title: IFN-γ induces hematopoietic stem cell myelopoiesis through Meis1 in tumor

city: guangzhou

first: Songqi

last: Zhu

state: guangdong

address: No. 74, Zhongshan 2nd Road, Yuexiu District

institute: Sun Yat-sen University

summary:
Background
Tumors associated overproduction of tissue-damaging myeloid cells and loss of lymphoid cell production were caused by chronic inflammation. Hematopoietic stem cells (HSCs) were the origin of all innate and adaptive immune cells and differentiate through a series of lineage-biased multipotent progenitors (MPPs) dependent on situations.
Methods
MC38 tumor and Lewis lung cancer models were performed to evaluate HSCs differentiation biased. Through elisa assay and bioinformatic analysis, the key pro-inflammatory cytokine was selected, which promoted myeloid-biased differentiation of HSCs. Next, the main transcription factor was found in tumor induced myeloid-biased differentiation. Finally, HSC-derived myeloid-derived suppressor cells (MDSCs) and impaired T cell functions were measured to evaluate the reason of tumor progression. By targeting myeloid-biased HSCs, Emapalumab was used to suppress tumor progression.
Results
Here we found HSCs preserved myeloid-biased differentiation in MC38 tumor and Lewis lung cancer models, which reflected extensive properties in tumor models, and was induced by one of pro-inflammatory cytokines, IFN-γ. Transcriptional profiling indicated Meis homeobox 1 (Meis1) was enriched in tumor primed HSCs, and ablation of Meis1 in HSCs prevented HSCs-associated myeloid cell differentiation. HSC-derived MDSCs, which were primary factors, promoted tumor progression. Targeting myeloid differentiated HSCs, combination of anti-PD-1 and Emapalumab, an anti-IFN-γ antibody, inhibited HSC-derived MDSCs and enhanced T cells associated adoptive immune response to suppress tumor progression. Myelodysplastic syndrome (MDS), which was displayed abnormal myeloid cell differentiation induced by hematopoietic failure, was improved by treated with Emapalumab or Meis1 inhibitor.
Conclusions
These results suggested that targeting HSCs was a new approach to treat tumor, and combination of PD-1 and Emapalumab might serve as a novel therapeutic strategy to improve the response and efficacy of anticancer therapy.

overall_design: RNA-seq profiling of HSCs from both normal and MC38 colon cancer C57BL/6J mice to investigate the mechanism underlying the myeloid-bias of HSCs induced by tumorigenesis.

first: Xue

first: Minyi

last: Zhao

first: Kexin

first: Weiwei

last: Ma

first: Ruiqing

last: Zhou

first: Uet

last: Yu

first: Bangxue

last: Jiang

first: Xiaoqing

last: Bai

first: Peng

last: Lei

first: Shunqing


title: Ribo-seq analysis of alternative splicing under PEG treatment in osfkbp20-1b mutant compared to wild-type (ZH11) rice.

status: Public on Jan 24 2026

city: Daejeon

first: Haemyeong

last: Jung

address: 125 Gwahak-ro, Yuseong-gu

department: Plant Systems Engineering Research Center

country: South Korea

institute: KRIBB

type: Expression profiling by high throughput sequencing

summary: To investigate whether intron containing transripts from alternative splicing are abundant in monosome of osfkbp20-1b upon drought stress, we analyzed Ribo-seq to identify the quantitative profiling and alternative splicing.

overall_design: Total RNA was precipitated from monosome and polysome of osfkbp20-1b or WT shoot and extracted in condition of 20% PEG-6000 for 6 h treatment using 1-week-old rices.

first: Hye Sun

last: Cho

first: Hyun Ji

last: Park


title: Transcriptome analysis of alternative splicing under PEG treatment in osfkbp20-1b mutant compared to wild-type (ZH11) rice

summary: To investigate whether observed changes in pre-mRNA splicing led to OsFKBP20-1b depletion upon drought stress, we analyzed RNA-seq to identify the quantitative profiling and alternative splicing.

overall_design: Oryza sativa. L (ssp. japonica) total RNA was extracted from osfkbp20-1b and WT shoot after mock or 20% PEG-6000 for 6 h treatment using 1-week-old rices.


title: Integrated Clinical Trial and Molecular Profiling Reveals Immune Drivers of Chronic Hand Eczema

city: Toulouse

first: Rüçhan

last: Ekren

address: CHU Purpan – BP 3028 –  Toulouse Cedex, 3

department: INFINITY

country: France

institute: Inserm UMR 1291

summary: Chronic hand eczema (CHE) is a painful, itchy and inflammatory skin disease of multifactorial origin. CHE can be categorized based on etiology and/or clinical presentation, including intertwined atopic-contact eczema-psoriasis traits, making it challenging to diagnose and treat. While being the most frequent work-related dermatosis, the underlying immune mechanisms remain unclear. Here we performed a randomized controlled study comparing dupilumab and placebo and demonstrated that CHE is a type 2 immunity driven disease, regardless of etiological factors or clinical presentation. We conducted a comprehensive molecular profiling of CHE patients of all etiologies and morphologies to identify potential common features and evaluated the consequences of blocking IL-4Rα during 16 weeks. This phase 2b randomized, multicenter, double-blind, placebo-controlled clinical trial included 94 adults with moderate to severe CHE persisting for at least six months and resistant to potent topical corticosteroids. We found that CHE patients share complex transcriptomic signatures with those of atopic dermatitis and psoriasis patients, with dysregulated genes involved in skin barrier, leukocyte migration, cytotoxicity, type 1, 2 and 3 immunity. Compared to placebo control, 16-week dupilumab treatment significantly improved clinical severity and quality of life of CHE patients, while largely restoring appropriate transcriptomic and proteomic programs related to skin barrier and immune homeostasis. These findings demonstrate that IL-4Rα signaling is a critical regulator of CHE pathological features, independent of atopic dermatitis background or environmental triggers, and propose reclassifying CHE as a type 2 immune disorder, with dupilumab or IL-4/13 targeted therapy as the mainstay treatment for moderate to severe disease.

overall_design: Hand skin biopsy samples from back or palm were collected from patients with moderate to severe chronic hand eczema (CHE) at baseline and at week 16. Arm or abdomen control skin samples were obtained from healthy donors matched for age and sex. The dataset includes patient samples for longitudinal analysis, along with healthy control samples serving as reference for non-lesional skin comparisons.

first: Perrine

last: Gery

first: Aurélie

last: Du-Thanh

first: Emilie

last: Bérard

first: Fatma

last: Jendoubi

first: Vanina

last: Lenief

first: Hugo

last: Rimet

first: Nadia

last: Raison-Peyron

first: Amel

last: Bouznad

first: Maria

middle: P

last: Konstantinou

first: Jonathan

last: Rioual

first: Lilian

last: Basso

first: Juliette

last: Mouiren

first: Manon

last: Boussier

first: Brigitte

last: Milpied

first: Cristina

last: Bulai Livideanu

first: Louise

last: Jaulent

first: Florence

last: Hacard

first: Marine

middle: A

last: Lefevre

first: Audrey

last: Nosbaum

first: Julien

last: Seneschal

first: Marc

last: Vocanson

first: Carle

last: Paul

first: Nicolas

last: Gaudenzio

first: Marie

last: Tauber


title: Type 2 lymphocytes restrict type 3 lymphocytes during liver fibrosis and co-localize in fibroblast niches

status: Public on Jan 23 2026

city: Tübingen

first: Jun-Hoe

last: Lee

address: Otfried-Müller-Str. 37

department: Quantitative Biology Centre (QBiC)

country: Germany

institute: University of Tuebingen

summary: Fibroblasts are dynamic structural cells that direct both beneficial tissue repair and pathologic organ fibrosis through interactions with tissue-resident type 2 and type 3/17 lymphocytes (T2L and T3L). We performed spatial transcriptomics to profile heterogenous fibroblast populations within fibrotic, adventitial, and parenchymal regions of resting and fibrotic murine livers as well as to determine their crosstalk with T2L and T3L. Our analysis suggests a spatially associated crosstalk between liver lymphocytes and fibroblast niches.

overall_design: Four mouse models with genetic depletion of IL-5+ lymphocytes and IL-17A+ lymphocytes were used for the analysis: 4-week CCl4- and placebo-treated IL5-Cre mice, 4-week CCl4-treated IL-5 deleter mice, and 4-week CCl4-treated IL-5;IL-17A double deleter mice.

first: Julia

last: Sbierski-Kind

first: Kelly M

last: Cautivo

last: Nilsson

first: Taeeun

last: Gu

first: Hyeewon

last: Seo

first: Hyun Je

last: Kim

first: Ari

last: Molofsky


title: Systemic immune correlates of long-term survival after Delta-24-RGD based on the therapeutic adenovirus for recurrent glioblastoma effect trial (TARGET)

city: Houston

first: Sanjay

last: Singh

state: TX

address: 6767 Bertner St

department: Neurosurgery

country: USA

institute: MD Anderson Cancer Center

summary: Purpose: Treatment of high grade gliomas, particularly glioblastoma (GBM), with the oncolytic adenovirus Delta-24-RGD has previously produced anti-tumor effects in phase 1 clinical trials. These effects are mediated through direct oncolysis and activation of an anti-tumor immune response. In this study, we combined  Delta-24-RGD with interferon gamma (IFN-𝛾), a potent activator of T-helper 1 CD8+ cell immune response. Patients and Methods: In the Phase 1b, multicenter, randomized, study (NCT02197169), we evaluated the combination of intratumoral injected Delta-24-RGD with subcutaneous administered IFN-𝛾 in 37 patients with recurrent high grade glioma and investigated potential systemic immune correlates of long-term survival. Twenty-seven patients were randomized 2:1 into two cohorts; Delta-24-RGD with IFN-𝛾 or Delta-24-RGD alone via a standard nashold biopsy needle. In an expansion cohort, 10 patients received intra-tumoral injected Delta-24-RGD via the MEMS Cannula (Neela Therapeutics). Results: Although the addition of IFN-𝛾 to Delta-24-RGD did not significantly increase the percentage of long term survivors compared to Delta-24RGF alone, the IFN-𝛾 cohort has the longest surviving patients after treatment (OS 44.2, 23.7, 20.6 and 20.1 months). Post-hoc analysis of plasma and peripheral blood mononuclear cells using viral phage immunoprecipitation sequencing antibody reactome profiling of viral epitopes (VirScan) and single cell RNA sequencing (scRNA seq) revealed that levels of circulating anti-adenovirus specific IgG and CD8+ NKT-like cells 2 months after treatment with Delta-24-RGD distinguished long term survivors from short term survivors. Conclusions:  Immunological fitness assessed by an anti-adenoviral specific antibody response and higher levels of activated CD8+ NKT-like cells after Delta-24-RGD treatment could be used as early surrogates of a robust systemic immune response that correlates with rate of tumor growth and long-term survival.

overall_design:
Cryopreserved peripheral blood mononuclear cells obtained from patients (n=7) enrolled in the study before and after treatment were sequenced. Viable CD3+ T-cells within peripheral blood mononuclear cells were stimulated overnight using anti-CD3/anti-CD28 co-stimulation. Single cell RNA-sequencing of stimulated CD3+ T-cells was performed using the 10x Genomics platform.

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

first: Chibawanye

middle: I

last: Ene

first: Thiagarajan

last: Venkataraman

first: Lynette

middle: M

last: Phillips

first: James

last: Long

first: Deep

first: Nam

middle: D

last: Tran

first: Frank

last: Tufaro

first: P

middle: J

last: Anand

first: Nicholas

last: Navin

first: Sujit

last: Prabhu

first: Jeffrey

middle: S

last: Weinberg

first: Benjamin

last: Larman

first: Candelaria

last: Gomez-Manzano

first: Juan

last: Fueyo

first: Frederick

middle: F

last: Lang


title: Single-cell transcriptomic comparison of the developing human fetal stomach and pluripotent stem cell-derived gastric organoids

city: Cincinnati

first: Daniel

middle: O.

last: Kechele

state: OH

address: 3333 Burnet Ave Location R3.034

department: Developmental Biology

institute: Cincinnati Children's Hospital Medical Center

summary: The goal of engineering increasingly complex in vitro human organoid models is to more accurately model human organogenesis and disease. Recently, human antral gastric organoids (hAGOs) were engineered to contain splanchnic mesenchyme (SM) and enteric neural crest cells (NCCs), resulting in the formation of functional three germ layer gastric organoids. It is unclear how three-germ layer hAGOs compare with the human fetal stomach and how the added germ layers alter gastric differentiation in vitro. To determine the robustness of hAGOs and how additional germ layers impact development, we benchmarked hAGO with and without added SM and NCC to a single cell atlas of the developing human stomach. A comparison of hAGOs in vitro to fetal organs confirmed that they were gastric and most similar to 7 week stomach with the epithelium comprised primarily of gastric precursors and surface mucous cells. The SM added to hAGOs formed fetal gastrointestinal-like mesenchyme whereas the NCCs in hAGOs differentiated into neuronal precursors and glial cells similar to those found in developing endodermal organs. The addition of SM and NCCs did not drastically alter the cellular diversity of the epithelium in vitro but maintained more uncommitted precursors similar to 7 week stomach. Following transplantation and growth for 10 weeks, hAGOs with SM grew and matured into tissue more similar to the 14 week fetal stomach. Bioinformatic inference of cell-cell communication confirmed known signaling crosstalk between germ layers but also identified new signaling candidates that may regulate tissue assembly. Together, these data show that three-germ layer hAGOs faithfully modeled the multilayer complexity of the fetal stomach at a single cell transcriptomics level and provided insight into human stomach development.

overall_design: Day 37 in vitro human antral gastric organoids with added splanchnic mesenchyme and/or neural crest cells (one to two biological replicates), day 35 HIO (one replicate), or HAGO with mesenchyme following 10 wk in vivo grown under mouse kidney capsule were dissociated to single cells were subjected to 10X single cell RNA sequencing.

middle: O

first: Jacob

middle: R

last: Enriquez

first: Konrad

last: Throner

first: Praneet

last: Chaturvedi

first: Guillermo

last: Sanchez

last: Wells


title: Loss of the O-GlcNAcylation in Hepatic Differentiation utilizing choline-deficient ethionine supplemented diet

status: Public on Jan 25 2026

city: Kansas City

first: Dakota

last: Robarts

state: KS

address: 3901 Rainbow Blvd

institute: University of Kansas Medical Center

summary:
We studied the effects of loss of hepatic O-GlcNAc Transferase (OGT), the enzyme that attaches the O-GlcNAc to protein, in a choline-deficient and ethionine (CDE) supplemented model.  We placed hepatocyte-specific OGT knockout mice (OGT-KO) and controls on the CDE diet for 2 weeks. We then performed RNA sequencing. We then repeated the 2-week CDE diet with the addition of a 7-day normal diet recovery period.
We then performed RNA-Sequencing on isolated RNA from whole liver lysate to determine differentially expressed genes.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for control and OGT-KO mice (equally pooled RNA from n of 3) with no recovery and a 7 day recovery after CDE diet. cDNA was sequenced using 2 lanes targeting 25 million reads/sample.

first: Sumedha

last: Gunewardena

first: Udayan

last: Apte


title: Targeting ubiquitin signaling vulnerabilities in KEAP1-inactivated lung cancer

first: Igor

last: Mačinković

department: 7Department for Immunity of Inflammation

institute: Medical Faculty Mannheim Heidelberg University

summary: Lung cancer cells rely on protein homeostasis regulators, particularly the ubiquitin-proteasome system (UPS), to sustain malignancy. Genetic alterations in UPS components, such as E3 ubiquitin ligases (E3s) and deubiquitinating enzymes (DUBs), are common and create context-dependent therapeutic dependencies. To investigate how these changes drive tumor formation, we conducted CRISPR screens on metabolically stressed murine lung cancer models and identified specific cancer vulnerabilities, including KEAP1. Although KEAP1 is frequently mutated in aggressive non-small cell lung cancers (NSCLC, ~15%), our findings reveal an unexpected proto-oncogenic role for KEAP1 in a genetically defined subset of NSCLC. Mechanistically, Keap1 deletion activated NRF2 and upregulated Aldh3a1. This led to elevated NADH/NAD⁺ ratios, triggered reductive stress, and suppressed tumor growth. Given the poor prognosis of KEAP1-mutated patients, combinatorial CRISPR dropout screens revealed druggable E3s and DUBs as Keap1-dependent co-vulnerabilities. Notably, depleting these co-dependencies such as the E3 ligases Herc2, Ubr4 and Huwe1 ablated the in vivo development of Keap1-inactivated tumors. We demonstrate that targeting the UPS represents an underexplored, promising therapeutic approach for patients with KEAP1-inactivated tumors, especially under metabolic stress.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for KPL, KP, and KPP primary murine lung tumor cell lines: KI696 (1µM) treatment vs. vehicle control (DMSO)

first: Varun

last: Shah

first: Oliver

last: Hartmann

first: Martin

last: Wegner

first: Cristian

last: Prieto-Garcia

first: Rubina

last: Kazi

first: Viktoria

last: von Heyl zu Herrnsheim

first: Amin

last: Wanli

first: Bianka

last: Bohnacker

first: Koraljka

last: Husnjak

first: Dmitry

last: Namgaladze

first: Mathias

last: Rosenfeldt

first: Manuel

last: Kaulich

first: Markus

middle: E

last: Diefenbacher

first: Ivan

last: Dikic


title: Spatial transcriptomic molecular characterization of pig dorsal root ganglion neurons [Visium]

city: Toronto

first: Shreejoy

last: Tripathy

state: Ontario

address: 250 College st.

country: Canada

institute: CAMH

summary: This dataset comprises 10X Visium spatial transcriptomics data from the pig dorsal root ganglia (DRG) of female pigs. It aims to map the spatial gene expression patterns within the DRG, offering insights into the molecular identity of neuronal populations, including nociceptors. This work provides a unique spatial perspective on gene expression, facilitating a deeper understanding of DRG molecular architecture and its implications in sensory processing.

overall_design: The study sourced DRGs from 7 female pigs, with tissues processed for Visium spatial transcriptomics. DRGs were fresh-frozen, sectioned, and prepared on Visium slides for spatial sequencing. The objective is to characterize spatial gene expression within pig DRGs, identifying distinct neuronal populations and their molecular markers.

first: Marisol

last: Moreno

first: Jannis

last: Körner

first: Derek

last: Howard

first: Angelika

last: Lampert

first: Theodore

last: Price


title: GID/CTLH E3 ligase complex control cell fate programs for sexual development of Plasmodium falciparum

city: Melbourne

first: Danushka

middle: Sujeeva

last: Marapana

state: VIC

address: 1G Royal Parade

country: Australia

institute: The Walter and Eliza Hall Institute of Medical Research

summary: Transmission of the malaria parasite Plasmodium falciparum requires the formation of specialised sexual cells called gametocytes. A hallmark of P. falciparum gametocyte development is its long duration, during which the parasite undergoes dramatic cellular remodelling including morphological, physiological and metabolic changes which result in the formation of a transmission ready, stage V gametocyte. Here we show that the PfGID E3 ubiquitin ligase complex regulates critical gametocyte cell fate programs through the targeted ubiquitination of key proteins. Deletion of PfGID complex components leads to an arrest in gametocyte development and a loss of transmission to mosquitoes. PfGID governs gametocyte development by fine-tuning the protein levels of two substrates: the ZFP36 family RNAbinding protein GD1, and PfDPL, a cryptochrome-like protein. Our findings reveal that PfDPL regulates the expression of male-specific proteins early in gametocyte development that are essential for gametogenesis. In parallel to the PfDPL controlled cell fate program the RNA binding protein GD1 regulates transcripts crucial for gametocyte development by holding them in a state of translational repression. These findings illuminate the intricate molecular choreography underlying Plasmodium sexual development and provide insights into how single-celled eukaryotes execute cell-fate programs to navigate complex life cycles and adapt to diverse host environments.

overall_design: RNA-seq profiling of wild type IGP2 and ∆GID1/2/7/8/9 gametocytes at day 3,6,9 and 12 of development.

first: Peter

last: Hickey

first: Matthew

middle: W

last: Dixon

first: Alan

last: Cowman


title: Conserved sleep disturbances in FOXP1 syndrome originate from developmental dysregulation of peptidergic signaling

city: Nijmegen

first: Nicholas

last: Raun

address: Geert Grooteplein 10

country: Netherlands

institute: Radboudumc

summary: We have profiled gene expression from whole dissected brains of FoxP mutant Drosophila melanogaster.

overall_design: Gene expression profiles in adult Drosophila brains were compared between FoxP mutants and their genetic background controls. 4 replicates per condition were used, each replicate was comprised of genetic material from 12 dissected fly brains.

first: Mireia

last: Coll-Tané

first: Anna

last: Castells-Nobau

first: Annette

last: Schenck


title: Inflammasome activation and oxidative stress in SARS-CoV-2 breakthrough infection and symptomatic rebound

city: BETHESDA

first: Cihan

last: Oguz

state: MD

address: NIHBC 29B BG RM 1NN20, 9000 ROCKVILLE PIKE

institute: NIH

summary: Despite the efficacy of therapeutics and vaccines in reducing risk of severe COVID-19, breakthrough infections and rebound symptoms after initial improvement have been reported. We evaluated critical inflammatory responses in vaccinated individuals presenting with early acute (EA), late acute (LA) and clinical rebound (REBOUND) symptoms using single cell RNA sequencing.

overall_design: We performed single cell RNA sequencing (scRNA-Seq) of peripheral blood mononuclear cells (PBMCs) samples from vaccinated patients presenting with early acute (EA), late acute (LA) and clinical rebound (REBOUND) symptoms of COVID-19. The experimental design for sequencing involved a total of 15 PBMC samples (13 patients) distributed across the three conditions: EA, LA, and REBOUND.

first: Silvia

middle: L

last: Lage

first: Joseph

last: Rocco

first: Francisco

last: Otaizo-Cassaquero

first: Adam

last: Rupert

first: Kristin

last: Boswell

first: Brian

last: Epling

first: Logan

last: Cook

first: Eduardo

last: Amaral

first: Elizabeth

last: Laidlaw

first: Frances

last: Galindo

first: Richard

last: Koup

first: Princy

last: Kumar

first: Rita

last: Poon

first: Glenn

last: Wortmann

first: Andrea

last: Lisco

first: Maura

last: Manion

first: Irini

last: Sereti


title: Commonalities in gene expression and methylation changes across two rat models of acquired epilepsy [RNA-seq]

city: Grand Forks

first: Junguk

last: Hur

state: ND

address: 1301 N. Columbia Rd. Stop 9037

department: Biomedical Sciences

institute: University of North Dakota

summary: Epileptogenesis, the process by which a normal brain develops epilepsy, is characterized by complex changes in DNA methylation and gene expression. In this study, RNA sequencing and reduced-representation bisulfite sequencing were utilized to investigate these molecular alterations in two distinct and widely used rat models of temporal lobe epilepsy: intrahippocampal electrical kindling and systemic kainic acid. These models, involving rats, differ significantly in their underlying mechanisms and histopathological outcomes, providing a unique opportunity to identify both shared and model-specific changes during epileptogenesis. By comparing these models, we uncovered common pathways that may reflect generalizable, model-independent mechanisms of epileptogenesis, alongside distinct changes that highlight the diverse molecular landscapes of each model. This integrative, multi-omics approach not only enhances our understanding of the molecular drivers of epileptogenesis but also underscores the importance of cross-model comparisons for uncovering robust and potentially therapeutic targets in epilepsy research. This dataset serves as a valuable resource for exploring the epigenomic and transcriptomic underpinnings of epilepsy.

overall_design: Adult male Sprague–Dawley rats (~170–280 g) were used to investigate molecular alterations during epileptogenesis in two distinct models of temporal lobe epilepsy: systemic kainic acid and intrahippocampal electrical kindling. Animals were housed under a 12:12 light/dark cycle with ad libitum access to food and water. In the systemic kainic acid model, rats underwent electrode implantation surgery, followed by incremental kainic acid injections to induce status epilepticus. In the intrahippocampal kindling model, rats were instrumented with hippocampal electrodes and subjected to twice-daily stimulations until fully kindled. Whole hippocampi were surgically dissected 24 hours after the last seizure, flash-frozen in liquid N2, and stored at -80°C. Total RNA and DNA were extracted from left hippocampal samples using Qiagen’s AllPrep DNA/RNA Mini Kit. RNA sequencing libraries were constructed using the NEBNext Ultra II RNA Library Prep Kit and sequenced with a single-end read length of 110 bases on an Illumina NovaSeq platform. Reduced representation bisulfite sequencing (RRBS) libraries were prepared following Msp1 digestion, bisulfite conversion, and PCR amplification, and sequenced with the same platform. The resulting RNA-seq and RRBS datasets provide comprehensive insights into gene expression and DNA methylation changes associated with epileptogenesis across these models.

first: Benton

last: Purnel

first: Detlev

last: Boison


title: Endogenous retroviruses synthesize heterologous chimeric RNAs to reinforce human early embryo development

city: HangZhou

first: Zhengyi

last: Li

state: ZheJiang

address: 866 Yuhangtang Rd, Hangzhou

department: Institute of Genetics

country: China

institute: Zhejiang University School of Medicine

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

overall_design: Refer to individual Series


title: Ageing promotes metastasis via activation of the integrated stress response [RNA-Seq OE]

city: Gothenburg

first: Volkan

last: Sayin

address: Medicinaregatan 1F

department: Department of Surgery

country: Sweden

institute: University of Gothenburg

summary: Lung cancer predominantly affects older individuals, yet how physiological aging influences tumor evolution remains poorly understood. Here, we show that aging reprograms the evolutionary trajectory of KRAS-driven lung adenocarcinoma, limiting primary tumor growth while promoting metastatic dissemination through epigenetic activation of the integrated stress response (ISR). The ISR effector ATF4 drives epithelial and metabolic plasticity, conferring metastatic competence. Mechanistically, aged tumor cells exhibit increased sensitivity to the PERK–eIF2α arm of the unfolded protein response, sustaining persistent ATF4 signaling. Targeting the ISR-ATF4 genetically or pharmacologically abolishes these adaptations and limits dissemination, whereas ATF4 overexpression alone is sufficient to induce metastasis. The aging–ATF4 axis imposes a dependency on glutamine metabolism, revealing a therapeutically actionable vulnerability. Clinical analyses confirm that ATF4 is enriched in aged tumors and correlates with poor survival and advanced-stage disease. Collectively, these results define epigenetic ISR–ATF4 activation as a causal driver of lineage plasticity and metastasis in aged tumors, revealing a therapeutic opportunity in older patients with lung adenocarcinoma, the most common yet understudied subset of lung cancer

overall_design: To investigate transcriptomic differences between Old and Young primary cultures from KP-Young and KP-Old mice with and without Atf4 over-expression.

first: Angana

last: Patel

first: Clotilde

last: Wiel


title: Commonalities in gene expression and methylation changes across two rat models of acquired epilepsy [RRBS]

type: Methylation profiling by high throughput sequencing


title: Chronic variable mild stress alters the transcriptome and signaling properties of the anterodorsal bed nuceleus of the stria terminalis in a sex-dependent manner

city: New Brunswick

first: Thomas

last: Degroat

state: NJ

address: 10 Suydam Street, Apt 12

department: Animal Sciences

institute: Rutgers University

summary: Chronic stress is a physiological state marked by dysregulation of the hypo-pituitary-adrenal axis and high circulating levels of stress hormones, such as corticosterone in mice or cortisol in humans. This dysregulated state may result in the development of mood disorders but the process by which this occurs is still unknown. The bed nucleus of the stria terminalis (BNST) serves as an integration center for stress signaling and is therefore likely an important area for the development of mood disorders. This project utilized a chronic variable mild stress (CVMS) paradigm to persistently stress mice for 6 weeks followed by RNA-Sequencing of the anterodorsal (ad) BNST and electrophysiology of corticotropin releasing hormone-expressing cells in the adBNST. Our results show significant sex-biases in the transcriptome of the adBNST as well as effects of CVMS on the transcriptome of the adBNST specifically in males. Female biased genes are related to synaptic transmission while male biased genes are related to RNA processing. Stress sensitive genes in males are related to synaptic transmission and synapse formation. Additionally, electrophysiology data showed that CVMS suppressed the M-current in males but not females. However, CVMS increased the strength of excitatory post-synaptic currents in females but not males. This suggests significant differences in how males and females process chronic stress. It also suggests that the BNST is more sensitive to chronic stress in males than in females.

overall_design: At 7-9 weeks of age, male and female mice were selected for either control conditions or chronic variable mild stress (CVMS). This resulted in 4 experimental groups with 15 mice each. After CVMS or control conditions, mice were anesthetized with ketamine, then the brain was dissections, sliced, and microdissected to isolate the anterodorsal bed nucleus of the stria terminalis. This occured 1 hour after the last stressor in CVMS mice, which was wet bedding. Tissue samples from 3 biological replicates were then pooled prior to RNA extraction. RNA-Sequencing had a sample size of n=5 for each group with no outliers.

first: Sarah

last: Paladino

first: Benjamin

last: Samuels

first: Troy

last: Roepke


title: Effect of IVNS1ABP mutation, knockout on gene expression during iPSCs differentiation to Neural Progenitors

city: La Jolla

first: FANG

last: YUAN

address: 10901 N Torrey Pines Rd

institute: Sanford Burnham Prebys

summary: A homozygous variant in IVNS1ABP was identified in three siblings, displaying progeroid features with severe neuropathy. The association between IVNS1ABP and aging has never been reported before. By generating isogenic iPSCs from the patients’ fibroblasts and differentiating the iPSCs into neural progenitor cells (NPCs), we found that mutant IVNS1ABP fibroblasts, iPSCs, and NPCs exhibited disrupted cytokinesis, DNA damage, and cellular senescence. Transcription analysis of isogenic iPSCs and iPSCs derived neural progenitors (NPCs) also showed impaired cytokinesis and senescence alteration.  Correspondingly, cerebral organoids displayed premature differentiation of NPCs to neurons. Molecular profiling as well as biochemical and cellular analysis revealed altered binding of mutant IVNS1ABP to actin and actin-associated proteins and dysregulated actin dynamics during cytokinesis. Taken together, we propose that IVNS1ABP mutation dysregulates actin polymerization and organization which is at least partly responsible for the cellular senescence phenotypes in this undiagnosed disease.

overall_design: To get insight into the gene’s affection in CNS (central nerve system), we corrected one patient iPSC line, and generated the mutation corrected isogenic iPSC line and KO iPSC line by CRISPR/Cas9. These iPSCs lines were further differentiated to NPCs. We then performed gene expression profiling analysis using data obtained from RNA-seq of the isogenic cell lines (CON, MT and KO), at two tome points (iPSCs and NPCs)

first: Fang

last: Yuan

first: Haofei

last: Wang

first: Su-Chun

last: Zhang


title: Ageing promotes metastasis via activation of the integrated stress response

overall_design: To investigate differences in transcriptomics between Old and Young primary cultures from KP-Young and KP-Old mice.

middle: H


type: Genome binding/occupancy profiling by high throughput sequencing


title: Ageing promotes metastasis via activation of the integrated stress response (ATAC-Seq)

overall_design: To investigate epigenetic differences between Old and Young primary cultures from KP-Young and KP-Old mice.


title: NR2F6 deletion revives CAR‑T cell function and induces antigen‑agnostic immune memory in solid tumors

city: Innsbruck

first: Dietmar

last: Rieder

address: Innrain 80

department: Biocenter

country: Austria

institute: Medical University of Innsbruck

summary: CAR‑T cell therapy is effective in hematologic malignancies but remains challenging in solid tumors owing to antigen heterogeneity and tumor microenvironment‑induced exhaustion. Here, gene editing of the nuclear receptor NR2F6 restores CAR‑T cell functionality, sustaining a TCF1⁺ progenitor‑exhausted T cell phenotype, enhancing metabolic fitness, and preserving cytotoxic potency under chronic antigen exposure. In immunocompetent models, Nr2f6‑deficient CAR‑T cells suppress solid tumor growth and induce robust, polyclonal host antitumor responses, as shown by protection in tumor re‑challenge experiments. Although infused CAR‑T cells disappear within 2 weeks, durable tumor control coincides with epitope spreading and secondary immune responses, likely via dendritic and other antigen‑presenting cell reactivation. Protection against antigen‑negative tumors and transferable immunity reveal a dual mode of direct cytotoxicity followed by durable immune reprogramming. This broadened host immunity may offset immune escape driven by antigen loss and tumor heterogeneity, establishing NR2F6 inhibition as a promising CAR‑T engineering strategy for durable, antigen‑agnostic solid‑tumor immunotherapy.

overall_design:
Bulk RNA sequencing: Transcriptional profiling of wildtype and Nr2f6 knockout CAR-T cells in co-culture with Panc02-EpCAM tumor cells at day 0, day 4 and day 8.
Single cell RNA sequencing: single cell transcriptomic profiling and V(D)J analysis of either naive or Nr2f6 knock-out CAR-T treated survivor mice challenged with Panc02-EpCAM negative tumors.

first: Dominik

last: Humer

first: Victoria

last: Klepsch

first: Gottfried

last: Baier


title: Energy-sensing molecule RORγ regulates Cholesterol Metabolism and Immune Signaling in Diabetic Kidney Disease and Aging

status: Public on Jan 22 2026

city: Shenzhen

first: Shu

last: Yang

address: 1017 Dongmen North Road, Luohu District, Shenzhen

institute: shenzhen people's hospital

summary: Aging is a major risk factor for diabetic kidney disease (DKD), with both conditions exhibiting similar renal pathology. We identify the energy-sensing molecule Retinoic acid-related orphan receptor γ (RORγ) as significantly downregulated in diabetic and aged kidneys. Tubule-specific RORγ deficiency exacerbates kidney injury, whereas its overexpression protects. Mechanistically, RORγ stabilizes insulin-induced gene 1 (INSIG1) by upregulating the deubiquitinase YOD1 and enhancing AMPK activity via CAB39, which together promote INSIG1 phosphorylation and subsequent stabilization. Stabilized INSIG1 potently blocks the ER-to-Golgi transport and activation of SREBP2 (cholesterol synthesis) and STING (inflammatory signaling). In diabetes, RORγ itself is suppressed transcriptionally by CTCF and functionally by impaired AMPK/SIRT1 signaling, which hinders its activation. Importantly, administration of a RORγ agonist or RORγ-enriched exosomes effectively alleviates diabetic kidney injury. Thus, RORγ emerges as a key regulatory node that mitigates DKD and renal aging by co-regulating AMPK-mediated metabolic and STING-driven innate immune pathways through INSIG1 stabilization.

overall_design: We induced RORγ overexpression in human TECs and conducted RNA sequencing (RNA-seq) analysis.


title: Mithramycin Alters EWS::FLI1 DNA Binding and RNA Polymerase II Processivity to Inhibit Nascent Transcription [CUT&Tag]

city: Ann Arbor

first: Patrick

last: Grohar

state: MI

address: 1600 Huron Pkwy

institute: University of Michigan Medical School

summary: Although many DNA binding natural products exert their effects through non-specific mechanisms, a therapeutic opportunity exists for a subset of these compounds that alter the expression or activity of specific driver oncogenes in specific cell contexts. In this study, we integrate CUT&Tag with Global Run-On Sequencing (CUT, Tag, and GRO) to show that the minor groove binding compound, mithramycin (MMA), inhibits the Ewing sarcoma oncogenic driver, the EWS::FLI1 transcription factor. MMA causes either an increase or decrease in EWS::FLI1 binding to chromatin at downstream target response elements to poison nascent transcription. The reversal of EWS::FLI1 activity is limited by non-specific effects of the drug on RNAPII processivity but can be optimized by continuous administration at low concentration to cause more precise reversal of the oncogenic transcriptome and striking Ewing sarcoma xenograft regressions. The activity in vivo is further improved with a less-toxic second-generation analog, AIT-102.

overall_design: CUT&Tag data using FLI1 antibody, H3K27ac antibody or IgG control following incubation with PBS solvent control or mithramycin at either 20 nmol/L for 72 hours or 100 nmol/L for 18 hours.

first: Rebecca

last: Kaufman


title: Mithramycin Alters EWS::FLI1 DNA Binding and RNA Polymerase II Processivity to Inhibit Nascent Transcription [RNA-seq]

overall_design: Bulk RNAseq data of TC32 with or without knockdown of EWS::FLI1 achieved with a 30-hr incubation with siEF or non-specific siNEG


title: Seq-Scope-eXpanded (Seq-Scope-X): Spatial Omics Beyond Optical Resolution

first: Jun Hee

last: Lee

address: 109 Zina Pitcher Pl

institute: University of Michigan

summary: Sequencing-based spatial transcriptomics (sST) enables transcriptome-wide gene expression mapping but falls short of reaching the optical resolution (200–300 nm) of imaging-based methods. Here, we present Seq-Scope-X (Seq-Scope-eXpanded), which empowers submicrometer-resolution Seq-Scope with tissue expansion to surpass this limitation. By physically enlarging tissues, Seq-Scope-X minimizes transcript diffusion effects and increases spatial feature density by an additional order of magnitude. In liver tissue, this approach resolves nuclear and cytoplasmic compartments in nearly every single cell, uncovering widespread differences between nuclear and cytoplasmic transcriptome patterns. Independently confirmed by imaging-based methods, these results suggest that individual hepatocytes can dynamically switch their metabolic roles. Seq-Scope-X also works in brain and colon, and can be adapted for spatial proteomics, profiling hundreds of barcode-tagged antibody stains at microscopic resolutions in mouse spleens and human tonsils. Together, these findings establish Seq-Scope-X as a transformative platform for ultra-high-resolution whole-transcriptome and proteome profiling, providing unparalleled precision and biological insights.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
Tissue Samples
Mouse liver, colon, and spleen tissues were collected from 8-week-old male C57BL/6 wild-type mice, and brain tissue was obtained from a 6-month-old male mouse. All animal procedures were approved by the Institutional Animal Care and Use Committee at the University of Michigan (protocol PRO00011369).
Human tonsil tissue was obtained from the UCLA Pathology Biobank as a discarded surgical specimen from an adult patient with chronic tonsillitis. The sample was fully de-identified prior to acquisition and classified as IRB-exempt under institutional and federal guidelines, with no access to identifiable patient information.
Seq-Scope-X Transcriptome Workflow
Fresh frozen tissues were cryosectioned, mounted on charged slides, fixed with formaldehyde, and permeabilized with methanol. Anchor probes were hybridized in a formamide-containing buffer under humidified conditions. Tissues were then embedded in a polyacrylate-based monomer solution, polymerized, and cleared using digestion buffer with Proteinase K.
Tissue expansion was performed by incubation in diluted SSC, and DAPI staining was used to assess tissue integrity. Expanded gels were trimmed for imaging and alignment, then placed onto Seq-Scope Chips. Probe release and transcript transfer were achieved by heat incubation, followed by standard Seq-Scope library preparation, omitting tissue digestion as tissues were not directly attached to the chip.
Seq-Scope-X Proteome Workflow
For spatial proteomic analysis, tissues were permeabilized with methanol, blocked with a BSA-containing solution, and incubated overnight with TotalSeq™-A oligonucleotide-tagged antibody cocktails. After washing and post-fixation, tissues were processed using the same embedding, clearing, and expansion steps as in the transcriptome workflow.
Library preparation was modified to capture antibody-bound DNA oligonucleotides. Following reverse transcription, antibody tag libraries were eluted, purified, amplified by AT-PCR and indexing PCR, size-selected to isolate ~250 bp fragments, and sequenced on an Illumina NovaSeq-X platform.
Data Processing and Analysis
Seq-Scope-X transcriptome data were processed using the Seq-Scope pipeline with adjustments for experimentally determined expansion factors, following the NovaScope and NEDA workflows. Processing included generation of spatial barcode maps, alignment to reference genomes, construction of spatial gene expression matrices, and clustering using Seurat v5.
Spatial factor discovery was performed using Latent Dirichlet Allocation, and FICTURE was used to project cell-type factors into raw pixel space. Microscopy images, which lacked fiducial markers, were aligned to transcriptomic data using QGIS and further processed with CellProfiler and Photoshop. Differential expression, clustering, and integration analyses were conducted on hexagonally binned data to enable spatial and functional interpretation.

first: Angelo

last: Anacleto

first: Weiqiu

last: Cheng

first: Hee Sun

last: Han

first: Hyun Min

last: Kang


title: Cytoplasmic mRNA decay by the anti-viral nuclease RNase L promotes transcriptional repression [S2P Pol II CUT&RUN]

city: Berkeley

first: Britt

middle: Aspen

last: Glaunsinger

state: CA

address: 565 Li Ka Shing Center

department: Department of Plant and Microbial Biology

institute: University of California, Berkeley

summary: Ribonuclease (RNase) L is an antiviral factor that promiscuously degrades viral and cellular RNA in the cytoplasm. This results in extensive translational reprogramming, altering mRNA processing and export. Here, we reveal that another major consequence of cytoplasmic RNase L activity is the repression of nascent RNA synthesis in the nucleus. This is not associated with altered nuclear RNA stability but instead results from transcriptional repression. For RNA polymerase II, repression is primarily associated with reduced occupancy of serine 2-phosphorylated polymerase in gene bodies, indicating an elongation defect. Prominent among the transcriptionally downregulated loci are immune-related genes, supporting a role for RNase L in tempering innate immune and inflammatory responses. RNase L activation also caused disruption of nucleoli and reduced RNA polymerase I and III transcription. Crosstalk between RNA decay and transcription thereby contributes to the large-scale modulation of gene expression in RNase L-activated cells.

overall_design: Pol II occupancy measurement by CUT&RUN of A549 WT or RNase L-KO cells either transfected with Lipofactamine RNAiMAX alone or with poly(I:C) for 4 hours (3 biological replicates per condition). For each replicate, an additional RNAiMAX-transfected WT sample was included for IgG control.

first: Xiaowen

last: Mao

first: Sherzod

last: Tokamov

first: Felix

last: Pahmeier

first: Azra

last: Lari

first: Jinyi

last: Xu

first: Eva

last: Harris


title: Rational design of immune gene therapy combinations via in vivo CRISPR activation screening of tumor microenvironment modulators

city: New Haven

first: Chuanpeng

last: Dong

state: CT

address: 850 West Campus Dr

department: Genetics

institute: Yale University School of Medicine

summary: The hostile tumor microenvironment (TME) remains a major challenge for cancer immunotherapy. Here, we performed TME-targeted in vivo CRISPR activation (CRISPRa) screen to identify factors that promote anti-tumor immunity, culminating in rationally designed immune gene therapy combinations. Multiplexed activation of genes encoding antigen presentation, T cell proliferation, co-stimulation, and migration (APCM) leads to enhanced anti-tumor responses. An APCM-focused CRISPRa screen in metastatic tumors identified CD80, TNFSF14, CXCL10, TNFSF18, TNFSF9, and IFNG as top immunostimulatory candidates. Further optimization pinpointed TNFSF9 (4-1BBL) + IFNG + IL12B (4II) as a potent therapeutic combination. AAV-4II enhanced antigen presentation, T cell activation, proliferation, cytotoxicity, and tumor infiltration. Preconditioning the TME with AAV-4II synergized with CAR-T and TCR-T cell therapies to suppress primary and metastatic solid tumors in vivo. These findings establish TME-targeted CRISPRa screening as a rapid route to develop immune gene therapy combinations against solid tumors.

first: Feifei

last: Zhang

first: Ryan

last: Chow

first: Sidi

last: Chen

first: Guangchuan

last: Wang


title: Canonical BAF complex orchestrates mesenchymal stem cell niche composition and fate via cofactor-guided chromatin remodeling

city: Los Angeles

first: Mingyi

address: 2250 Alcazar Street, CSA103, HSC

department: Center for Craniofacial Molecular Biology

institute: University of Southern California


title: Step-wise signal integration governs adaptive programming of lymphocytes [bulkRNA-seq and ATAC-seq 6hr Stim]

city: New York

first: Hyunu

last: Kim

state: NY

address: 417 E 68th St

department: Immunology

institute: Memorial Sloan Kettering Cancer Center

summary: Lymphocyte differentiation depends on activation via antigen and cytokines during the immune response to infection. How the timing and integration of these signals program the epigenetic and functional fate of these cells is not completely understood. In this study, we find that inflammatory cytokine signals received by innate and adaptive lymphocytes have a context-dependent role for immune memory formation. Without preceding and sufficient antigen receptor signaling, inflammatory cytokines drive terminal differentiation into short-lived effector cells. In contrast, sufficient antigen-receptor signaling redirects inflammatory cytokine signals to promote memory differentiation via cooperation of STAT and AP-1 transcription factors. By this crucial epigenetic mechanism, optimally equipped lymphocytes are selected for memory formation rather than a terminal effector cell fate. Whereas T cells are hardwired to be shielded from premature inflammatory signals, NK cells rely on coincidental early antigen receptor signaling for adaptive responses. Together, step-wise integration of antigen and cytokine signaling optimizes both effector and memory differentiation, allowing for promiscuous recruitment into the acute immune response while promoting avidity maturation in memory populations of both innate and adaptive lymphocytes.

overall_design: Bulk RNA-seq and ATAC-seq of in vitro stimulated NK cells (with the indicated stimulations) as well as NK cells isolated from MCMV-infected mice taken after 1 day post infection (2-4 replicates each).

first: Simon

last: Grassmann

first: Joseph

last: Sun


title: Step-wise epigenetic signal integration governs adaptive programming of cytotoxic lymphocytes [CUT&RUN STAT1 STAT5 cJun]

overall_design: CUT&RUN of stimulated NK and CD8+ T cells


title: RORγ drives non-small cell lung cancer progression by upregulating the NGF signalling

city: Guangzhou

first: Guodi

last: Cai

state: Guangdong Province

address: 132, Waihuandonglu, Daxue Cheng

department: School Of Pharmaceutical Sciences

institute: Sun Yat-Sen university

summary: Lung cancer remains one of the most prevalent and lethal malignancies worldwide, with non-small cell lung cancer (NSCLC) representing the most common subtype—highlighting the critical need for novel therapeutic approaches. Here, we identify the retinoic acid receptor-related orphan receptor gamma (RORγ) as a key driver of NSCLC progression. Integrative bioinformatics and immunohistochemical analysis revealed that RORγ is highly expressed in NSCLC tissues and that its expression correlates with poor patient prognosis. Functionally, elevated RORγ significantly enhanced the proliferation, migration, and invasion capabilities of NSCLC cells. Conversely, treatment with the RORγ antagonist or genetic silencing of RORγ potently suppressed these malignant phenotypes both in vitro and in vivo. Mechanistically, RORγ directly binds to the promoter region of NGF, stimulates NGF gene transcription, and thereby promotes NSCLC progression. RORγ antagonists suppress NGF expression and inhibit its downstream signalling pathways, whereas exogenous NGF supplementation or overexpression of NGF notably reverses the inhibitory effects of RORγ antagonists on NSCLC cells. Taken together, these results establish RORγ as a critical regulator of NSCLC and a promising therapeutic target for NSCLC treatment.

overall_design: H157 cells were treated with vehicle (DMSO) or W6134 (2.5 μM) for 48 hours before total RNA extraction. The extraction steps of total RNA were according to the manufacturer's protocol of the Vazyme Super FastPure Cell RNA Isolation Kit (Vazyme Biotech, Nanjing, China). Transcriptomic sequencing of RNA-seq libraries were validated through MGISEQ2000 machine (BGI Tech, China). Enrichment analysis of co-downregulated genes (expression changes of ≥ 1.5-fold) in both cell lines following W6134 treatment was performed using R (v4.2.1), with the most significantly enriched pathways visualized via volcano plots (considering p adjust (FDR) < 0.05 as statistically significant).

first: Yechun

last: Zeng

first: Junjian


title: Analysis of LARP6 impact on RNA localisation to cell protrusions of Glioblastoma cells

city: Oxford

first: Faraz

middle: K.

last: Mardakheh

address: South Parks Road

department: Department of Biochemistry

country: United Kingdom

institute: University of Oxford

summary: LARP6 is a conserved RNA-binding domain that regulates the localisation of Ribosomal Protein mRNAs to the protrusions of mesenchymal-like cells. Our results had revealed that in addition to its folded La-module RNA binding domain, LARP6 makes direct contacts with its RNA targets via its disordered N-terminal region, which precedes the La-module. To assess the contribution of this region to the regulation of RNA localisation by LARP6, we carried out a spatial transcriptomics analysis of U-87 MG Glioblastoma cells, treated with scrambled control vs LARP6 3'UTR targeting siRNAs, with or without rescuing the LARP6 expression using a doxycycline-inducible full-legth or delta N-terminal mutant of LARP6. The cells were subjected to siRNA knockdown for 72hrs, before being seeded on 3um transwell filters and allowed to protrude through the pores for 90 mins. The protrusions and cell-bodies on opposite sides of the filter were isolateed, with total RNA extracted and subjected to RNA-sequencing using Lexogen QUANTSEQ 3' mRNA sequencing library preparation. Three independent biological replicates of each experiment were performed.

overall_design: A total of three independent experiments were performed, each with the following conditions: 1- U87-MG control cells + scrambled (scr) siRNA; 2- U87-MG control cells + LARP6 3'UTR targeting (si3UTR) siRNA; 3- U87-MG cells + Full-length (FL) myc-LARP6 + scr siRNA; 4- U87-MG cells + FL myc-LARP6 + si3UTR; 5- U87-MG cells + delta-NTR myc-LARP6 + scr siRNA; 6- U87-MG cells + delata-NTR myc-LARP6 + si3UTR;  Each sample was then fractionated into protrusion and cell-body fractions using transwell filters, before RNA extraction and sequencing using Lexogen's Quantseq 3' mRNA sequencing. For more details, please see the associated preprint: https://doi.org/10.1101/2024.09.20.614075.

first: Federica

last: Capraro

middle: K

first: Maria

last: Conte


title: Step-wise epigenetic signal integration governs adaptive programming of cytotoxic lymphocytes [ATAC-seq AP1inhibitor]

overall_design: ATAC-seq of stimulated NK cells


title: ISL1: A Novel Neuroendocrine Subtype in Small Cell Lung Cancer Predicts Durable Response to Lurbinectedin

city: Indianapolis

first: Misty

last: Shields

state: IN

address: 980 W. Walnut St

institute: Indiana University

summary: Small cell lung cancer (SCLC) is a recalcitrant thoracic malignancy known for acquired chemoresistance, early metastatic spread, and poor overall survival. Treatment with lurbinectedin, a DNA minor groove alkylating agent, provides durable efficacy in a subset of patients. In this study, we aim to identify and validate predictive biomarkers to lurbinectedin in small cell lung cancer patients. Within the ISL1 “high” lines, 1,105 genes were uniquely downregulated following lurbinectedin, including ISL1, RBMS3, PARD3B, SIX1, SOX2-OT, AURKA, and ASCL1. Downregulation of select MYC paralogs was additionally observed in the ISL1 “high” lines. Over 1,100 genes were additionally identified to be uniquely upregulated in the ISL1 “high” lines, including ATF3, BEST1, and DDIT3. ISL1 “low” lines showed significantly fewer unique expression changes following lurbinectedin (35 downregulated, 25 upregulated). Regardless of ISL1 status, 83 genes were globally downregulated, including LSAMP and MACROD2, while only 14 genes were globally upregulated following lurbinectedin, including TONSL, CDT1, and CHTF18.

overall_design: For the RNA-seq, two ISL1 “high” (H209, H187) and two ISL1 “low” (H82, SHP-77) cell lines were treated in biological triplicates with 0.1 nM lurbinectedin (or DMSO vehicle) for 24 h before harvesting for RNA extraction and sownstream RNA-seq.

first: Katherine

last: Minton

first: Tianhao

last: Zhou


title: Canonical BAF complex orchestrates mesenchymal stem cell niche composition and fate via cofactor-guided chromatin remodeling [CUT&Run DKO]

summary: The canonical BAF (BRG1/BRM-associated factor) chromatin remodeling complex plays a pivotal role in governing stem cell behavior, yet how it regulates adult stem cell niche remains unclear. Here, we show that ARID1-containing cBAF complex orchestrates the spatial organization of the mesenchymal stem cell niche and fate in the adult mouse incisor. Dual loss of ARID1A and ARID1B in Gli1+ mesenchymal stem cells using conditional knockout mouse models disturbs chromatin accessibility in a cell-type-specific manner and alters cofactor recruitment, leading to niche cell disorganization, disrupting progenitor cells (transit-amplifying cells, TACs) fate commitment during tissue homeostasis. Single-cell multi-omics profiling and in vivo functional validations reveal that the cBAF complex partners with DLX2 to coordinate niche cell composition and recruits FOXO1 and DLX2 to balance TAC proliferation and differentiation. Our findings establish cBAF as a master regulator of chromatin state and microenvironment architecture, essential for maintaining adult mesenchymal stem cell function and tissue homeostasis.

overall_design: DKO mouse incisor proximal end tissue were collected and digested into cells, then underwent the process following the CUT&RUN protocol.


title: The deacetylase Sir2 is the primary sensor driving transcriptional changes in response to low NAD+ in the yeast Kluyveromyces lactis

city: Buffalo

first: Charikleia

last: Karageorgiou

address: 109 Cooke Hall, Mary Talbert Way

department: Department of Biological Sciences

institute: University at Buffalo

summary: The coenzyme NAD+ (nicotinamide adenine dinucleotide) is a critical electron carrier in central metabolism and is required for cellular health. It is proposed that cells sense intracellular NAD+ levels using sirtuin deacetylases, which require NAD+ for their enzymatic activity.  We tested this hypothesis by examining how intracellular NAD+ levels affect expression of Sir2-repressed genes in the yeast Kluyveromyces lactis. Because K. lactis cannot synthesize NAD+, we could create a gradient of intracellular NAD+ levels by growing cells in varying concentrations of the precursor nicotinic acid. We found that as NAD+ levels decreased, acetylation of histones at target promoters increased, as did expression of these genes. RNA-Seq analysis revealed that genes induced in low nicotinic acid include some that would restore NAD+ levels, such as the high-affinity nicotinic acid transporter TNA1, and some that would enable long term survival, such as genes promoting sporulation. Most genes induced in low nicotinic acid (100 of 114 or 88%) were also induced in the absence of Sir2. Moreover, in sir2Δ cells, few transcriptional changes occurred in response to low nicotinic acid. Thus, Sir2 is the primary sensor responsible for the transcriptional response to low NAD+ in K. lactis. In addition, the degree of induction varied across NAD+ levels, suggesting that Sir2 behaves as a rheostat, tuning gene expression to NAD+ availability.

overall_design: Kluyveromyces lactis wild-type (WT; CBS2359) and sir2Δ strains were grown in yeast nitrogen base supplemented with nicotinic acid (NA) at four concentrations, 15 to 400 μg/L, to create a gradient of intracellular NAD⁺. Cultures were harvested at mid-log phase (OD₆₀₀ ≈ 1.0). For each strain × condition combination, two independent biological replicates were collected (17 total RNA-seq libraries).

first: Mahasweta

last: Acharjee

first: Kristen

last: Humphrey

first: Vincent

last: Lactaoen

first: Omer

last: Gokcumen

first: Laura

last: Rusche


title: Step-wise signal integration governs adaptive programming of lymphocytes

first: Hyunu

last: Kim

overall_design: Refer to individual Series


title: Induction of antigen-presenting monocyte-derived dendritic cells by nanoparticles inhibits metastasis and relieves immunosuppression in the metastatic niche

first: Lonnie

last: Shea

institute: University of Michigan- Ann Arbor

summary: Myeloid immune cells play a major role in establishing a suitable microenvironment for metastatic tumor cells. Dysregulated myeloid cells suppress antigen-presentation pathways and effector T cell responses at distal organs, and reprogramming these cells may enhance anti-tumor cytotoxicity. Targeting myeloid cells with poly(lactide-co-glycolide) nanoparticles, which possess intrinsic immunomodulatory properties, can promote monocyte maturation to inhibit metastasis. Intravenously delivered nanoparticles made with polyvinyl alcohol, but not other surfactants, reduce the accumulation of neutrophils at the metastatic niche and induce the differentiation of monocytes into antigen-presenting monocyte-derived dendritic cells. The internalization of nanoparticles was linked to the upregulation of gene expression programs in monocyte-derived dendritic cells associated with antigen presentation and T cell stimulation, and ligand-receptor network modeling supports increased activation of Th1 cells by these monocyte-derived dendritic cells. Nanoparticle administration increased the proportion of CD4 cells with Th1 and Th17 phenotypes and did not inhibit metastasis in mice where monocytes or T cells were depleted, indicating that interactions between monocyte-derived dendritic cells and T cells are essential to the mechanism of action. Collectively, our findings demonstrate that nanoparticles can reprogram circulating monocytes into monocyte-derived dendritic cells to modulate the metastatic niche and enhance antigen presentation to stimulate intrinsic T cell responses.

overall_design: Lungs were isolated from female BALB/c 4T1-tumor bearing mice at D14 post-inoculation (inoculated with 50 uL of 2e6 4T1 cells/mL). Mice were treated with saline (control) or 1mg of NPs every three days starting at D1 post-inocluation (D1, 4, 7, 10, 13 NP treatments). Cells were then prepared for flow-assisted cell sorting by staining with AF488-CD45 and sorted into CD45+NP+, CD45+NP-, and CD45- populations on the Bigfoot Cell Sorter. Sorted samples were fixed with the 10x Chromium Next GEM Single Cell Fixed RNA Sample Preparation Kit following manufacturer instructions. Fixed samples were submitted to the University of Michigan Advanced Genomics Core for library preparation with the 10x Single Cell Fixed RNA Hybridization & Library Kit and Single Cell Fixed RNA Mouse Transcriptome Probe Kit following manufacturer guidelines for the 10x Single Cell Gene Expression Flex platform. Samples were sequenced on the NovaSeq X 10B flow cells (300 cycle) at a depth of approximately 25,000 reads per cell.

first: Jeffrey

middle: A

last: Ma

first: Kate

middle: V

last: Griffin

first: Kathryn

last: Kang

first: Agustina

last: Diener

first: Ian

last: Schrack

first: Elizabeth

last: Bealer

first: Laila

last: Rad

first: Rebecca

last: Pereles

first: Jacqueline

last: Jeruss


title: Canonical BAF complex orchestrates mesenchymal stem cell niche composition and fate via cofactor-guided chromatin remodeling [CUT&Run]

first: Mingyi

last: Zhang

overall_design: Control mouse incisor proximal end tissue were collected and digested into cells, then underwent the process following the CUT&RUN protocol.


title: Non-invasive epidermis sampling for DNA methylation-based prediction of skin cancer phenotypes

city: Heidelberg

first: Oliver

last: Gilliam

address: Im Neuenheimer Feld

institute: German Cancer Research Center

type: Methylation profiling by genome tiling array

summary: The epidermis is uniquely exposed to the effects of environmental factors such as ultraviolet radiation, which induce progressive genetic and epigenetic modifications contributing to aging and the onset of keratinocyte carcinomas. DNA methylation is the best-characterized epigenetic modification and a valuable biomarker for assessing epidermal health. However, broad screening approaches have been hindered by the limited quantity and quality of the genomic DNA obtained from the epidermis and the resulting need for invasive sampling methods. Here we describe an integrated method that enables the non-invasive sampling of epidermal DNA for subsequent analysis by DNA methylation microarrays. This procedure combines a gel-based adhesive tape for keratinocyte collection, a robust gDNA extraction protocol and a curated selection of microarray probes optimized for low-input DNA conditions. Analysis of >100 corresponding methylomes demonstrates that our approach can be used for both the training of epigenetic clocks capable of predicting epidermal age with high accuracy, as well as the investigation of various DNA methylation-based biomarkers relevant to keratinocyte cancer development. These findings underscore the potential of our method for broad and non-invasive skin health assessment and cancer prevention strategies.

overall_design: We aimed to profile skin epidermis using the TapeLift, a non-invasive sampling method of epidermal DNA. DNA methylation analysis was performed with the EPIC V2 methylation bead chip.

first: Manuel

last: Rodríguez-Paredes

first: Yan

last: Feng

first: Katrin

last: Wegner

first: Günter

last: Raddatz

first: Elke

last: Grönniger

first: Frank

last: Lyko


title: Cytoplasmic mRNA decay by the anti-viral nuclease RNase L promotes transcriptional repression [S5P Pol II CUT&Run]

first: Britt

last: Glaunsinger

first: Xiaowen

last: Mao

first: Sherzod

last: Tokamov

first: Felix

last: Pahmeier

first: Azra

last: Lari

first: Jinyi

last: Xu

first: Eva

last: Harris


title: Canonical BAF complex orchestrates mesenchymal stem cell niche composition and fate via cofactor-guided chromatin remodeling [scATAC-seq]

overall_design: Single-cell transposase-accessible chromatin were obtained from the digested proximal region of mouse incisor of at 4 days post-tamoxifen induction for DKO mice at the age of 1 month.


title: EBF1 regulates sensory establishment in the cochlea by positioning the medial boundary of the prosensory domain and restricting proliferation of the sensory progenitor population

city: Seattle

first: Joshua

middle: William

last: Hahn

state: WA

address: 3747 W Stevens Wy NE

department: Department of Neurobiology & Biophysics

institute: University of Washington

summary: In our previous study, we reported that Ebf1 excision throughout the inner ear epithelium and before the onset of cochlear development leads to dramatic sensory expansion in the cochlea by neonatal stages. Ebf1 conditional knockout cochleae possess over twice as many sensory cells as littermate controls and develop ectopic sensory patches in their Kölliker’s organs. To better understand the mechanism behind EBF1’s role in restricting sensory establishment, we performed multiome sequencing in our current study. EBF1 is a traniption factor best known for its importance in B cell lineage specification, during which it acts as both an activator and a repressor. Our results indicate that EBF1 prevents the Kölliker’s organ cells from being recruited to the prosensory domain by promoting expression of Prdm16 and repressing expression of Jag1 and Sox2. We also found that EBF1 may promote cell cycle exit by repressing Ccnjl expression. In summary, medial expansion of the prosensory domain, together with delayed cell cycle exit in the developing cochlear epithelium, underlies the robust increase in sensory cells seen in Ebf1 conditional knockouts.

overall_design: To enable investigation of EBF1-dependent changes in cochlear development at the single cell level, we performed multiome sequencing, combining single nucleus RNA sequencing (snRNA-seq) and single nucleus ATAC sequencing (snATAC-seq), on mouse cochlea at E14.5 and E16.5 in control mice and in a Ebf1 conditional knockout model.

first: Kathryn

middle: G

last: Powers

first: Juliette

last: Wohlschlegel

first: Olivia

last: Bermingham-McDonogh


title: Cytoplasmic mRNA decay by the anti-viral nuclease RNase L promotes transcriptional repression [4sU-seq]

overall_design: Nascent RNA profiling by 4sU-seq of A549 WT or RNase L-KO cells either transfected with Lipofactamine RNAiMAX alone or with poly(I:C) for 4 hours (3 biological replicates per condition).


title: iCLIP analysis of full-length and deletion mutants of myc-LARP6

first: Faraz

last: Mardakheh

summary: Intrinsically disordered regions (IDRs) are prevalent in RNA-binding proteins (RBPs), yet their roles in RNA interactions remain poorly defined. We examined the structured and disordered RNA-binding activities of LARP6, an RBP with a diverse RNA-binding repertoire. U87 glioblastoma cells stably expressing myc-tagged full-length or various deletion mutants of LARP6 under a doxycycline switch were induced to express myc-LARP6 variants at near endogenous levels, before individual-nucleotide resolution UV-crosslinking and immunoprecipitation (iCLIP) was performed to assess each variants' RNA-binding targets on the transcriptome. A total RNA-seq experiment was also performed on the cells in parallel to distinguish between changes in RNA bidning and those that are affected via expression level variations.

overall_design:
iCLIP of myc-LARP6 from full-length (FL), N-terminal Region deleted (deltaNTR), La-module deleted (delta LaMod), N-terminal domain deleted (deltaNTD),  and C-terminal region deleted (deltaCTR1) U87 cells, along with untransfected control cells was performed as indicated in (https://doi.org/10.1101/2024.09.20.614075).
To normalise iCLIP differences based on total RNA variations, an rRNA depletion whole transcriptome sequencing of each stably expressing U87 cell-line following LARP6 induction was also performed in parallel, using short single read (SE50) and long paired end read (PE150) sequencing. These were used as input control.

first: Federica

last: Capraro

first: Maria

last: Conte


title: Canonical BAF complex orchestrates mesenchymal stem cell niche composition and fate via cofactor-guided chromatin remodeling [RNA-Seq]

first: Mingyi

last: Zhang

overall_design: Transcriptomes were obtained from the digested proximal region of mouse incisor of at 4 days post-tamoxifen induction for DKO mice at the age of 1 month.


title: CD74⁺ Myeloid Cells across Brain Pathologies

city: Madrid

first: Manuel

last: Valiente

address: Melchor Fernández Almagro, 3

country: Spain

institute: CNIO

summary: In this study, we conducted a comprehensive analysis of single-cell RNA sequencing data from immune cells isolated from the brain tissue of mouse models of Alzheimer’s disease (AD), multiple sclerosis (MS), and brain metastasis (BrM). Our findings reveal a shared transcriptional signature among CD74⁺ myeloid cells across these conditions, indicating a conserved inflammatory response that may be amenable to therapeutic targeting. These results highlight the role of CD74⁺ myeloid cells as a unifying component of the immune landscape in diverse neurological disorders and lay the groundwork for future investigations into targeted interventions aimed at mitigating these pathologies.

overall_design: scRNA-seq from CD45+ immune cells isolated from brain tissue of mouse models for Alzheimer's Disease, Multiple Sclerosis, and Brain Metastasis.

first: Angel

last: Marquez-Galera

first: Laura

last: Alvaro-Espinosa

first: Jose

middle: P

last: Lopez-Atalaya

first: Carolina

last: Hernandez-Oliver


title: Comparison of CD74+ vs CD74- microglia/macrophages from the brain TME from 2 different type of tumors (B16/F10-BrM & H2030-BrM)

summary: To investigate the properties of CD74+ microglia/macrophages compared to the CD74- microglia/macrophages in brain metastasis.

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of CD74+ microglia/macrophages compared to CD74- microglia/macrophages isolated from 4 experiments of B16/F10-BrM brain metastasis (pool of at least 3 brains each) and 4 experiments of H2030-BrM brain metastasis (pool of at least 3 brains)

first: L

last: Álvaro

first: C

last: Hernández Oliver

first: M


title: Canonical BAF complex orchestrates mesenchymal stem cell niche composition and fate via cofactor-guided chromatin remodeling [scRNA-seq]

overall_design: Single-cell transcriptomes were obtained from the digested proximal region of mouse incisor of at 4 days post-tamoxifen induction for DKO mice at the age of 1 month.


title: Step-wise signal integration governs adaptive programming of lymphocytes [scRNA-seq]

first: Hyunu

last: Kim

overall_design: scRNA-seq of NK cells isolated from spleen of C57BL/6 mice upon MCMV infection on day 0-4.

first: Simon

last: Grassmann

first: Endi

last: Santosa

first: Joseph

last: Sun


title: TP53-TAU axis regulates microtubule bundling to control alveolar stem cell mediated regeneration

city: Durham

first: Purushothama Rao

last: Tata

email: pt93@duke.edu, tata.lab@yahoo.com

state: NC

address: 303 Research Dr., Alexander Sands Building, Room- 451, BOX 3709

department: Department of Cell Biology

institute: Duke University School of Medicine

summary: To assess the morphological dynamics during the differentiation of alveolar epithelial type 2 cells (AT2s) into alveolar epithelial type 1 cells (AT1s), we established an ex vivo differentiation model in 2-dimensional cultures with defined conditions using purified AT2s from mouse lungs.

overall_design: Purified murine AT2s were seeded on collagen-1 or fibronectin with serum-free feeder-free medium. We performed bulk RNA sequencing on cells collected from collagen-1 (for AT2s maintenance) or fibronectin-coated plates harvested on days 5 (for alveolar transitional cell states induction) and days 9 (for AT1s induction).

first: Satoshi

last: Konishi

first: Aleksandra


title: Spatiotemporal molecular profiling of macrophage-fibroblast crosstalk defines checkpoints orchestrating onset and resolution of inflammation [scATAC-Seq]

status: Public on Jan 21 2026

city: Berlin

first: Gerhard

last: Krönke

address: Virchowweg 11

department: Rheumatology and clinical immunology

institute: Charite Berlin

summary: The molecular details of macrophage-fibroblast crosstalk during the onset and resolution of inflammatory disease remain incompletely understood. Here, we apply a scRNAseq-, scATACseq- and bulk RNAseq-based bioinformatic modelling approach to map heterocellular signaling circuits of synovial macrophage and synovial fibroblast (SF) subsets during various stages of inflammatory arthritis. While SFs function as key pacemakers of synovial inflammation, individual subsets of synovial macrophages support both the perpetuation and the resolution of arthritis. While pro-inflammatory Il1b+ macrophages dominate the early stages of inflammation, these cells also retain a substantial intrinsic plasticity that is characterized by chromatin remodeling and an eventual differentiation into Spp1+ macrophages. These cells display a terminally-differentiated phenotype, suppresses activation of pro-inflammatory SFs, and initiates the resolution of arthritis by secretion of regulatory mediators including osteopontin. Our data highlight the dichotomous character of macrophage-fibroblast crosstalk and define the cellular and molecular checkpoints that control the onset and resolution of immune-mediated inflammatory diseases.

overall_design: We generated scATACseq data of myeloid Cd45+Cd11b+Ly6G- cells isolated from murine paws at three timepoints during K/BxN serum transfer arthritis, at steady state, day5 and day9.

first: Katharina

last: Weishaupt

first: David

last: Chambers

first: Maria

last: Dzamukova

first: Ivana

last: Androšević

first: Jean-Philippe

last: Auger

first: Darleen

last: Hüser

first: Sébastien

last: Trzebanski

first: Andreas

last: Ramming

first: Anika

last: Grüneboom

first: Georg

last: Schett

first: Steffen

last: Jung

first: Markus

last: Hoffmann


title: Spatiotemporal molecular profiling of macrophage-fibroblast crosstalk defines checkpoints orchestrating onset and resolution of inflammation [RNA-seq]

overall_design: We generated RNAseq data of synovial fibroblasts, either wildtype or fibroblasts derived from K/BxN serum transfer mice, stimulated in vitro with either Fgf2, Opn or a combined treatment


title: Spatiotemporal molecular profiling of macrophage-fibroblast crosstalk defines checkpoints orchestrating onset and resolution of inflammation [scRNA-seq]

overall_design: To extend previously generated scRNAseq data in GSE134691 and GSE129087 we profiled myeloid cells and stromal cells from murine paws to have 3 timepoints during K/BxN serum transfer arthritis at days 0, 5 and 9. Specifically we sequenced Cd45+Cd11b+Ly6G- myeloid cells at day 9 and Cd45- stromal cells at day 0 and day5.


title: Step-wise signal integration governs adaptive programming of lymphocytes [CUT&RUN STAT4]

first: Hyunu

last: Kim

overall_design: STAT4 CUT&RUN of stimulated NK and CD8+ T cells

first: Simon

last: Grassmann

first: Joseph


title: Step-wise signal integration governs adaptive programming of lymphocytes [bulkRNA-seq and ATAC-seq]

overall_design: Bulk RNA-seq and ATAC-seq of in vitro stimulated NK cells (with the indicated stimulations) as well as NK cells isolated from MCMV-infected mice taken after 1 day post infection (2--4 replicates each).

first: Endi

last: Santosa

last: Sun


title: Human liver-derived organoids recapitulate Oropouche virus infection and manifestation, enabling antiviral drug discovery

city: Rotterdam

first: Qiuwei

last: Pan

address: Wytemaweg 80

institute: Erasmus University Medical Center

summary: Oropouche virus (OROV) is a neglected, re-emerging arbovirus that typically causes self-limiting febrile illness but can also result in severe complications. Currently, there are no approved vaccines or treatments for OROV infection. We integrated clinical data from OROV-infected patients with human liver-derived organoid models to investigate the virus's impact on the liver and evaluate repurposed antivirals. Patient blood tests show elevated liver enzymes, suggesting OROV-associated hepatic dysfunction. OROV isolates productively infect liver organoids and induce severe cellular damage. Transcriptomic profiling reveals strong virus-host interactions, including activation of interferon-stimulated genes and cell death pathways. Pharmacological inhibition of the interferon pathway enhances OROV replication, whereas treatment with therapeutic interferon-α suppresses the infection. Molnupiravir, a clinically approved antiviral targeting viral RNA-dependent RNA polymerase, markedly inhibits OROV replication and mitigates virus-induced cytopathology. Combining molnupiravir with interferon-α resulted in synergistic antiviral activity, indicating the complementarity of virus-targeted and host-directed strategies.

overall_design: Organoids cultured from adult human liver tissue were infected with both OROV isolates, OROV-1967 (strain RIVM/OROV/TRVL9760) and OROV-2024 (strain IRCCS-SCDC_1/2024_OROV-2024). Infected organoids were harvested at 1- 48-, and 96-hours post-infection. A treatment group was established using organoids infected with the OROV-2024 isolate and treated with 1 μM NHC treatment from 1 hour to 96 hours post-inoculation. As negative controls, uninfected organoids were cultured under same conditions for 96 hours. Total RNA was extracted from all samples using the MachereyNagel NucleoSpin RNA II Kit (Bioke, Netherlands) and quantified with the Bioanalyzer RNA 6000 Picochip. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads for cDNA synthesis and library construction by Novogene. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. RNA sequencing was conducted using a paired-end 150 bp (PE 150) sequencing strategy via Illumina platforms.

first: Jiajing

last: Li

first: Xin

last: Wang


title: Loss of JAK1 Function Causes G2/M Cell Cycle Defects Vulnerable to KIF18A Inhibition [Cal27 CRISPR Screen]

city: Cambridge

first: Vanessa

middle: Martine

last: Kelley

state: MA

address: 300 Binney

department: Gerstner Center for Cancer Diagnostics

institute: The Broad Institute

summary: Therapeutic resistance to DNA damage is a significant challenge in oncology. To gain insight into biological mechanisms that cause DNA damage resistance and to inform strategies for achieving synergy with therapeutic radiation, we performed parallel pooled genetic CRISPR-Cas9 screening for survival in high-risk head and neck squamous cell carcinoma (HNSCC) subtypes. Surprisingly, in addition to known mediators of radiotherapy response, including ATM, DNAPK, and NF-κB signaling, loss of JAK1 was identified as a driver of tumor cell radioresistance. Knockout of JAK1 in HNSCC increased cell survival by enhancing the DNA damage-dependent G2/M cell cycle arrest and delaying progression to radiation-induced mitotic catastrophe. In line with this finding, both JAK1 knockout and kinase inhibition with abrocitinib prevented subsequent formation of radiation-induced micronuclei. Loss of JAK1 function did not affect canonical CDK1 signaling but instead reduced activation of PLK1 and AURKA, two kinases with auxiliary roles in the regulation of G2 and M phase progression. Correspondingly, using both EdU labelling and live cell imaging techniques, JAK1 loss was found to cause prolonged metaphase, mitotic slippage, and progression to tetraploidy. Targeting the mitotic kinesin KIF18A with the small molecule sovilnesib exacerbated mitotic stress and enhanced the efficacy of radiation. These studies establish KIF18A inhibition as a strategy to counteract the protective G2/M cell cycle arrest induced by DNA damage and to thus enhance tumor cell sensitivity to radiation therapy.

overall_design: We performed a kinome-focused (Brunello gRNA library) CRISPR screen on the Cal27 HNSCC cell line with radiation as a selection pressure.  Three seperate experimental replicates of the Cal27 cells were either irradiated or treated with a control regimen.  Sequencing was then performed to determine gRNAs that were enriched or depeletd in the irradiated samples compared to unirradiated samples.

first: Marta

last: Baro

first: William

last: Gasperi

first: Nicholas

last: Ader

first: Hannah

last: Lea

last: Contessa


title: Antagonism between blue and red light-signalling controls thallus flatness in Marchantia polymorpha

city: Rehovot

first: Zohar

last: Meir

state: Shfela

address: Herzl 234

department: Mathematics & CS

country: Israel

institute: Weizmann Institute of Science

summary: The growth orientation of the Marchantia polymorpha thallus – a system of dorsiventralized, indeterminate axes – is modulated by light. We show that red and blue light act antagonistically to control thallus flatness, with red light signalling promoting epinasty and blue light signalling promoting hyponasty. We found that loss-of-function mutations in the blue light receptor MpPHOT led to epinasty, while loss-of-function mutations in the red light receptor MpPHY resulted in hyponasty. We hypothesize that these antagonistic activities of blue and red light signalling are balanced in white light, resulting in the development of flat thalli. Using time-resolved transcriptomics, we identified genes that were rapidly induced upon light exposure. Among these genes were all six members of the M. polymorpha BBX gene family. Mutants harbouring loss-of-function mutations in two of the six MpBBX transcription factors developed defective thalli. Mpbbx1 loss-of-function mutants formed hyponastic thalli, while Mpbbx5 loss-of-function mutants developed epinastic thalli. Double mutants Mpbbx1 Mpbbx5 grew flat, supporting the hypothesis that they function antagonistically. Together, these data indicate that phototropin-mediated blue light and phytochrome-mediated red light signalling antagonistically modulate thallus flatness, and that BBX transcription factors also act antagonistically to regulate thallus flatness.

overall_design: To examine light-responsive gene expression in Marchantia polymorpha, wild-type was grown under white light conditions, followed by a dark adaptation period and subsequent exposure to distinct light qualities. Plants were subjected to white, blue, red, or far-red light, as well as continued darkness, and samples were collected across a time course to capture early and late transcriptional responses. Total RNA was isolated from biological replicates for each condition and time point, and transcriptome-wide gene expression was quantified by RNA sequencing. Sequencing data were processed using a bioinformatic pipeline to map reads to the M. polymorpha reference genome and quantify transcript abundance. Gene expression levels were compared across treatments relative to the dark reference to identify differentially expressed genes, enabling a systematic analysis of light-quality- and time-dependent transcriptional responses.

first: Johannes

last: Rötzer

first: Liam

last: Dolan


title: Age-Related Decline in NCKX4-Mediated Calcium Clearance Accelerates Aortic Remodeling and Drives Early Vascular Aging

first: Guilherme Henrique

last: Souza Bomfim

address: 1 Washington Square Village 2R

department: Department of Molecular Pathobiology

institute: New York University (NYU)

summary: Aging is the primary nonmodifiable risk factor for cardiovascular diseases (CVDs), with older women facing a greater risk of CVDs than age-matched men. Vascular smooth muscle cells (VSMCs) dysfunction and impaired calcium (Ca2+) handling are recognized as central contributors to arterial stiffening and calcification. However, the molecular and functional determinants of Ca2+ clearance that drive vascular aging remain poorly understood. We identify the (Na+)-sodium/Ca2+-calcium (K+)-potassium-dependent exchanger 4 (NCKX4) as a crucial functional regulator of VSMCs Ca2+ clearance and vascular integrity. NCKX4 (encoded by Slc24A4) expression was significantly reduced in aortas from aged (72-78 weeks) mice, with a pronounced decline in females. Aged-related loss of NCKX4 impaired Ca2+ clearance function and increased calcium-phosphate mineralization. Young (12-15 weeks) Nckx4⁻/⁻ mice revealed fragmentation of elastic fibers, collagen accumulation, wall thickening, and extracellular matrix (ECM) remodeling, all hallmarks of vascular aging that closely resembled those of aged wild-type mice. Transcriptomic profiling showed that loss of NCKX4 alters pathways linked to Ca2+-integrin signaling, ECM turnover and mineralization, including dysregulation of anchorage integrins, microfibril-stabilizing, osteogenic drivers and pro-fibrotic integrins. These findings reveals that an impaired Ca2+ clearance promotes maladaptive inside-out integrin signaling, disrupting VSMCs anchorage, ECM homeostasis and mineralization. Our results establish NCKX4 as a previously unrecognized determinant of vascular aging, whose decline accelerates premature arterial remodeling and calcification. This study therefore, positions NCKX4 as a potential mechanistic link between age, sex-dependent vulnerability, and vascular stiffening, with implications for novel therapeutic strategies targeting Ca2+ handling in CVDs prevention.

overall_design: RNA-seq profiling of aortic tissue from young (Y, 12-15 weeks) and aged (A, 72-78 weeks) female wild-type (WT) and their knockdown Slc24a4 (Nckx4-/-) mice.


title: Loss of JAK1 Function Causes G2/M Cell Cycle Defects Vulnerable to KIF18A Inhibition [Detroit562 RNAseq]

overall_design: We performed RNA Sequencing on Detroit562 HNSCC cell lines.  The NT2 cell line was transduced with a non-targeting control gRNA, and the JAK1 knockout (KO) cell line was transwduced with a JAK1-targeting gRNA.  JAK1 KO was confirmed via Western blot.  Three seperate experimental replicates of the Detroit562 NT2 and JAK1 KO cell lines were submitted for sequencing.


title: Loss of JAK1 Function Causes G2/M Cell Cycle Defects Vulnerable to KIF18A Inhibition

overall_design: We performed RNA Sequencing on Cal27 HNSCC cell lines.  The NT2 cell line was transduced with a non-targeting control gRNA, and the JAK1 knockout (KO) cell line was transwduced with a JAK1-targeting gRNA.  JAK1 KO was confirmed via Western blot.  Three seperate experimental replicates of the Cal27 NT2 and JAK1 KO cell lines were submitted for sequencing.


title: Engineering Human Bone Marrow-derived Mesenchymal Stromal Cell Aggregates for Enhanced Extracellular Vesicle Secretion in a Vertical-Wheel Bioreactor

city: Tallahassee

first: li

last: sun

state: FL

address: 1115 West Call st.

institute: FSU College of Medicine

type: Non-coding RNA profiling by high throughput sequencing

summary: Human mesenchymal stem/stromal cells (hMSCs) hold significant potential for regenerative medicine due to their anti-inflammatory and pro-angiogenic secretome. In particular, 3D hMSC aggregates secrete EVs that have enhanced anti-inflammatory and immunomodulatory properties. However, safety and efficacy concerns associated with stem cell therapy have led to the discovery of cell-free approaches utilizing hMSC-derived extracellular vesicles (EVs). Despite their therapeutic promise, the clinical application of hMSC-EVs is limited by low production yield. This study investigates the scalable generation of hMSC-EVs from 3D aggregates in a novel Vertical-Wheel Bioreactor (VWBR) through shear stress-mediated biochemical cues, promoting cargo expression relevant to nerve regeneration and neuropathic treatment. Bone marrow-derived hMSCs were cultured as 3D aggregates in VWBRs and exposed to two different culture media—αMEM/FBS (serum-containing) and DMEM/F12/B27 (serum-free)—under three agitation speeds (25, 40, and 64 rpm). Metabolite and gene analyses were performed to assess EV biogenesis, focusing on ESCRT machinery markers. Results showed that hMSCs cultured in VWBR exhibited higher expression of EV biogenesis genes and glycolytic genes compared to static culture. αMEM/FBS (serum-containing) condition was more robust than DMEM/F12/B27 (serum-free) condition. EV yield (EV number per cell) increased by 3-10 fold (in serum-containing medium) in VWBR compared to static culture, with size of 120-180 nm and EV marker expression. microRNA-sequencing of the EVs shows the upregulation of miR-29a-3p, miR-451a, miR-224-5p, miR-16-5p, miR-133a-3p, and miR-143-3p, etc., reflecting a combination that enhances EV biogenesis, promotes metabolic reprogramming, and supports immunomodulatory behavior characteristics. Functional assays demonstrated that the generated EVs effectively modulated Schwann cell responses under neural inflammation, supporting their therapeutic potential. These findings highlight the role of VWBR-driven hydrodynamics in promoting EV production from 3D hMSC aggregates. This study advances the knowledge of dynamic aggregation and metabolic influence on 3D hMSC-EV production and fundamentally scale up the preconditioned techniques used to promote hMSC aggregation and the consequent EV secretion.

overall_design: Human bone marrow-derived mesenchymal stem/stromal cells (hMSCs) were cultured in regular 2D or 3D conditions. EVs were collected and total RNA was isolated for sequencing.

first: Li


title: Loss of JAK1 Function Causes G2/M Cell Cycle Defects Vulnerable to KIF18A Inhibition [Detroit562 CRISPR Screen]

overall_design: We performed a kinome-focused (Brunello gRNA library) CRISPR screen on the Detroit562 HNSCC cell line with radiation as a selection pressure.  Three seperate experimental replicates of the Detroit562 cells were either irradiated or treated with a control regimen.  Sequencing was then performed to determine gRNAs that were enriched or depeletd in the irradiated samples compared to unirradiated samples.


title: The role of Fibulin-2 during cardiac regeneration in zebrafish

city: Montreal

first: Rubén

last: Marín-Juez

address: 3175 Chem. de la Côte-Sainte-Catherine

institute: CHU Sainte-Justine

summary: We used a 10X Genomics single-cell RNA sequencing approach to compare the single-cell transcriptome of heart ventricles from fbln2sjr3-/- and wild-type siblings, at uninjured state and at 4 days post-cryoinjury.

overall_design: Uninjured WT heart ventricles (pool of 4), cryoinjured WT heart ventricles at 4 days post-cryoinjury (pool of 4), uninjured fbln2sjr3-/- heart ventricles (pool of 4), cryoinjured fbln2sjr3-/- heart ventricles at 4 days post-cryoinjury (pool of 4) and cryoinjured fbln2sjr7-/- heart ventricles at 4 days post-cryoinjury (pool of 4) were extracted for single-cell dissociation and library preparation.

last: Marin Juez

first: Gülsüm

last: Kayman-Kürekçi

first: Gursimran

last: Kaur Bajwa

first: Gregor

last: Andelfinger

first: Séverine

last: Leclerc

first: Emilie

last: de Chantal

first: Darrell

last: Belke

first: Justin

last: Deniset

first: Shaoqiu

last: Zhang


title: MYRF Controls Mesothelium Specification, Signaling, and Plasticity [scRNA-Seq]

city: La Jolla

first: Gidsela

last: Luna

state: California

address: 9500 Gilman Dr

institute: UC San Diego

summary: The mesothelium is a squamous monolayer that ensheathes internal organs and lines the body cavities. Aside from facilitating tissue sliding, its additional functions remain poorly understood. Here, we study the mesothelium through investigating myelin regulatory factor (Myrf), a transcription factor expressed in the mesothelium and a top mutated gene in congenital diaphragmatic hernia (CDH), a developmental disorder that affects the lung and diaphragm. In mice, inactivation of Myrf early in embryogenesis resulted in CDH and defective mesothelium specification, compromising its role as a signaling center for lung growth. Inactivation after mesothelium specification led to additional defects, including enhanced differentiation into various mesenchymal cell types, causing a striking accumulation of elastin-expressing smooth muscle/myofibroblasts encasing the lung, mimicking pleuroparenchymal fibroelastosis (PPFE), a rare adult lung condition. Compound mutants demonstrate that MYRF functions synergistically with YAP/TAZ in mesothelium differentiation. Together, these findings highlight the complex role of the mesothelium in development and disease.

overall_design: Myrf mutant and control mesothelial cells were isolated by fluorescent activated cell sorting (FACS) and analyzed using scRNA-Seq

first: Jamie

middle: M

last: Verheyden

first: Chunting

last: Tan

first: Estelle

last: Kim

first: Ziai

last: Zhu

first: Michelle

last: Hwa

first: Jugraj

last: Sahi

first: Yufeng

last: Shen

first: Wendy

last: Chung

first: David

middle: J

last: McCulley

first: Xin

last: Sun


title: MYRF Controls Mesothelium Specification, Signaling, and Plasticity [RNA-Seq]

overall_design: RNA-Seq profiling of the E13.5 Tbx4tetOcre;MyrfE6 mutant lung and cre control


title: Induction of a renal developmental cell state is associated with chemotherapy resistance in favorable-histology Wilms tumor

city: Memphis

first: Hongjian

last: Jin

state: TN

address: 262 Danny Thomas Place

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hospital

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

overall_design: Refer to individual Series


title: IOP-induced blood-retinal barrier compromise contributes to RGC death in glaucoma

city: New York

first: Simon

last: John

address: 630 West 168th Street

institute: Columbia University

summary: The integrity of the blood-retinal barrier (BRB) has been largely unexplored in glaucoma. We reveal that elevated intraocular pressure (IOP) partially compromises the BRB in two human-relevant inherited mouse models of glaucoma (DBA/2J and Lmx1bV265D). Experimentally increasing IOP in mouse eyes further confirms this. Notably, the compromise induces subtle leakage, happening without bleeding or detected endothelial cell junction disruption, and it precedes neurodegeneration. Leakage occurs from peripheral veins in the retinal ganglion cell layer with a concomitant loss of the transcytosis inhibitor MFSD2A. Supporting this, bulk RNA sequencing of retinal veins revealed upregulated vesicular transport and downregulated Wnt signaling in hypertensive versus control veins. Transmission electron microscopy confirmed intact tight junctions in D2 glaucoma mice, while increased vesicles suggest enhanced transcytosis. In human glaucoma eyes, albumin immunostaining showed BRB leakage in retinal veins, mirroring our mouse findings. Importantly, stabilizing β-catenin in retinal endothelial cells prevents both vascular leakage and neurodegeneration in the DBA/2J model. The occurrence of leakage in all 3 high IOP models and in human glaucoma indicates that BRB compromise may be a common, yet overlooked, mechanism in glaucoma. These findings suggest that IOP-induced BRB compromise plays a critical role in glaucoma, offering a new therapeutic target.

overall_design: 9 months old DBA/2J and DBA/2J-Gpnmb+/SjJ were intraperitoneally injected with 0.33 mg/g body weight sodium fluorescein (AK-FLUOR, Akorn). 5 minutes after injection, mice were euthanized by cervical dislocation, eyes enucleated and retinal veins were dissected using super fine forceps (Dumont, NC9497215) under the fluorescent dissection scope. 4 major veins from the same mouse, including main branches were combined as one sample. Total RNA was extracted using RNeasy Micro kit (Qiagen, 74004). RNA concentration and quality (RIN) was measured by Bioanalyzer. About 100 pg total RNA (RIN>9) were reverse transcribed to cDNA using SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara). The library was prepared using Nextera XT (Illumina) and sequenced by Aviti Element. Bulk RNA-seq data was aligned to GRCm38 and gencode M23 and quantified by Kallisto. Transcript quantifications were imported into R framework for downstream analysis.

first: Chi


title: MYRF Controls Mesothelium Specification, Signaling, and Plasticity [CUT&Run]

overall_design: E16.5 wildtype mesothelial cells were stained with surface markers and sorted by flow cytometry for H3K27ac CUT&RUN.


title: Hypusination of the translation factor eIF5A regulates mitochondrial tRNA processing to promote prostate cancer aggressiveness

city: Nice

first: Michel

last: KAHI

address: 151 Route Saint Antoine

institute: INSERM U1065

summary: We studied the involvement of the hypusination pathway in prostate cancer progression using various models, including patient-derived tumor organoid cell lines and in vivo mouse models. We employed different omics techniques to identify the molecular mechanisms linking hypusination to the aggressiveness of prostate cancer.

overall_design: We performed RNA-seq on DU145 cells treated for 24 h with GC7 at a concentration of 40 µM. And we carried out polysome-profiling followed by sequencing of polysome-associated mRNAs (i.e. heavy ribosome-bound fractions), as well as sequencing of the cytoplasmic (total) mRNA fraction. This combined approach was designed to compare changes at the transcriptome level (via RNA-seq) and at the translatome level (via polysome-associated mRNAs), thus allowing us to assess how inhibition of hypusination affects not only mRNA abundance, but also mRNA translation (ribosome loading) in DU145 prostate cancer cells.

last: Kahi

first: Anne

last: Vincent

first: JeanJacques

last: Diaz

first: Frederic

last: Bost