title: Airway epithelial hyperactivation of JAK-STAT signaling impairs type-III IFN responses during RSV infection in Down Syndrome [SingleCell RNA-seq]

city: Washington,DC

first: Nino

last: Gustavo

state: Washington,DC,

address: Sheikh Zayed Campus,111 Michigan Avenue,

department: Center for Precision Medicine and Genomics Research

institute: Childrens National Hospital

summary: Trisomy 21 (TS21) or Down syndrome (DS) causes a ninefold increase in the mortality risk in children from otherwise non-lethal respiratory syncytial virus (RSV) infection. However, it is not known if this lethality is due to increased viral infectivity, or downstream antiviral response. We analyzed the pediatric airway epithelial cells (AECs) - the primary point of viral entry and defense and found that the antiviral IFN-JAK/STAT signaling response is hyperactivated in T21 cells relative to euploid cells. This is associated with decreased RSV infection in TS21 AECs. Conversely, upon exposure to RSV, both the induction of IFN signaling and type-III IFN production are diminished in TS21 AECs and in patients in vivo. Treating TS21 AECs with JAK inhibitor alleviated the baseline type-III IFN upregulation without impairing their ability to activate IFN response upon viral exposure. This identifies a potential approach to mitigate the impact of RSV on children with DS.

overall_design:
To investigate the cellular landscape of Trisomy21 samples in comparison to Euploid samples, we performed single cell RNAseq on cell  cultures of nasal airway epithelium  cells (AECs)
An euplooid (BR61) and a trisomy 21 (TS21-6), Airway epithelium cell sample, was treated with sucrose solution (mock treatment) or RSV treated. A total of 8 samples were obtained, with 2 technical replicates each per genotype anc condition.

first: Elizabeth

last: Chorvinsky

first: Surajit

last: Bhattacharya

first: Betelehem

last: Solomon Bera

first: Allison

last: Welham

first: Claire

last: Lawlor

first: Diego

last: Preciado

first: Jose

last: Gomez

last: Gutierrez

first: Hiroki

last: Morizono

first: Jyoti

last: Jaiswal

first: Gustavo

last: Nino


title: Transcriptome of the liver tissue from Hyal1-knock out mice

status: Public on Dec 12 2025

city: Houston

first: Hari

middle: Krishna

last: Yalamanchili

state: Texas

address: 1250 Moursund St

department: Pediatrics

country: USA

institute: Children’s Nutrition Research Center

type: Expression profiling by high throughput sequencing

summary: Hyaluronidase-1 (Hyal1) is a lysosomal hyaluronidase that intracellularly hydrolyzes hyaluronan. The analysis of Hyal1's roles in hepatic gluconeogenesis from standard and obese conditions benefits from a model organism with Hyal1 deletion. Here, RNA-seq data of liver tissue from wild-type or Hyal1 knock-out mice fed with a low-fat or high-fat diet for 14 weeks.

overall_design: 12 samples

first: Xi

last: Chen

first: Michelle

last: Dias

first: Yi

last: Zhu


title: TAF2 and MYC

city: Richmond

first: Mikhail

last: Dozmorov

state: VA

address: 830 E Main St

department: Biostatistics

institute: Virginia Commonwealth University

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: The role of Yin Yang 1 in mouse KMWT1 glioma cells

summary: The effects s of YY1 were evaluated on proliferation, migration, and gene expression of KMWT1 mouse glioma cells.

overall_design: Expression of YY1 was KD and gene expression was examined by RNA-seq (relative to the control siRNA)

first: Karli

last: Mockenhaupt

first: Alexandra

last: Gonsievski

first: Tomasz

last: Kordula


title: Role of STARD10 in human pancreatic β-cells

city: Singapore

first: Adrian

middle: Kee Keong

last: Teo

state: Singapore

address: 61 Biopolis Drive, Proteos

department: Stem Cells and Diabetes Laboratory

country: Singapore

institute: IMCB, A*STAR

summary: Purpose: To compare the transcriptome profile between WT and STARD10 KO pancreatic β-like cells at different timepoints

overall_design: Methods: Differentiate WT and STARD10 KO human embryonic stem cells (hESCs) into pancreatic β-like cells which are then used in this study

first: Nur

last: Amirruddin

first: Shawn

last: Hoon

middle: K


title: TAF2 and MYC cooperate to promote hepatocellular carcinoma

summary: In order to check the tumorigenic property of TAF2, either alone or in combination with MYC, we used Sleeping Beauty (SB) transposase-mediated somatic integration in combination with hydrodynamic tail vein injection (HTVI) technique in FVB mice. TAF2 alone did not induce tumor, MYC overexpression induced tumors at a variable levels, while both TAF2 and MYC overexpression resulted in profound development of HCC.

overall_design: FVB/NJ mice (6 weeks old weighing approximately 20 g) from The Jackson Laboratory were used for hydrodynamic injection of plasmids. For each mouse pT3-EF1H-TAF2 (20 microg) or pT3-EF1alphaH-MYC (20 microg) vector was mixed with pCMV-SB vector (0.8 microg), diluted in 2 ml of saline, sterilized with a 0.22 micron filter and injected via tail vein within 5-8 seconds. In combination of pT3-EF1alphaH-TAF2 (20 microg) and pT3-EF1alphaH-MYC (20 microg), 1.6 microg pCMV-SB was used. Five weeks after injection mice were sacrificed and tumors were subjected to RNA-seq

first: Saranya

middle: C

last: Reghupaty

first: Devanand

last: Sarkar


title: Fibroblast-like cells in mesothelioma can derive from tumor cells

city: Milan

first: Jose

middle: Manuel

last: Garcia-Manteiga

address: Via Olgettina 58

department: Center for Translational Genomics and Bioinformatics

country: Italy

institute: OSR - San Raffaele Scientific Institute

summary: Pleural mesothelioma (PM) is an aggressive cancer that originates from mesothelial cells lining the pleura. To identify the different cell types in mesothelioma and their relationships, we performed single-cell RNAseq analyses of non-malignant pleura biopsies, PM biopsies and PM patient-derived organoids. Gene expression profiles of mesothelial and mesothelioma cells are very similar, suggesting that mesothelioma cells retain most properties of mesothelial cells. Surprisingly, in PM patient-derived organoids mesothelioma cells can acquire a fibroblast-like gene expression profile. Indeed, in most of the original PM biopsies a fraction of cells within the cluster of cancer-associated fibroblasts (CAFs) appear derived from tumor cells, with which they share the same genomic rearrangements. We confirmed by immunohistochemistry, and thus at the protein level, that cancer-derived fibroblast-like cells (CDFs) express smooth muscle actin, as most CAFs do, but have lost the same tumor suppressor proteins as the cognate mesothelioma cells. We propose that mesothelioma cells can become CDFs because they retain the ability of mesothelial cells to differentiate into fibroblasts. CDFs are thus tumor cells with fibroblast-like gene expression associated to tumors, and fulfil the definition of CAFs. CAFs generally support tumor progression, and in most tumors derive from resident fibroblasts or circulating mesenchymal cells. Our finding that a subset of CAFs derive from tumor cells, at least in mesothelioma, challenges current understanding of CAF origin. We suggest that interfering with the mesothelioma-to-CAF transition might offer an avenue to moderate tumor progression and resistance to therapy.

overall_design: Three non-tumoral pleura, five mesothelioma tumor biopsies were extracted from patients and 3 patient-derived-organoids were isolated in culture and analyzed by single-cell RNASeq

middle: M

first: Eltjona

last: Rapaj

first: Rossanna

last: Mezzapelle

first: Marco

middle: E

last: Bianchi


title: Novel Role of Endothelial CD45 in Regulating Endothelial-to-Mesenchymal Transition in Atherosclerosis

status: Public on Dec 11 2025

city: Boston

first: Kulandaisamy

last: Arulsamy

state: MA

address: 300 Longwood Ave.

department: Cardiology Department

institute: Boston Children's Hospital

summary:
Background: Protein-tyrosine-phosphatase CD45 is expressed in all nucleated cells of the hematopoietic system but has also been detected in mitral valve endothelial cells (ECs) undergoing endothelial-to-mesenchymal transition (EndoMT). Interestingly, our recent study indicated that activation of the endogenous CD45 promoter in human endothelial colony-forming cells (ECFCs) also induced expression of multiple EndoMT marker genes. We hypothesize that CD45 may contribute to atherosclerosis, a prevalent cardiovascular disease dependent on EndoMT.  However, the detailed molecular mechanisms underlying how CD45 contributes to EndoMT and the impact of therapeutic manipulation of CD45 expression in atherosclerosis are entirely unknown.
Method: We generated a tamoxifen-inducible EC-specific CD45-deficient mouse strain (EC-iCD45KO) on an ApoE-deficient (ApoE-/-/C57BL/6) background and fed them a Western diet to produce atherosclerosis. We enriched mouse aortic ECs with anti-CD31 beads to perform single-cell RNA sequencing. Cellular, biochemical,  and molecular approaches were used to investigate the effect of endothelial CD45-specific deletion on EndoMT and lesion development in ApoE-/- model of atherosclerosis.
Results: Endothelial ApoE-/- CD45-deficient mice showed reduced lesion development, plaque macrophages, and expression of cell adhesion molecules when compared to ApoE-/- controls.
Single-cell RNA sequencing revealed that loss of endothelial CD45 reduces EndoMT marker expression and TGF-β signaling in atherosclerotic mice, which is associated with the reduction of lesions in the ApoE-/- mouse model. Mechanistically, the loss of CD45 results in increased FGFR2 in mouse aortic ECs and KLF2 expression in the aortic root. Consistently, endothelial CD45-deficiency inhibits EndoMT and TGF-β signaling.
Conclusions: These findings demonstrate that genetic depletion of endothelial CD45 protects against EndoMT-driven atherosclerosis by promoting FGFR2 and KLF2 expression while inhibiting TGFβ signaling and EndoMT. Thus, targeting endothelial CD45 may be a novel therapeutic strategy to reduce  EndoMT and treat atherosclerosis.

overall_design: We generated a tamoxifen-inducible EC-specific CD45-deficient mouse strain (EC-iCD45KO) on an ApoE-deficient (ApoE-/-/C57BL/6) background and fed them a Western diet to produce atherosclerosis. We enriched mouse aortic ECs with anti-CD31 beads to perform single-cell RNA sequencing (10X Genomics). Cellular, biochemical,  and molecular approaches were used to investigate the effect of endothelial CD45-specific deletion on EndoMT and lesion development in ApoE-/- model of atherosclerosis.

first: Qianman

last: Peng

first: Yao

last: Wei Lu

first: Hong

first: Kaifu

first: Joyce

last: Bischoff


title: Asparagine synthetase and G-protein coupled estrogen receptor are critical responders to nutrient supply in KRAS mutant colorectal cancer

city: New Haven

first: Lingeng

last: Lu

state: CT

address: 60 College Street

department: Chronic Disease Epidemiology

institute: Yale School of Public Health

summary: Survival differences exist in colorectal cancer (CRC) patients by sex and disease stage. However, the potential molecular mechanism(s) are not well understood. Here we show that asparagine synthetase (ASNS) and G protein-coupled estrogen receptor-1 (GPER1) are critical sensors of nutrient depletion and linked to poorer outcomes for females with CRC. In a 3D spheroid model of isogenic SW48 KRAS wild-type (WT) and G12A mutant (MT) cells grown under a restricted nutrient supply, we found that glutamine depletion inhibited cell growth in both cell types, whereas ASNS and GPER1 expression were upregulated in KRAS MT versus WT.  Estradiol decreased growth in KRAS WT but had no effect on MT cells.  In a clinical colon cancer cohort of The Cancer Genome Atlas, both high GPER1 and ASNS expression were associated with poorer overall survival for females only in advanced stage tumors. These results suggest KRAS MT cells have mechanisms in place that respond to decreased nutrient supply, typically observed in advanced tumors, by increasing the expression of ASNS and GPER1 to drive cell growth. Furthermore, KRAS MT cells are resistant to the protective effects of estradiol under nutrient deplete conditions.  The findings indicate that GPER1 and ASNS expression in the link of nutrient supply and KRAS mutations shed additional light on the mechanisms behind sex differences in metabolism and growth in CRC and have clinical implications in the precision management of KRAS MT CRC.

overall_design: To investigate the effect of glutamine depletion and estradiol (E2) supplementation on gene expression in human female CRC SW48 cell lines, we grew SW48 KRAS WT and its isogenic SW48 KRAS (G12A/+) MT cells in DMEM medium in the presence/absence of glutamine (0, 4 mM) and E2 (0, 10 uM) using a hanging-drop 3D model.  We then performed gene expression profiling analysis using data obtained from RNA-seq of 2 different cells at 4 different treatment conditions.   This study was also supported in part by American Cancer Society Research Scholar

first: Caroline

last: Johnson

first: Sajid

last: Khan


title: DNA methylation and lncRNA expression control asynchronous DNA replication at specific imprinted gene domains [Capture Repli-seq]

city: Gif-sur-Yvette

first: Benoit

last: Moindrot

address: 1, avenue de la terrasse

country: France

institute: Institute for Integrative Biology of the Cell

summary: Besides genome-wide patterns of replication timing (RT), some genes display allelic replication asynchrony in stem cells, brought about by stochastic events and genetic polymorphisms. Whether epigenetic modifications control asynchronous replication remains unclear. We explored mammalian imprinted domains, where parental DNA methylation imprints mediate allele-specific gene expression. Our genome-wide and locus-specific assays in mono-parental and hybrid mouse ESCs reveal pronounced RT asynchrony—which is parent-of-origin dependent and lost upon neural differentiation—at the Dlk1-Dio3 and Snrpn domains, which both comprise lncRNA polycistrons.  Generating a range of mutant lines, we find that asynchronous replication at Dlk1-Dio3 is mediated by differential DNA methylation, and that the lncRNA Meg3 controls early replication across parts of the domain on the maternal chromosome.  RT thereby becomes unlinked from 3D chromatin architecture as assayed by Hi-C.  The combined replication timing, DNA methylation, 3D chromatin structure and gene expression data highlight how parental methylation imprints and lncRNA expression control replication and can override RT domain organisation.

overall_design: Capture Repli-seq in mESC cells (BJ1 and JB1 genetic background). NPC samples were obtained by in-vitro differentiation of mESCs. Delta-Meg3-C1, Zfp57-/- and Zfp57-/-Meg3pro-/- cell lines were obtained by CRISPR-Cas9 deletion. Sh-1 cells were obtained in Kota et al., 2014.

first: Yui

last: Imaizumi

first: François

last: Charon

first: Daan

last: Noordermeer

first: Robert

last: Feil


title: Dictionary of human intestinal organoid responses to secreted niche factors at single cell resolution

city: South San Francisco

first: Michelle

last: Chen

state: CA

address: 1 DNA Way

department: Cell & Tissue Genomics

institute: Genentech, Inc.

summary: The intestinal epithelium is often a site of pathology, such as in inflammatory bowel disease (IBD), and its maintenance is highly modulated by interactions with the microenvironment. However, a systematic understanding of how the myriad of niche cues impact distinct epithelial cell types in a diseased context is still lacking. To address this gap, we first benchmarked diverse human colonic organoid injury models against IBD tissue and established a disease-relevant model of epithelial inflammation using TNFɑ, IFNɣ, and IL1β. Using this system, we built a dictionary of epithelial responses to 79 secreted niche factors at single cell resolution via donor-pooled, multiplexed single cell RNA-sequencing (scRNA-seq). The comprehensive nature of our atlas allowed us to map relationships between perturbations, infer the function of less well-characterized ligands, and identify cell type-specific perturbed pathways. Finally, we established the relevance of organoid-derived gene programs by mapping them to single cell and spatial atlases of human IBD tissue. Our resource offers a global view of epithelial responses to microenvironmental cues in a physiologically relevant disease context and generates new hypotheses for signaling factors that may be involved in epithelial homeostasis and repair.

overall_design: Using the low-dose cytomix model, we generated a molecular dictionary of epithelial responses to secreted niche factors in human colon organoids across 3 donors via multiplexed scRNA-seq


title: Airway epithelial hyperactivation of JAK-STAT signaling impairs type-III IFN responses during RSV infection in Down Syndrome [Bulk RNA-seq]

first: Nino

last: Gustavo

summary: Trisomy 21 (TS21), commonly known as Down syndrome (DS), increases mortality risk due to respiratory syncytial virus (RSV) in children by nearly 9-fold. Interferon (IFN)-mediated JAK/STAT antiviral signaling is altered in DS given that four IFN receptor genes reside on chromosome 21. This study unveils an interferonopathy in TS21 pediatric airway epithelial cells (AECs), the primary point of entry and defense against RSV. Relative to euploid cells, TS21 AECs show reduced RSV infection levels accompanied by baseline hyperactivation of IFNJAK/STAT antiviral signaling. Conversely, in response to RSV infection, both the induction of IFN signaling and type-III IFN production are reduced in TS21 AECs compared to controls. JAK inhibition mitigates baseline IFN hyperactivation and increases type-III IFN antiviral response in TS21 AECs. Our findings identify hyperactivation of IFN-JAK/STAT in AECs of children with DS as a potentially targetable mechanism for reducing the lethal impact of RSV infection in this vulnerable population.

overall_design: Three infant AECs were plated at  1.5 x 10^5 cells/well on collagen coated 6 well dishes (pureCol) for approximately 24 hours .  After 24hr of plating,  the cells were transitioned to serum free media. The cells were treated the next day with either IFN-λ/IL-29 (100ng/mL) or IFN β (1ng/mL) in serum free media.

first: Elizabeth

last: Chorvinsky

first: Surajit

last: Bhattacharya

first: Betelehem

last: Solomon Bera

first: Allison

last: Welham

first: Claire

last: Lawlor

first: Diego

last: Preciado

first: Jose

middle: L

last: Gomez

first: Maria

middle: J

last: Gutierrez

first: Hiroki

last: Morizono

first: Jyoti

last: Jaiswal

first: Gustavo

last: Nino


title: Gene expression analysis of control and TAF2 knockdown clones of HuH-7 cells

first: Mikhail

last: Dozmorov

summary: We created stable clones of HuH-7 cells expressing either control, scrambled shRNA (C2) or TAF2 shRNA (T7, T20) and performed RNA-seq on these clones to identify genes that are regulated by TAF2.

overall_design: RNA was harvested from C2, T7 and T20 cells and RNA-seq was performed using an Illumina platform.

first: Saranya

last: Reghupaty

first: Devanand

last: Sarkar


title: GSDME-controlled pyroptosis promotes muscle repair by coordinating tissue resident macrophages and fibro-adipogenic progenitors [RNA-seq]

city: shanghai

first: Qi

last: Cao

address: NO.325 Guohe Road

country: China

institute: Second Military Medical University

summary: GSDME (Gasdermin E) is a critical protein known for its role in pyroptosis, a form of programmed cell death associated with inflammation. We demonstrated that GSDME as a crucial mediator in muscle repair, particularly in the context of muscle damage induced by cardiotoxin (CTX). Specifically, we found that GSDME-controlled pyroptosis promotes muscle repair by coordinating the activities of tissue-resident macrophages and fibro-adipogenic progenitors (FAPs).

overall_design: To simulate a muscle injury repair model, CTX (cardiotoxin) was injected into the thigh muscles of wild-type (WT) mice. Samples were collected from both the injection group and the control (unloaded) group to assess the effects of the model.To explore the function of the Gsdme, we conducted detailed experiments in both WT and knockout (KO) mice. Gastrocnemius muscles were harvested from WT injection groups and KO injection groups at four different time points: Day 1, Day 4, Day 7, and Day 14 post-injection. Each group included biological triplicates. These samples were then subjected to RNA sequencing (RNA-seq) analysis.

first: Q

first: P

last: Wang


title: An Inducible CRISPRi system for phenotypic analysis of essential genes in Pseudomonas aeruginosa

first: Jaryd

last: Sullivan

address: 185 Cambridge St

institute: Massachusetts General Hospital

summary: Precise and tunable genetic tools are essential for high throughput functional genomics. To address this need in the important gram-negative pathogen Pseudomonas aeruginosa, we developed and characterized a tightly regulated CRISPRi system that enables precise and tunable repression of essential genes. The system utilizes a rhamnose-inducible promoter to control both the Streptococcus pasteurianus-derived dCas9 and gene-specific sgRNAs, each encoded on separate plasmids for modularity and efficiency. The combination of tight regulation and high conjugation efficiency facilitated the rapid and facile construction of strains with regulated depletion of 16 essential genes spanning diverse pathways. Comparison of phenotypes across the different genetically depleted strains, including growth rate, susceptibility to antibiotics, and changes in transcriptional programs, revealed novel aspects of gene function or small molecule mechanism of action. Finally, the rhamnose-inducible CRISPRi system supports the generation and stable maintenance of pooled mutant libraries, thereby paving the way for future genome-wide, systematic assessment of individual gene vulnerabilities, which will provide critical insights for target prioritization in antibiotic discovery efforts against this recalcitrant pathogen.

overall_design: RNAseq of 18 CRISPRi strains at various times (6, 10 hours of induction), and with various concentrations of CRISPRi inducer (0%, 0.0125%, 0.05% rhamnose)

first: Sullivan

last: Jaryd

first: Warrier

last: Thulasi

first: Hung

last: Deb


title: APC coordinates GSK3 phosphorylation of SETD8 to suppress colorectal cancer

first: Zvi

middle: I

last: Cramer

address: 30 Caldwell St

institute: University of Pennsylvania

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Mutations in the tumor suppressor APC initiate CRC in part by preventing the GSK3 kinase from phosphorylating β-CATENIN, leading to its stabilization and transactivation of mitogenic target genes. While the importance of β-CATENIN phosphorylation by GSK3 is well-established, APC regulation of GSK3 activity upon other targets with potential oncogenic relevance are not understood. Here, we identify the H4K20 methyltransferase SETD8 as target of APC-coordinated GSK3 phosphorylation in the intestinal epithelium. We found that phosphorylation by GSK3 restrains the oncogenic activity of SETD8, with loss of phosphorylation sensitizing mice to oncogenic insults. Mechanistically, loss of SETD8 phosphorylation in tumors results in a loss of H4K20me1 deposition at oncogenic cholesterol biosynthesis and fetal intestinal genes, allowing for their activation at least in part through gain of YAP accessibility. These results underscore the importance of SETD8 in CRC and represent a novel β-CATENIN-independent oncogenic consequence of APC loss.

overall_design: To investigate how SETD8-dependent T140 phosphorylation regulates YAP/TEAD chromatin engagement in APC-null colorectal cancer organoids, we performed CUT&RUN profiling of YAP/TEAD binding

first: Christopher

last: Lengner

first: Mario

middle: A

last: Blanco

first: Ning

last: Li


title: Single cell RNA sequencing of rat lung after Glenn or sham surgery

city: Milwaukee

first: Andrew

middle: D

last: Spearman

state: Wisconsin

address: 8701 Watertown Plank Rd

institute: Medical College of Wisconsin

summary: Pathogenesis of single ventricle pulmonary arteriovenous malformations is not well understood. We used single cell RNA sequenicng (scRNA-seq) to investigate the molecular changes at single cell resolution early after Glenn or sham surgery.

overall_design: scRNA-seq profiling of rat lung tissue 3 weeks after Glenn or sham surgery

first: Pan

last: AY

first: Spearman

last: AD


title: Early-life stromal niches orchestrate B lymphopoiesis at the brain’s borders

first: Beth

last: Stevens

state: Massachusetts

address: 3 Blackfan Circle, 12220 Center for Life Sciences

summary: Single cell RNA sequencing of murine brain border and bone marrow tissues at postnatal day (P)14 to profile early-life immune cells and their stromal/endothelial niches in these organs.

overall_design: Dura mater, brain and attached leptomeninges/choroid plexus, calvarial bone marrow, and tibial bone marrow were extracted from three C57BL/6J mice at P14 for single cell RNA sequencing.

first: Samuel

last: Marsh

first: Alec

last: Walker


title: Differences in mRNA expression in young vs mature adult Drosophila hindguts

city: Durham

first: Jessica

last: Sawyer

state: NC

address: PO Box 3813

institute: Duke University

summary: Tissue maintenance in the presence of cell death-promoting insults requires a host of molecular mechanisms. Many studies focus on cell renewal through regeneration, while fewer studies explore mechanisms that promote cell longevity despite cell death stimuli. Here, we reveal that the adult Drosophila hindgut ileum is an excellent model for studying tissue maintenance by long-lived cells. Hindgut ileal enterocytes resist the damaging detergent SDS and upstream caspase signaling by head-involution-defective (hid). This hid-induced death insensitivity arises early in adulthood and is associated with numerous transcriptional changes. We interrogated 82 of these transcriptional changes in a candidate screen for enhancers of hid-induced death in the ileum. Top among our screen hits is an immunoglobulin family cell adhesion gene, CG15312, that maintains the adhesion protein FasIII on cell membranes. In hid-expressing ileal cells, CG15312 loss causes cell death and pyknotic nuclear clustering. We name this conserved gene low on-membrane fas and enhancer of hid (loofah). Our findings reveal a new mechanism linking cell adhesion and cell death resistance in a long-lived cell type. Our work establishes a new model for studying tissue preservation.

overall_design: RNAseq profiling of wildtype young and mature adult Drosophila hindgut cells.

first: Donald

middle: T

last: Fox


title: Reciprocal interactions between EMT and BMP signalling drive collective cell invasion

city: Cambridge

first: Benjamin

last: Steventon

address: Downing Street

department: Department of Genetics

country: United Kingdom

institute: University of Cambridge

summary: During collective cell invasion, epithelial-to-mesenchymal transition (EMT) and morphogen signalling-mediated cell fate specification are traditionally viewed as a linear cascade: morphogens drive cell fates that activate EMT programs. Here, we uncover reciprocal coupling between EMT initiation and BMP signalling mediated by SNAI2 and SMAD1. Using substrate-induced EMT in ex vivo explants, we demonstrate that EMT initiation upregulates SMAD1 expression, priming cells for BMP signalling competence across germ layers. Single-cell RNA sequencing reveals SNAI2 and SMAD1 co-expression in EMT initiation regions, and SNAI2 overexpression is sufficient to induce ectopic SMAD1 expression in vivo. While BMP signalling is dispensable for EMT initiation, it regulates cell fate proportions, dispersal dynamics, precursor region depletion rates, and migration directionality. This coupling provides a mechanism for synchronising cell fate specification with invasion progression during axis elongation, positioning EMT as a process that actively modulates morphogen competence to coordinate tissue-level cell behaviours during collective cell invasion.

overall_design: Bulk RNA sequencing of APS and PNP explants before (0h) and after (24h) migration on human fibronectin-coated glass. Sample names have been re-named since the experiment: MSP is APS_0h, MSP_EXPLANT is APS_24h, NP is PNP_0h, and NP_EXPLANT is PNP_24h.

first: Yuri

last: Takahashi


title: Heat-Shock Pathway Activation by TRC-051384 Protects Spiral Ganglion Neurons from Noise-Induced Hearing Loss [RNA-Seq]

city: Chicago

first: Jeffrey

last: Savas

state: Illinois

address: 303 E. Chicago Avenue, Ward 12-013

department: Neurology

institute: Northwestern University

summary: Noise-induced hearing loss (NIHL) is a major public health problem caused by damage to cochlear hair cells, synapses, and spiral ganglion neurons (SGNs). However, effective treatments are completely lacking. We investigated cellular stress responses induced by loud noise in a mouse model of cochlear synaptopathy and tested whether selective activation of the dominant pathway identified could confer protection. RNA sequencing and spatial transcriptomics revealed that noise exposure elicited a robust but transient upregulation of endoplasmic reticulum chaperones and proteasome subunits in SGNs and supporting cells. To target this response, we administered TRC051384, a small-molecule activator of the heat shock transcription factor Hsf1, prior to noise exposure. TRC051384 crossed the blood–labyrinth barrier and reached the cochlea, induced heat shock protein gene expression, and restored ubiquitin–proteasome function in SGNs. Notably, TRC051384 treatment improved auditory brainstem response recovery, preserved Wave I amplitudes, and maintained ribbon synapse density. These findings establish proteotoxic stress in SGNs as a central driver of NIHL and identify HSF1 activation as a promising therapeutic strategy.

overall_design: Bulk RNA-seq was performed on cochlear tissue from 16-week-old CBA/CaJ mice subjected to acoustic overexposure. Mice were divided into four groups (N = 3 per group): Control – mock-exposed (no noise). Noise-exposed, 0 hr – exposed to 2 hours of 100 dB SPL broadband noise and sacrificed immediately after exposure. Noise-exposed, 2 hr – sacrificed 2 hours post-exposure. Noise-exposed, 4 hr – sacrificed 4 hours post-exposure. Noise-exposed, 8 hr – sacrificed 8 hours post-exposure.

middle: N

first: Seby

last: Edassery

first: Miguel

last: Ramirez


title: Evaluation of the efficacy of radiodynamic therapy using talaporfin sodium in human pancreatic cancer MIA PaCa-2 xenograft models

city: Kitakyushu

first: Junko

state: Fukuoka

address: 2-7 Hibikino, Wakamatsu-ku

department: Graduate School of Information, Production and Systems

country: Japan

institute: Waseda University

summary: We investigated changes in gene expression in MIA PaCa-2 human pancreatic cancer xenografts in nude mice after radiodynamic therapy using talaporfin sodium.

overall_design:
MIA PaCa-2 human pancreatic cancer cells were implanted subcutaneously into immunodeficient mice to establish xenograft tumors.
Once tumors reached the experimental size, animals were randomly assigned to four treatment groups:
1. NT (control): no treatment.
2. TS: talaporfin sodium administration only.
3. XT: X-ray irradiation only.
4. TS-XT: combination of talaporfin sodium and X-ray irradiation.
Talaporfin sodium was administered intravenously at 10 mg/kg, 2 hours prior to each irradiation session.
X-ray irradiation was delivered at 3 Gy per day for three consecutive days (total dose = 9 Gy).
Tumors were excised 25 days after the final irradiation, and total RNA was extracted from each tumor.
RNA sequencing was performed to investigate changes in gene expression profiles among the four treatment groups.

first: Teppei

last: Yamaoka


title: CD38 endows local antigen-specific Foxp3+ Treg cells with stress resilience for compartmentalized control of CNS inflammation

city: Munich

first: Thomas

last: Korn

email: thomas.korn@tum.de, c.sie@tum.de

address: Ismaninger Str. 22

department: Experimental Neuroimmunology

country: Germany

institute: Technical University of Munich

summary: Foxp3-expressing regulatory T (Treg) cells protect from systemic autoimmunity. However, little is known about the significance of Treg cells in inflammation-experienced tissues. Using experimental autoimmune encephalomyelitis (EAE), we show that Treg cells accumulate and persist in the central nervous system (CNS) until long after the resolution of the bulk of the inflammatory infiltrate. CNS-specific local depletion of post-inflammatory Treg cells, but not systemic depletion of Treg cells, immediately rekindles autoimmune inflammatory flares in the CNS by residual local effector T cells. Expression of the NAD-consuming ecto-enzyme CD38 is crucial for the functional adaptation of post-inflammatory CNS Treg cells to a stressful microenvironment, in which access to IL-2 is limited. CD38 counteracts ADP-ribosylation of the IL-2R and, thus, maintains its high sensitivity to IL-2. Their fully functional high-affinity IL-2 receptor prevents the loss of tissue-resident antigen-specific Treg cells. These "stress-tolerant" CNS Treg cells impede the collapse of immune homeostasis in the CNS once acute inflammation is controlled.

overall_design: We profiled the transcriptome of spleen, visceral adipose tissue, and CNS Foxp3+ Treg cells, along with Foxp3- conventional Th cells (Tconv), isolated from Foxp3 (GFP) reporter mice at different EAE disease stages (Naïve, Pre-onset, Peak, Recovery) using bulk RNA-seq. Additionally, we employed the same experimental design to isolate cells from Foxp3ERT2-Cre Rosa26LSL-tdTomato mice at the Recovery stage. Utilizing Tamoxifen labeling and the Foxp3 fate-mapping system, we sorted stable (Foxp3-GFP+, tdTomato+) and unstable (Foxp3-GFP+, tdTomato−) populations and performed bulk RNA-seq analysis.

first: Andreas

last: Muschaweckh

first: Hsin-Hsiang

last: Chen

first: Rupert

last: Öllinger

first: Christopher

last: Sie


title: Bulk RNA-seq: CD31 sorted lung cells after Glenn or sham surgery and diet modification

first: Andrew

last: Spearman

summary: Pathogenesis of single ventricle pulmonary arteriovenous malformations is not well understood. We performed bulk RNA sequenicng (RNA-seq) on isolated lung CD31+ cells to investigate the molecular changes in lung endothelial cells early after Glenn or sham surgery in rats on different diet modifications.

overall_design: RNA-seq profiling of microbead sorted CD31+ lung cells 3 weeks after Glenn or sham surgery. Post-surgical rats were on 1 of 3 modified diets: Vitamin A control, Vitamin A deficient diet, or Vitamin A excess diet.

first: AY

last: Pan

first: AD


title: FABP4, marker of worse prognosis in cardiovascular disease, induces neutrophil’s proatherogenic phenotype which is modulated by semaglutide

city: Santiago de Compostela

first: David

last: Sánchez-López

state: A Coruña

address: Travesía Da Choupana S/n

country: Spain

institute: Institute of Health Research of Santiago de Compostela: Instituto de Investigacion Sanitaria de Santigao de Compostela

summary: Dysfunctional epicardial adiposity is a risk factor for coronary artery disease (CAD). Its genesis is associated with an upregulation of fatty acid binding protein 4 (FABP4) levels, which might exert paracrine inflammatory and atherogenic mechanisms on the cardiovascular system. We aimed to study the prognosis of patients with high systemic FABP4, its association with a neutrophil proatherogenic phenotype, involved mechanisms and its modulation by semaglutide, a glucagon-like peptide-1 receptor agonist (GLP-1ra). Higher plasma FABP4 levels than 50 ng/mL were associated with heart failure (HF) onset during follow-up. In patients with CAD, these levels were associated with pro-inflammatory and pro-atherogenic neutrophil profile markers as MPO, NGAL and CD11b, analysed by real-time PCR. The group of patients with the highest FABP4 levels exhibited higher levels of MMP9, CXCR2, and CD11b in neutrophils. A preclinical model, based on neutrophils and coronary endothelial cells, determined the effects of FABP4 on neutrophils' respiratory burst, by flow cytometry, activity of NF-kB, by western blot checking IkBa phosphorylation, CD11b integrin expression levels and adhesion to coronary endothelial cells. A modulation of the neutrophils' transcriptome, analysed by RNA-seq, and plasma chemokine CCL5 levels suggested changes in leukocyte migration and platelet activation pathways in patients who reduced plasma FABP4 levels after semaglutide treatment. Thus, supraphysiological levels of FABP4 induce pro-inflammatory and proatherogenic mechanisms in neutrophils and coronary endothelial cells. Its modulation by semaglutide could explain its benefits on coronary artery disease (CAD).

overall_design: Neutrophils (isolated by PolymorphPrep) from patients (n=11) with obesity and cardiovascular disease were isolated before and after semaglutide treatment for 6 months.

last: García-Vega

first: J

last: Viñuela

first: Isabel

last: Ferreirós-Vidal

first: Diego

last: Iglesias-Álvarez

first: José

last: Martínez-Cereijo

first: Laura

last: Reija-López

first: Ángel

last: Fernández-González

middle: R

last: González-Juanatey

first: Sonia

last: Eiras


title: TRMT112 Drives A Tumor Growth and Metastasis-Promoting Program in Triple-Negative Breast Cancer

city: Birmingham

first: Dongquan

state: AL

address: AB1170 1720 2nd Ave. South

institute: University of Alabama at Birmingham

summary: Ribosomal RNA Modifying Proteins (RRMPs) are integral to ribosome biogenesis, executing post-transcriptional modifications that influence translation fidelity and efficiency. Dysregulation of RRMPs has been increasingly implicated in cancer progression, yet their collective role across malignancies remains largely unexplored. Here, we performed a multi-omics analysis of 22 RRMPs across diverse cancer types using The Cancer Genome Atlas, the Molecular Taxonomy of Breast Cancer International Consortium, and additional high-throughput datasets. Our analysis revealed widespread genomic alterations and transcriptional dysregulation of RRMPs across malignancies, with distinct expression patterns in breast cancer subtypes. Notably, Triple-Negative Breast Cancer (TNBC) exhibited the highest RRMPs enrichment, which correlated with increased genomic instability including elevated tumor mutational burden and aneuploidy scores, and poor survival outcomes. Among the RRMPs, tRNA methyltransferase activator subunit 11-2 (TRMT112) emerged as a key regulator of tumor progression. Functional assays demonstrated that TRMT112 knockdown in TNBC cells significantly reduced proliferation, migration, invasion, and metastatic potential, whereas its overexpression enhanced these tumorigenic properties. Polysome profiling and RNA sequencing of actively translated transcripts revealed that TRMT112 reprograms the translational landscape by promoting pro-metastatic and stromal remodeling pathways while suppressing immune-related processes. In vivo studies using an orthotopic breast cancer model further confirmed that TRMT112 depletion impairs tumor growth and reduces metastatic burden. Collectively, our findings establish RRMPs as critical modulators of cancer progression and identify TRMT112 as a key driver of aggressive phenotypes in TNBC. The dysregulation of TRMT112 across breast cancer subtypes highlights its potential as both a prognostic biomarker and a therapeutic target. These insights provide a mechanistic foundation for future interventions aimed at targeting TRMT112-driven translational programs in aggressive breast cancer.

overall_design:
To investigate how silencing or overexpressing TRMT112 affects transcript translation and associated protein networks, we performed polysome profiling in the breast cancer cell lines MDA-MB-231, SUM159, and BT-549. Polysomes were isolated from these cells using a sucrose gradient fractionation system.
RNA-seq was subsequently performed on the polysome fractions to identify transcripts actively translated by ribosomes under TRMT112 knockdown and overexpression conditions. This approach allowed us to assess how TRMT112 modulates translational activity and impacts gene expression at the level of protein synthesis.

first: Lalita

last: Samant

first: Rajeev

first: Amr

last: Elhamamsy


title: Discrete and cell-specific hypoxic responses in Arabidopsis roots resolved by single-nuclei transcriptomics

city: Winnipeg

first: Claudio

last: Stasolla

state: MB

address: 66 Dafoe Road

department: Plant Science

country: Canada

institute: University of Manitoba

summary: With the intensification of unpredictable flooding events because of global warming, there is a need to understand how root cells perceive and respond to oxygen deprivation. The use of high-throughput single-nuclei RNA sequencing (snRNA-Seq) allows the examination of gene expression profiles in discrete cell types. Here, root tips segments of Arabidopsis seedlings were subjected to normoxic (21% oxygen) or hypoxic (4% oxygen) treatments for 4h and analyzed by snRNA-Seq. Hypoxia induces a major transcriptome rewiring, most prominent in the meristematic root cells, with the exclusion of the quiescent center (QC), which is vulnerable to low oxygen. Changes in carbon and nitrogen metabolism by low oxygen were centered around increasing demand for carbohydrate to drive substrate phosphorylation via fermentation, reduction of nitrate to sustain energetic processes, and the bypass of the TCA cycle via aminotransferase upregulation. In conclusion, the use of snRNA-Seq provides a high-resolution atlas of gene expression events defining root cell-specific responses to low oxygen.

overall_design: Arabidopsis roots were subjected to 4h of normoxic (21% oxygen) or hypoxic (4% oxygen) conditions. Nuclei were isolated from 1cm root tips and analyzed with snRNA-seq.

first: Robert

last: Hill

first: Sean

last: Robertson

first: Abir

middle: U

last: Igamberdiev

first: Mohammed

last: Mira

first: Olivia

last: Wilkins


title: Single-cell multi-omic characterization of the soybean root response to cyst nematode infection

city: ATHENS

middle: J.

last: Schmitz

state: GA

address: B416 Davison Life Sciences Department of Genetics University of Georgia 120 East Green Street

department: Genetics

institute: University of Georgia

summary: Soybean cyst nematodes parasitize soybean roots by inducing the formation of multinucleate syncytia to feed and complete their life cycle. However, the molecular basis of syncytia initiation and development remains limited. Here, we generated an integrated single-nucleus RNA and chromatin accessibility profile of soybean roots from infected and uninfected plants. We profiled 56,448 high-quality nuclei and identified all major root cell types, including distinct subpopulations enriched with syncytial nuclei. Transcriptomic and chromatin accessibility analyses support their procambium cell signature that progresses through distinct stages associated with immune suppression, cell fusion, and endoreduplication. Integrative gene expression and transcription factor motif chromatin accessibility analyses identified CAMTA1, as a key transcriptional repressor of defense-related genes including receptor-like kinases (RLKs), whereas MYB, MYB-related, and E2F as transcriptional activators that coordinate cell wall remodeling, chromatin modification and DNA replication, respectively, across developmental trajectories. These findings provide mechanistic insights into host reprogramming during nematode parasitism and a foundational resource for engineering nematode-resistant soybean.

overall_design: To dissect the molecular responses of soybean roots to SCN infection and track syncytium development, we performed snRNA-seq and scATAC-seq on mock-inoculated and SCN-infected soybean roots from the susceptible genotype Williams 82 at 5 days post-inoculation (DPI) with two biological replicates. The soybean roots were inoculated with infective J2 and allowed to infect the roots for 24 hours after which the roots were washed to remove any J2 that had not yet penetrated the roots. This step allowed for the collection of root tissue with a higher percentage of sedentary life stages of SCN enabling the capture of a mix of initial syncytial cells through developing syncytia up to a maximum of ~4 days old.

first: Xuan

last: Zhang

first: Vinavi

last: Gamage

first: Melissa

last: Mitchum


title: CD8 T cells cross-restricted by HLA-B*57 and HLA-E*01 recognize HIV Gag with different functional profiles [dataset 1]

first: Kevin

middle: James

last: Maroney

state: Alabama

address: 1001 20th Street S, 1501, Ascend Apartments

summary: Few non-classical HLA-E restricted HIV-specific epitopes have been described, and even less is known about the functional profile of responding CD8 T cells (CD8s). This study evaluates the functional characteristics of CD8s targeting the Gag epitope (KAFSPEVIPMF or KF11) based on their restriction by either HLA-E (E-CD8s) or HLA-B57 (B57-CD8s). CD8s from 8 people with HIV (PWH) were cocultured with KF11 peptide presented by cell lines expressing HLA-B*57:01, HLA-E*01:01 or E*01:03. CD8s were analyzed through single-cell (sc) RNA and TCR sequencing. Additionally, supernatants were analyzed for soluble proteomics using a Luminex assay. B57-CD8s secreted higher levels of cytotoxic cytokines such as IFNγ, while E-CD8s produced more chemotactic cytokines, including RANTES, CXCL10 (IP-10), and IL27confirmed through scRNAseq. Despite distinct cytokine profiles, TCR clonotypes stimulated by KF11 were cross-restricted by HLA-B*57 and HLA-E*01/03. In vitro T cell reporter assays clearly demonstrated this cross-restriction.  A TRAV5-containing metaclonotype cluster was seen in PWH with lower viral loads. These findings demonstrate that HIV-specific CD8s in PWH exhibit cross HLA-B*57 and HLA-E*01/03 restriction, resulting in functionally distinct immune responses that may contribute to HIV control.

overall_design:
CD8+ T cells were isolated from PBMC's of 1 HIV+ controller (C) Ci10004, noncontroller (NC) Ci10076, and ART+ noncontroller (ART+ NC)  Ci10074, or just PBMC's were used. These CD8+ T cells were co-cultured with HLA-null cell line 721.221ΔE transduced with nothing (null), HLA-B*57, E*01:01, or E*01:03, either loaded with no HIV-1 gag KF11 (unstimulated) or loaded with KF11 (stimulated). Alternatively, PBMC's from these same people with HIV (PWH) were unstimulated or stimulated with peptide. This stimulation (co-culture or PBMC) was performed for 18 hours before staining with oligo-tagged antibodies (hashtagging), then CITE-seq and fluorophore-tagged antibody cocktail. An equal number of Activated and unactivated CD8+ T cells in each of these conditions were then sorted into the same tube for each of the 3 PWH (3 tubes of 10 multiplexed conditions each). These were then used for library construction. There were 10 conditions (5 HLA/PBMC conditions - null, E01, E03, B57, PBMC X 2 stimulation conditions (unstimulated, stimulated with KF11)) per PWH, for 30 conditions total. After this, GEX, CITE-seq, and TCR data generated 2 separate sets of files (GEX and CITE-seq were both in GEX_FB)  for each multiplexed of 3 samples. Demultiplexing was performed as described in the manuscript to generate 30 conditions X 3 sample types (but GEX and feature barcoding were demultiplexed to the same GEX_FB file from which CITE-seq and GEX information was obtained) = 60 files. Through the pipeline and based on folder structure, metadata was applied holistically and 30 sets of conditions, each with TCR, GEX, and CITE-seq data were assembled into a single Seurat file at which point downstream analysis was performed. Though CD8 T cells were sorted with high purity, some of the co-cultured cell line was also incorrectly sorted and formed a distinct cluster far from all other clusters which was also used for analysis of the source of Luminex-identified cytokines - thus, the "cell line" column indicates the co-cultured HLA-expressing cell line as well, as this may be relevant for that cluster.
Please note that processed data files generated from both GEX and FB raw files are linked to the correpsonding GEX records.

first: Kevin J.

first: Michael A.

last: Rose

first: Allisa K.

last: Oman

first: Abha

last: Chopra

first: Hua-Shiuan

last: Hsieh

first: Zerufael

last: Derza

first: Rachel

last: Waterworth

first: Mark A.

last: Brockman

first: Spyros A.

last: Kalams

first: Anju

last: Bansal

first: Paul A.

last: Goepfert


title: RNA-seq analysis of the impact of PU.1 deletion on RELM-a+ macrophages from peritoneal macrophages in CAIA mice

city: Hefei

first: Yilong

last: Fang

address: Meishan Road

institute: Anhui medical university

summary: This study found that the deletion of PU.1 significantly altered the gene expression profiles related to ferroptosis and inflammation in peritoneal derived RELM-a⁺ macrophages of CAIA mice in vitro.

overall_design: To further investigate the role of PU.1 in the ferroptosis of RELM-a+ ESM, RELM-a+ macrophages from peritoneal macrophages were analyzed in vitro.

first: Jiajie

last: TU


title: Single cell RNA seq of the major cell types in the larva of the sea star, Patiria miniata

city: Providence

first: Nathalie

last: Oulhen

state: RI

address: 185 meeting street

institute: Brown university

summary: Echinoderms are invertebrate deuterostomes closely related to chordates and have become a tractable model for study of the evolution of mechanisms involved in development, primordial germ cell specification, and regeneration. Sea urchins rely on inherited mechanisms for germline formation while sea stars rely instead on cell-cell inductive signaling mechanisms. Here, we present a single cell RNA sequencing of the sea star Patiria miniata day3 larva, and its integration into the datasets of the first four days of development. We identified each cell cluster of the larva using marker genes for in situ RNA hybridization and found that, surprisingly, the primordial germ cells share many gene expression profiles with cells in the coelomic pouches, and that the ectodermal epithelium is quite heterogenous. This dataset from the sea star provides a developmental trajectory of gene expression leading to each major cell type in the larva, providing a foundation for comparative analysis with other echinoderm species in parsing out mechanisms of developmental specification, regeneration, and germ line formation.

overall_design: Adult P. miniata animals were collected by Peter Halmay (San Diego Fishermen's Working Group). Embryos were cultured as described previously (Fresques et al., 2016). Embryos were cultured in filtered (0.2 μm) sea water collected at the Marine Biological Laboratories in Woods Hole, MA, USA, until the appropriate stage for dissociation. All embryos used in the study resulted from the mating of one male and one female to ensure complete comparative capability. Multiple fertilizations were initiated in this study and timed such that the appropriate stages of embryonic development were reached at a common endpoint. The embryos were then collected and washed twice with calcium-free sea water, and then suspended in hyalin-extraction media (HEM) for 10-15 min, depending on the stage of dissociation. When cells were beginning to dissociate, the embryos were collected and washed in 0.5 M NaCl, gently sheared with a pipette, run through a 40 μm Nitex mesh, counted on a hemocytometer and diluted to reach the appropriate concentration for the scRNA-seq protocol. Equal numbers of embryos were used in each time point and at no time were cells or embryos pelleted in a centrifuge.

first: Gerardo

last: Reyes

first: Stephany

last: Foster

first: Gary

last: Wessel


title: Functional Role of THRAP3 in Modulating Thyroid Hormone–Mediated Gene Networks in C2C12 Myotubes

city: Nagakute

first: Taku

last: Fukushima

state: Aichi

institute: Aichi Medical University

summary: Thyroid hormone (TH) secreted by the thyroid gland plays essential roles in regulating metabolism, development, and nervous system function. Thyroid hormone receptor-associated protein 3 (THRAP3) is a nuclear coactivator that interacts with the thyroid hormone receptor (TR) and facilitates target gene regulation through the mediator complex. Although this mechanism has been well studied in other tissues, the specific role of THRAP3 in skeletal muscle remains unclear. Here we investigated the function of THRAP3 in skeletal muscle using Thrap3 knockout (KO) C2C12 cells. Loss of THRAP3 significantly suppressed the expression of key myogenic regulatory factors, including Myod1, Mef2c, and myosin heavy chain genes, resulting in impaired myogenic differentiation and muscle diameter. Furthermore, we found that THRAP3 influences triiodothyronine (T3)-induced gene expression, suggesting that it cooperatively modulates thyroid hormone signaling in muscle cells. Taken together, our findings identify THRAP3 as a novel regulator of myogenesis and indicate that it supports T3 activity by coordinating thyroid hormone–responsive gene expression in skeletal muscle.

overall_design: RNA-seq plofiling of Thrap3 Ctrl and knockout C2C12 cells with or without T3 treatment at day 6 of myogenic differentiation.

first: Iori

last: Sakakibara


title: Hybrid Endometrial-Derived Hydrogel and Human Endometrial Organoids Synergize for Uterine Regeneration in an Immunocompetent Murine Model

city: Badajoz

first: María

last: Gómez Álvarez

state: Badajoz

address: Parque de Cornalvo, 29

institute: IVI Foundation

summary: Study question: Can human endometrial organoids (hEOs) synergize with a hybrid endometrial-derived hydrogel (HG) to regenerate the endometrium in an immunocompetent murine model of Asherman’s Syndrome/Endometrial Atrophy (AS/EA)? Summary answer: The combination of HG+hEOs was biocompatible in an immunocompetent murine model, restored endometrial thickness and glandular structure, reduced fibrosis and ferroptosis, promoted angiogenesis and regenerative immune pathways, but failed to fully restore fertility, likely due to the prolonged retention of the synthetic hydrogel component. Main results and the role of chance: No systemic immune alterations or hematological abnormalities were detected post-treatment, indicating that the combined treatment was compatible and safe in mice. Fourteen days after treatment, HG+hEOs treatment significantly restored endometrial thickness and gland density, reduced collagen deposition and iron accumulation (ferroptosis), and enhanced vascularization compared to the PBS condition (p < 0.05), reaching levels comparable to SHAM controls. RNA sequencing of the murine endometria confirmed restoration of transcriptomic profiles and upregulation of angiogenesis, cell proliferation, and regenerative immune pathways in the HG+hEOs group. However, fertility outcomes (pregnancy rate and embryo number) remained significantly impaired in all conditions, with no statistical improvement over the PBS group. Mice injected with PM confirmed that fertility impairment was linked to the presence of synthetic hydrogel in previously damaged uteri.

overall_design: First, an AS/EA model was established in female C57BL/6 mice via uterine injury using 70° ethanol. After 4 days of endometrial damage, hEOs were co-injected with HG into the uterine horns. Animals (n = 46) were divided into four conditions: SHAM, PBS, HG and HG+hEOs. Two weeks post-injection, a subset of mice (n = 21) was sacrificed for biocompatibility, histological, and transcriptomic analyses. Functional recovery of the endometrium was assessed in the remaining animals (n = 21) through fertility outcome evaluation. In addition, two groups treated with PuraMatrix (PM) alone were also included (n = 12), with (n = 7, PM damaged) or without (n = 5, PM non-damaged) endometrial damage, to address inconsistencies observed in fertility outcomes.


title: Integrated  stress response and Drug-Induced Acute Kidney Injury: Involvement of ATF4-STAT1-GBP2 Signaling

city: Ningbo

first: Xiaoyan

last: Sun

address: 247 Renmin Road, Jiangbei District, Ningbo City, Zhejiang Province, China

institute: Fudan University,The First Affiliated Hospital of Ningbo University,

summary: Background: Pyroptosis plays a critical role in eliminating pathogens and facilitating tissue repair; however, sustained pyroptosis-driven inflammation accelerates kidney injury and disease progression. Thus, elucidating the mechanisms governing pyroptosis is essential for developing effective therapies for inflammatory kidney diseases such as acute kidney injury (AKI), which currently lacks specific treatment options. Methods: Changes in tubular epithelial cells following drug-induced AKI were assessed using single-cell RNA sequencing, immunohistochemistry, and immunofluorescence. Mechanistic insights were obtained through RNA sequencing, genomic manipulation, transcriptomic profiling, luciferase reporter assays, co-immunoprecipitation, and Western blotting. Tubular epithelial cell fate was further evaluated using transgenic mouse models and pharmacological interventions. Results: We identified activating transcription factor 4 (ATF4) as a key regulator of inflammation in drug-induced AKI. As the master regulator of the integrated stress response, ATF4 was markedly upregulated in renal tubules and positively correlated with kidney dysfunction in both human and murine AKI models. The specific deletion of ATF4 in tubular epithelial cells significantly ameliorated kidney dysfunction, inflammation, and mitochondrial apoptosis, whereas ATF4 activation exacerbated these pathological features. Mechanistically, ATF4 suppression inhibited STAT1 phosphorylation and disrupted its interaction with GBP2, thereby attenuating NLRP3 inflammasome activation, preventing tubular epithelial cells' pyroptosis, and improving kidney function. Notably, inhibition of ATF4—either pharmacologically using our prioritized integrated stress response antagonist ERMT1 or through engineered nanobiologics-mediated silencing of tubular epithelial cells—significantly reduced renal inflammation and injury. Conclusions: ATF4 promoted pyroptosis in drug-induced AKI through STAT1–GBP2 signaling.

overall_design: Transcriptional profiling was performed via high-throughput RNA sequencing (RNA-seq) on murine renal tissues. The study cohort comprised a total of nine samples, stratified into three distinct experimental groups with three biological replicates per group (n=3):Vehicle-treated  controls (ATF4_flox/flox + Vehicle);Cisplatin-treated mice (ATF4_flox/flox + Cisplatin);Cisplatin-treated Atf4 knockout mice (Atf4-/- + Cisplatin).

first: Wei

last: Chen


title: Redefining the Spectrum of EBV-Positive Diffuse Large B-Cell Lymphoma and EBV-Positive Classic Hodgkin Lymphoma

city: Isehara

first: Shunsuke

last: Nagase

address: 143 Shimokasuya

institute: Tokai University

summary: Epstein–Barr virus-positive (EBV+) diffuse large B-cell lymphoma (DLBCL) and EBV+ classic Hodgkin lymphoma (CHL) are major B-cell lymphomas with EBV infection in elderly patients. Although they are regarded as distinct clinicopathologic entities, distinguishing EBV+ CHL from EBV+ DLBCL is often challenging because of their overlapping histological and immunophenotypic features. We characterized the spectrum of EBV+ large B-cell lymphoma in 57 patients aged ≥50 years, including 35 EBV+ DLBCL (12 polymorphic DLBCL [pDLBCL] and 23 monomorphic DLBCL [mDLBCL]) and 22 EBV+ CHL. Gene expression profiling revealed interferon-γ (IFNγ)-enrichment with overexpression of indoleamine 2,3-dioxygenase 1 (IDO1), an immunosuppressive enzyme, in more than half of pDLBCL (5/8), but less in mDLBCL (3/19) and CHL (1/19). Fluorescence in situ hybridization showed a higher frequency of 9p24.1-altered cells in CHL (54%; interquartile range [IQR], 42%–89%), but lower in pDLBCL (18%; IQR, 12%–23%) and mDLBCL (5%; IQR, 0%–30%). Notably, immunohistochemical expression of PDL1 was higher in pDLBCL than in mDLBCL, suggesting IFNγ-mediated upregulation. DLBCL with EBV latency type III (n = 13) exhibited lower tumor PDL1 expression and reduced IDO1-enriched microenvironment. Multivariate analysis of the total cohort revealed that both EBV latency type III and Eastern Cooperative Oncology Group performance status ≥2 were independently associated with shorter overall survival. EBV+ large B-cell lymphoma spectrum was reclassified into four molecular groups: (1) EBV latency type III suggestive of immune senescence (n = 10, 22%), (2) high proportion of 9p24.1-alteration (n = 9, 20%); (3) high IFNγ signature score (n = 9, 20%), and (4) low IFNγ signature score (n = 18, 39%). Moreover, these groups were identified using surrogate immunohistochemical markers: EBNA2, PDL1, and IDO1. In conclusion, the molecular studies assessing tumor–host interaction enhances understanding of the EBV+ large B-cell lymphoma spectrum and benefits pathological diagnosis and clinical management.

overall_design: GEP was performed on 47 samples: 19 EBV+ CHL and 28 EBV+ DLBCL (8 pDLBCL and 20 mDLBCL).

first: Naoya

last: Nakamura

first: Yara

middle: Y

last: Kikuti

first: Joaquim

last: Carreras

first: Yuki

last: Tanigaki

first: Makoto

last: Orita

first: Atsushi

last: Ito

first: Haruka

last: Ikoma

first: Hiroshi

last: Kawada

first: Yohei

last: Masugi


title: Neurotoxicity of Propylene Glycol Butyl Ether: Multiomic Evidence from Human BrainSpheres

city: Lausanne

first: Marie-Gabrielle

last: Zurich

address: Rue de Bugnon, 7

department: Department of Biomedical Sciences (DBS)

country: Switzerland

institute: University of Lausanne

summary: Exposure to solvents may contribute to the development of neurodevelopmental and neurodegenerative diseases. Glycol ethers consist in a widely used class of organic solvents leading to workers and consumers exposure via many applications. Ethylene glycol ethers are gradually being replaced by propylene glycol ethers thought to be less toxic. However, their neurotoxicity is not systematically assessed before placing them on the market. Therefore, this study investigated the potential neurotoxicity of propylene glycol butyl ether (PGBE) for which no official occupational limit has been established. To this aim, new approach methodologies have been used. Human induced pluripotent stem cells-derived BrainSpheres model was exposed to PGBE and to its assumed human main metabolite, 2-butoxypropanoic acid (2BPA). An integrative multiomic approach (transcriptomics, proteomics, metabolomics and lipidomics) was adopted to assess molecular alterations, derive benchmark concentrations and define potential mechanisms of action. PGBE was neurotoxic at occupationally relevant exposure concentrations. This was shown for the first time in human cells. Although PGBE was more cytotoxic than 2BPA, both compounds showed very similar neurotoxicity. PGBE and 2BPA strongly affected the cell cycle, induced oxidative stress and perturbed energy and lipid metabolism. They also targeted specific nervous system processes, such as axon guidance and synapse organization. Finally, 2BPA might trigger ferroptosis by increased iron uptake. Our in vitro results show an urgent need for public health authorities to carefully assess the risk glycol ethers pose to humans, to properly protect the workers as well as individuals in the general population unknowingly exposed from indoor air contaminations.

overall_design: Human induced pluripotent stem cells (hiPSC)-derived 3D brain cultures called BrainSpheres were exposed once to propylene glycol butyl ether (PGBE) at 5, 10 and 20 mM and to 2-butoxypropanoic acid (2BPA) at 5, 10 and 20 mM for 24h, or repeatedly at each medium change to the same consentrattions for 1 week. Untreated BrainSpheres were uses as contros. BrainSpheres were collected at the end of the treatment, washed and kept at -80°C. 4 replicates were prepared for each compound, concentration and time-point, for a total of 64 samples.

first: David

last: Lopez-Rodriguez

last: Pamies

first: Julien

last: Boccard

first: Isabel

last: Meister

first: Mathieu

last: Galmiche

first: Tatjana

last: Sajic

first: Estelle

last: Maret

first: Noéline

last: Héritier

first: Massimo

last: Frangiamone

first: Aurélien

last: Thomas

first: Nancy B.

last: Hopf

first: Serge

last: Rudaz


title: oHSV-mediated JAG1 blockade induces glioma senescence-associated secretory phenotype to increase macrophage activation and sensitize to cetuximab-mediated senolysis

city: Augusta

first: Balveen

last: Kaur

address: CN-3205, 1410 Laney-Walker Blvd

department: Pathology

institute: Augusta University

summary: Oncolytic HSV-1 (oHSV) treatment induces Notch signaling and myelosuppression in the tumor microenvironment (TME) of preclinical models. In the clinic, upregulation of JAG1 gene expression was observed in recurrent high-grade glioma patients treated with CAN-3110. Since JAG1 is expressed on both glioma cells and tumor-associated macrophages (TAMs), and its expression correlated with a worse prognosis, we engineered a JAG1-antagonizing oHSV (OncoD-0J1) and interrogated its impact on the tumor and myeloid TME. OncoD-0J1 antagonized JAG1-mediated Notch signaling and had a significant therapeutic advantage in vivo, which relied on Notch signature in tumor cells. Kinome profiling revealed that OncoD-0J1 treatment suppressed CDK1, resulting in a G2/M cell cycle checkpoint as seen by cell cycle analysis. Cell cycle arrest led to senescence and correlated with increased reactive oxygen species, p62 accumulation, autophagosome accumulation, and senescence-associated beta-galactosidase activity. This resulted in increased production of inflammatory chemokines and DAMPs such as IL-1β and extracellular ATP. RNA sequencing of murine macrophages co-cultured with infected human tumor cells showed enrichment of chemotactic and pro-inflammatory pathways as well as increased Fc receptor activation following OncoD-0J1 infection. Single-cell RNA sequencing and flow cytometric analysis of F4/80+ cells isolated from infected tumors showed a shift from tumor-supporting TAMs to inflammatory macrophages upon OncoD-0J1 treatment. Senescent cells showed heightened EGFR activation as a mechanism to escape death, which created a unique vulnerability for cetuximab as a senolytic agent. Combination therapy reduced EGFR signaling and induced macrophage-mediated antibody-dependent cellular cytotoxicity, thereby increasing the anti-tumor therapeutic response of OncoD-0J1 as a monotherapy.

overall_design: Primary GBM cells were infected with OncoD or OncoD-0J1 at a multiplicity of infection (MOI) of 0.02 (GBM12) and 0.05 (GBM28) for 1 hour and media was changed to 0.05% FBS DMEM (n=4). Infected tumor cells were overlaid with serum-starved murine RAW 264.7 cells at a 1:1 ratio.  6 hours after co-culture, total RNA was isolated using the Rneasy Plus kit from Qiagen, and samples were submitted for bulk RNA sequencing.

first: Kimberly

last: Rivera-Caraballo

first: Tae Jin

last: Lee

first: Arnoneel

last: Sinha

first: Marco

last: Orecchioni

first: Karina

last: Vazquez-Arreguin

first: Shilpa

last: Sharma

first: Kimya

last: Jones

first: Upasana

last: Sahu

first: Sara

last: Murphy

first: Bangxing

last: Hong

first: Ravindra

last: Kolhe

first: Ashok


title: oHSV-mediated JAG1 blockade induces glioma senescence-associated secretory phenotype to increase macrophage activation and sensitize to cetuximab-mediated senolysis I

overall_design: Glioma cell line LN229 was transfected with sJAG1-expressing plasmid and stably selected with puromycin (1ug/mL). Cells were individually plated in four replicates overnight. Next day, total RNA was isolated using the Rneasy Plus kit from Qiagen and samples were submitted for bulk RNA sequencing.


title: Socially Responsive Yolk Steroids Correlate with Early Extraembryonic Gene Expression

city: Bloomington

first: Center for Genomics and Bioinformatics

last: IU

state: IN

address: 1001 E Third St

department: Biology

institute: Center for Genomics and Bioinformatics

summary: Here, we identify socially sensitive yolk hormones and explore their relationship with transcript-wide gene expression patterns in extra-embryonic tissues during early embryonic development in male and female house sparrows (Passer domesticus). To enable the latter, we additionally characterized how yolk hormones change across development to identify the period during which maternally derived hormones are present. We exposed captive-breeding house sparrows to simulated territorial intrusions throughout the yolking period and collected eggs to measure >30 yolk hormones using LC-MS-MS. We additionally collected unmanipulated eggs from the aviary and the wild and incubated them to one of three timepoints: embryonic day 0 (ED0), ED3, or ED5. We characterized how yolk hormones changed across development and then explored relationships between transcript-wide gene expression levels in ED3 extra-embryonic tissues and levels of yolk hormones that are responsive to social stimuli.

overall_design: Eggs were unmanipulated and incubated to embryonic day (ED) 3 or 5. RNA was collected from extraembryonic and brain tissues.

first: Jasmeen

first: Ryan

last: Paitz

first: Taylor

last: Verrett

first: Alexandra

middle: B

last: Bentz


title: Single-Cell Sequencing Reveals the Impact of Mild Traumatic Brain Injury on the Hippocampus

city: Chengdu

first: Weibo

last: Liang

address: Renmin South Road

institute: Sichuan University

summary: To elucidate molecular features of the cells of Hippocampus, their progeny at each differentiation stage, and surrounding cells in hippocampus undercontrolled cortical impact (CCI)  conditions, >15000 cells were profiled from matched hippocampus of 3 mice that had received CCI and 3 sham-operated controls.Cell type specific gene expression responding to (mild traumatic brain injury, mTBI) were revealed, some of which were closely associated with pathogenesis post-injury. Furthermore, the diverse cell to cell interaction networks uncovered an array of cellular processes under mTBI.  Our gene expression atlas provides extensive resources for future researches regarding mTBI induced pathogenesis, its therapeutic interventions or diagnostic tests.

overall_design: Hippocampus mRNA profiles of 8~10-week old mTBI and Sham mice were generated by  scRNA-Seq.

first: Xiameng

last: Chen

first: Manrui

last: Li


title: Human PSC-derived organoids model sympathetic ganglion development and its functional crosstalk with the heart

city: Shanghai

first: Jinkui

last: Zhu

state: Shanghai

address: 393 Middle Huaxia Road, Pudong, Shanghai, 201210, China.

department: School of Life Science and Technology

institute: ShanghaiTech University

summary: The sympathetic ganglia are essential components of the nervous system that regulate various aspects of involuntary body functions. Recapitulating sympathetic ganglion development with three-dimensional (3D) organoids is challenging and has not been achieved. Here, we report a method to differentiate human pluripotent stem cells into 3D neural organoids that resemble peripheral sympathetic ganglia, producing both neurons and glial cells of the ganglia in a self-organized manner. We developed an organoid system to construct functional connections between the sympathetic ganglia and one of their peripheral targets, the heart, by fusing human sympathetic ganglion organoids (hSGOs) and heart-forming organoids. Notably, this system enables the evaluation of signaling controls (i.e., nerve growth factor [NGF] signaling) on human sympathetic-to-cardiac innervation and reveals the reciprocal impacts between the sympathetic and cardiac lineages during their co-development. Our study provides a physiologically relevant platform for understanding the development of human sympathetic ganglia, their crosstalk with peripheral targets, and related diseases.

overall_design: scRNA-seq data profiles of hSGOs and hHFOs generated in this study.

first: Yantong

last: Liu

first: Yangfei

last: Xiang


title: Systems Genetics of Lifespan and Senescence in Drosophila melanogaster

city: Greeenwood

first: Maryam

last: Nasiri Aghdam

state: SC

address: 114 Gregor Mendel Cir

institute: Clemson University

summary: As global populations age, understanding the genetic basis of variation in lifespan becomes increasingly important. We used an outbred population derived from 37 inbred, sequenced lines from the Drosophila Genetic Reference Panel. We performed whole genome sequencing on pools of young and old flies, separately for males and females, to identify variants and genes associated with increased lifespan. We identified 742 variants in females and 428 in males, most of which were sex-specific; only 53 genes and 6 variants were shared between males and females, with some variants exhibiting sexually antagonistic patterns. Of the 1,117 mapped genes, 665 had human orthologs and many were associated with disease phenotypes. Gene Ontology analyses revealed enrichment for genes affecting nervous system development and mitochondrial functions. We conducted RNA sequencing of male and female heads, bodies, and reproductive tissues weekly up to 10 weeks of age. We identified nearly 2,600 genes with significant age-related changes, that were enriched in mitochondrial, metabolic, immune, and neuronal pathways. A total of 185 of these genes had variants associated with lifespan from the first study. Construction of interaction networks using all age-significant genes and their interacting partners revealed 25 xQTL-containing hub genes with human orthologs, including blw, klu, Dronc, ATP5PD, mEFTu1, levy, and Socs36E. Context-dependent correlation analysis revealed tissue- and sex-specific expression patterns among age-associated genes, highlighting xQTL genes with strong tissue-specific regulation. These findings illustrate how systems genetics can identify conserved pathways and candidate genes relevant to human aging and longevity.

overall_design: We used an outbred population derived from 37 sequenced inbred lines of the Drosophila Genetic Reference Panel. Whole-genome sequencing was performed on pooled young and old flies, separately by sex, to identify lifespan-associated variants and genes. Additionally, we conducted weekly RNA sequencing of male and female heads, bodies, and reproductive tissues up to 10 weeks of age.

first: Desiree

last: Unselt

first: Maria

last: Adonay

first: Tatania

middle: V

last: Morozova

first: Gunjan

middle: H

last: Arya

first: Lavanya

last: Turlapati

first: Vijay

last: Shankar

first: Robert

last: Anholt

first: Trudy

last: Mackay


title: Topoisomerase II inhibitors CX-5461 and Doxorubicin differ in their cardiotoxicity profiles

city: Galveston

first: Michelle

middle: C.

last: Ward

address: 301 University blvd.

institute: UTMB

summary: CX-5461 (CX) is a clinical-stage anticancer agent originally identified as an RNA polymerase I inhibitor, but more recently recognized for its ability to target the beta isoform of topoisomerase II (TOP2B). This isoform is also inhibited by anthracyclines such as Doxorubicin (DOX), a widely used chemotherapy drug known to cause cardiotoxicity. To investigate whether CX shares similar cardiotoxic potential, we compared its effects to DOX in human induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs) from six donors. Both drugs induced cell death, yet CX was markedly less cytotoxic than DOX, with an approximate 20-fold difference in potency. At sub-lethal concentrations, DOX led to significant DNA damage, whereas CX did not. Transcriptome analysis was performed across three timepoints following treatment with low and high sub-micromolar doses of each drug. Gene expression profiling revealed that DOX triggered extensive transcriptional reprogramming involving thousands of genes, while CX elicited a more restrained response affecting only hundreds. Time-course comparisons showed partial overlap in gene response trajectories, with CX-responsive genes representing a subset of the broader DOX-induced network. These shared genes were enriched for pathways involved in chromosome segregation and DNA replication. Importantly, analysis of genes located within functionally validated loci implicated in anthracycline-induced cardiotoxicity demonstrated that DOX altered the expression of ~80% of these genes, whereas CX had no measurable effect. These findings suggest that although CX can engage certain transcriptional programs similar to DOX, its overall impact on cardiomyocytes is substantially attenuated and does not resemble the cardiotoxic signature characteristic of DOX exposure.

overall_design: We generated RNA-seq data from iPSC-derived cardiomyocytes differentiated from six healthy individuals, including three females (Individuals 1–3) and three males (Individuals 4–6). Cardiomyocytes were treated with 0.1 µM or 0.5 µM of CX-5461 (CX), Doxorubicin (DOX), or vehicle control (VEH) for 3, 24, or 48 hours.

first: Sayan

last: Paul

first: José

last: Gutiérrez

first: Alyssa

last: Bogar

middle: C


title: ATAC-Seq Reveals the Impact of Mild Traumatic Brain Injury on the Hippocampus

first: Weibo

last: Liang

summary: To elucidate the epigenomic features of hippocampal cells following mTBI, approximately 50,000 nuclei were profiled from matched hippocampal tissues of three mice subjected to controlled cortical impact (CCI) and three sham-operated controls. Cell type-specific chromatin accessibility changes in response to mTBI were identified.

overall_design: Chromatin accessibility profiles of the hippocampus from 8- to 10-week-old mTBI and sham mice were generated using ATAC-Seq.

first: Xiameng

last: Chen

first: Manrui

last: Li


title: The comparison of iPSCs and fibroblasts in Apodemus speciosus

city: Kagoshima

first: Sumito

last: Matsuya

address: 1-21-24 Korimoto

department: Joint Faculty of Veterinary Medicine

institute: Kagoshima university

summary: Compare gene expression status of iPSCs and fibroblasts in Apodemus speciosus.

overall_design: We performed RNA-seq analysis on Apodemus speciosus iPSCs, embryoid bodies and fibroblasts.

first: Hiroyuki

last: Imai

first: Naoki

last: Iwamori

first: Kaoru

last: Fujino

first: Yusuke

last: Sakurai

first: Toshiki

last: Yoshimura

first: Kenji

last: Watanabe

first: Wataru

last: Fujii

first: Yoichi

last: Mizukami

first: Masashi

last: Tsujio

first: Ken

last: Kusakabe

first: Kiyoshi

last: Kano


title: Bulk RNA sequencing of hippocampal neurons from TMSB4X conditional knockout (CKO) mice following mTBI

summary: We generated a neuron-specific tdTomato red fluorescent protein-expressing Tmsb4x-CKO mouse model, Thy-1Cre/+ROSA26tdTomato/+ Tmsb4xf/y mice. This model specifically knocks out Tmsb4x in neurons while expressing the tdTomato fluorescent protein. We subsequently performed FACS to sort hippocampal neurons and extracted tdTomato+ cells for bulk RNA sequencing. The sequencing results revealed specific gene expression changes in the hippocampal neurons of CKO mice following mTBI.

overall_design: RNA-seq  profiles of the hippocampal neurons from Tmsb4x-CKO+mTBI mice(n=3), WT+mTBI mice(n=3), WT+Sham mic(n=3)e were generated.


title: CD8 T cells cross-restricted by HLA-B*57 and HLA-E*01 recognize HIV Gag with different functional profiles [dataset 2]

city: Birmingham

first: Kevin

last: Maroney

institute: University of Alabama at Birmingham

summary: Few non-classical HLA-E restricted HIV-specific epitopes have been described, and even less is known about the functional profile of responding CD8 T cells (CD8s). This study evaluates the functional characteristics of CD8s targeting the Gag epitope (KAFSPEVIPMF or KF11) based on their restriction by either HLA-E (E-CD8s) or HLA-B57 (B57-CD8s). CD8s from 8 people with HIV (PWH) were cocultured with KF11 peptide presented by cell lines expressing HLA-B*57:01, HLA-E*01:01 or E*01:03. CD8s were analyzed through single-cell (sc) RNA and TCR sequencing. Additionally, supernatants were analyzed for soluble proteomics using a Luminex assay. B57-CD8s secreted higher levels of cytotoxic cytokines such as IFNγ, while E-CD8s produced more chemotactic cytokines, including RANTES, CXCL10 (IP-10), and IL27confirmed through scRNAseq. Despite distinct cytokine profiles, TCR clonotypes stimulated by KF11 were cross-restricted by HLA-B*57 and HLA-E*01/03. In vitro T cell reporter assays clearly demonstrated this cross-restriction.  A TRAV5-containing metaclonotype cluster was seen in PWH with lower viral loads. These findings demonstrate that HIV-specific CD8s in PWH exhibit cross HLA-B*57 and HLA-E*01/03 restriction, resulting in functionally distinct immune responses that may contribute to HIV control.

overall_design: CD8+ T cells from 8 people with HIV (PWH), specifically 4 controllers (C), 2 noncontrollers (NC), 1 elite controller (EC), and one noncontroller on antiretroviral therapy (ART+ NC) were used for this assay. Initially, indicated condition cell lines (41A3.CD4, 41A3.CD4.B57, 41A3.CD4.E01, 41A3.CD4.E03) were pulsed with KF11 peptide at 10 ug/mL for 2 hrs at 37°C before peptide was washed off with 1X serum-free media (SFM). CD8+ T cells were then isolated from PBMCs using the StemCell Easy-Sep CD8 Enrichment kit (cat. NC0050243) and coincubated with peptide-pulsed cell lines as indicated for 18 hrs in the presence of α-CD28 and -49d. Cells were then stained with Aqua LIVE/DEAD stain (Thermo Fisher Scientific), anti-CD3-PacBlue, -CD4-AlexaFluor780, -CD8-AlexaFluor700, -CD14/16/19/56-PerCP-Cy5.5 (dump channel, all separate antibodies), -CD69-APC, -CD137-PE, -CD94-PE-Cy7, and -CD107a-FITC. As per gating strategy shown in Figure S1A, single cell lymphocytes were gated on, followed by live cells (Aqua -), CD4/dump -/-, CD8+ CD3-dim, CD69/137+.. Cells which fit this gating strategy and met the criteria of having a CD3-dim activated response to the given HLA pulsed with KF11 significantly (and 3X) higher than 41A3.CD4 also pulsed with KF11 were then sorted into a 96-well plate containing the lysis buffer previously described using the Aria II FACS sorter. scTCR and scRNA-seq was performed as previously described (Bansal et al. 2021).

first: Kevin J.

first: Michael A.

last: Rose

first: Allisa K.

last: Oman

first: Abha

last: Chopra

first: Hua-Shiuan

last: Hsieh

first: Zerufael

last: Derza

first: Rachel

last: Waterworth

first: Mark A.

last: Brockman

first: Spyros A.

last: Kalams

first: Anju

last: Bansal

first: Paul A.

last: Goepfert


title: Z-DNA formation induces the totipotent-like state and primes Zscan4-dependent chromatin compartmentalization [methyl-seq]

city: Paris

first: Yann

last: Loe-Mie

address: 25 rue du Dr Roux

department: Computational Biology

institute: Institut Pasteur

type: Methylation profiling by high throughput sequencing

summary: A remarkable transition during murine development is the progression from the 1-cell embryo to the 2-cell stage, accompanied by the activation of a specific set of embryonic genes, epigenome reprogramming, and nuclear architecture reorganization. Some of these characteristics are recapitulated in vitro with the spontaneous emergence of 2-cell-like cells from mouse embryonic stem cells, which exhibit a transcriptomic signature resembling the 2-cell stage, including the expression of genes such as Dux, Zscan4, and the repetitive element MERVL, and a more relaxed chromatin state. Here, we show that inter-and intra-chromosomal interactions, driven by Zscan4 chromatin factors, form during this transition and segregate into a distinct genomic compartment (Z compartment). Mechanistically, the formation of Z-DNA, an alternative DNA conformation regulated by polyamine levels, promotes the emergence of totipotent-like cells and the establishment of the Z compartment. This compartment is characterized by a decrease in active histone marks and a reduced expression of genes associated with differentiation and late developmental processes. Overall, these findings suggest that Z-DNA formation may play a dual role, first in activating ZGA genes and later in guiding genome compartmentalization to safeguard the totipotent-like state by restricting the expression of non-ZGA genes within a permissive chromatin environment.

overall_design: Methyl-seq experiments were performed in 2CLCs and ESCs in triplicates.

first: Shireen

last: Shajahan

first: Jack-Christophe

last: Cossec


title: Z-DNA formation induces the totipotent-like state and primes Zscan4-dependent chromatin compartmentalization

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

overall_design: Refer to individual Series


title: oHSV-mediated JAG1 blockade induces glioma senescence-associated secretory phenotype to increase macrophage activation and sensitize to cetuximab-mediated senolysis III

first: Balveen

last: Kaur

overall_design: Athymic nude mice were implanted with 200,000 GBM12 cells for 2 weeks and injected with 100,000 PFU of control OncoD or OncoD-0J1 for 3 days, after which  tumor-bearing brain hemispheres were harvested for F480-positive cell isolation. These cells were submitted for single-cell RNA sequencing.

first: Kimberly

last: Rivera-Caraballo

first: Tae Jin

last: Lee

first: Arnoneel

last: Sinha

first: Marco

last: Orecchioni

first: Karina

last: Vazquez-Arreguin

first: Shilpa

last: Sharma

first: Kimya

last: Jones

first: Upasana

last: Sahu

first: Sara

last: Murphy

first: Bangxing

last: Hong

first: Ravindra

last: Kolhe

first: Ashok


title: Beta-Hydroxybutyrate but not NMN supplementation mimics caloric restriction reducing early mortality in Daphnia

city: Johnson City

first: Lev

last: Yampolsky

state: Tennessee

address: 811 Lazywood Dr

department: Biological sciences

institute: East Tennessee State University

summary: NAD+ homeostasis is an important determinant of lifespan and may be a key mechanism of caloric restriction (CR) expansion of lifespan. Ketone bodies such as beta-hydroxybutyrate (BHB) that regulate NAD+ abundance and NAD+ precursors such nicotinamide mononucleotide (NMN), are known to extend life in experimental animals and ameliorate age-related conditions in humans. We tested the hypothesis that chronic BHB and NMN exposure can extend lifespan similarly to the effect of CR treatment in a model organism Daphnia, a freshwater zooplankton crustacean.  We also measured fecundity, lipofuscin accumulation, and lipid investments into offspring in Daphnia fed the full diet, full diet with BHB, NMN, and combined treatments, and fed the CR diet (25% of the full diet).   We show that BHB exposure, but not NMN exposure, reduces early life mortality in fully fed Daphnia to levels similar to those observed under CR without compromising fecundity. We also observed that in a combined exposure cohort, NMN nearly eliminates the beneficial effect of BHB. None of the treatments affected lipofuscin accumulation, but the NMN and the combined treatment mimicked the effect of CR on neonate size in older females. An RNAseq experiment comparing the two diets and the two exposure treatments showed showed that BHB-treated Daphnia change expression of a variety of genes, including genes with known longevity extending effects, but differential expression of few genes is consistent with the effects of CR and their functionality is not clear.

overall_design: Clone’s provenance and maintenance  The experiment was conducted using two parthenogenetically maintained isolates of D. magna, GB-EL75-69 and IL-M1-8, previously characterized as a long-lived and a moderately long-lived genotypes, respectively (Beam et al. 2024). These clones have been originally extracted, respectively, from a permanent lake in London, UK, and an intermittent summer-dry pond in Jerusalem, Israel. The two clones will be referred to thereafter as the GB and IL clones. Both have been obtained from Basel University Daphnia stock collection (Basel, Switzerland) and maintained in the lab for over 5 years in modified ADaM zooplankton medium (Klüttgen et al. 1994; https://evolution.unibas.ch/ebert/lab/adam.htm) at 20 ºC on the diet of the green alga Scenedesmus acutus (synonym: Tetradesmus obliquus) grown in the lab on constant light in Jüttner et al. (1983) algal medium. To obtain animals for the experimental cohorts, three juvenile females of each clone were taken out of the stock cultures and maintained individually in 20 mL of ADaM medium, fed with 2E5/mL Scenedesmus cells per day, thus initiating three replicate cohorts. Second or thirds clutch offspring of these progenitor grandmothers were collected within 24 hours of birth and maintained in 100 mL glass jars under the same conditions, serving as mothers of the experimental animals. Experimental design  Offspring of the maternal generation were collected from mothers in each of replicate and each of the two clones in the same manner and split, within 24 hours of birth, into ad libitum treatment receiving 4E5/mL Scenedesmus cells per day and CR treatment, fed 1E5/ml Scenedesmus cells per day. These two deitary treatments will be hereafter referred to as Control400 (full diet) and Control100 (CR diet). These individuals were kept in 100 mL glass jars until the age of 6-7 days, at which point they were transferred, in groups of 5, into 50 mL plastic tubes with the bottoms cut off and replaced by 1mm nylon. These tubes were placed into racks, 32 tubes per rack, and each rack was placed into a 4L glass aquarium filled with ADaM medium to achieve 20 mL volume per Daphnia. Food has been added to these aquaria daily with the concentration of 1E5 and 4E5 cells per mL in the two diet treatments and the medium was replaced every 4 days. Census was taken every other day and medium volume and food quantity was adjusted to account for attrition in the cohorts.  Racks containing tubes with Daphnia were removed from the holding aquaria for 2 hours every day and placed, after rinsing in fresh ADaM medium, into trays containing either 2.5 mM BHB, or 0.1mM NMN solutions in ADaM, or a solution of both chemicals together, at the same concentrations. Control cohorts in each of the diet treatments were placed for the same amount of time into identical trays containing ADaM medium. Thus, individuals from the two clones shared the exposure handling and solution, and all treatments shared the medium and food outside of exposure times. This resulted in the following treatments: Control400 (full diet), full diet with BHB exposure, full diet with NMN exposure, full diet with exposure to both BHB and NMN, and Control100 (CR diet).  RNAseq experiment  At the age of 752 days (i.e. at about 10% cohort mortality in the CR treatment and about 20% mortality in the full diet control) 3 females per clone were sampled from each of the control, CR, and BHB treatments and 2 females per clone from the NMN treatment, resulting in the total of 22 samples. Females were sampled at the same phase of the ovary/molting cycle by being selected within 24 hours after egg-laying. These freshly laid eggs were removed from the brood chambers and whole body somatic tissues of the females were homogenized in liquid nitrogen and total RNAs were immediately extracted using Qiagen RNeasy Plus Mini kit. RNA library preparation was performed using NEBNext Ultra II Directional RNA Library prep Kit (NEB, Lynn, MA) following the manufacturer's protocols. The libraries were sequenced with Illumina Novoseq 6000, S4 flow cell, PE100. The quality check of Indexed sequences was performed by Fastqc, and indexed sequences were trimmed using an adaptor sequence by TrimGalore-0.4.5.  Sense reads were mapped to D. magna Xinb3 reference transcriptome (BioProject ID: PRJNA624896; D. Ebert and P. Fields, personal communication; Fields et al., in preparation) using STAR (Dobin et al. 2013) and genes with differential expression (DE) among treatments and between clones were identified using DEseq2 (Love et al. 2014). Overall transcriptional differences among treatments were visualized by PCA on TPM (transcripts per million reads) data on genes in which at least one DEseq2 was significant with |log2(FC)|>1 and padj<0.1. In order to pinpoint genes with expression pattern consistent with mortality differences between treatments the following criteria were used: 1) a significant difference between each BHB or NMN treatment and the full diet control as specified above and 2) mean TMP intermediate between the full diet and CR controls. Additionally, we specifically identified genes in which mean TPM was intermediate between the two controls in the IL clone, in which mortality difference between BHB and full diet control was the stronger of the two clones.

first: A

last: Pearse


title: Z-DNA formation induces the totipotent-like state and primes Zscan4-dependent chromatin compartmentalization [RNA-Seq]

first: Yann

last: Loe-Mie

overall_design: RNAseq experiments were performed in ESCs and 2CLCs after different treatments.

first: Shireen


title: Z-DNA formation induces the totipotent-like state and primes Zscan4-dependent chromatin compartmentalization [Hi-C]

overall_design: HiC experiments were performed in ESCs and 2CLCs after different treatments.

last: Shajahan

first: Jack-Christophe


title: A systems approach reveals SMARCD3 regulon drives alternate growth signaling and vulnerability to MEK inhibitors in everolimus resistant breast cancer cells

city: Duarte

first: Aritro

last: Nath

state: California

address: 1500 E Duarte Rd

department: Medical Oncology & Therapeutics Research

institute: City of Hope

summary: Estrogen receptor-positive breast cancer (ER+BC) represents nearly 75% of all breast tumors, with nearly 20-40% patients eventually developing metastases. Everolimus is an mTOR inhibitor which has been approved for use in combination with exemestane in patients with metastatic ER+BC. However, many patients eventually develop resistance to everolimus leading to poor survival outcomes. Systematic characterization of the molecular phenotypes underlying everolimus resistance could reveal new therapeutic targets for metastatic ER+BC. We analyzed transcriptomic profiles from multiple pairs of everolimus resistant or sensitive ER+BC cell lines, to identify signaling mechanisms that distinguish resistant cells both at baseline and under everolimus treatment. Using a linear mixed-effects model, we identified strong activation of the growth-factor signaling meta-phenotype in resistant cells at baseline, which persisted even under everolimus treatment. This meta phenotype included alternate growth signaling mechanisms including IGF1R/insulin, ESR1, RAS and MAPK signaling. To understand the regulatory mechanism behind alternate growth-factor signaling activation, we adopted a network reconstruction architecture to identify SMARCD3 regulons as key transcriptional regulatory networks in resistant cells. In a neo-adjuvant trial for ER+BC patients, the expression levels of SMARCD3 and its regulon’s activity were significantly elevated in tumors refractory to everolimus. To develop a therapeutic strategy against everolimus resistance, we used transcriptomic and drug sensitivity profiles of 926 cancer cell lines treated with 395 compounds. We found that the activation of SMARCD3 regulons was consistently associated with sensitivity to several known MEK1/2 inhibitors, including trametinib. To validate these findings, we evaluated the efficacy of everolimus in combination with trametinib and demonstrated that the combination treatment significantly reduced the growth of resistant cells compared to everolimus. Our results demonstrate that everolimus resistant ER+BC cells utilize alternate growth-factor signaling to escape therapeutic control. We found that this phenotype is strongly linked with activation of the SMARCD3 regulons and can be therapeutically targeted using MEK1/2 inhibitors.

overall_design: The samples are sensitive or everolimus-resistant CAMA-1, MCF-7 and T47D ER+ breast cancer cell lines treated with DMSO (control) or everolimus.

first: Eric

middle: F

last: Medina

first: Elena

last: Farmaki

first: Jason

last: Griffiths

first: Andrea

last: Bild