes versicolor to engineer enhanced tolerance to hydrothermal liquefaction aqueous phase

city: Urbana

first: Lauriebeth

last: Leonelli

state: Illinois

address: 1206 W Gregory Dr.

department: Department of Agricultural and Biological Engineering

institute: University of Illinois Urbana-Champaign

summary: Industrial wastewater contains a variety of persistent pollutants that are difficult to treat and pose risks to ecosystems. One such stream, hydrothermal liquefaction aqueous phase (HTL-AP), is a toxic yet nutrient- rich byproduct generated during conversion of biomass to biocrude oil. HTL-APs are chemically diverse, posing significant challenges to implementing robust treatment methods for detoxification and nutrient reclamation. Fungi exhibit a wide breadth of metabolic capabilities that respond dynamically to their environment, making them a resilient and versatile solution for degrading or transforming recalcitrant compounds from streams such as HTL-AP. Understanding the genetic basis of fungal tolerance in such environments is critical to fully realize their bioremediation capacity. This work leverages transcriptomic analyses to identify key gene families broadly associated with fungal stress tolerance, providing insight into the molecular mechanisms driving acclimation to various inhibitors. The white-rot fungus Trametes versicolor was subjected to three distinct HTL-APs and identify consistently upregulated genes encoding NAD(P)-binding proteins, alpha/beta-hydrolases, aldo/keto reductases, and cytochrome P450s across all conditions, suggesting broad activation of redox and detoxification pathways. These results advance our understanding of fungal stress responses and lay the groundwork for future functional annotation efforts to support the development of new, stress-tolerant strains capable of reclaiming nutrients from diverse and hostile waste environments.

overall_design: RNAseq was used to perform differential gene expression analysis on triplicate samples of wild type Trametes versicolor cultivated in culture media (control) and three different types of HTL-AP-supplemented media (treatment) condtions. The three aqueous phase types were food waste (FW), salad dressing waste (SD), and algal biomass waste (AB).

first: Rachel

last: Dalke

first: Liam

last: Reynolds

first: Paul

middle: C

last: Davidson

first: Qi

last: Jing

first: Yuanhui

last: Zhang

first: Laurie

middle: B


title: Diabetes-Induced Hearing Loss via Next-Generation Sequencing Research Model

city: Taipei

first: Shing-Hwa

last: Liu

address: No.1 Jen Ai road section 1

department: College of Medicine

country: Taiwan

institute: National Taiwan University

summary: Emerging evidence implicates the cochlea as a potential site of injury, yet the underlying molecular mechanisms remain poorly defined. In this study, we employed a streptozotocin (STZ)-induced type 1 diabetic mouse model to investigate cochlear dysfunction and region-specific transcriptomic alterations. Auditory brainstem response testing revealed significant hearing threshold elevation and reduced outer hair cell function in diabetic mice. RNA sequencing of microdissected cochlear regions including modiolus, lateral wall, and organ of corti, identified hundreds of differentially expressed genes per region, with the lateral wall exhibiting the most extensive transcriptional changes.

overall_design: To investigate the global transcriptional effects of diabetes on cochlear subregions, RNA sequencing was performed on the modiolus, lateral wall, and organ of corti isolated from control and streptozotocin-induced diabetic mice (n = 3 per group).

first: Ting-Hua

last: Yang


title: Core clock genetic control in the mouse hepatic stellate cell (HSC) EMS404

overall_design: Triplicate biological RNA samples from EMS404 cells treated with TGFb or not after transfection with a control, scrambles siRNA or a Bmal1 targeting siRNA were analyzed by RNA sequencing.  Cells were treated with 10ng/mL TGFb


title: Establishment of Patient-Derived Succinate Dehydrogenase-Deficient Gastrointestinal Stromal Tumor Models for Predicting Therapeutic Response

city: La Jolla

first: Mark

last: Antkowiak

state: CA

address: 3855 Health Sciences Dr

department: Surgery

institute: University of California, San Diego

summary:
Purpose: Gastrointestinal stromal tumor (GIST) is the most common sarcoma of the gastrointestinal tract, with mutant succinate dehydrogenase (SDH) subunits (A-D) comprising less than 7.5% (i.e., 150-200/year) of new cases annually in the United States. Contrary to GISTs harboring KIT or PDGFRA mutations, SDH-mutant GISTs affect adolescents/young adults, often metastasize, and are frequently resistant to tyrosine kinase inhibitors (TKI). Lack of human models for any SDH-mutant tumors, including GIST, has limited molecular characterization and drug discovery.
Experimental design: We describe methods for establishing novel patient-derived SDH-mutant (mSDH) GIST models and interrogated the efficacy of temozolomide on these tumor models in vitro and in clinical trials of patients with mSDH GIST.
Results: Molecular and metabolic characterization of our patient-derived mSDH GIST models revealed that these models recapitulate the transcriptional and metabolic hallmarks of parent tumors and SDH deficiency. We further demonstrate that temozolomide elicits DNA damage and apoptosis in our mSDH GIST models. Translating our in vitro discovery to the clinic, a cohort of patients with SDH-mutant GIST treated with temozolomide (n = 5) demonstrated a 40% objective response rate and 100% disease control rate, suggesting that temozolomide represents a promising therapy for this subset of GIST.
Conclusions: We report the first methods to establish patient-derived mSDH tumor models, which can be readily employed for understanding patient-specific tumor biology and treatment strategies. We also demonstrate that temozolomide is effective in patients with mSDH GIST who are refractory to existing chemotherapeutic drugs (namely, TKIs) in clinic for GISTs, bringing a promising treatment option for these patients to clinic.

overall_design:
We describe methods for establishing novel patient-derived SDH-mutant (mSDH) GIST models and interrogated the efficacy of temozolomide on these tumor models in vitro and in clinical trials of patients with mSDH GIST. We established patient-derived SDH-mutant GIST cell lines for SDHA, SDHB, and SDHC-GIST individually. Comparative gene expression profiling analysis of RNAseq data for three patient-derived SDH-mutant GIST cell lines and their parent tumors
SD437A = SDHA, SD424B = SDHB, SD435C = SDHC-GIST

first: Mayra

last: Yebra

first: Shruti

last: Bhargava

first: Avi

last: Kumar

first: Adam

middle: M

last: Burgoyne

first: Chih-Min

last: Tang

first: Hyunho

last: Yoon

first: Sudeep

last: Banerjee

first: Joseph

last: Aguilera

first: Thekla

last: Cordes

first: Vipul

last: Sheth

first: Sangkyu

last: Noh

first: Rowan

last: Ustoy

first: Sam

last: Li

first: Sunil

middle: J

last: Advani

first: Christopher

middle: L

last: Corless

first: Michael

last: Heinrich

first: Razelle

last: Kurzrock

first: Scott

last: Lippman

middle: T

last: Fanta

first: Olivier

last: Harismendy

first: Christian

last: Metallo

first: Jason

middle: K

last: Sicklick


title: Adaption to chronic hypercapnia drives time- and site-dependent changes in brainstem cardiorespiratory nuclei.

city: Wauwatosa

first: Ibrahim

last: Vazirabad

state: Wisconsin

address: 8915 W Connell Ave

department: Physiology

institute: Medical College of Wisconsin

summary: Traditional mechanisms of respiratory neuroplasticity to not fully describe the temporal pattern of ventilatory adaptations to chronic hypercapnia. To gain insights into novel mechanisms that may underly such adaptations, we performed bulk-tissue RNA sequencing from three key brainstem cardiorespiratory site involved in acute chemosensitivity (the retrotrapezoid nucleus; RTN), respiratory rhythm generation (the ventral respiratory column, VRC), and peripheral information integration (the nucleus tractus solitarius, NTS) during three different time-points of acclimatization to chronic hypercapnia (3 hours (h), 24h, and 7 days (d)). We hypothesized that chronic hypercapnia induces both time- and region-dependent transcriptional changes that may partially underly ventilatory and chemoreceptive adaptations.

overall_design: Brainstem tissue for bulk-tissue RNA sequencing was collected from 5 groups (n=6/group) of adult (≥2 years), outbred (Alpine, Saanen, Toggenburg, etc.), female goats, which were randomly assigned to different environmental CO₂ exposures. One group (Group 1) was housed in room air for 24 hours and served as the baseline control for goats exposed to either 3 hours (Group 2) or 24 hours (Group 3) of  6% inspired CO₂ (InCO₂). An additional group of goats were housed for 7 days of room air (Group 4) and served as the main comparison for goats housed at 6% InCO₂ for 7 days (Group 5).  For biopsy collection, goat brainstems were cryosectioned (−20°C) in 0.1-mm increments until the opening of the central canal to the 4th ventricle was visible (obex; 0 mm). From this landmark, additional 0.5-mm sections were made to span the following regions: 0–2 mm, 2–4 mm, and 8–10 mm from obex. Punch biopsies were collected using a 13-gauge (~1.8mm diameter) stainless-steel tube targeting three key brainstem regions:  1) nucleus of the solitary tract (NTS; 0–2 mm rostral to obex); 2) ventral respiratory column (VRC; 2–4 mm rostral to obex), to include the pre-Bötzinger complex  (PreBotC) ventrolateral and nucleus ambiguus (nAmb); and 3) the retrotrapezoid nucleus (RTN; 8–10 mm rostral to obex) (Figure 1B). Tissue samples were stored at −80°C until RNA isolation was performed. RNA extraction and sequencing were performed in two batches at the Mellowes Center for Genomic Sciences and Precision Medicine ‘Omics Core (RRID:SCR_022926). Groups 1–3 were processed in the first batch, and Groups 4–5 in the second.

first: Kirstyn

last: Grams

first: Matthew

middle: R

last: Hodges

first: Gary

last: Mouradian

middle: Y

first: Suzzane

middle: E

last: Neumueller

first: Hubert

middle: V

last: Forster


title: co-cultures of mesenchymal cells with epithelial organoids promote fusion into bioengineered liver tissues by ECM remodeling

city: Utrecht

first: Frank

last: van Steenbeek

state: Select State/Province

address: Yalelaan 104

country: Netherlands

institute: Utrecht University

summary: Human liver tissue engineering holds promise for transplantation but faces challenges replicating liver complexity. In the present study, we created bioengineered liver tissues (BLTs) utilizing three different cell types; human intrahepatic cholangiocyte organoids (ICOs), hepatic stellate cells (HSCs), and mesenchymal stromal cells (MSCs). Co-culturing with HSCs and MSCs accelerated growthand spontaneous fusion resulted in complex liver-like tissue structures. In a dynamic suspension culture, BLTs had a more compact morphology and higher expression of hepatic markers, including ALB, CYP3A4, and MRP2. We further showed that animal-derived Matrigel can be replaced by a synthetic polyisocyanide (PIC)-based hydrogel for BLTs. Importantly, PIC-based hydrogel further promoted the maturation of BLTs assessed by parameters as intracellular protein levels, morphological analysis, and metabolic activity. Transcriptomic analyses revealed mechanisms underlying tissue formation and function. To conclude, our strategy  yields functional liver tissues  suitable for disease modelling, drug screening, and toxicity tests, and form an important basis for future development of larger liver tissues for in vivo transplantation.

first: Shicheng

last: Ye

first: Zhenguo

last: Wang

first: Luc

last: van der Laan

first: Jos

last: Malda

first: Bart

last: Spee

last: Van Steenbeek

first: Kerstin

last: Schneeberger


title: Tolerability and Safety of Nintedanib and Immunosuppression in Autoimmune Inflammatory Myopathy and Progressive Pulmonary Fibrosis

city: MONTREAL

first: David

last: Langlais

state: QC

address: 740 Ave Dr Penfield, rm 4203, McGill Genome Centre

department: Human Genetics

institute: McGill University

summary: Introduction: Autoimmune-inflammatory myopathy related interstitial lung disease (AIM-ILD) are often progressive and fibrotic. Given the rarity of this disease, little is known about the safety and tolerability of nintedanib, an anti-fibrotic treatment, in combination with immunosuppression in this population. The objective of this single-arm, open-label trial was to assess safety and tolerability of nintedanib in AIM-ILD, and to determine if peripheral blood cell gene expression changes with administration of nintedanib. Methods: Patients with progressive, fibrotic AIM-ILD on background immunosuppression enrolled in this trial were given nintedanib for 24 weeks. Primary endpoint was the percentage of subjects who took 90% or more of the study drug doses. Secondary endpoints included safety (adverse events) and efficacy (lung function) outcomes. Bulk RNA sequencing of peripheral blood  was performed at baseline and each subsequent visits to examine gene expression. Results: Eleven participants were enrolled, of which nine completed the study visits as per protocol at 24 weeks. The trial was discontinued due to slow recruitment. Only 3 (27%) participants took 90% or more doses of nintedanib. Drug compliance ranged from 27% to 95%. The most common adverse events were diarrhea, nausea / vomiting, and abdominal pain. There were no significant changes in lung function over time. No difference in gene expression over time was identified. Conclusions: Our trial was limited by small sample size and challenging recruitment, making clear conclusions on safety and tolerability difficult. The nintedanib treatment did not induce measurable gene expression changes in peripheral blood. Based on this small population, tolerability of nintedanib with immunosuppression in AIM-ILD appears challenging.

overall_design: RNA-Seq on whole blood before and after (subsequent visits) oral Nintedanib administration.

first: Benoit

last: Brilland

first: Deborah

last: Assayag


title: ASK1-induces FGF21 expression in the liver

city: Zurich

first: Stephan

last: Wueest

address: Lenggstrasse 30

institute: University Children's Hospital Zurich

summary: Increasing circulating fibroblast growth factor 21 (FGF21) concentrations may be an appealing strategy to prevent/treat obesity. Herein we identify apoptosis signal regulating kinase 1 (ASK1) as an inducer of hepatic FGF21 production. High fat diet (HFD)-fed liver-specific ASK1 overexpressing mice (ASK1+hep) revealed increased hepatic expression and circulating levels of FGF21.

overall_design: RNA-sequencing of liver samples harvested from control (ASK1f/f) and ASK1 overexpressing (ASK1+hep) mice after 7 weeks of HFD.

first: Daniel

last: Konrad

first: Anne

last: Goergen


title: Targeting CPSF73, the mRNA 3' End Processing Endonuclease, Reverses the Epithelial-Mesenchymal Transition in Cancer Cells

first: Claire

last: Moore

address: 150 harrison Ave

institute: Tufts university school of medicine

summary: Metastasis is a major contributor to cancer-related mortality and therapeutic failure. Cancer cells acquire metastatic potential by losing epithelial characteristics and gaining mesenchymal properties through the epithelial-mesenchymal transition (EMT). Differential poly(A) site (PAS) usage, known as alternative polyadenylation (APA), generates mRNA isoforms differing in coding sequence, subcellular localization, stability, or translation efficiency. In cancer, 3′UTR shortening increases expression of proto-oncogenes by escaping miRNA-mediated repression. High expression of CPSF73, which cleaves mRNA precursors at PASs, is associated with unfavorable prognoses in cancer patients. However, the role of APA in regulating EMT remains poorly understood. In this study, we show that catalytic inhibition of CPSF73 attenuates cancer cell proliferation and promotes EMT reversal in MDA-MB-231, MCF7, A549, and HepG2 cells. Global profiling of APA changes following CPSF73 inhibition revealed widespread 3′UTR lengthening and suppression of intronic PASs in MDA-MB231 cells. APA shifts were observed in key EMT-related genes, accompanied by decreased expression of corresponding proteins across all four cell lines. We used antisense morpholino oligonucleotides to block the proximal PAS of AKT2, shifting the balance of AKT2 mRNA isoforms toward the long isoform. This shift caused EMT reversal, marked by reduced AKT2 protein expression, changes in EMT-related markers, and impaired invasion by MDA-MB-231 cells. Together, these findings identify APA-mediated 3'UTR lengthening, with functional consequences in EMT-related genes, as a coordinated mechanism promoting EMT reversal, highlighting a significant connection between APA and the EMT process. Interfering with these APA changes may offer a promising therapeutic strategy to suppress metastasis, with potential efficacy across multiple pathways.

overall_design: 3′ end-focused RNA-seq of MDA-MB-231 breast cancer cells, untreated or treated for 72 hours with JTE-607, a small-molecule inhibitor of CPSF73.

first: Marzieh

last: Naseri

first: Luyang


title: Vehicle vs CXCL10 expression in 4MOSC1 buccal tumors

city: San Diego

first: Cheyanne

middle: Kristen

last: Shinn

address: 9500 Gilman Drive, MC 0684

summary: To explore changes in the immune status of the TME induced by IT CXCL10 administration in 4MOSC1 tumors, we employed the nCounter PanCancer Mouse Immune Profiling gene expression platform (NanoString Technologies), which surveys 770 immune-related gene signatures, thereby enabling broad characterization of immune cell populations and inflammatory status.

overall_design: RNA expression of Vehicle treated vs CXCL10 treated 4MOSC1 buccal tumors harvested at day 10 post tumor engraftment

first: Robert

last: Saddawi-konefka


title: PIKfyve-regulated lipid metabolism as a therapeutic vulnerability in neuroendocrine prostate cancer

city: Ann Arbor

first: Arul

last: Chinnaiyan

state: Michigan

address: 1500 E. Medical Center Dr

institute: University of Michigan

summary: Neuroendocrine prostate cancer (NEPC) is a lethal, androgen receptor (AR)-independent subtype of prostate cancer that often arises after AR pathway inhibition and has limited treatment options. We hypothesized that NEPC might be susceptible to metabolic interventions targeting PIKfyve. Here, we identify the lipid kinase PIKfyve as overexpressed in advanced prostate cancers and find that NEPC cells are especially dependent on PIKfyve-driven lipid metabolism. Pharmacological PIKfyve inhibition triggered rapid apoptosis in NEPC cells. Mechanistically, AR pathway loss in NEPC reprogrammed tumor cells to tolerate sustained stress through autophagy. PIKfyve blockade forced NEPC cells to rely on de novo lipid synthesis for survival, and accordingly, dual inhibition of PIKfyve and de novo lipid synthesis synergistically suppressed NEPC tumor growth. These findings reveal a unique metabolic vulnerability in NEPC and suggest that targeting PIKfyve-dependent lipid metabolism could be a promising therapeutic strategy for this aggressive prostate cancer subtype.

overall_design:
1. RNA profiling of LTL331R-CL cells after DMSO, ESK981, Apilimod, and PIK5-33d treatment for 6 hours under normal serum condition and serum starvation condition.
2. RNA profiling of xenograft tumor samples from four AR+ (MDA-PCa-146-12, VCaP, CRPC-VCaP, LNCaP) and five NEPC tumor types (LTL610, LTL331R, NCI-H660, LTL352, LTL545).
3. RNA profiling of xenograft tumor samples from LTL352 or LTL545 treated with Vehicle, ESK981, or Apilimod for 5 days.
4. RNA profiling of xenograft tumor samples from LTL331R  treated with Vehicle, ESK981, TVB-2640, or ESK981 in combination with TVB-2640 for 5 days.

first: Yang

last: Zheng

first: Yuanyuan

last: Qiao

first: Yuping

last: Zhang

first: Gabriel

last: Cruz

first: Fengyun

last: Su

first: Rui

first: Xuhong

last: Cao


title: Transcriptomic changes from resulting from DARPP-32 or DDR1 knockdown

city: Nottingham

first: Sarah

middle: Joanne

last: Storr

state: Nottinghamshire

address: Biodiscovery Institute

institute: University of Nottingham

summary: Breast or ovarian cancer cells with either DARPP-32 (PPP1R1B) or DDR1 knockdown prior to RNA Sequencing to identify transcriptomic changes associated with gene expression


title: The Polycomb Protein EED Constrains the SCLC Neuroendocrine Phenotype and Drives Lung Cancer Histological Transformation [ATAC-seq]

first: Yixiang

last: Li

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

summary: Lung cancer is comprised of distinct histological subtypes including lung adenocarcinoma (LUAD) and small cell lung cancer (SCLC). Although histological subtypes of lung cancer are often mutually exclusive, patients can present with combined LUAD and SCLC histology tumors. Moreover, LUADs can histologically transform to SCLC through lineage plasticity as a mechanism of resistance to targeted therapies, which most often occurs in EGFR-Mutant LUAD with concurrent RB1 and TP53 inactivation after treatment with EGFR inhibitors. The mechanisms that promote LUAD to SCLC histological transformation are poorly understood. Expression of genes associated with PRC2 activity increase during LUAD to SCLC histological transformation, but it is unknown whether PRC2 is a causative driver of histological transformation in lung cancer. To study the role of the PRC2 complex in SCLC tumorigenesis, we used CRISPR-based somatic gene editing to make SCLC genetically-engineered mouse models (GEMMs) deficient for PRC2 through inactivation of EED; PRC2’s core scaffolding subunit. Strikingly, EED inactivation caused complete histological transformation from ASCL1-positive SCLC to LUAD through an intermediate NEUROD1-positive/NCAM-positive cell state. Mechanistically, SCLC to LUAD histological transformation is initiated when PRC2 inactivation de-represses bivalent genes marked by both H3K27me3 and K3K4me3 including RAS, PI3K, and MAPK pathway genes as well as NEUROD1. Lastly, we developed an EGFR-Mutant LUAD GEMM with concurrent RB1 and TP53 inactivation where EGFR inhibition can promote SCLC transformation and a metastatic phenotype; both of which are completely abrogated by EED inactivation. Together, these findings show that the PRC2 complex is required to drive ASCL1-positive neuroendocrine SCLC with its loss promoting the LUAD phenotype nominating PRC2 inhibition as a therapeutic strategy to block SCLC transformation.

overall_design: ATAC-seq profiling of EED-WT or EED-Mutant RPR2 GEMM tumors.

first: Matthew

last: Oser


title: Atomistic TCR-ligand interactions instruct memory T-cell differentiation and crossreactivity [RNA-seq]

first: Jonathan

middle: S.

last: Duke-Cohan

address: 450 Brookline Avenue JF517

department: Medical Oncology

summary: While memory T-cells provide protective immunity against specific pathogens, their post-encounter differentiation into central (TCM) and/or effector (TEM) subpopulations remains enigmatic. We thus explored the CD8 T-cell receptor (TCR) repertoire of 242 murine TCRαβ clonotypes directed against an immunodominant influenza A virus (IAV) peptide/major histocompatibility complex (pMHC) ligand, the nucleoprotein NP366-374/Db, leveraging single-cell transcriptomics with paired TCR sequencing, mechanosensing metrics, and in vivo memory development plus TCR-pMHC structural analyses. Polar TEM and more variegated TCM repertoires as well as bipotential “bipolar” clonotypes (TBP) revealed weak force-dependent bonding parameters associated with heterosubtypic IAV crossreactivities. TCM and TEM polarities manifest pMHC binding skewed to TCRβ- versus TCRα-subunit mechanotransduction, respectively, unlike the more signaling-balanced TBP TCRs. In sum, TCR diversity anticipates pathogen evolution whereas divergent signaling regulates memory fate.

overall_design: RNA-Seq profiling of retrogenic T cells, each variant expressing a unique influenza-specific T cell receptor, isolated from retrogenic mice as naive CD8 T cells and cultured in vitro for up to 66 h on spleen cells presenting the influenza NP366 peptide with sampling at several time points

first: Aoi

last: Akitsu

middle: S

first: Ellis

last: Reinherz


title: The Polycomb Protein EED Constrains the SCLC Neuroendocrine Phenotype and Drives Lung Cancer Histological Transformation [Bulk RNA-seq]

overall_design: RNA-seq profiling of 1. EED-WT and EED-Mutant tumors from genetically engineered mouse model with deletion of Rb1, Trp53, and Rbl2. 2. SCLC cell line derived from RPR2 genetically engineered mouse model  and genetic inactivation of EED with two sgRNA and non-targeting control using CRISPR-Cas9. 3. EED-Mutant RPR2 LUAD cell lines 1339 and 1344 overexpressing WT EED or inactive EED. 4. EGFR-Mutant LUAD GEMM tumor with concurrent Rb1 and Trp53 mutation with or without EGFR turned off or EED genetic inactivation.

first: Hyeonseo

last: Cho


title: The Polycomb Protein EED Constrains the SCLC Neuroendocrine Phenotype and Drives Lung Cancer Histological Transformation [ChIP-seq]

overall_design: H3K27ac ChIP-seq profiling of EED-WT or EED-Mutant RPR2 GEMM tumors. EED, H3K27me3, and H3K4me3 ChIP-seq profiling of EED-WT RPR2 GEMM tumors.

first: Shweta

last: Kukreja

first: Rong

first: Xintao

last: Qiu

first: Henry

last: Long