title: C18orf21/RMP24 and Nepro/RMP64 are RNase MRP-specific subunits required for 40S ribosome biogenesis

status: Public on Aug 11 2025

city: Cambridge

first: Jimmy

last: Ly

state: Massachusetts

address: 455 main street

department: Biology

institute: Whitehead Institute

summary: RNase P and RNase MRP are evolutionarily-related ribonucleoprotein complexes that share common protein subunits, but carry out distinct site-specific endonuclease activities. Here, we identify two RNase MRP-specific proteins C18orf21 (RMP24) and Nepro (RMP64). C18orf21 contains a structurally similar N-terminal domain to Rpp21, but has a distinct subcellular localization and RNA-binding specificity, allowing C18orf21 to uniquely associate with RNase MRP. We ectopically express C18orf21 (RNase MRP specific), Nepro (RNase MRP specific), Rpp21 (RNase P specific), and Rpp14 (shared subunit), with a C-terminal GFP and performed RIP-seq to identify bound RNAs. Our data provide a model to understand C18orf21 physical interactions along with its role in ribosomal RNA processing. In addition to this, we knock out C18orf21, Rpp21, and Rpp14 and analyze their transcriptome. We additionally analyze rRNA intermediates in knockout cells.

overall_design: Biological replicates for RIP-seq were defined as replicate doxycycline inductions of GFP transgenes.Biological replicates for RNA-seq experiments were defined as repliate lentiviral infections/knockouts. N=2 biological replicates were performed for each experiment.

first: Eric

last: Smith

first: Iain

last: Cheeseman


title: Chronic IFN-γ Exposure Drives Divergent Cellular and Molecular Responses in Glioblastoma Subtypes

status: Public on Aug 12 2025

city: Santa Monica

first: Santosh

last: Kesari

state: California

address: 2200 Santa Monica Blvd

department: Translational Neuro-oncology

country: USA

institute: Saint John Cancer Institute

type: Expression profiling by high throughput sequencing

summary: Background: Glioblastoma (GBM) is an aggressive primary brain tumor with poor prognosis and limited treatments. Interferon-gamma (IFN-γ) plays a complex role in modulating immune and tumor responses, and its long-term impact on GBM remains unclear. Methods: Human GBM cell lines U87 and U251 were subjected to up to 28 days of chronic IFN-γ exposure and assessed for morphology, gene expression, protein dynamics, and cytokine secretion. RNA sequencing, automated Western blotting, and single-cell proteomics were employed to uncover distinct cellular and molecular adaptations to prolonged IFN-γ signaling. Results: Chronic IFN-γ exposure induced significantly divergent phenotypic changes in U87 and U251 cells. U87 cells formed neurosphere-like structures and upregulated STAT1/STAT3 signaling, suggesting an immunogenic response. In contrast, U251 cells displayed elongated morphologies and activated PI3K-Akt and Erk pathways, promoting survival and immune evasion. Differential gene expression analysis highlighted unique temporal profiles, with U251 cells exhibiting higher expression of immune resistance genes such as PD-L1 and VEGF. Secretome profiling further demonstrated contrasting cytokine landscapes: U87 cells secreted pro-inflammatory cytokines, while U251 cells produced immunosuppressive factors. Conclusions: Chronic IFN-γ exposure drives distinct molecular and phenotypic changes in GBM subtypes, reflecting their intrinsic heterogeneity. While IFN-γ enhances immune activation, prolonged exposure may also promote immune escape. These findings emphasize the need for therapeutic strategies combining IFN-γ with immune checkpoint inhibitors and targeted pathway modulation to optimize GBM treatment outcomes.

overall_design: This study investigates the temporal and cell line–specific effects of chronic IFN-γ exposure in human glioblastoma cell lines. U87-MG and U251-MG cells were treated with 1 μg/mL IFN-γ continuously over 28 days. Samples were collected at defined time points (Day 0, 3, 14, and 28), with additional withdrawal conditions at Day 28 (IFN-γ removed after Day 14). RNA was isolated for transcriptomic analysis by bulk RNA-sequencing. Each group includes three biological replicates. The experimental design enables assessment of sustained IFN-γ signaling and reversibility upon treatment cessation across distinct GBM subtypes.

first: Rahbarlayegh

last: Elnaz

first: Wojcinski

last: Alexander

first: Nomura

last: Natsuko

first: Kesari

middle: R

last: Parnav

first: Juarez

middle: M

last: Tiffany

last: Santosh


title: An unbiased survey of distal element-gene regulatory interactions with direct-capture targeted Perturb-seq

status: Public on Aug 15 2025

city: Stanford

first: Jesse

last: Engreitz

state: CA

address: 450 Serra Mall

department: Genetics

institute: Stanford University

summary: We developed a new framework for highly powered, unbiased CRISPR screens of distal regulatory elements, including an optimized experimental method (Direct-Capture Targeted Perturb-seq (DC-TAP-seq)), a random design strategy, and a comprehensive analytical pipeline that accounts for statistical power. Using pilot datasets from K562 and WTC11 cells, we benchmarked DC-TAP-seq against conventional scRNA-seq and TAP-seq for capture efficiency, guide detection, and knockdown assessment. Applying this optimized framework, we systematically perturbed ~1,400 randomly selected candidate regulatory elements across the two cell types and revealed key features of the human regulatory landscape. We found that most regulatory interactions have small effect sizes (<10%), occur over short genomic distances (<100 kb), and often involve CTCF-bound elements lacking classical enhancer marks. Housekeeping genes were regulated by distal elements with ~2-fold weaker effect sizes compared to other genes. Our results highlight limitations in existing CRISPR datasets and predictive models, and demonstrate the utility of DC-TAP-seq for building more comprehensive maps of distal regulation in the human genome.

overall_design: We generated pilot datasets from K562 and WTC11 cells to develop and optimize DC-TAP-seq, a targeted single-cell RNA-seq method for capturing both gene expression and guide RNAs. To benchmark assay performance, we also generated conventional scRNA-seq and TAP-seq datasets from K562. We use the pilot datasets for comparisons of capture efficiency, guide detection, and knockdown assessment.

first: Judhajeet

last: Ray

first: Evelyn

last: Jagoda

first: Glen

last: Munson

first: Vasundhara

last: Singh

first: Dulguun

last: Amgalan

first: Chad

last: Munger


title: Single-cell multi-omics profiling of PBMCs from SLE patients pre- and post-dual-target (BCMA/CD19) CAR-T therapy

status: Public on Aug 08 2025

city: Zhongshan

first: Ming

last: Hong

state: Guangdong

address: NO. 2 Sunwen East Road

country: China

institute: Zhongshan City People's Hospital

summary: We employed single-cell RNA sequencing combined with BCR/TCR profiling to study PBMCs from 5 SLE patients before treatment and after peripheral B-cell reconstitution following dual-target (BCMA/CD19) CAR-T therapy. PBMCs were analyzed to characterize dynamic immune cell subsets, BCR/TCR clonal expansion, and SLE-related pathways. This study provides a single-cell landscape of dual-target CAR-T therapy in SLE, offering insights into efficacy and potential biomarkers.

overall_design: Following dual-target (BCMA/CD19) CAR-T therapy for SLE, PBMCs from five patients were collected before treatment and after peripheral B-cell reconstitution, isolated by density gradient centrifugation, and analyzed using single-cell RNA sequencing with BCR/TCR profiling.

first: Zhenghao

last: He


title: ApoE4 disrupts intracellular trafficking and iron homeostasis in an improved iPSC-based model of human brain endothelial cells [scRNA-seq]

status: Public on Aug 09 2025

city: Basel

first: Martina

last: Pigoni

address: Grenzacherstrasse 124

department: NRD

country: Switzerland

institute: Hoffmann-La Roche

summary: Transferrin receptor in brain endothelial cells can deliver therapeutic antibodies to the brain via transcytosis across the blood-brain barrier. Whether receptor transport remains intact in Alzheimer’s disease is still a major open question. Here, we investigated whether apolipoprotein E4 (ApoE4), the major genetic risk factor for Alzheimer’s disease, altered intracellular transport in human brain endothelial cells. To achieve this, we first developed an optimized protocol for induced pluripotent stem cells based on a defined chemical cocktail and extracellular-matrix support to differentiate brain endothelial cells (iCE-BECs). Multi-omic profiling and functional transport assays showed that iCE-BECs have a brain endothelial gene signature and recapitulate receptor-mediated transcytosis of a clinically validated BrainshuttleTM antibody against transferrin receptor. Engineered iCE-BECs homozygous for ApoE4 had altered spatiotemporal organization of early endosomes, increased transferrin receptor expression and reduced cytoplasmic iron. Our data revealed that ApoE4 can impact intracellular transport and iron homeostasis at the BBB in a cell-autonomous manner. This finding could be relevant for the brain delivery of therapeutic antibodies for Alzheimer’s disease.

overall_design: To assess the quality of endothelial cells obtained with our optimized protocol vs published protocols, we differetiated iPSC differentiated in brain endothelial cells using our improved protocol ( iCE-BECs ) to brain endothelial cells differentiated with already pulished protocol (iEC, Patsch-derived protocol) and the same cells treated with Rep Sox (iEC-rep). "Condition 1" corresponds to "Protocol 1"in the manuscript (iEC), "Condition 2" corresponds to "Protocol 2" in the manuscript (iEC-rep) and "Condition 3" corresponds to "Protocol 3" in the manusctipt (iCE-BECs).

first: Roberto

last: Villasenor Solorio

first: Barbara

last: Hoellbacher


title: ApoE4 disrupts intracellular trafficking and iron homeostasis in an improved iPSC-based model of human brain endothelial cells [bulk RNA-seq]

overall_design: To assess the quality of endothelial cells culture obtained with our optimized protocol vs published protocols, we differetiated iPSC differentiated in brain endothelial cells using our improved protocol (iCE-BECs) to brain endothelial cells differentiated with already pulished protocol (iEC, Patsch-derived protocol) and the same cells treated with Rep Sox (iEC-rep). "Condition 1" corresponds to "Protocol 1"in the manuscript (iEC), "Condition 2" corresponds to "Protocol 2" in the manuscript (iEC-rep) and "Condition 3" corresponds to "Protocol 3" in the manusctipt (iCE-BECs). This Bulk RNA-seq analysis allows an evaluation of the culture.

first: Lia

last: D'Abate


title: NDF-FACT phase separation condensates are required for RNA Polymerase II transcription elongation through chromatin [RNA-Seq]

status: Public on Aug 05 2025

city: Piscataway

first: Jia

last: Fei

state: NJ

address: 604 Allison Rd

department: Department of Molecular Biology and Biochemistry

institute: Rutgers University

summary:
How the facilitates chromatin transcription (FACT) complex enables RNA polymerase II to overcome chromatin barriers in cells remains poorly understood—especially given the limited direct interactions of FACT with polymerases, DNA or nucleosomes. Here we demonstrate that phase separation, mediated by nucleosome destabilizing factor (NDF), is a key mechanism enabling the function of FACT during transcription elongation. Through biochemical and single-molecule assays, we found that NDF−FACT condensates create specialized biochemical environments that enhance transcription efficiency approximately 20-fold compared with FACT alone. These dynamic condensates form on transcribing RNA polymerase II and travel along chromatin, where they promote efficient nucleosome
disassembly at barriers while retaining histones on DNA to preserve chromatin integrity. In human stem cells, disruption of these condensates leads to genome-wide transcriptional defects and chromatin instability, mirroring the effects of FACT depletion. By showing that phase separation enhances FACT function during transcription elongation, our study reveals a key mechanism that preserves chromatin integrity and transcriptional homeostasis in human stem cells.

overall_design: RNA-seq analysis of NDF_WT and NDF_K161A mutant cells.

first: Ziwei

last: Li

first: Francesca

last: Burgos-Bravo

first: Kevin

last: Xu

first: Chen

first: Kelvin

middle: Y

last: Kwan

first: Alexander

middle: B

last: Tong

first: Zelin

last: Shan

first: Huan

last: Wang

first: Motoki

last: Takaku

first: Joey

first: Zheng

last: Shi

first: Dmitry

last: Lyumkis

first: Carlos

last: Bustamante


title: Phase-separated NDF−FACT condensates facilitate transcription elongation on chromatin [CUT&Run]

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: CUT&RUN of NDF in NDF-degron cells treated with DMSO and Auxin for 1h or 2 h; CUT&RUN of NDF in NDF_WT and NDF_K161A mutant cells.


title: Identification of endogenous G-quadruplexes (G4s) in human, mouse, and pig (ATAC-Seq)

status: Public on Aug 06 2025

city: Wuhan

first: Zhen-Xia

last: Chen

state: Hubei

address: No.1 Shizishan Street

department: College of Life Science and Technology

institute: Huazhong Agricultural University

summary:
G4s are non-canonical four-stranded structures and emerge as novel genetic regulatory elements. Endogenous G4s (eG4s) can form quadruplex structures and induce double strand breaking during DNA replication, and thus contributing to genomic instability and genome evolution. Besides, eG4s are closely associated with gene expression regulation, and both their stimulative and repressive roles in the genome have been elucidated. Although functions of several specific G4s have been reported, a systematical identification and characterization of eG4s is still unconducted. Here we applied Cleavage Under Targets and Tagmentation (CUT&Tag) for mapping eG4s across human, mouse, and pig at high resolution and low background. We analyzed their genomics distribution, evolutionary conservation, dynamics, regulation, and impacts on gene expression in a single framework.
ATAC-seq

sample_organism:
Homo sapiens
Sus scrofa

platform_organism:
Homo sapiens
Sus scrofa

overall_design: We conducted ATAC-seq experiment on genomic DNA extracted from human (SW620) and pig (PK15 and ST) cells in two biological replicates.

first: Sheng

middle: H

last: Qian

first: Ling


title: Identification of endogenous G-quadruplexes (G4s) in human, mouse, and pig (CUT&Tag)

summary:
G-quadruplexes (G4s) are non-canonical four-stranded structures and emerge as novel genetic regulatory elements. Endogenous G4s (eG4s) can form quadruplex structures and induce double strand breaking during DNA replication, and thus contributing to genomic instability and genome evolution. Besides, eG4s are closely associated with gene expression regulation, and both their stimulative and repressive roles in the genome have been elucidated. Although functions of several specific G4s have been reported, a systematical identification and characterization of eG4s is still unconducted. Here we applied Cleavage Under Targets and Tagmentation (CUT&Tag) for mapping eG4s across human, mouse, and pig at high resolution and low background. We analyzed their genomics distribution, evolutionary conservation, dynamics, regulation, and impacts on gene expression in a single framework.
CUT&Tag using G4-specific antibody, BG4

sample_organism:
Homo sapiens
Sus scrofa
Mus musculus

platform_organism:
Homo sapiens
Sus scrofa
Mus musculus

overall_design: We performed G4 CUT&Tag experiment on genomic DNA extracted from human, mouse, and pig cells in biological triplicate. HCT116, SW620, A549, HT29, 293T, HepG2, and NCM460 were from human, c2c12 and 3T3 were from mouse, and PK15 and ST were from pig. We sequenced a total of 30 samples.


title: Brain pericytes derived from human pluripotent stem cells retain vascular and phagocytic functions under hypoxia

status: Public on Aug 01 2025

city: Los Angeles

first: Ruslan

last: Rust

address: 1501 San Pablo Street

institute: University of Southern California

summary: The integrity and function of the blood-brain barrier (BBB) are largely regulated by pericytes. Pericyte deficiency leads to BBB breakdown and neurological dysfunction in major neurological disorders including stroke and Alzheimer’s disease (AD). Transplantation of pericytes derived from induced pluripotent stem cells (iPSC-PC) has been shown to restore the BBB and improve functional recovery in mouse models of stroke and pericyte deficiency. However, the molecular profile and functional properties of iPSC-PC under hypoxic conditions, similar to those found in ischemic and neurodegenerative diseases remain largely unexplored. Here, we demonstrate that iPSC-PC under severe hypoxia retain essential functional properties, including key molecular markers, proliferation rates, and the ability to migrate to host brain vessels via function-associated PDGFRB-PDGF-BB signaling. Additionally, we show that iPSC-PC exhibit similar clearance of amyloid beta (Aβ) neurotoxins from AD mouse brain sections under both normoxic and hypoxic conditions. These findings suggest that iPSC-PC functions are largely resilient to hypoxia, highlighting their potential as a promising cell source for treating ischemic and neurodegenerative disorders.

overall_design: iPSC-derived pericytes are cultured under normoxic and severe hypoxic conditions, then harvested after defined exposure times, and their RNA is extracted for bulkRNA sequencing to compare gene expression profiles between conditions.


title: Nutrient-driven TOR signalling controls a chromatin-associated complex for orchestrating plant growth and stress tolerance.

city: Beijing

first: xinjian

last: He

address: No. 7, zhongguancun life science park road, changping district

institute: National Institute of Biological Sciences

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

overall_design: Refer to individual Series

first: Xin

middle: J


title: Phase-separated NDF−FACT condensates facilitate transcription elongation on chromatin [PRO-Seq]

first: Jia

overall_design: Pro-seq analysis of NDF_WT and NDF_K161A mutant cells.

first: Ziwei

first: Francesca

first: Kevin


title: SRSF12 is a primate-specific splicing factor that induces a tissue-specific gene expression program

first: Jimmy

last: Ly

summary: Alternative splicing expands proteomic diversity and is tightly regulated by splicing factors, including the serine/arginine-rich (SR) protein family. Here, we analyze the poorly characterized protein SRSF12. Although SRSF12 is conserved across vertebrates, it is poorly expressed in most mammals, and we find that SRSF12 knockouts in mice do not result in overt physiological or transcriptomic alterations. In contrast, SRSF12 is more highly expressed in primates where it is predominantly expressed during meiosis and in the brain. SRSF12 localizes to splicing speckles in cultured human cells and interacts with the core splicing factors. Strikingly, ectopic expression of SRSF12 in human cells induces widespread transcriptional changes, activating testis- and brain-specific gene expression programs. SRSF12 overexpression also leads to mitotic arrest and cell death, phenotypes that require both its structured RNA recognition motif and intrinsically disordered arginine/serine-rich C-terminal domain. Together, our results suggest that SRSF12 has evolved primate-specific expression to regulate testis- and brain-specific genes.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Biological replicates for RNA-sequencing were defined as replicate doxycycline inductions of GFP transgenes, n = 3. Biological replicates for animal work represent different animals, n = 2.

first: Ly

last: Jimmy

first: Cady

last: Sarah

first: Haug

last: Sofia

first: Khalizeva

last: Ekaterina

first: Cheeseman

last: Iain


title: KDM6A and B-mediated transcriptional activation of EWSR1-FLI1 targets coordinates demethylase dependent and independent mechanisms in Ewing sarcoma

status: Public on Aug 18 2025

city: Barcelona

first: Enrique

last: Blanco

address: Dr. Aiguader 88

department: Gene Regulation, Stem Cells and Cancer

country: Spain

institute: Center for Genomic Regulation (CRG)

summary: Ewing Sarcoma (EwS) is a highly aggressive tumor arising in bones and soft tissues driven by the fusion oncoprotein EWSR1::FLI1. This aberrant transcription factor binds to GGAA microsatellites, causing epigenetic reprogramming through the formation of active neo-enhancers in a permissive cellular context. Inhibition of the oncogene remains challenging, and current efforts seek to exploit emergent epigenetic treatments targeting EWSR1::FLI1 cofactors. In EwS, neo-enhancers are characterized by strong enrichment of the active H3K27ac mark and concomitant lack of the repressive H3K27me3 mark. These regions are typically decorated with high levels of H3K27me3 prior to EWSR1::FLI1-activation. Here, upon expression of EWSR1::FLI1 in human pediatric mesenchymal stem cells, considered the putative cell of origin of EwS, we unraveled the genome-wide redistribution of H3K27me3. Stemming from these results, we elucidated the contribution of the H3K27me3 demethylases KDM6A/UTX and KDM6B/JMJD3 in the transcriptional activity of EWSR1::FLI1 induced enhancers. KDM6A had a demethylase-independent role in recruiting BRG1 at EWSR1::FLI1-primed enhancers containing single GGAA motifs, which was critical for EwS tumor growth. Conversely, KDM6B demethylated H3K27me3 at specific EWSR1::FLI1-active enhancers, co-localizing with BRG1 at GGAA repeats. Loss of KDM6B impaired the growth of EwS tumor xenografts. These results highlight KDM6 demethylases as EWSR1::FLI1 functional partners with potential as targets for treating EwS.

overall_design: ChIP-seq experiments and RNA-seq experiments. CTRL stands for Control, KD stands for knocked-down conditions, and KO stands for knocked-out conditions of KDM6A and KDM6B, and EWSR1-FLI1. Induction means EWSR1-FLI1 induction

first: Elisabeth

last: Figuerola-Bou

first: Sara

last: Sanchez-Molina


title: Phase-separated NDF−FACT condensates facilitate transcription elongation on chromatin [ChIP-Seq]

last: Fei

overall_design:
ChIP-seq analysis of NDF, Spt16 and Pol II in iPSC cells; ChIP-seq of NDF, Spt16, Pol II and LEDGF in iPSC cells treated with 1,6-hexanediol and vehicle; ChIP-seq of Spt16 and Pol II in NDF-degron cells treated with DMSO and Auxin for 1h or 2 h; ChIP-seq of NDF in Spt16-degron cells treated with DMSO and Auxin 4 h; ChIP-seq of NDF in NDF_WT and NDF_K161A mutant cells.

MNase-seq in NDF-degron cells treated with DMSO and Auxin for 2 h

MNase-seq in NDF_WT and NDF_K161A iPSC cells

last: Li

last: Burgos-Bravo

last: Xu

first: Chen

first: Kelvin

last: Kwan

first: Alexander

last: Tong

first: Zelin

last: Shan

first: Huan

last: Wang

first: Motoki

last: Takaku

first: Joey

first: Zheng

first: Dmitry

first: Carlos


title: A human microphysiological model of afferent DRG nociceptor-spinal cord dorsal horn circuitry

city: Madison

first: Randolph

middle: S

last: Ashton

state: WI

address: 330 N Orchard St.

department: Biomedical Engineering and Wisconsin Institute for Discovery

institute: University of Wisconsin-Madison

summary: We generated single cell RNA-seq data to measure the transctiptional profiles of cervicothoracic human pluripotent stem cell-derived dorsal horn spheroids cultured together with human DRG spheroids in an in-vitro model of the dorsal root ganglion-spinal horn dorsal horn pain circuit. hPSC derived dorsal horn interneurons were generated using our previously established protocol and aggregated into spheroids. These spheroids were cultured in a microphysiological device for 5 weeks together with human DRG spheroids created using hiPSC derived nociceptors purchased from Anatomic Inc. In toal we recovered the transcriptomes of 28,445 cells. Analysis verified the presence of the dI4/dI5 cells of the superficial dorsal horn which are implicated in the modeled pain circuit. These cells also expressed a high level of late-born neuronal markers NFIB and Neurod2.

overall_design: The data consist of single cell RNA-seq measurements taken from 2 cocultures of hiPSC derived dHINs and DRG nociceptors from Anatomic Inc after 5 weeks culture in a microphysiological device.

first: Frank

last: Seipel

first: Kevin

last: Pollard

first: Nisha

last: Iyer

first: Michael

last: Moore


title: Cancer systems immunology reveals myeloid—T cell interactions and B cell activation mediate response to checkpoint inhibition in metastatic breast cancer

first: Jesse

last: Kreger

address: 1050 Childs Way

summary: Sensitization of the immune-suppressed tumor microenvironment (TME) of breast cancer by histone deacetylase inhibition shows promise, but the mechanisms of sensitization are unknown. We investigated the TME of breast-to-lung metastases by combining experimental and clinical data with theory. Knowledge-guided subclustering of single-cell RNA-sequencing data and cell circuits analysis identified 39 cell states and salient interactions, of which myeloid, T cell and B cell subpopulations were most affected by treatment. Using functional immunologic assays, we verified that inhibition of the ICAM pathway partially recapitulated treatment effects. Mathematical modeling of tumor-immune dynamics confirmed that tumor reduction required simultaneous modulation of multiple TME interactions. We found evidence that treatment affected anti-tumor antibody production. Analysis of patient biopsies via spatial proteomics corroborated preclinical findings: in responders we observed increased B cell activation, mature tertiary lymphoid structures, and increased CD8+ T cell—macrophage distances with treatment. Overall, this study provides a framework for the discovery of cell-cell interactions that govern responses in complex TMEs.

overall_design:
Lung metastases from NeuN mice (NT2.5-LM) under six different treatment conditions (V, E, EP, EC, EPC, PC) were dissected. Tumor microenvironment samples were analyzed using scRNA-seq.
V: vehicle condition
E: HDAC inhibitor (entinostat) only
EP: entinostat and anti-PD-1 (nivolumab)
EC: entinostat and anti-CTLA-4 (ipilimumab)
EPC: entinostat and anti-PD-1 and anti-CTLA-4
PC: anti-PD-1 and anti-CTLA-4

first: Edgar

last: Gonzalez

first: Yingtong

last: Liu

first: Xiaojun

last: Wu

first: Arianna

last: Barbetta

first: Aaron

middle: G

last: Baugh

first: Batul

last: Al-Zubeidy

first: Julie

last: Jang

first: Sarah

last: Shin

first: Matthew

last: Jacobo

first: Vered

last: Stearns

first: Roisin

last: Connolly

first: Won

last: Ho

first: Juliet

last: Emamaullee

first: Adam

middle: L

last: MacLean

first: Evanthia

middle: T

last: Roussos Torres


title: Phase-separated NDF−FACT condensates facilitate transcription elongation on chromatin [TT-Seq]

first: Jia

last: Fei

overall_design: TT-seq and DRB/TT-seq analysis of NDF_WT and NDF_K161A mutant cells.

first: Ziwei

last: Li

first: Francesca

last: Burgos-Bravo

first: Kevin

last: Xu

first: Chen

first: Kelvin

last: Kwan

first: Alexander

last: Tong

first: Zelin

last: Shan

first: Huan

last: Wang

first: Motoki

last: Takaku

first: Joey

first: Zheng

last: Shi

first: Dmitry

last: Lyumkis

first: Carlos

last: Bustamante


title: Identification of endogenous G-quadruplexes (G4s) in human, mouse, and pig

first: Zhen-Xia

last: Chen


title: Brief exposure to oral antibiotics has age-dependent effects on morphine reward and gene expression in the medial prefrontal cortex of adolescent and adult mice_1

city: Winston-Salem

first: Rebecca

last: Hofford

state: NC

address: 115 S Chestnut St

department: Translational Neuroscience

institute: Wake Forest School of Medicine

summary: Adolescence is a critical period for the initiation of problematic drug use, which significantly increases the risk of developing substance use disorders later in life. This heightened vulnerability is partly attributed to the immaturity of the prefrontal cortex, a brain region both essential for decision-making and implicated in drug reward. During adolescence, peripheral systems, such as the gut microbiome, also undergo substantial changes. Emerging evidence suggests that disruptions to the gut microbiome can influence gene expression and drug reward behaviors in rodent models. In this study, we investigated the effects of oral antibiotics on morphine reward and prefrontal cortical gene expression in adolescent and adult mice. Using oral antibiotics to transiently disrupt the microbiome, we found that short-term antibiotic exposure reduced morphine place preference specifically in adolescent mice. In a separate cohort, we observed that antibiotic treatment altered the transcriptomic response to morphine in the medial prefrontal cortex across all age groups. Notably, the transcriptomic changes induced by antibiotics and morphine were age-specific, with distinct gene expression patterns observed in adolescents compared to adults. These findings establish a foundation for future research into the role of the gut microbiome in opioid reward and highlight potential gene pathways underlying age-dependent differences in opioid sensitivity.

overall_design: Male C57BL/6J wild type mice adolescent (start PND 25) or adult (start PND 55) given oral antibiotics (Abx) or remained on water and were given injections (s.c.) of saline or morphine (15 mg/kg) for 5 days.

first: Jonathon

middle: P

last: Sens

first: Ava

last: Shipman

first: Violet

last: Kimble

first: Christina

last: Coric

first: Katherine

last: Meckel

first: Drew

middle: D

last: Kiraly


title: Single cell sequencing of the effects of blocking lymphotoxin alpha in the mesenteric lymph node and spleen

city: New York

first: Emma

middle: Claire

last: Erlich

state: NY

address: 417 E 68th St

institute: Memorial Sloan Kettering

summary: TNFDARE+/- mice develop TNF-driven transmural ileitis and mesenteric inflammation, and lose body mass, reminiscent of human Crohn’s disease. Here, we report that B cells regulate body mass and intestinal permeability during ileitis in a manner that is linked to lymphotoxin (LT)-a but not LTb, whereas B cell LTab2 promoted mesenteric TLS that suppressed lymphatic outflow. Using genetic approaches and neutralizing reagents, we connect LTa3, a ligand for TNFRs, expressed by activated follicular B cells to their appearance in draining lymph nodes and the generation or persistence of IgA+ ileal plasma cells. Some of the same B cells also expressed TNF. Opposite to LTa, expression of TNF by B cells was disadvantageous to the development of IgA+ ileal plasma cells, suggesting counterbalancing interplay between LTa3 and TNF in ileitis. These data highlight a multi-faceted role of B cells in ileitis that includes an unexpected role for B cell-derived LTa3 in the maintenance of body weight.

overall_design: We used single cell RNA sequencing to compare the immune cells that had trafficked from the ileum to either the mesenteric lymph node or the spleen under four conditions to understand how blocking lymphotoxin alpha homotrimer can alter the immune system. All mice had undergone a bone marrow transplant 30 weeks previously. Half had received WT bone marrow and half received bone marrow from TNFdARE mice, who have aberrantly stable tumor necrosis factor (TNF) mRNA and subsequently develop Crohn's disease-like ileal inflammation; both donors universally expressed the photoconvertible protein KikGR. A day prior to photoconversion, mice were dosed with either an anti-LTa3 antibody or an isotype control forming four groups: 1) WT mice given an isotype control, 2) WT mice given the anti-LTa3 antibody, 3) TNFdARE mice given an isotype control or 4) TNFdARE mice given the anti-LTa3 antibody. Surgery was performed on anesthetized mice to photoconvert haematopoietically derived cells in the ileum. The mesenteric lymph nodes and spleen were collected 20 hours later.

middle: C

first: Quazim

middle: A

last: Alayo

first: Ayoung

last: Kim

first: Jichang

last: Han

first: Rachel

last: Mintz

first: Christopher

last: Huckstep

first: Heather

last: Ruiz

first: Rachael

last: Field

first: Taylor

last: Dunning

first: Leila

last: Saleh

first: Mark

last: Hoofnagle

first: Alexei

middle: V

last: Tumanov

first: Farshid

last: Guilak

first: Jonathan

last: Brestoff

first: Rafael

last: Czepielewski

first: Gwendalyn

last: Randolph


title: Study of MED1 acetylation in ER positive breast cancer cells [RNA-Seq III]

first: Douglas

last: Barrows

address: 1230 York Ave

institute: Rockefeller University

summary: Chromatin occupancy of MED1 and other Mediator components, as well as Pol II, were studied in MCF7 cells. MED1 acetylation affects chromatin occupancy of its related factors, which was analyzed with CUT&RUN-seq, ChIP-seq and sequential ChIP-seq assay (by pan-acetyl-lysine antibody) with MED1 KR mutant (HA tag) where acetylation residues were replaced. Combined with RNA seq analysis for gene expression in MCF7 cells with MED1 KO and KR/KQ MED1 ectopic expression, the role of MED1 acetylation in gene transcription control was investigated.

overall_design: ChIP-seq and/or CUT&RUN-seq for MED1 and other Mediator compoments, as well as Pol II, were conducted in MCF7 cells. In addition to normal MCF7 cells, the cells with depletion of endogenous MED1 and ectopic expression of WT or KR mutant MED1 (HA tag) were also tested. Sequential ChIP-seq by FLAG (for MED1) antibody and pan-acetyl-lysine antibody were conducted. RNA seq (for mature mRNA) was conducted for MCF7 cells with MED1 KO (vs control), and 6KR/Q MED1 ectopic expression (Vs WT MED1 expression).

first: Ran

last: Lin

first: Thomas

last: Carroll

first: Robert

last: Roeder


title: Study of MED1 acetylation in ER positive breast cancer cells [CUT&Run]


title: Study of MED1 acetylation in ER positive breast cancer cells [RNA-Seq IV]


title: Single cell transcriptome for three Drosophila intestinal derived cell lines

city: Bloomington

first: Arthur

last: Luhur

state: IN

address: 1001 E Third St, DGRC Department of Biology

institute: Indiana University

summary: We report the single cell transcriptome for three distinct Drosophila intestinal derived cell lines.

overall_design: Cells were harvested from defined passage to be used for single cell transcriptome analysis.

first: Daniel

last: Mariyappa

first: Andrew

last: Zelhof


title: TSC SEGA Atlas [snRNA-seq]

city: Clemson

first: David

middle: Matthew

last: Feliciano

state: South Carolina

address: 132 Long Hall

department: Biological Sciences

institute: Clemson University

summary: Tuberous Sclerosis Complex (TSC) is a genetic disorder characterized by benign growths called hamartomas that can be a significant cause of morbidity and mortality. Hamartomas are found along the neurocutaneous axis including along the brain’s ventricles near the boundaries of the striatum. They can be categorized by size and include small subependymal nodules (SENs) or larger subependymal giant cell astrocytomas (SEGAs). SEGAs are associated with changes in neurological presentation and are a substantial cause of hydrocephalus if left untreated. Immunohistochemistry, electron microscopy, and bulk RNA sequencing have been used to examine SEGA cellular composition. However, there remains considerable debate over the results because bulk techniques do not parcellate transcriptomic changes within individual cells and SEGAs contain cells with abnormal morphology that betray canonical classification. Here, we describe a quantitative analysis of SEGA cell identities based on single nuclei RNA sequencing.

overall_design: Single Nuclei RNA Sequencing of Tuberous Sclerosis Complex Subependymal Giant Cell Astrocytomas and Caudate Nucleus from Human Patients

first: Trudy

last: Mackay

first: Vijay

last: Shankar


title: Immunopathogenesis of lethal H5N1 avian influenza virus clade 2.3.4.4b infection in macaques

city: Boston

first: Dan

last: Barouch

state: MA

address: 3 Blackfan Cir

department: CVVR

institute: Beth Israel Deaconess Medical Center

summary: The H5N1 avian influenza virus clade 2.3.4.4b outbreak represents a major pandemic threat for humans, with some reported cases of severe and fatal respiratory illness. A key unanswered question is the pathogenesis of severe H5N1 disease following respiratory infection. In this study, we explored mechanisms of pathogenesis of severe H5N1 disease in cynomolgus and rhesus macaques following infection with the H5N1 isolate A/Texas/37/2024 (huTX37-H5N1). Cynomolgus macaques developed severe pneumonia that was lethal in 100% of macaques by 7 days post-infection. By contrast, rhesus macaques demonstrated dose-dependent mortality, and surviving animals showed protective immunity against high-dose re-challenge. A multi-omics analysis demonstrated that H5N1 infection was characterized by robust induction of proinflammatory cytokines, innate immune cells, complement, coagulation, apoptosis, and immune exhaustion pathways. Taken together, our data indicate inflammation and immune dysregulation as key mechanisms of H5N1 pathogenesis in nonhuman primates.

sample_organism:
Macaca fascicularis
Macaca mulatta

platform_organism:
Macaca fascicularis
Macaca mulatta

overall_design: This study was performed in accordance with an approved Animal Care and Use Committee protocol and following recommendations from the Guide for the Care and Use of Laboratory Animals of the Office of Animal Welfare, National Institutes of Health and the Animal Welfare Act of the US Department of Agriculture, in an AAALAC-accredited facility. The macaques were placed in high biocontainment (BSL-3) inside a climate-controlled room with a fixed 12-hour light-dark cycle. Animals were singly housed during the H5N1 challenge period in HEPA filtered microisolator caging (Rockville Steel, MD). They were provided a commercial monkey chow, treats, and fruit twice daily with water ad libitum. Animals that were noted to have reduced appetite were provided Gatorade. Environmental enrichment was provided with manipulanda and commercial toys. The animals were monitored at least twice daily (AM/PM) throughout the study. All sample processing and sample removal from high biocontainment followed approved biosafety protocols. 9 outbred Mauritian-origin cynomolgus monkeys (Macaca fascicularis) and 9 outbred Indian-origin rhesus macaques (Macaca mulatta), adult male and female ages 3-13 were randomly allocated to groups. All monkeys were housed at Bioqual, Rockville, MD. In the first study, 9 cynomolgus macaques were inoculated with 109 TCID50 H5N1 by the combination IN+IT route (N=6) or by the IN only route (N=3). In the IN+IT group, 3 animals were utilized for PET-CT imaging and were not sampled for BAL to avoid interference with the imaging. The virus was administered as 1 ml by the intranasal (IN) route and/or 1 ml by the intratracheal (IT) route. In the second study, 9 rhesus macaques were inoculated with 109, 107, or 105 TCID50 (N=3/group) H5N1 by the IN+IT routes. On day 28 following initial infection, the surviving rhesus macaques (N=6) were re-challenged with 109 TCID50 H5N1.

first: Hanne

last: Andersen

first: Malika

last: Aid-Boudries


title: Vagal TRPV1+ sensory neurons regulate myeloid cell dynamics and protect against influenza virus infection

first: Adam

last: Haber

address: 665 Huntington Ave

department: Environmental Health

institute: Harvard T.H. Chan School of Public Health

summary: Influenza viruses are a major global cause of morbidity and mortality. While vagal TRPV1+ nociceptive sensory neurons are known to mediate defenses against harmful agents, their function in lung antiviral defenses remains unclear. Our study reveals that both systemic and vagal-specific ablation of TRPV1+ nociceptors reduce survival in mice infected with influenza A virus (IAV). Despite no difference in viral load, mice lacking TRPV1+ neurons exhibited increased viral spread, exacerbated lung pathology, and elevated levels of pro-inflammatory cytokines. Loss of TRPV1+ neurons altered the lung immune landscape, including an expansion of neutrophils and monocyte-derived macrophages. Transcriptional analysis revealed impaired interferon signaling in these myeloid cells and an imbalance in distinct neutrophil sub-populations in the absence of nociceptors. Furthermore, antibody-mediated depletion of myeloid cells during IAV infection significantly improved survival, underscoring a role of TRPV1+ nociceptors in preventing pathogenic myeloid cell states that contribute to IAV-induced mortality.

overall_design: To define the role of TRPV1+ neurons in regulating the immune compartment of the lung during IAV infection, we performed single-cell RNA sequencing of lung immune cells isolated from vehicle and RTX-treated naïve animals or IAV PR8-infected animals at 7 days post-infection

first: Nicole

last: Almanzar

first: Daping

last: Yang

first: Jingya

last: Xia

first: Swalpa

last: Udit

first: Prabhu

last: Joshi

first: Sandeep

last: Adhikari

first: Daisy

last: Hoagland

first: Stephen

last: Yeung

first: Camille

last: Khairallah

first: Tomas

last: Huerta

first: Antonia

last: Wallrapp

first: Benjamin

last: Umans

last: Sarden

first: Ozge

last: Erdogan

first: Nadia

last: Baalbaki

first: Jiawei

last: Hou

first: Anna

last: Beekmayer-Dhillon

first: Juhyun

last: Lee

first: Kimberly

last: Meerschaert

last: Liberles

first: Ruth

last: Franklin

first: Bryan

last: Yipp

first: Kamal

last: Khanna

first: Pankaj

last: Baral

first: Isaac

last: Chiu


title: Elevation of KIR+CD8+ T cells during human pregnancy

city: PITTSBURGH

first: Jing

last: Li

state: PA

address: 5117 Centre Ave 2.26b

institute: University of Pittsburgh

summary: During pregnancy, immune responses must balance fetal protection from infections with tolerance of the semi-allogeneic fetus. However, the mechanisms regulating maternal-fetal tolerance remain poorly understood. Recently, we identified KIR+CD8+ T cells as a previously underappreciated regulatory subset important for suppressing self-reactivity in human autoimmune and infectious diseases. To better understand what other roles these cells might play, we asked whether they are active during pregnancy. We first observed an increased frequency of KIR+CD8+ T cells in the peripheral blood of pregnant women at the second trimester, especially in those carrying a male fetus. In vitro, KIR+CD8+ T cells inhibited the alloreactive responses of maternal T cells against irradiated cord blood cells and suppressed HY-specific CD8+ T cells from mothers with a male fetus. Therefore, the higher induction of KIR+CD8+ T cells in mothers carrying a male fetus may help suppress additional allogenic responses triggered by Y chromosome antigens. Longitudinal analysis showed that KIR+CD8+ T cells undergo expansion and differentiate into functional cytotoxic cells during pregnancy. Single cell RNA-seq analysis of decidual CD8+ T cells from early pregnancy revealed elevated number and activity of KIR+ CD8+ T cells at the maternal-fetal interface. In addition, increased levels of KIR+CD8+ T cells correlated with pregnancy disorders (e.g., spontaneous abortion and preeclampsia). Taken together, our findings suggest an important role of KIR+CD8+ T cells in the maintenance of maternal tolerance by suppressing fetal-specific alloreactive T cells. They may also be useful as predictive biomarkers or drug targets for human pregnancy disorders.

overall_design: PBMCs from pregnant women collected at different time points throughout pregnancy or in the postpartum period were labeled with unique tags using a BD™ Hu Single Cell Sample Multiplexing Kit (no. 633781) for 20 min at room temperature. Cells were then washed three times with PBS, after which the barcoded PBMCs were pooled and stained with viability dye and flow antibodies. Live KIR+CD8+ T cells were sorted into sample buffer and immediately loaded onto the BD Rhapsody Cartridge using the BD Rhapsody Cartridge Reagent Kit (no. 633731) per manufacturer’s instructions. Single-cell cDNA was prepared using the BD Rhapsody cDNA Kit (no. 633773). This was followed by the preparation of single-cell mRNA, TCR, and tag libraries using the BD Rhapsody™ TCR/BCR Multiomic Assay for Targeted Kit (catalog no. 666622), along with primers from the BD Rhapsody Immune Response Panel (399 genes; catalog no. 633750) and custom primers. Sequencing was carried out using NovaSeq (Illumina, San Diego, CA) in Stanford Genomics Sequencing Center and Novogene.


title: Aurora kinase A promotes trained immunity via regulation of endogenous S-adenosylmethionine metabolism

city: Guangzhou

first: Mengyun

address: Xingang Road

institute: SYSU

summary: Innate immune cells can acquire a memory phenotype, termed trained immunity, but the mechanism underlying the regulation of trained immunity remains largely elusive. Here, we demonstrate that inhibition of Aurora kinase A (AurA) dampens trained immunity induced by β-glucan. ATAC-seq and RNA-seq analysis reveals that AurA inhibition restricts chromatin accessibility of genes associated with inflammatory pathways such as JAK-STAT, TNF and NF-κB pathways. Specifically, AurA inhibition promotes nuclear localization of FOXO3 and the expression of glycine N-methyltransferase (GNMT), a key enzyme responsible for adenosylmethionine (SAM) consumption. Metabolomic analysis confirms a reduction in SAM level upon AurA inhibition. As a result of SAM deficiency, trained mouse macrophages exhibit decreased H3K4me3 and H3K36me3 enrichment on gene regions of Il6 and Tnfα. Additionally, the tumor inhibition effect of β-glucan is notably abolished by AurA inhibition. Together, our findings identify an essential role of AurA in regulating trained immunity via a methylation-dependent manner by maintaining endogenous SAM level through mTOR-FOXO3-GNMT axis

overall_design: Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq) in trained BMDMs

first: Xiaojun

last: Xia


title: Study of MED1 acetylation in ER positive breast cancer cells [RNA-Seq II]

first: Douglas

last: Barrows

first: Ran

last: Lin

first: Thomas

last: Carroll

first: Robert

last: Roeder


title: Consistent self-organized emergence of hyaline cartilage in hiPSC-derived multi-tissue organoids

city: Minneapolis

first: Huzefa

last: Husain

state: MN

address: 312 Church St., Nils Hasselmo Hall 7-256

department: Biomedical Engineering

institute: University of Minnesota

summary: Existing protocols for in vitro hyaline cartilage production utilizing human induced pluripotent stem cells (hiPSCs) have several challenges including a complex culturing process that uses undefined culture media, phenotypic instability, and batch-to-batch variability of the cell product. Here, our primary objective is to describe a simple, xeno- and feeder-free protocol for the generation of hyaline cartilage utilizing multi-tissue organoids (MTOs). We investigated gene regulatory networks during hiPSC-MTO differentiation using RNA sequencing and bioinformatics analyses, as well as histological and immunohistochemical methods. Interplays between bone morphogenetic protein (BMP) and neural fibroblast growth factor (FGF) pathways associated with the phenotypic transition of MTOs are described. Comparisons across transcriptomes revealed that the expression of chondrocyte-specific genes in MTOs correlates strongly with fetal lower limb chondrocytes. Single-cell RNA sequencing findings confirmed that the majority of cells belonged to the chondrogenic lineage and that they were similar across MTO batches, suggesting uniformity of the culture process. Collectively, these findings demonstrate the consistent emergence of hyaline cartilage in MTOs and the molecular pathways that govern this process, thereby establishing an accessible source of functional chondrocytes for future therapeutic evaluations.

overall_design:
To investigate the inter- and intra-variabliiaty of gene expression profiles of Multi-Tissue Organoids (MTOs) generated from hiPSCs
Explore the cellular diveristy within MTOs

middle: I

first: Manci

first: Juan

middle: E

last: Abrahante

first: Natalia

last: Mancipe

first: Amanda

last: Vegoe

first: Yi

middle: W

last: Chai

first: Beth

last: Lindborg

first: Marc

last: Tompkins

first: Brenda

last: Ogle

first: Peter

last: Larsen

first: Timothy

last: O'Brien

first: Ferenc

last: Toth


title: TET-deficient knockout cells transit between pluripotent states and exhibit precocious germ cell differentiation

city: Edinburg

first: Sara

last: Gonzalez Brito

email: saraglezbr@gmail.com, s1659595@ed.ac.uk

state: Scotland

address: 5 Little France Dr

country: United Kingdom

institute: University of Edinburgh

summary: TET1, TET2 and TET3 are DNA demethylases with critical roles during early embryonic development and cell differentiation. To assess the contributions of TET proteins to cell function during early development, single and compound knockouts of Tet genes in mouse pluripotent embryonic stem cells (ESCs) were generated. ESCs lacking all alleles of Tet1 and Tet2, or all alleles of Tet1, Tet2 and Tet3 form epiblast-like cells and epiblast stem cells in culture, indicating that TET proteins are not required to transit between naïve, formative and primed pluripotency. Moreover, in differentiation protocols, ESCs with double-knockouts of Tet1 and Tet2 or triple-knockouts of Tet1, Tet2 and Tet3 do not differentiate normally , fail to activate somatic gene expression and retain expression of pluripotency transcription factors. Therefore, TET1 and TET2, but not TET3 act redundantly to facilitate somatic differentiation. Importantly, ESCs with double knockouts of Tet1 and Tet2, or triple knockouts of Tet1, Tet2 and Tet3 cells do differentiate into primordial germ cell-like cells (PGCLCs). Furthermore, PGCLC differentiation of Tet1, Tet2 double knockouts, or Tet1, Tet2, Tet3 triple knockouts occurs with high efficiency in the presence or absence of PGC-promoting cytokines. Moreover, acquisition of a PGCLC transcriptional programme occurs more rapidly in the absence of TET proteins. These results establish TET proteins as key regulators enabling epiblast cells to choose between somatic and germline fates. The functions of Tet1 and Tet2, but not Tet3 are required to enable epiblast cells to undergo somatic differentiation and in the absence of TET protein function, epiblast cell differentiation defaults to the germline.

overall_design: Wild type and TET tripple knockout (TET-TKO) cells were differentiated into first EpiLCs and then PGCLC aggregates in the presence or absence of cytokines. Cells were collected at day 0 (EpiLCs), day 2 and day 6 of differentiation, total RNA was extracted, depleted for rRNA and sequenced using the NextSeq 2000 platform.

first: Raphaël

last: Pantier

first: Elisa

last: Barbieri

first: Ella

last: Thomson

first: Tulin

last: Tatar

last: Colby

first: Man

last: Zhang

first: Ian

last: Chambers


title: Semaphorin 3E-Plexin-D1 pathway regulates ovulation, granulosa cell luteinization, and ovarian angiogenesis in mice

city: Ithaca

last: Ren

address: 203 Morrison Hall

department: Animal Science

institute: Cornell University

summary: Ovulation is induced by the luteinizing hormone surge and accompanied by granulosa cell luteinization and ovarian angiogenesis. Sema3E-Plexin-D1 pathway regulates angiogenesis in other tissues, but its role in the ovary was unknown. We report herein that the expression of Sema3E and its receptor, Plexin-D1, is dynamically regulated in the mouse ovary downstream of the LH surge. This regulation is mediated by CCAAT/enhancer-binding proteins α and β through modulating chromatin accessibility. Intraovarian injection of recombinant Sema3E results in reduced ovulation, impaired corpus luteum formation, and aberrant ovarian angiogenesis. These in vivo physiological abnormalities are consistent with altered expression of genes regulating these processes, and with data from in vitro cultured granulosa cells and/or ovarian stromal tissues treated with Sema3E or Plexin-D1 neutralizing antibody. Our findings shed light on the important role of Sema3E-Plexin-D1 pathway in the ovary, pinpointing it as a potential therapeutic target for fertility and infertility management.

overall_design:
To explore the functional impact of evaluated Sema3E in the mouse ovary, we performed intraovarian injection of mouse recombinant Sema3E or IgG before hCG stimulation during standard superovulation.
We then isolated ovarian granulosa cells and ovarian stromal tissue at 8 h post-hCG from ovaries injected with IgG vs Sema3E and performed bulk RNA-sequencing analysis.

first: Hanxue


title: Inhibiting endothelial Rhoj blocks pro-fibrotic vascular intussusception and angiocrine factors to sustain lung regeneration

city: Chengdu

first: Jie

last: Ma

address: No.17 People's South Road

institute: Sichuan university

summary: Proliferation of vascular endothelial cells (ECs) is critical for providing sufficient cells lining the neo-vascular lumen.  Moreover, expanding ECs need to undergo multiple steps to line new lumen,  functionalizing anti-thrombotic and anti-inflammatory interface that prevents extravasation of inflammatory cells, maintains blood perfusion, and facilitates cellular crosstalk. Therefore, productive angiogenesis in regeneration requires formation of endothelial tight junction, arrangement of endothelial apical lumen, and alignment of basolateral side juxtaposed with alveolar epithelial cells.  As a result, we used single cell RNA sequencing (scRNA-seq) to detect the function of diverse EC clusters.

overall_design: Endothelial cells of WT mice in the sham operation group and endothelial cells of WT mice and conditional knockout mice on day 7 after PNX were selected for single cell sequencing

first: Liyin

first: Xu

first: Lanlan

first: Hua

first: Yulei

last: Zhu

first: Xingming

last: Huang

first: Ting

first: Xiangdong

last: Tang

first: Yuan

last: Wang

first: Lu

last: Chen

first: Qiang

last: Pu

first: Liming

last: Yang

first: Zhongwei

last: Cao

first: Bi-Sen

last: Ding


title: OKN-007 is an Effective Anticancer Therapeutic Agent Targeting Inflammatory and Immune Metabolism Pathways in Endometrial Cancer.

city: Oklahoma city

first: Bethany

last: Hannafon

state: OK

address: 975 NE 10th Street

department: Obstetrics and Gynecology

institute: University of Oklahoma Health Sciences Center

summary:
Advanced-stage endometrial cancer patients typically receive a combination of platinum and paclitaxel chemotherapy. However, limited treatment options are available for those with recurrent disease, and there is a need to identify alternative treatment options for the advanced setting. Our goal was to evaluate the pre-clinical efficacy and mechanism of action of the anti-cancer drug Oklahoma Nitrone 007 (OKN-007) alone and in combination with carboplatin and paclitaxel in endometrial cancer. The effect of OKN-007 on the metabolic viability of endometrial cancer cells in both two- and three-dimensional (2D and 3D) cultures, as well as on clonogenic growth, in vitro was assessed. We also evaluated OKN-007 in vivo using an intraperitoneal xenograft model and targeted gene expression profiling to determine the molecular mechanism and gene expression programs altered by OKN-007. Our results showed that endometrial cancer cells were generally sensitive to OKN-007 in both 2D and 3D cultures. OKN-007 displayed a reduction in 3D spheroid and clonogenic growth. Subsequent targeted gene expression profiling revealed that OKN-007 significantly downregulated the immunosuppressive immunometabolic regulatory enzyme indolamine 2,3-dioxygenase 1 (IDO1) (-11.27-fold change) and modulated upstream inflammatory pathways that regulate IDO1 expression (interferon- (IFN-), Jak-STAT, TGF-β, and NF-kB), downstream IDO1 effector pathways (mTOR and aryl hydrocarbon receptor (AhR)) and altered T-cell co-signaling pathways. OKN-007 treatment reduced IDO1, SULF2, and TGF-β protein expression in vivo, and inhibited TGF-β, NF-kB, and AhR- receptor-mediated nuclear signaling in vitro. These findings indicate that OKN-007 surmounts pro-inflammatory, immunosuppressive, and pro-tumorigenic pathways and is a promising approach for the effective treat endometrial cancer.
Targeted mRNA expression profiling was performed using the nCounter ® Tumor Signaling 360™ Panel (NanoString Technologies), which comprises 780 genes involved in cancer-related pathways and internal reference genes. Raw data were normalized and log2 transformed using the geNorm algorithm, differential expression (DE) was determined using the Generalized Linear Model (GLM), and Gene Set Analysis (GSA) was used to summarize the directed global significance score by calculating the change in regulation within each defined gene set relative to the baseline.  Pathway enrichment was also calculated for gene sets as defined in multiple databases, including WikiPathways, REACTOME, MSigDB, and Gene Ontology, and FDR adjustment and p-Elim pruning scores were calculated when appropriate. DE, GSA, and other pathway enrichment were conducted using ROSALIND software (v. 3.38.5.1).  Genes with >1.5-or <1.5-fold change at P < 0.05 were considered significantly differentially expressed.

overall_design: For this study, 4–6-week-old female athymic Nude-Foxn1 nu mice (Envigo) were used. Tumors were established by intraperitoneal injection of CS99 cells (1x10^6 /100 μL). Mice were randomized into four groups: 1. Untreated Control (UT) (regular drinking water), 2. OKN-007 (150 mg/kg daily in drinking water), and 3.Carboplatin/paclitaxel C-T (50 mg/kg and 15 mg/kg, respectively, once weekly, intraperitoneally), 4. OKN-007/Carboplatin/paclitaxel (150 mg/kg, 50 mg/kg, and 15 mg/kg, intraperitoneal  C-T administered once weekly; OKN-007 was administered daily in drinking water). Portions of the dissected tumors were snap-frozen, then transferred to RNA-later Ice (Invitrogen), and RNA and proteins were extracted using the mirVana PARIS kit (Invitrogen).

first: Sugantha

last: Elayapillai


title: Study of MED1 acetylation in ER positive breast cancer cells [ChIP-seq]

first: Douglas

last: Barrows

first: Ran

last: Lin

first: Thomas

last: Carroll

first: Robert

last: Roeder


title: Study of MED1 acetylation in ER positive breast cancer cells [HiCAR-seq]


title: Study of MED1 acetylation in ER positive breast cancer cells [RNA-seq]


title: Effect of polyIC administration on gene expression in decidual tissues of E13.5 mice

city: Hefei

first: Qi

middle: wu

last: Bian

state: Anhui

address: Division of Life Sciences and Medicine, 443 Huangshan Road

department: Life sciences and medicine

institute: University of Science and Technology of China

summary: Previous research indicate that maternal immune activation (MIA) correlated with increased frequency of autism spectrum disorder (ASD) in offspring. Our data sugests that aberrant decidual NK cells are required for MIA-induced neurodevelopment and behavioral disorders. To determine what triggers dNK cells to react to MIA at the maternal-fetal interface, we evaluated the DEGs of decidua tissue samples from dams triggered with polyIC or saline control.

overall_design: Decidual tissues were isolated from saline- or polyIC-treated dams at E13.5 for whole-genome transcriptome analyses by RNA-seq.

first: Qiwu


title: Effect of polyIC administration on gene expression in decidual NK cells of E13.5 mice

summary: Previous research indicate that maternal immune activation (MIA) correlated with increased frequency of autism spectrum disorder (ASD) in offspring. Our data sugests that maternal NK cells facilitate MIA-induced neurodevelopment and behavioral disorders. To determine how aberrant maternal NK cells instruct the developmental trajectory of the fetal brain environment, we evaluated the DEGs of decidua NK cells from dams triggered with polyIC or saline control.

overall_design: Decidual NK cells were isolated from saline- or polyIC-treated dams at E13.5 for whole-genome transcriptome analyses by RNA-seq.


title: Study of MED1 acetylation in ER positive breast cancer cells

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

overall_design: Refer to individual Series


title: Bulk RNA sequencing of de novo and radiation-recurrent head and neck squamous cell carcinoma tumors

status: Public on Jul 31 2025

city: Milwaukee

first: Abdullah

middle: A.

last: Memon

state: Wisconsin

address: 9200 W Wisconsin Ave

department: Department of Otolaryngology and Communication Sciences

institute: Medical College of Wisconsin

summary: We performed bulk RNA sequencing on head and neck squamous cell carcinoma (HNSCC) tumors to identify, characterize, and select specifc cancer-testis antigens (CTAs) as potential precision immuno-oncologic targets. Specifically, we compared CTA expression between previously untreated (de novo) tumors and radiation-recurrent tumors to assess expression patterns in different clinical settings.

overall_design: Tumor samples were taken from patients undergoing standard-of-care surgical resection. Samples were categorized based on whether patients presented with a de novo HNSCC or underwent biopsy for an in-field recurrence in a previously irradiated tumor bed at the time of salvage surgery.

first: Joseph

last: Zenga


title: Aryl hydrocarbon receptor ligands drive pancreatic cancer initiation and progression through pro-tumorigenic T cell polarization

city: Ann Arbor

first: Timothy

last: Frankel

state: MI

address: 1500 East Medical Center Dr

institute: University of Michigan

summary: Here, we aimed to determine whether AhR ligands found in cigarette smoke, such as TCDD, promote pancreatic dysplasia and PDAC progression. We utilized an orthotopic mouse model of PDAC and collected pancreatic tissue from mice treated with either TCDD or a vehicle control and performed single-cell RNA sequencing to assess changes in the tumor microenvironment.

overall_design: Pancreata from orthotopic model of pancreatic tumorigenesis collected and subjected to single cell RNA sequencing.

first: Brian

last: Griffith

first: Padma

last: Kadiyala

first: Katelyn

last: Donahue

first: Ahmed

last: Elhossiny


title: Single-cell sequencing of dorsal root ganglion from IMQ-induced psoriasiform dermatitis mice.

city: wuhan

first: Jian

last: Jiang

address: jiefang avenue

institute: hospital

summary: We divided the e male C57BL/6 mice into two groups: a non-treatment group and an IMQ-induced psoriasiform dermatitis group. The dorsal root ganglia of the mice were extracted, enzymatically digested, and then enriched using Percoll. Subsequently, single-cell RNA sequencing was performed.

overall_design: a non-treatment group (named C-DRG) and an IMQ-induced psoriasiform dermatitis group(named I -DRG).

first: Xin

last: Liu


title: Targeting Triple-Negative Breast Cancer Using Allogeneic Stem Cell-Engineered Mesothelin-Specific CAR-NKT Cells with Potent Antitumor Activity

city: Los Angeles

first: Yichen

last: Zhu

state: California

address: 610 Charles E Young Drive S

institute: University of California, Los Angeles

summary: Triple-negative breast cancer (TNBC) is an aggressive subtype of breast cancer characterized by the lack of ER, PR, and HER2 expression. Its aggressive behavior, high degree of tumor heterogeneity, and immunosuppressive tumor microenvironment (TME) are associated with poor clinical outcomes, rapid disease progression, and limited therapeutic options. Although chimeric antigen receptor (CAR)-engineered T cell therapy has shown certain promise, its applicability in TNBC is hindered by antigen escape, TME-mediated suppression, and the logistical constraints of autologous cell production. In this study, we employed hematopoietic stem and progenitor cell (HSPC) gene engineering and a feeder-free HSPC differentiation culture to generate allogeneic IL-15-enhanced, mesothelin-specific CAR-engineered invariant natural killer T (Allo15MCAR-NKT) cells. These cells demonstrated robust and multifaceted antitumor activity against TNBC, mediated by CAR- and NK receptor-dependent cytotoxicity, as well as selective targeting of CD1d+ TME immunosuppressive cells through their TCR. In both orthotopic and metastatic TNBC xenograft models, Allo15MCAR-NKT cells demonstrated potent antitumor activity, associated with robust effector and cytotoxic phenotypes, low exhaustion, and a favorable safety profile without inducing graft-versus-host disease. Together, these results support Allo15MCAR-NKT cells as a next-generation, off-the-shelf immunotherapy with strong therapeutic potential for TNBC, particularly in the context of metastasis, immune evasion, and treatment resistance.

first: Yan-Ruide

last: Li

first: Lili

last: Yang


title: Derivation of Embryonic Stem Cells Across Avian Species

city: Pasadena

first: Xi

last: Chen

address: 1200 E. California Blvd

institute: California Institute of Technology

summary: Chimeric and germline-competent embryonic stem cells (ESCs) have been derived from mice and rats, but not from other species. Here, we report the development of conditions for the derivation of ESCs from chickens and several other avian species. Chicken ESCs express core pluripotency markers and can efficiently differentiate into cells of all three germ layers. Furthermore, chicken ESCs can form high rates of chimerism when injected into chicken embryos both ex ovo and in ovo. More importantly, chicken ESCs can give rise to germ cells both in vitro and in ovo, indicating that chicken ESCs are germline competent. Interspecies chimeras can also be generated by injecting other avian ESCs into chicken embryos. Establishment of germline competent avian ESCs opens up a new avenue for producing genetically engineered avian species.

sample_organism:
Anser cygnoides
Coturnix japonica
Struthio camelus australis

overall_design: We derived embryonic stem cell lines using primary cells from EGK.X stage embryos of quail, goose and ostrich. We then performed gene expression profilling analysis using data obtained from RNA-seq of quail, goose and ostrich ES cell lines. Each type of sample was prepared in duplicate.

first: Qi-Long

last: Ying


title: Affymetrix SNP array data of salivary gland tumors in AFAP family

city: Montreal

first: Fiona

last: Chan Pak Choon

state: QC

address: 3755 Côte-Sainte-Catherine

department: Human Genetics

country: Canada

institute: McGill University

type:
Genome variation profiling by SNP array
SNP genotyping by SNP array

summary: Copy-number and loss of heterozygosity analysis of salivary gland tumors in a proband with attenuated familial adenomatous polyposis (AFAP), using Affymetrix OncoScan and CytoScan HD arrays

overall_design: Three tumor DNA samples from one individual were analysed: two FFPE-derived parotid basal cell adenocarcinomas (BCACs) using the OncoScan CNV Assay, and one fresh frozen submandibular BCAC using the CytoScan HD Array Arrays were processed using Affymetrix ChAS v4.2 with the hg19 genome build

last: Chan-Pak-Choon

first: Catherine

last: Beaumont

first: José

last: Camacho Valenzuela

first: Josianne

last: Leblanc

first: Sonja

last: Dahlum

first: Reiner

last: Siebert

first: François

last: Thuot

first: Marc

last: Pusztaszeri

first: Jacinthe

last: Chênevert

first: Paz

last: Polak

first: Tania

last: Cruz Marino

first: Barbara

last: Rivera

first: William

last: Foulkes


title: Effect of downregulated P4HA2 on gene expression during brachytherapy of KYSE30 cells

city: Nanjing

first: Jian

last: Lu

address: 87 Dingjiaqiao Road,

institute: Zhongda Hospital, Southeast University

summary: Lineage-specific endoplasmic reticulum-related genes and proteins are crucial for the radiosensitivity of tumor cells. Here, we report that the P4HA2 protein is a key regulator in the brachytherapy of esophageal cancer. Downregulation of P4HA2 leads to increased radiosensitivity of tumor cells, which can be rescued by exogenous P4HA2. Additionally, P4HA2 interacts with ATAD3A to regulate the sensitivity of esophageal cancer to brachytherapy, and the underlying mechanism remains unknown. In summary, our data provide a molecular framework for exploring the changes in gene lineages after P4HA2 downregulation and brachytherapy.

overall_design: RNA-seq analysis of wild-type KYSE30 cells (control) and their knockdown derivatives under cumulative 4 Gy of brachytherapy (ShP4HA2 + brachytherapy).

first: Xijuan

last: Yao


title: A Histone-Centric Multi-Omics Study Shows that Increased H3K4 Methylation Sustains Triple Negative Breast Cancer Phenotypes

city: Milan

first: Tiziana

last: Bonaldi

address: Via Adamello 16

department: Department of Experimental Oncology

country: Italy

institute: European Institute of Oncology

summary: Altered histone post-translational modifications are frequently associated with cancer. Here, we applied mass-spectrometry to study the epigenetic landscapes of breast cancer subtypes, with a particular focus on triple-negative breast cancers (TNBCs), a heterogeneous group lacking welldefined molecular targets and effective therapies. The analysis of over 150 tumors revealed epigenetic signatures that discriminate TNBCs from the other BC subtypes, and that distinguish TNBC patients with different prognoses. Employing a multi-OMICs approach integrating epigenomics, transcriptomics, and proteomics data, we investigated the mechanistic role of increased H3K4 methylation in TNBCs, demonstrating that H3K4me2 sustains the expression of genes associated with the TNBC phenotype. Through CRISPR-mediated editing, we established a causal relationship between H3K4me2 and gene expression for several targets. Furthermore, treatment with H3K4 methyltransferase inhibitors reduced TNBC cell growth in vitro and in vivo. Collectively, our result unraveled a novel epigenetic pathway implicated in TNBC pathogenesis and suggests new opportunities for targeted therapy.

overall_design: ChIP-seq data of the histone modification H3K4me2 in MDA-MB-231 cell line. Cells were treated with the OICR-9429 inhibitor (antagonist of the WDR5 domain), with DMSO or untreated. For the quantitative comparison between cells treated with the inhibitor and cells treated with DMSO, 5% Drosophila spike-in was added before the incubation with antibodies.

first: Roberta

last: Noberini

first: Giulia

last: Robusti

first: Alessandro

last: Vai

first: Evelyn

last: Oliva Savoia

first: Maria Giovanna

last: Jodice

first: Giovanni

last: Bertalot

first: Betül

last: Çat

first: Isabella

last: Pallavicini

first: Giuseppina

last: Bonizzi

first: Maria

last: Capra

first: Nicola

last: Fusco

first: Federico

last: Zambelli

first: Salvatore

last: Pece

first: Giulio

last: Pavesi

first: Saverio

last: Minucci


title: Cancer-induced nerve injury promotes resistance to anti-PD-1 therapy [scRNA-seq II]

city: Kingston

first: Sebastien

last: Talbot

state: ON

address: 18 Stuart st

department: DBMS

institute: Queen's University

summary: Peri-neural invasion (PNI) is a well-established poor prognostic factor in multiple cancer types. However, the mechanisms driving the PNI's detrimental clinical effect remain elusive. Here, we provide clinical and mechanistic insights into PNI and cancer-induced injury of tumor-associated nerves (TANs) and their role in resistance to anti-PD-1 therapy. Our work demonstrates that poor response to anti-PD-1 therapy in cutaneous squamous cell carcinoma (cSCC), melanoma, and gastric cancer is associated with PNI and TANs injury. Ultrastructural electron microscopy analysis reveals that direct contact between cancer cells and nerve fibers leads to cancer-induced nerve injury (CINI) via myelin degradation. Injured neurons respond by autonomously initiating an interleukin (IL)-6 and interferon (IFN) type I inflammatory response. This inflammatory response alters the immune activity in the peri-neural niche in melanoma, cSCC, and pancreatic adenocarcinoma, leading to an immuno-suppressive activity aimed at nerve healing and regeneration. As the tumor grows, the CINI burden increases, the inflammatory signal within the niche becomes chronic, and eventually skews the general immune tone within the tumor microenvironment to a suppressive and exhaustive state. The CINI-driven anti-PD-1 resistance can be reversed by targeting multiple steps in the CINI signaling process: denervating the tumor, conditional knockout of the transcription factor mediating the injury signal within neurons (cKO-Atf3), knockout of the IFN-a receptor signaling (Ifnar1-/-), or by combining anti-PD-1 and anti-IL-6-receptor blockade. Our findings demonstrate the direct immuno-regulatory roles of TANs and their therapeutic potential.

overall_design: Six-week-old male and female littermate control (Trpv1wt::Diptheria-Toxinfl/wt) mice were intradermally injected in the left paw with 2×105 B16F10 cells or non-tumorigenic keratinocytes (MPEK-BL6). Seven days later, tumor-infiltrating neurons (or neurons in MPEK-injected skin) were retrogradely labeled by an acute intra-tumor injection of AAV9-CAG-mCherry-WPRE-SV40p (10 µL, 5.5×109). Fourteen days post-inoculation, mice were euthanized, and the L3–L5 dorsal root ganglia (DRG) were harvested and digested. Most CD45+ cells were depleted using the MagniSort Mouse CD45 Depletion Kit (Invitrogen, #8804-6864). The remaining neurons were resuspended in FACS buffer (PBS with 2% fetal calf serum and EDTA) and stained with Viability Dye eFluor 780 (eBioscience, 65-0865-14) at 4 °C for 15 minutes. Subsequently, nuclei were stained with SYTO 40 (10 µM, Thermofisher, #S11351) for 5 minutes at room temperature to distinguish cells from axonal debris. Cells were then purified by FACS on a BD FACSAria IIu cell sorter and subjected to single-cell barcoding using the Chromium Next GEM Single Cell 3′ GEM, Library, and Gene Expression v3.1 system (10x Genomics). Libraries were sequenced on an Illumina NovaSeq X platform, generating 120 million total reads. Reads were aligned to the mouse reference genome using Cell Ranger (10x Genomics) and analyzed with Seurat. Low-RNA-content and dead cells were excluded (nFeature_RNA > 100, percent.mt < 25%). AAV9 expression was not detected and therefore subsequent analysis was performed using principal component analysis which identified 19 clusters, and which were assigned cell types using known markers and the Tabula Muris reference atlas. Clusters were grouped into major cell types for comparing gene expression under different conditions. Four biological replicates per group were analyzed to compare B16F10-injected mice and keratinocyte-injected mice. To increase statistical robustness, a pseudobulk approach was used by averaging expression for each cell type in each sample, followed by differential expression analysis with DESeq2. Gene set enrichment analysis (GSEA) was then used to evaluate gene ontology gene sets.

first: Mohammad

last: Balood

first: Frederico Omar Gleber

last: Netto


title: Cancer-induced nerve injury promotes resistance to anti-PD-1 therapy [scRNA-seq]

overall_design: B16F10-mCherry-OVA melanoma cells (5 × 105) were inoculated intradermally into the flank of eight-week-old male and female mice whose nociceptor neurons were either permissive (NaV1.8WT::ATF3fl/fl) or resistant (NaV1.8cre::ATF3fl/fl) to injury. Ten days after tumor inoculation, the tumors were excised, minced with a razor blade, and digested for 30 minutes in DMEM containing 10 mM HEPES, 1.6 mg/mL collagenase IV (Sigma, #C5138), and 10 μg/mL DNase I (Sigma, #4942078001). The resulting cell suspensions were filtered through a 40 μm mesh, and samples from two mice were pooled for each experiment. After red blood cell lysis (Gibco, #A10492-01), cells were stained with Zombie Aqua viability dye (BioLegend, #423105) and a FITC anti-mouse CD45 antibody (BioLegend, #103107). Approximately 500,000 live immune cells, which included ~80% CD45+ cells, were sorted on a BD FACSAria III cell sorter into a collection buffer (PBS, 0.04% BSA, and 50% FBS; Sigma, #F4135), then fixed and prepared for single-cell library construction using the Chromium 10x Fixed RNA kits (#PN-1000414 and #PN-1000497). Libraries were sequenced on an Illumina NovaSeq X, and reads were aligned to the mouse reference genome using Cell Ranger (10x Genomics). Low-quality cells (nFeature_RNA ≤ 100 or percent.mt ≥ 5%) were excluded from downstream analysis in Seurat, and the remaining cells were clustered using 20 principal components at a resolution of 0.8, yielding 10 distinct clusters. These clusters were annotated using standard markers and the Tabula Muris reference atlas, then grouped by major cell type (B cells, CD8+ T-cells, CD4+ T-cells, Tregs, and myeloid cells) to compare gene expression between experimental conditions. To investigate differences between conditional knockout (cKO) and intact (control) mice, a single library was used to define inflammation markers with the Seurat FindMarkers function. Four biological replicates per group (cKO vs. controls) were generated, and gene-expression comparisons were averaged for each cell type and sample.

first: Karine

last: Roversi

first: Amin Reza

last: Nikpoor

first: Tuany

last: Eichwald


title: Robustness of urinary extracellular vesicle-derived miRNA profiles over multiple days and the impact of urine concentration

city: Yushima, Bunkyo-ku, Tokyo

first: Atsushi

last: Satomura

address: 5F ITP Hongo Office , 2-25-7

country: Japan

institute: Craif

type: Non-coding RNA profiling by high throughput sequencing

summary: Urinary extracellular vesicle (EV)-derived microRNAs (miRNAs) have emerged as promising noninvasive biomarkers for disease prediction. However, fluctuations in urine concentration throughout the day may influence miRNA abundance and profiles, potentially limiting their clinical utility. To ensure the broader applicability of urinary miRNAs in disease prediction, it is essential that their profiles remain stable regardless of collection time. In this study, we systematically examined factors influencing urinary miRNA abundance and assessed the stability of miRNA profiles. We collected serial urine samples from healthy individuals over three days, and performed small RNA sequencing to analyze urinary miRNA profiles in relation to various urine concentration parameters. Total miRNA counts were negatively correlated with urine volume and positively correlated with urine concentration indicators, including specific gravity and creatinine levels. miRNA profiles remained stable across different times and days when samples with low miRNA counts were excluded. These findings indicate that urine dilution—primarily due to fluid intake—is a major cause of variation in urinary miRNA abundance. Our results highlight the importance of collecting adequately concentrated samples and provide foundational insights for developing standardized urine collection protocols to enhance the reliability of urinary miRNAs as biomarkers.

overall_design: miRNA-seq of urinary miRNA over 3 days from 6 healthy individuals.

first: Yoriko

last: Ando

first: Motoki

last: Mikami

first: Mika

last: Mizunuma

first: Yuki

last: Ichikawa


title: A metabolite sensor CtBP2 is secreted in response to shifts in cellular energy status to maintain systemic/organismal health

city: Tsukuba

first: Motohiro

last: Sekiya

address: 1-1-1 Tennodai

institute: University of Tsukuba

summary: While intracellular metabolic homeostasis is coordinated by metabolite-sensing molecules, intercellular (cell-to-cell) metabolic harmonization remains underexplored. Here we describe an intercellular (cell-to-cell) communication system regulated by a metabolite sensor C-terminal binding protein 2 (CtBP2). CtBP2 is secreted via exosomes in response to reductive metabolism, which is suppressed by excessive oxidative stress. A series of pro-longevity agents, such as metformin, resveratrol and hydrogen sulfide, induce CtBP2 secretion, and administration of exosome CtBP2 extends lifespan in mice. Consistent with these findings, serum CtBP2 concentrations are higher in human subjects from families with a history of longevity and exhibit an age-dependent decline. Healthspan is also improved by exosome CtBP2 as exemplified by protection against frailty in mice and elevated serum CtBP2 levels are associated with less cardiovascular diseases in human. These health benefits could be attributed to the adequate increase of reduction potentials that induces activation of Forkhead box M1 (FoxM1) and AMP-activated protein kinase (AMPK). Our findings illustrate a metabolic system that presents potential as a target for future clinical applications.

overall_design: CtBP2 is a metabolite sensor that accommodate metabolites using its Rossmann fold pocket. We created mouse embryonic fibroblast cells with mutations in CtBP2's Rossmann fold. We isolated exosomes from wild-type MEF or the mutant MEF and treated IMR90 human fibroblast cells with those exosomes (200 microg/ml) for 1.5 days (WT1-4 and Mut1-4, respectively). RNA was isolated and regular RNA-seq was performed.


title: Transcriptional profiling of striatum from the Q140 mouse model of Huntington's disease, from A rare genetic variant confers resistance to neurodegeneration across multiple neurological disorders by augmenting selective autophagy

first: Riki

last: Kawaguchi

state: CA

address: 760 Westwood Plaza, Room 37-420

department: Department of Psychiatry and Neurology Department of Psychiatry

summary: Striatum isolated from 6 m/o wildtype, Q140 knock-in mice in the presence or absence of Alfy overexpression. Alfy overexpression achieved by knockin of human WDFY3 cDNA into Rosa26 locus. Total RNA seq analysis.

overall_design: Striata from 6 m/o Q140 and WT in the presence or absence of Alfy overexpression. Total RNA. 4 males and 4 females per genotype. N=8 per group. Littermates used

first: Katherine

middle: R

last: Croce

first: Peter

last: Langfelder

last: Wang

first: William

middle: X

last: Yang

first: Ai

last: Yamamoto


title: KCTD10 is a sensor for co-directional transcription-replication conflicts

city: Rochester

first: Jake

last: Kloeber

address: 200 First Street SW

department: Oncology

institute: Mayo Clinic

summary: During DNA replication, the replisome must remove barriers and roadblocks including the transcription machinery. Transcription-replication conflicts (TRCs) occur when there are collisions between the replisome and transcription machinery, and are increasingly recognized as an important source of mammalian genome instability. How cells facilitate replisome bypass at sites of TRCs is incompletely understood. Here we show that the CUL3-KCTD10 E3 ligase senses TRCs and promotes remodeling of the RNA polymerase complex to allow replisome bypass. We found that the substrate adaptor KCTD10 interacts with the replisome and the transcription machinery and regulates both in unstressed conditions. These bivalent interactions allow KCTD10 to detect co-directional TRCs and facilitate higher-order assembly of KCTD10 complexes that recruit CUL3 to induce the ubiquitination and removal of the RNA polymerase factor TCEA2. In the absence of KCTD10, there is increased retention of TCEA2 and the RNA polymerase complex, causing an accumulation of TRCs and increased DNA damage. Our results demonstrate how replication can proceed through transcriptionally active regions, utilizing a unique bridging function of the CUL3-KCTD10 complex. These findings provide a framework for how the coordination between transcription and replication may contribute to the maintenance of genome stability.

overall_design: The submission includes samples from CUT&RUN experiments performed using HeLa cells expressing FLAG-tagged KCTD10. The primary objective of the study is to determine the location of KCTD10 binding genome-wide.

first: Kloeber

last: Jake

first: Chen

last: Bin

first: Huang

last: Jinzhou

first: Lou

last: Zhenkun


title: INFLAMMATION-INDUCED SENESCENT-LIKE GLIA REWIRE CELLULAR NETWORKS IN MULTIPLE SCLEROSIS [scRNAseq_organoids]

first: Edoardo

last: Pedrini

state: Lombardy

address: Via Olgettina 60

department: Division of Neuroscience

institute: Hospital San Raffaele

summary: In multiple sclerosis (MS), chronic compartmentalized inflammation is thought to drive relentless clinical deterioration. Here, we investigate the link between unresolved parenchymal inflammation and cellular senescence in MS progression. Single-cell transcriptomic analysis of human brain tissue reveals an accumulation of senescent-like glial cells in diseased white matter, especially in chronic active lesions, and to a lesser extent in the cortex. Spatial transcriptomics show gradients of senescence-like signatures extending from lesion cores to periplaque regions, alongside rewired cellular networks. Experimental induction of senescence in MS hiPSC-derived neural organoids demonstrates that microglia are especially vulnerable to inflammation-induced senescence, which can be partially rescued by CNS-penetrant anti-inflammatory drugs. At the patient level (n=500), increased 3T MRI-estimated brain-age is observed, especially in individuals with more than four chronic active lesions. These findings suggest that chronic inflammation might accelerate senescence-like processes, potentially contributing to disease progression, and that its modulation might help limit further propagation.

overall_design: single cell transcriptomic profile of 8 Organoids samples treated with different stimuli

first: Francesca

last: Fagiani

first: Maria

middle: S

last: Martire

first: Gaia

last: Gastoldi

first: Colin

last: Bulcke

first: Jing-Ping

last: Lin

first: Elena

last: Brambilla

last: Ruffini

first: Carolina

last: Peri

first: Dragan

last: Maric

first: Gianvito

last: Martino

first: Paola

last: Panina-Bordignon

last: Calabresi

first: Pietro

last: Maggi

first: Daniel

last: Reich

first: Martina

last: Absinta


title: Cholangiocytes’ Primary Cilia Regulate DNA Damage Response and Repair

city: Austin

first: Estanislao

last: Peixoto

address: 801 16th Ave NE

institute: Hormel Institute, University of Minnesota

summary: Primary cilia have been considered tumor-suppressing organelles in cholangiocarcinoma (CCA), though the mechanisms behind their protective role are not fully understood. This study investigates how the loss of primary cilia affects DNA damage response (DDR) and DNA repair processes. Human cholangiocyte cell lines were used to examine the colocalization of DNA repair proteins at the cilia and assess the impact of experimental deciliation on DNA repair pathways. Deciliation was induced using shRNA knockdown or CRISPR knockout of IFT20, IFT88, or KIF3A, followed by exposure to the genotoxic agents cisplatin, methyl methanesulfonate (MMS), or irradiation. Cell survival, cell cycle progression, and apoptosis rates were evaluated, and DNA damage was assessed using comet assays and γH2AX quantification. An in vivo liver-specific IFT88 knockout model, generated using Albumin-Cre/Lox recombination, was used to study the loss of primary cilia in the liver. Results showed that RAD51 localized predominantly at the base of the cilium, while ATR, PARP1, CHK1, and CHK2 were also detected within the ciliary shaft. Deciliated cells displayed dysregulation in critical DNA repair pathways. These cells also showed reduced survival and increased S-phase arrest after genotoxic challenges as compared to ciliated cells. Enhanced DNA damage was observed via increased γH2AX signals and comet assay results. An increase in γH2AX expression was also observed in our in vivo model, indicating elevated DNA damage. Additionally, key DDR proteins such as ATM, p53, and p21, were downregulated in deciliated cells after irradiation. This study underscores the crucial role of primary cilia in regulating DNA repair and suggests that targeting cilia-related mechanisms could present a novel therapeutic approach for CCA.

overall_design: Normal Human Cholangiocytes cell line (NHC) were stably transfected with non-target (NT) and IFT88 specific shRNAs in induce deciliation. Next-generation sequencing (RNAseq) was used to further study the consequences of ciliary lost.

first: Seth

last: Richard

first: Kishor

last: Pant

first: Juan

last: Abrahante

first: Wioletta

last: Czaja

first: Sergio

last: Gradilone


title: Altered translation elongation contributes to key hallmarks of aging in killifish brain (tRNA-Seq)

city: Stanford

first: Jae Ho

last: Lee

address: 318 Campus Drive E200

department: Biology

institute: Stanford University

summary:
Aging is a major risk factor for neurodegeneration and is characterized by diverse cellular and molecular
hallmarks. To understand their origin, we studied the effects of aging on the transcriptome, translatome,
and proteome in the brain of short-lived killifish. We identified a cascade of events in which aberrant
translation pausing led to altered abundance of proteins independently of transcriptional regulation. In
particular, aging caused increased ribosome stalling and widespread depletion of proteins enriched in
basic amino acids. These findings uncover a potential vulnerable point in the aging brain's biology –
the biogenesis of basic DNA- and RNA-binding proteins. This vulnerability may represent a unifying
principle that connects various aging hallmarks, encompassing genome integrity, proteostasis and the
biosynthesis of macromolecules.

overall_design: Analysis of tRNA abundance and charging in the young and aged killifish brain.

first: Till

last: Balla

first: Antonio

last: Marino

first: Domenico

last: Di Fraia

first: Jae

middle: H

first: Judith

last: Frydman

first: Alessandro

last: Cellerino

last: Ori

first: Danny

last: Nedialkova


title: Altered translation elongation contributes to key hallmarks of aging in killifish brain (RNA-Seq)

overall_design: Comparative analysis of  Transcriptome of Nothobranchius furzeri from different age groups.

first: Philipp

last: Koch

first: Christoph

last: Englert

first: Cinzia

last: Caterino

first: Hanna

last: Reuter

first: Marco

last: Groth


title: Altered translation elongation contributes to key hallmarks of aging in killifish brain (Ribo-Seq)

overall_design: Comparative analysis of  translatome(Ribosome profiling) of Nothobranchius furzeri liver from three age groups (5wph, 12wph, and 39wph)


title: INFLAMMATION-INDUCED SENESCENT-LIKE GLIA REWIRE CELLULAR NETWORKS IN MULTIPLE SCLEROSIS [Spatial transcriptomic]

first: Edoardo

last: Pedrini

overall_design: Visium profile of 12 slices of human brain tissue from progressive MS patients.

first: Francesca

last: Fagiani

first: Maria

last: Martire

first: Gaia

last: Gastoldi

first: Colin

last: Bulcke

first: Jing-Ping

last: Lin

first: Elena

last: Brambilla

last: Ruffini

first: Carolina

last: Peri

first: Dragan

last: Maric

first: Gianvito

last: Martino

first: Paola

last: Panina-Bordignon

first: Peter

last: Calabresi

first: Pietro

last: Maggi

first: Daniel

last: Reich

first: Martina

last: Absinta


title: High-throughput diversification of protein-ligand surfaces to discover chemical inducers of proximity

city: Boston

first: Scott

last: Armstrong

address: 450 Brookline Ave

department: pediatric oncology

institute: Dana Farber Cancer Institute

summary: Chemical inducers of proximity (CIPs) stabilize biomolecular interactions, often causing a privileged rewiring of cellular biochemistry. While rational design strategies can expedite the discovery of heterobifunctional CIPs, molecular glues have predominantly been discovered by serendipity. Envisioning a prospective approach to discover molecular glues for a pre-selected target, we hypothesized that pre-existing ligands could be systematically decorated with chemical modifications to discover protein-ligand surfaces that are tuned to cooperatively engage another protein interface. Using high-throughput chemical synthesis to diversify a ligand for the transcriptional coactivator ENL with 3,163 structurally diverse chemical building blocks, we discovered a compound dHTC1 that elicits potent, selective, and stereochemistry-dependent degradation of ENL by induced binding to CRL4CRBN. Unlike prior CRBN-based degraders, dHTC1 binds the ligase with high affinity only after forming the ENL:dHTC1 complex, relying on a hybrid interface of protein-protein and protein-ligand contacts. Altogether, this study points toward an expanded chemical space for co-opting the therapeutically important substrate receptor, CRBN, and a second proof-of-concept extending this approach to BRD4 further validates high-throughput chemistry as a facile tool to discover new degraders

overall_design: To compare gene expression changes in mouse-cell depleted bone marrow cells from an MV4;11 xenograft, 4 mice per group received 3 doses of vehicle, (R)-dHTC1 or (S)-dHTC1 50 mg/kg i.p. BID. Samples were collected 1 hour after the last dosing. RNA sequencing was performed with samples from 3 individual mice per group.

first: Daniela

last: Wenge

first: Charlie

last: Hatton


title: RNA-seq of dorsal root ganglion from IMQ-induced psoriasiform dermatitis mice.

first: Jian

last: Jiang

summary: We divided the male C57BL/6 mice into two groups: a non-treatment group and an IMQ-induced psoriasiform dermatitis group. We isolated the C3-C5 ganglia from male mice, then preserved them in RNA stabilization solution. RNA was extracted using Trizol, followed by transcriptome sequencing.

overall_design: To explore changes in the DRG of mice under psoriatic conditions, we performed transcriptomic sequencing on the DRG tissues from IMQ-induced psoriatic dermatitis mice and naive mice.

first: Xin

last: Liu

first: Shiying


title: INFLAMMATION-INDUCED SENESCENT-LIKE GLIA REWIRE CELLULAR NETWORKS IN MULTIPLE SCLEROSIS [snRNAseq Brain]

first: Edoardo

last: Pedrini

overall_design: nuclei trascriptomic profile from 4 White Matter samples and 19 Cortex samples

first: Francesca

last: Fagiani

first: Maria

last: Martire

first: Gaia

last: Gastoldi

first: Colin

last: Bulcke


title: Select chromatin complexes are essential drivers of pathogenic enhancer activity and gene expression in Ewing sarcoma [ChIP-Seq]

summary: Using ChIP-seq we assessed the changes occuring at EWS::FLI1 enhancer regions following perturbation of EWS::FLI1, MLL3/4 and p300/CBP.

overall_design: Using previously described EWS::FLI1 degrader cell lines (A673-dHALO and EWS::502 dTAG) we assessed the changes in the epigenetic landscape at EWS::FLI1 enhancers compared to MLL3/4 genetic deletion and p300/CBP perturbation using small molecule inhibitor A485 and degrader dCBP1.

first: Laura

last: Godfrey

first: Charles


title: Peripherally administered androgen receptor-targeted antisense oligonucleotide rescues spinal pathology in a murine SBMA model

city: New Haven

first: Changwoo

last: Lee

state: CT

address: 295 Congress

department: Neuroscience

institute: Yale University

summary: Degeneration of the neuromuscular system is a characteristic feature of spinal and bulbar muscular atrophy (SBMA), a CAG/polyglutamine (polyQ) expansion disorder caused by mutation in the androgen receptor (AR). Using a gene targeted mouse model of SBMA, AR113Q mice, we demonstrate age-dependent degeneration of the neuromuscular system that initially manifests with muscle weakness and atrophy and progresses to include denervation of neuromuscular junctions and lower motor neuron soma atrophy. Using this model, we tested the hypothesis that therapeutic intervention targeting skeletal muscle during this period of disease progression arrests degeneration of the neuromuscular system. To accomplish this, AR-targeted antisense oligonucleotides were administered subcutaneously to symptomatic AR113Q mice to reduce expression of polyQ AR in peripheral tissues but not in the spinal cord. This intervention rescued muscle atrophy, neuromuscular junction innervation, lower motor neuron soma size, and survival in aged AR113Q mice. Single-nucleus RNA sequencing revealed age-dependent transcriptional changes in the AR113Q spinal cord during disease progression which were mitigated by peripheral AR gene silencing. Our findings underscore the intricate interplay between peripheral tissues and the central nervous system in SBMA and emphasize the therapeutic effectiveness of peripheral gene knockdown in symptomatic disease.

overall_design: Single-nucleus RNA-sequencing was performed of SBMA knock-in (KI; AR113Q), ASO-injected SBMA KI, and wild-type (WT) littermate control mice at 26 and 52 weeks of age to examine the complex and dynamic interplay between diverse cell populations in the SBMA lumbar over time and and peripheral ASO injection.

first: Zhigang

last: Yu

first: Janghoo

last: Lim

first: Andrew

last: Lieberman