title: Ascorbic acid increases CD8+ T cells by binding Myh9 protein and enriching gut microbiota Akkermansia muciniphila, improves cognitive levels in middle-aged mice [scRNA-seq]

city: Shanghai

first: Hailiang

last: Liu

address: NO 1239, siping road

institute: Tongji university

summary: Immunosenescence hastens the process of systemic aging and impacts cognitive function, with antioxidants potentially ameliorating these consequences. This research systematically assessed the impact of ascorbic acid (vitamin C) on immunosenescence and cognitive function in middle-aged and elderly mice. The findings demonstrated a notable rise in peripheral blood lymphocytes, a decline in myeloid immune cells, and enhanced cognitive performance. In vitro studies indicated that ascorbic acid facilitated the differentiation of mouse hematopoietic stem cells (HSCs) and spleen monocytes into CD8+ T cells, with its efficacy primarily mediated by its interaction with the binding protein Myh9. Additionally, a positive correlation was observed between CD8+ T cells and cognitive function. Furthermore, a distinction exists between the efficacy of oral and intravenous administration of ascorbic acid in enhancing cognitive function, potentially attributable to the modulation of the gut microbiome Akkermansia muciniphila. Intravenous delivery notably enhances A. muciniphila abundance and significantly enhances cognitive performance in middle-aged and elderly mice, whereas oral ascorbic acid supplementation increases CD8+ T cell count and cognitive function in this demographic only when co-administered with A. muciniphila. This study demonstrated that the administration of ascorbic acid can mitigate immunosenescence and, in conjunction with A. muciniphila, improve cognitive function in mice. These findings offer a mechanistic rationale for utilizing immunomodulatory interventions to enhance cognitive function, underscoring the significance of selecting the optimal route of administration for achieving the intended effects.

overall_design: We implemented single cell transcriptomic analyses of PBMC from young, aged and aged mice treatment with AA for 1 month .


title: APC coordinates GSK3 phosphorylation of SETD8 to suppress colorectal cancer [ChIP-seq]

status: Public on Dec 04 2025

city: Boston

first: Zvi

middle: I

last: Cramer

state: MA

address: 30 Caldwell St

country: USA

institute: University of Pennsylvania

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Colorectal cancer (CRC) is the second-leading cause of cancer-related deaths with increasing incidence globally. Mutations in the tumor suppressor APC initiate CRC at least in part by preventing the GSK3 kinase from phosphorylating β-CATENIN, leading to its constitutive stabilization and transactivation of mitogenic target genes. While the importance of β-CATENIN phosphorylation by GSK3 is well-established, APC regulation of GSK3 activity upon other targets with potential oncogenic relevance are not understood. Here, we identify the H4K20 methyltransferase SETD8 as target of GSK3 phosphorylation requiring functional APC in the intestinal epithelium. We found that phosphorylation by GSK3 restrains the oncogenic activity of SETD8, with loss of phosphorylation sensitizing mice to oncogenic insults. Mechanistically, phosphorylation alters the role of SETD8 in transcriptional regulation, most notably by preventing it from activating oncogenic YAP signaling and an oncogenic fetal-like transcriptional program. These results underscore the importance of SETD8 in CRC and represent a novel β-CATENIN -independent oncogenic consequence of APC loss.

overall_design: To determine the  effects of SETD8 T140 phosphorylation on H4K20me1 in colorectal cancer, we overexpressed human WT or T140D SETD8 in murine colorectal tumoroids and then delivered sgRNAs targetting endogenous murine Setd8 via lentivirus. H4K20me1 was performed 4 days after lentiviral infection

first: Christopher

middle: J

last: Lengner

first: Mario

middle: A

last: Blanco


title: Ascorbic acid increases CD8+ T cells by binding Myh9 protein and enriching gut microbiota Akkermansia muciniphila, improves cognitive levels in middle-aged mice [RNA-seq]

country: China

type: Expression profiling by high throughput sequencing

summary: We implemented transcriptomic analyses of hippocampus of 8-9M mice.

overall_design: These mice with the treatment of AA for 30 days.


title: Molecular targets of colorectal cancer transformation revealed by single-cell sequencing

city: Nanjing

first: yang

last: sun

state: Jiangsu

address: Nanjing University Academy of Sciences, No. 163 Xianlin Avenue, Qixia District, Nanjing City, Jiangsu Province

department: Life Sciences

institute: Nanjing University

summary: Ulcerative colitis (UC) is associated with a significant risk of colorectal cancer transformation, which is considered one of its major complications. Prolonged chronic inflammation in the colon mucosa can lead to carcinogenesis due to various factors including dysregulation of cell proliferation and apoptosis, abnormal activation of the immune system, as well as DNA damage and repair abnormalities. Furthermore, the release of inflammatory mediators may directly or indirectly promote the formation and growth of cancer cells. The AOM/DSS mouse model is widely utilized to mimic the process of human colorectal cancer development, including chronic inflammation, carcinogenesis, and tumor progression. The model involves the administration of azoxymethane (AOM), a carcinogenic substance that induces DNA mutations and damage in colonic epithelial cells, leading to the initiation of colorectal cancer. Subsequently, dextran sulfate sodium (DSS), a chemical compound that induces intestinal inflammation, is administered through drinking water. The mice are subjected to cycles of DSS treatment interspersed with recovery periods, during which colitis-associated colorectal tumorigenesis occurs. The assessment typically involves monitoring of colon length, tumor formation, and histopathological examination. The mechanisms underlying colorectal cancer transformation in UC remain incompletely understood. However, research suggests that controlling inflammation, implementing standardized treatment protocols, and regular surveillance through colonoscopy and follow-up are crucial for both prevention and early detection of carcinogenesis. Therefore, further investigations into the mechanisms of colorectal cancer transformation in UC and the development of novel prevention and treatment strategies are essential for improving the prognosis and quality of life of UC patients.

overall_design: scRNA-seq profiling of colorectal adenoma cancerous tissue single cell suspension.

first: Li-Sha

last: Zhou

first: Yi-nuo

last: Ma

first: Yang

last: Sun


title: Renal denervation attenuates cardiac inflammatory responses via renal afferent nerve-splenic nerve axis after myocardial ischemic injury

first: Youming

last: Zhang

address: Jimo Road 150, Shanghai 200120, PR China

institute: Shanghai East Hospitol

summary: The study was designed to investigate the effects of renal denervation (RDN) on global gene expression changes in splenic CD11b+ cells after myocardial infarction (MI). Bilateral RDN was performed one day after MI. Then, splenic CD11b+ cells were isolated the from RDN group or MI group on day 5 after MI, and subjected to bulk RNA- sequencing.

overall_design: Splenic CD11b+ cells were isolated from either RDN group or MI group using flow cytometry. Then cells were lysed and total RNA was isolated for sequencing. Three biological replicates were performed for each group

first: Bing

last: Yang


title: Deciphering the Sperm RNA Code of Aging with PANDORA-seq

city: Salt Lake City

first: Qi

last: Chen

state: Utah

department: Department of Human Genetics

institute: university of utah

type: Non-coding RNA profiling by high throughput sequencing

summary: Sperm aging impacts male fertility and offspring health, highlighting the need for reliable aging biomarkers to guide reproductive decisions. Using PANDORA-seq, a novel method to comprehensively profile small non-coding RNAs (sncRNAs), we identified an "aging cliff" in mouse sperm RNA profiles-a sharp age-specific transition marked by significant shifts in genomic and mitochondrial tRNA-derived small RNAs (tsRNAs) and rRNA-derived small RNAs (rsRNAs). Notably, rsRNAs embedded in sperm heads exhibited a transformative length shift, with longer rsRNAs increasing and shorter ones decreasing with age, suggesting altered biogenesis with age. Remarkably, this sperm rsRNA length shift was consistently observed in two independent human aging cohorts, highlighting its evolutionary significance. Moreover, a combination of tsRNAs and rsRNAs (tsRNA/rsRNA cocktails) resembling those in aged sperm induced transcriptomic changes in embryonic stem cells, impacting metabolism and neurodegeneration pathways, mirroring the phenotypes observed in offspring of aged sperm. These results reveal new insights of sperm aging, highlighting the conserved rsRNA length shift in mice and humans, with translational potential for fertility and intergenerational health

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Mature sperm and sperm heads were collected from the cauda epididymis of male C57BL/6J mice aged 10, 30, 50, 70, and 90 weeks. Between 3 and 4 replicates were sequenced for each sample using PANDORA-seq and traditional sncRNA-seq. For paried human sperm heads, 8 donors provided two semen samples each over a span of 6 to 23 years. All human sperm head samples were sequenced using PANDORA-seq. For non-paired 47 human sperm head(cross-sectional cohort), 47 donors provide semen samples, and the sperm heads were only sequenced using PANDORA-seq. For the RNA-seq experiment, mESCs were transfected with vector, young_comb sncRNA mixture and old_comb sncRNA mixture seperately, After 24 hours of transfection, the total RNA were harvested by Trizol reagent for transcriptome RNA sequencing through polyA enrichment strategy.

first: Junchao

last: Shi

first: Xudong

first: Tong


title: Primate resident memory T cells activate humoral and stromal immunity [CITE-seq]

city: Minneapolis

first: David

last: Masopust

address: 2101 6th St. SE

institute: University of Minnesota

summary: CD8 resident memory T cells (Trm) comprise a small population of frontline sentinels compared to the large tissues they surveil. CD8 Trm make outsized contributions to immune protection from infection, yet underlying mechanisms are not well understood. This study interrogated mechanisms of Trm function in primates. We show that intravenous immunization of macaques with an SIV-gag-containing heterologous prime-boost-boost vaccine establishes memory T cells in >30 tissues, including visceral and mucosal compartments. We next developed methods for reproductive tract CD8 Trm reactivation in vivo. Upon antigen-sensing, CD8 Trm activated local stromal, parenchymal, and innate and adaptive immune cells. Stromal and parenchymal cells accentuated leukocyte homing and antiviral defenses. B and plasma cells were mobilized in the vaginal mucosa and bloodborne CD4 T cells were recruited and adopted an infection-resistant phenotype. In conclusion, Trm repurpose abundant neighboring stromal, parenchymal, and immune cells to amplify alarm signals and activate diverse host defenses.

overall_design: Female Indian Rhesus macaques were SIV-gag vaccinated. Animals were challenged intravaginally with CM9 peptide for 24h or left unchallenged. CITE-sequencing was performed on a mix of vaginal and cervical cells that were unsorted or sorted for leukocytes.

first: Vineet

last: Joag

first: Benjamin

last: Bimber


title: Primate resident memory T cells activate humoral and stromal immunity [Bulk RNA-seq]

overall_design: Female Indian Rhesus macaques were SIV-gag vaccinated. Animals were challenged intravaginally with CM9 peptide for 24 or 48h or left unchallenged. Bulk RNA sequencing was performed on all cells from the vagina, ectocervix, endocervix, or uterus or from a combination of cervical and vaginal CM9-specific CD8 T cells.


title: Characteristics of immunity system in postoperative delirium patients by single-cell transcriptomic analysis

city: Chengdu

first: Juan

last: Wu

state: Sichuan

address: No. 37 Guo Xue Alley, Wuhou District

department: Anesthesiology

institute: West China Hospital of Sichuan University

summary: Background: Postoperative delirium (POD) is the most complication after cardiac surgery, and associated with increased mortality and decreased long term cognition ability. Our study aimed to explore the characteristics of immunity system in POD patients. Methods: This prospective study included patients scheduled for selective on-pump cardiac surgeries, who were divided into Non-POD and POD group according to whether POD occurred within 30 days after surgery. Multi-channel spectral flow cytometry, single-cell sequencing and plasma cytokines measurement were performed to describe the characteristics of immunity system in POD patients before surgery and at 24 hours after surgery. Results: A total of 120 patients were included, and 12 were diagnosed as POD within 30 days after surgery. T cells and B cells were activated in POD patients before and after surgery, and the upregulation of related genes contributed to the activation of chemotaxis in GZMK+ CD8+ T cells and memory B cells, which was confirmed by the elevation of CCL3 and CXCL8 concentration in plasma and the increased expression of chemotaxis related ligands-receptors pairs (CCL16_CCR1 and CXCL13_CXCR5). The inflammation response was enhanced in CD4+ T cells, which was confirmed by the activation of many cytokines related pathways and increased plasma level of IL-17 and IL-4 in POD patients before and after surgery. In monocytes, antigen presentation process and complement response were enhanced in POD patients before and after surgery, which was confirmed by the increased relative abundance of antigen presentation related surface markers (CD80, HLA-DR), activation of gene sets related to antigen binding and complement activation, and increased expression of related ligands-receptors pair (HLA-A_KIR3DL1 and C3_C3AR1).

overall_design: We performed single-cell RNA sequencing of peripheral blood mononuclear cells from patients with or without POD at Pre-surgery and at 24 hours after surgery. The sequencing profiles were used to cluster the cells into the following four immune cell types based on expression of well-established markers: monocytes, T cells, B cells, and natural killer cells.


title: Influence of epigenetic modifications on gene expression in Fusarium oxysporum

city: Jena

first: Tongta

last: Sae-Ong

address: Adolf-Reichwein-Straße 23

department: Microbiome Dynamics

country: Germany

institute: Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute (Leibniz-HKI)

summary: The influence of the heterochromatic marks H3K36me3 and H3K27me3 was elucidated by deletion and (cross-)complementation experiments. Gene expression was analyzed under axenic conditions and in planta by RNA-seq, and epigenetic profiles were assessed by ChIP-seq.

sample_organism:
Fusarium graminearum
Fusarium oxysporum f. sp. lycopersici

overall_design: Axenic cultivation F. oxysporum: NO3 2 days; in planta: 6 DPI. Axenic cultivation F. graminearum: ICI+60 mM glutamine 3 days. Material was subjected to RNA extraction for RNA-seq, and was crosslinked with formaldehyde prior to ChIP-seq using indicated antibodies.

first: Slavica

last: Janevska

first: Umer

last: Farooq

first: Antonio

last: Di Pietro

first: Manuel

last: Sánchez López-Berges


title: Hijacking the transcriptional potential of the BAF complex for therapeutic purposes via induce proximity

city: Cambridge

last: Mayhew

address: 500 Technology Square, Suite 700

institute: Foghorn Therapeutics

summary: The BAF (Brg/Brahma-associated factors) complex, also referred to as the mammalian Switch/Sucrose-Nonfermentable (mSWI/SNF) chromatin remodeling complex, plays a pivotal role in epigenetically regulating diverse transcriptional programs. BAF’s chromatin remodeling activity, which enhances accessibility to transcriptional machinery, is critical for gene regulation. We hypothesize that redirecting endogenous BAF complexes to “turn on” therapeutically relevant genes offer an additional approach for disease treatment. Using chronic myelogenous leukemia K562 cells stably expressing the FIRE-dCas9 system (K562-FIRE) and rapamycin as a chemical inducer of proximity (CIP) via CRISPR/Cas9 and FKBP/FRB dimerization, we redirected endogenous BAF complexes to the promoter of fetal hemoglobin (HBG) using pooled small guide RNAs (sgRNAs) targeting the HBG1 promoter. RNA-seq analysis showed a statistically significant increase in HBG1 and HBG2 gene expression in rapamycin treated cells over the DMSO treated controls.

overall_design: K562 cells stably expressing the FIRE-dCas9 system (K562-FIRE) were profiled via RNA-seq to test whether endogenous BAF could activate expression of HBG1 gene expression using sgRNAs targeting the HBG1 promoter (sgHGB1) or non-targeting sgRNAs (sgNT) after 24 h of 10 nM rapamycin or DMSO treatment.

first: Lionel

last: Chia

first: Dave

last: Lahr

first: Asad

last: Taherbhoy


title: m6A epitranscriptome analysis of hypothalamus arcuate nucleus mRNAs by MeRIP-Seq in female rats

first: xiaoqin

last: yin

address: 355 Luding Road, Putuo District

institute: School of medicine, Shanghai Jiao Tong University

type: Methylation profiling by high throughput sequencing

summary: To explore the role of m6A during puberty, we performed m6A epitranscriptome analysis hypothalamus arcuate nucleus mRNAs by MeRIP-Seq in female rats at different developmental stages.

overall_design: Comparative gene expression profiling analysis of MeRIP-Seq data for female rats at different developmental stages in the arucate nucleus of hypothalamus.

first: Shaolian

last: zang

first: Pin

last: Li

first: Xiaoqin

last: Yin


title: Effect of different N-terminal catalytic activity of RNase E compared to full-length RNase E  on whole transcriptome expression profile of E. coli soft-agar plate culture

city: Taipei

first: Sue

last: Lin-Chao

address: 128 Academia Road, Section 2, Nankang,

department: Institute of Molecular Biology

country: Taiwan

institute: Academia Sinica

summary: RNase E is involved in the post-transcriptional gene regulation of a broad spectrom of RNA species involving in different biological processes. Frequently RNase E cooperates with different enzymes such as RNA degradosome components in the post-transcriptional regulation. As the regulation as a whole RNA degradosome is complicated and might differ case by case, we would like to seperate the effect of  catalytic activity of RNase E per se and the effect of RNA degradosome. On the other hand, the physiology of bacterial growth in liquid culture is different from that on swmming plate culture. In real growing enviromnent, in which E. coli grows in the gut of warm-blooded organism, is a condition more like in soft-agar system instead of liquid culture that commonly adapted in laboratory study. To study the regulatory role of RNase E per se and RNA degradosmoe in gene regualtion of soft-agar culture, we used two different length of N-terminal RNase E which give different catalytic acitvity and compared theire effect of the transcriptome expressional level of strain with full-length RNase E.Here we found different groups of transcript that was regulated by merely RNase E catalytic acitivity, effect of RNA degradosome, or both. Altogether, our data give insight into the complex regulation of RNase E/RNA degradosome in transcripts involved in different biological processes of soft-agar growing system.

overall_design: To separate the effect of RNA degradosome (which assemble on the C-terminal part of RNase E), we compared RNase E C-terminal deletion strain with plasmid ectopically expressing full-length RNase E to that expressing only N-termianl of RNase E protein. To further differentiate whether RNase E catalytic activity also have regulatory role on individual transcript, we compare the effect of Rne600 (encodes 1-599 aa of N-terminal RNase E, have membrane binding domain and has higher catalytic activity) to that of Rne500 (encodes 1-499 aa of N-terminal RNase E, does not have membrane binding domain and has lower catalytic activity). RNA samples were isolated from bacterial culture grown on 0.35% soft-agar LB plate after 24 h incubation.

first: Wei-Syuan

last: Wang

first: Shu-Yung

last: Tung

first: Chen-Hsin

last: Yu


title: CAG repeat-selective compunds reduce abundance of expanded CAG RNAs in patient and murine models of SCAs II

city: Albany

first: Cara

middle: T

last: Pager

state: NY

address: 1400 Washington Avenue

institute: University at Albany, State University of New York

summary: Spinocerebellar ataxias (SCAs) are a genetically heterogenous group of >40 devastating neurodegenerative conditions for which clinical care currently focuses on managing symptoms. Across these diseases there is a large unmet need for therapies that address underlying disease mechanisms. In this study, we utilised the shared CAG repeat expansion mutation causative for a large subgroup of SCAs, to develop a novel disease-independent and mechanism agnostic small molecule screening approach to identify compounds with therapeutic potential across CAG SCAs. Using this screening approach, we identified the FDA approved microtubule inhibitor Colchicine and a novel CAG-repeat binding compound that reduce expression of disease associated transcripts across SCA1, 3 and 7 patient derived fibroblast lines and the Atxn1154Q/2Q SCA1 mouse model in a repeat selective manner. Furthermore, we demonstrate that our lead candidate rescues dysregulated alternative splicing in Atxn1154Q/2Q mice. This work provides the first example of small molecules capable of targeting the underlying mechanism of disease across multiple CAG SCAs.

overall_design: SCA1 knock-in mice were treated via intraperitoneal injection with either DMSO alone (4 mice) or Hit 2 dissvolved in DMSO (4 mice) along with 4 wild-type mice also injected with DMSO. After treatments the cerebella were removed and RNA extracted for RNA-seq.

first: Hannah

middle: K

last: Shorrock

first: Asmer

last: Aliyeva

first: Jesus

last: Frias

first: Victoria

last: DeMeo

first: Claudia

middle: D

last: Lennon

first: Cristina

middle: C

first: Amy

last: Mascorro

first: Sharon

last: Shaughnessy

first: Hormoz

last: Mazdiyasni

first: John

last: Cleary

first: Kaalak

last: Reddy

first: Sweta

last: Vangaveti

first: Damian

middle: S

last: Shin

first: J

last: Berglund


title: Molecular mechanisms of activity dependent survival in the adult EC

city: Houston

first: Caleb

last: Wood

state: TX

address: 1 Baylor Plaza

institute: Baylor College of Medicine

summary: Entorhinal cortex layer II (ECII) neurons are some of the first cells to degenerate in Alzheimer’s Disease. Losing this region is impactful for cognition as ECII projections form the major cortical input into the hippocampus. To dissect the behavioral impact of ECII loss on hippocampal function, the Jankowsky lab created a chemogenetic mouse model in which ECII neurons express an engineered chloride channel (GlyCl) that prevents neuronal firing upon binding a systemically-delivered ligand. Using this model, we unexpectedly discovered that ECII neurons are particularly vulnerable to silencing and may require activity for survival. This study aims to determine the transcriptional changes correlating to degenerative phenotypes observed after electrical silencing of adult entorhinal cortex neurons.

overall_design: mRNA profiles of subdissected entorhinal cortex from adult (2-4 mos) Nop-tTA x TRE-GlyCl-9531 mice at subsequent days post GlyCl-activation compared to vehicle control.

first: Joanna

middle: L

last: Jankowsky


title: N6-methyladenosine modification of cLMNB1 overcomes osimertinib resistance by destabilizing FGFR4 in non-small cell lung cancer

first: yuxian

last: Qian

address: baiziting no.42

institute: Nanjing medical university

summary: Background: Osimertinib resistance is the main challenge of the treatment in EGFR mutant lung adenocarcinoma (LUAD). The role of N6-methyladenosine (m6A) modification of circular RNAs (circRNAs) in osimertinib-resistant LUAD remains largely unknown. Methods: Parental and resistant cell lines, as well as human and mouse lung tissue samples were implemented. We used MeRIP-seq and circRNA-seq to screen the potential circRNA candidate that influenced osimertinib resistance. The sensitivity of LUAD cells was detected by Cell Counting Kit-8 (CCK-8) assay. The interaction between circRNA and proteins was validated by RNA immunoprecipitation and RNA pulldown. We generated circRNA encapsulated in lipid nanoparticle (LNP). Bioluminescence imaging assay was used for the monitoring of orthotopic transplantation model. Results: It was observed that circRNA LMNB1 (cLMNB1) exhibited elevated levels of m6A modification and diminished expression in osimertinib-resistant LUAD. cLMNB1 increased the sensitivity of LUAD to osimertinib in vitro and in vivo. METTL3 increased the m6A modification of cLMNB1 and inhibited its expression through the reading protein YTHDF2. cLMNB1 acted as a scaffold between Fibroblast growth factor receptor 4 (FGFR4) and E3 ubiquitin-protein ligase CBL (c-Cbl), enhancing the ubiquitin-dependent degradation of FGFR4. cLMNB1 with mutation of m6A modification site (cLMNB1-mut) encapsulated in LNP increased the efficacy of osimertinib in resistant LUAD. Conclusions: Our findings demonstrated that METTL3 and YTHDF2 mediated cLMNB1 degradation in m6A-dependent manner, and cLMNB1 destabilized FGFR4 protein in a ubiquitin-dependent way. We propose cLMNB1-mut as a nucleic acid drug that can overcome osimertinib resistance for its efficacy in osimertinib-resistant pre-clinical models in LUAD.

overall_design: Examing the m6A modification levels of total RNA of PC9OR and PC9 cells, each with 3 replicates

first: Yuxian

first: Xing

last: Zhang


title: CAG repeat-selective compunds reduce abundance of expanded CAG RNAs in patient and murine models of SCAs I

first: Cara

last: Pager

overall_design: RAN-Seq was performed on parental and stably transfected HEK293T cells expressing CAG containing integrands at high (clone 37) and low (clone 15) levels.

first: Hannah

last: Shorrock

first: Asmer

first: Jesus


title: Study on the molecular mechanism of relapse and drug resistance in T lymphoblastic lymphoma/leukemia

city: Guangzhou

first: Xiao-Peng

last: Tian

address: 651 Dong Feng RD East

department: Department of Medical Oncology

institute: Sun Yat-sen University Cancer Center

summary: Increasing evidence shows that non-coding RNA in peripheral blood is closely related to drug resistance and relapse of T lymphoblastoma/leukemia. The main focus of this study is to observe the relationship between circular RNA(circRNA) and drug resistance and relapse status of lymphoblastoma/leukemia.

overall_design: The samples were divided into two groups according to drug sensitivity and drug resistance, and circDNA sequencing was performed on the peripheral blood samples of the two groups.CircRNAs were predicted by CIRI software and calculated the expression by junction reads at back-splicing sites then normalized by SRPBM. Differentially expressed genes between groups were predicted using edgeR software. |log2 FC| >1 and P value < 0.05 were considered thresholds for differentially expressed circRNAs


title: Depletion of P2X4 receptors alleviates prostate cancer bone  metastasis through reducing cancer cell invasiveness and  enhancing cell adhesion activities

city: Sheffield

first: Jiepei

last: He

state: Yorkshire

address: Medical School, Beech Hill Road

department: Oncology and metabolism

country: United Kingdom

institute: University of Sheffield

summary: The P2X4 receptor (P2X4R) is a receptor for ATP that is highly expressed in many cancer types including prostate cancer and is positively associated with tumourigenesis. To understand the role of P2X4R in prostate cancer bone metastasis gene P2RX4 was knocked out in human prostate cancer PC3 cells using the CRISPR/Cas9 system. Animal studies demonstrated that targeting P2X4R suppresses the process of tumour bone metastasis. RNA-seq was performed to understand the further mechanism for P2X4R deficiency correlated reduction in prostate cancer tumourigenicity. The results demonstrated that P2X4R deficiency in PC3 cells caused dramatically up-regulate the anti-tumour genes (CLDN18, ADAMTS12 and PRB2), and it also significantly increased cell adhesion function and characteristic of the epithelia gene (CLDN18), which may inhibit cancer cell invasion and delay the process of PCa bone metastasis. These findings provide important insights into the underlying biology of P2X4R and prostate cancer progression.

overall_design: Knockouting out P2X4R in prostate cancer cell line PC3 using CRISPR/Cas9. Comparative gene expression profiling analysis of RNA-seq data for PC3 WT and P2X4R knockout.

first: Ning

last: Wang

first: Yuhan

last: Zhou

first: Arredondo

last: Carrera

first: Alison

last: Gartland


title: Hydrostatic pressure driven vascular degeneration in cirrhosis [pLSEC]

city: Beijing

first: Yi

last: Long

address: Jinchun Road

institute: Tsinghua university

summary: The role of pathological vascular degeneration in cirrhosis remains poorly understood. In this study, we engineered multidimensional vascular models to replicate the pathological characteristics of liver sinusoidal endothelial cells (LSECs) at various fibrosis stages. Our investigation revealed that LSEC response to hydrostatic pressure is matrix stiffness-dependent, with LSECs survival when cultured on soft matrices, while those cultured on hard matrices experiencing cellular damage. The biomimic vascular in vitro model enabled us to identify GPR116 as a crucial membrane receptor of LSECs to sense and respond to hydrostatic pressure. GPR116 is specifically expressed in liver endothelial cells, and silencing GPR116 effectively protected the endothelial cells from hydrostatic pressure-induced damage on hard matrix, consequently inhibiting hepatic stellate cell activation and collagen remodeling. Thus, our findings highlight GPR116 as an indispensable pressure sensor in hepatic sinusoidal endothelium, playing a pivotal role in vascular remodeling during cirrhosis.

overall_design: To validate the biomimicry of the in vitro model, we compared the transcriptome similarity between mouse LSECs cultured in vitro and LSECs in different stages of hepatic fibrosis. We isolated primary LSECs(pLSECs) from healthy mice were cultured on substrates with varying stiffness (1.5 kPa, and 11 kPa) and subjected to different hydrostatic pressure (10mmHg and 20mmHg).  The pLSECs cultured on 1.5 kPa substrates under 10mmHg is Soft+LP group.The pLSECs cultured on 11 kPa substrates under 20mmHg is Stiff+HP group.  pLSECs were isolated from mice with early hepatic fibrosis (4W) and cirrhosis (12W) induced with CCl4 for 4 and 12 weeks respectively. pLSECs from normal mouse(NC), Soft+HP group and Stiff+HP group were analyzed by RNA-seq. Differentially expressed genes (DEGs) analysis revealed drastic changes of LESCs during fibrosis progression in vivo (NC versus 4W versus 12W) and during in vitro culture (NC versus Soft+LP versus Stiff+HP) .

first: Yanan

last: Du


title: Hydrostatic pressure driven vascular degeneration in cirrhosis [pLSEC WT/KO]

overall_design:
To investigate the role of GPR116 in vascular remodeling, we use conditional knockout mice (GPR116fl/fl Cdh5CreERT2) to selectively suppress GPR116 expression in endothelial cells. Subsequently, we induced liver fibrosis using CCl4 for 12 weeks to simulate late-stage fibrosis. We isolated primary LSEC from KO and WT mouse.
Comparative gene expression profiling analysis of RNA-seq data for primary LSEC from KO and WT mouse.


title: Hepatic hypertension on-a-chip identifies GPR116 as a hydrostatic pressure mechanosensor to regulate vascular injury in cirrhosis

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

overall_design: Refer to individual Series


title: Photo-sensitive oligonucleotides combined with topologically imposed light gradients enable spatially-resolved single-cell transcriptomics and epigenomics

city: Santa Barbara

first: Robert

middle: Anthony

last: Piscopio

state: CA

address: 2002 BioEngineering Bldg, CNTR for Bioengineering

institute: University of California, Santa Barbara

summary: The organization of cells within a tissue plays a critical role in tuning cellular function. Several methods have been recently developed to capture the transcriptome of single cells while retaining positional information. However, these genome-wide sequencing methods typically do not have the spatial resolution of individual cells and are limited to quantifying positional information within an arranged lattice, thereby failing to capture regions of nonoverlapping tissue. Further, these methods are generally limited to profiling fixed cells with reduced mRNA capture efficiency compared to standard scRNA-seq. In addition, existing methods lack modularity and cross-platform compatibility, thereby limiting most of these techniques from jointly profiling the genome-wide epigenetic state of cells. To overcome these limitations, we present scSTAMP-seq (single-cell Spatial Transcriptomic And Multiomic Profiling), an approach that employs cholesterol-tagged photolabile oligonucleotides that incorporate into cell membranes, enabling us to “stamp” the position of each cell using patterned light prior to tissue dissociation and single-cell sequencing. Applied to live cells, scSTAMP-seq efficiently captures spatially resolved single-cell transcriptomes and at a high resolution for all cells within a field of view. Furthermore, we showcase the dynamic spatial resolution provided by light gradients, enabling us to accurately map the position of individual cells. Finally, we show that scSTAMP-seq is modular and can be seamlessly integrated with various downstream single-cell sequencing technologies. We demonstrate this by performing scRNA-seq using plate- and droplet-based methods, and by performing joint epigenome and transcriptome sequencing from the same cell while preserving positional information. Collectively, these results demonstrate that scSTAMP-seq is a sensitive and high-throughput technology for mapping single-cell transcriptomes and epigenomes at the spatial resolution of individual cells.

overall_design: scSTAMP-seq profiles live Hela and U2OS cell cultures throughout the study. Live cell samples were incubated with photocleavable hashtag oligos (PHOs) that embed into the cell membrane through cholesterol modifications to oligonucleotide anchors that hybridize with PHOs, enabling one to "stamp" the position of each cell using spatially imposed light gradients prior to tissue dissociation and single-cell sequencing. By quantifying the extent of PHO cleavage that is proportional to light exposure of each cell, together with mRNA from the same cell, enables single-cell transcriptomics that retains positional information of cells within a sample. For precise spatial light patterning (~500 nm), a digital micromirror device (DMD) was used to deliver UV light to illuminate cell samples. For greater illumination area of cell samples, a UV LED floodlight was implemented.

first: Alex

last: Chialastri

first: Chieh

first: Mikolaj

last: Godzik

first: Weiyue

first: Lauren

last: Li

first: Kellie

last: Heom

first: Neha

last: Saxena

first: Maxwell

middle: Z

last: Wilson

first: Siddharth

last: Dey


title: Gene expression profiles of  hippocampal astrocytes in mesial temporal lobe epilepsy model mice

city: Tokyo

first: Ryuta

last: Koyama

address: 7-3-1 Hongo Bunkyo-ku

department: Graduate School of Pharmaceutical Sciences

country: Japan

institute: University of Tokyo

summary: Mesial temporal lobe epilepsy (MTLE) with hippocampal sclerosis accounts for the majority of refractory epilepsies in adults. Recently, astrocytes have attracted attention as a novel target for anti-seizure medications. We purified hippocampal astrocyte RNA from intrahippocampal kainic acid-injected MTLE model mice using RiboTag AAV and investigated the gene expression profiles of astrocytes in the epileptic hippocampus. By comparing the astrocytic RNA sequence data with whole hippocampal RNA, we identified gene expression profiles that are specific to epileptic hippocampal astrocytes.

overall_design: Three biological replicates were analyzed for each of the three conditions (AAV delivery only, AAV delivery + kainic acid injection, and AAV delivery + PBS injection). For collection of astrocytic RNA, AAV expressing EGFP-Rpl10a in astrocytes was injected into the right hippocampus of mice. 3~4 hippocampi were homogenized as one sample, and RNA was purified from a part of the clear supernatant as input sample. In addition, astrocytic translational RNA bound to ribosomes was immunoprecipitated by GFP tag and RNA was purified as IP sample.

first: Shinichi

last: Kinoshita


title: Hydrostatic pressure driven vascular degeneration in cirrhosis [6H]

overall_design: To explore the mechanisms of GPR116 response to hydrostatic pressure, we compared the DEGs between shControl LSECs and shGPR116 LSECs under 20 mmHg hydrostatic pressure treatment and untreated conditions.

last: long


title: Association of Neutrophil Gene Expression with 28-Day Ventilator Weaning in COVID-19 ARDS Patients (part 2)

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

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

summary: Rationale COVID-19 can cause ARDS, a life-threatening condition that requires long-term ventilation. Neutrophil activation is a key mediator of lung injury in ARDS. However, the relationship between peripheral neutrophil RNA expression at the time of severe illness and 28-day ventilator weaning has not yet been clarified. Objectives To clarify the relationship with 28-day ventilator weaning and whole blood RNA sequencing analysis in COVID-19 patients. Moreover, single-cell RNA-seq was performed on neutrophils to analyze changes in gene expression levels for each fraction. Methods Bulk sequencing was performed using whole blood from 28 COVID-19 ARDS patients (9 in the non-ventilator weaning group and 19 in the ventilator weaning group) and 16 healthy controls. Next, single-cell RNA-seq was performed on neutrophils isolated from peripheral blood of 5 COVID-19 ARDS patients (3 in the non-ventilator weaning group and 2 in the ventilator weaning group) and 6 healthy individuals. Measurements and Main Results Although there was no clear difference between the non-ventilator weaning group and the ventilator weaning group in bulk RNA-seq using whole blood, the result of single-cell RNA-seq revealed clear differences between the non-ventilator weaning group, the ventilator weaning group, and healthy individuals. Conclusions Our study suggests that gene expression in neutrophils at the time of severe illness in COVID-19 ARDS patients may be associated with 28-day ventilator weaning.

overall_design: Granulocytes were isolated from whole blood using gradient centrifugation and RBC lysis buffer

first: Masakazu

last: Ishikawa

first: Hiroshi

last: Ito

first: Jumpei

last: Yoshimura

first: Yuchen

last: Liu

first: Shuhei

last: Sakakibara

first: Fuminori

last: Sugihara

first: Hisatake

last: Matsumoto

first: Haruhiko

last: Hirata

last: Ogura

first: Jun

last: Oda

last: Okuzaki


title: Association of Neutrophil Gene Expression with 28-Day Ventilator Weaning in COVID-19 ARDS Patients


title: T-bet high and low sorted CD4 T cells after acute infection

city: Berlin

first: Max

last: Löhning

address: Chariteplatz 1

institute: DRFZ

summary: The purpose of this study was to understand in detail how T-bet+ CD4 T cells differ depending on their quantitative T-bet levels after acute LCMV infection. For this, the murine T-bet ZsGreen reporter system was used for sorting cells ex vivo without manipulation according to their T-bet brightness into high and low expressors. The bulk RNA Sequencing of these cells showed that T-bet high cells (n=3) have a rather cytotoxic profile, while T-bet low cells (n=3) upregulate multiple Tfh associated markers while still strongly depicting a Th1 phenotype. Overall, only up to 5% of the expressed genes differed between high and low expressors. Furthermore, the bulk ATAC-sequencing also confirmed strong overlap in chromatin accessability of high (n=2) and low (n=2) expressors. Only a couple of the highly differentially expressed genes from the RNA-Seq data also showed differences in chromatin accessability at the TSS. This study provides a further insight into the quantitative differences of T-bet expressing CD4 T cells.

overall_design: Naive Smarta CD4 T cells from T-bet ZsGreen donors (Thy1.1+) were transferred into T-bet ZsGreen recipients (Thy1.2+), which were infected shortly after with LCMV Arm (200pfu). On day 10 p.i. the cells were harvested from the spleen and lymph nodes of the mice. The cells were FACS sorted according to their T-bet ZsGreen brightness into High and Low sorted fractions and bulk RNA- and ATAC-Sequencing was performed. Cells generated in 3 (RNA-seq) or 2 (ATAC-seq) independent experiments were used for the analysis.

first: Valerie

last: Plajer

first: Adrián

last: Madrigal-Avilés

first: Maria

last: Dzamukova

first: Nayar

last: Durán-Hernández

first: Katrin

last: Lehmann

first: Mir-Farzin

last: Mashregi

first: Caroline

last: Peine


title: Hydrostatic pressure driven vascular degeneration in cirrhosis [4H24H]

first: Yi

last: Long

overall_design: To investigate how liver blood vessels respond to hydrostatic pressure stimulation, we collected cells cultured in 2D vessels on a substrate with a stiffness of 11 kPa.  Transcriptome sequencing of LSECs exposed to pressure stimulation at 20mmHg for 0 hours, 4 hours, and 24 hours were conducted respectively in order to identify membrane-integrated proteins as potential mechanosensors.

first: Yanan

last: Du


title: IL-22 induces Paneth cell metaplasia in the colonic epithelium of ulcerative colitis, promoting wound healing via REG3A [mouse RNA-seq]

status: Public on Dec 03 2025

city: Kiel

first: Joana

middle: P.

last: Bernardes

state: SH

address: Am Botanischen Garten 11

department: Systems Immunology

institute: IKMB

summary: Paneth cell metaplasia (PCM) is a phenomenon in which Paneth cells, typically found in the small intestine, appear in the colonic epithelium of patients with ulcerative colitis (UC). Our study demonstrates that the PCM occurrence correlates with disease duration and active inflammation. Furthermore, we reveal that the inflammation-induced cytokine IL-22 suppresses Notch signaling, thereby promoting PCM formation in the colonic epithelium while simultaneously inducing REG3A expression in metaplastic niches. In vitro, we show that Reg3a directly enhances cell proliferation and promotes wound healing using mouse colonic organoids. In vivo, Reg3aΔIEC mice in both acute and chronic DSS-induced colitis models exhibit delayed wound healing. Additionally, studies conducted with patient-derived human colonic organoids revealed that REG3A administration stimulates cell proliferation and accelerates wound healing. These findings underscore a novel protective role of PCM-mediated REG3A in the colonic epithelium of patients with UC.

overall_design: RNA-seq analysis comparing Reg3afl/fl and Reg3aΔIEC mouse colonic organoids.

first: Muto

last: Tomohiro

first: Go

last: Ito

first: Hiromune

last: Katsuda

first: Yui

last: Hiraguri

first: Satoru

last: Fujii

first: Kurara

last: Yamamoto

middle: P

first: Finn

last: Hinrichsen

first: Uchida

last: Hitoshi

first: Yasuhiro

last: Nemoto

first: Mayumi

last: Kinoshita

first: Eri

last: Ooshina

first: Kouhei

first: Shuji

last: Hibiya

first: Sayaka

last: Nagata

first: Fenja

last: Schuran

first: Shiro

last: Yui

first: Penelope

last: Pelczar

first: Samuel

last: Huber

first: Stefan

last: Schreiber

first: Philip

last: Rosenstiel

first: Mamoru

last: Watanabe

first: Ryuichi

last: Okamoto


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Wac B Cell Conditional Knockout Activated B Cells Transcriptomes

city: Shenzhen

first: Yuxing

last: Li

address: No. 1088 Xueyuan Avenue

institute: Southern University of Science and Technology

summary: To investigate the function of Wac in the regulation of B cell activation and plasmablasts differentiation, we used Cre-Loxp system to generate Wac conditional knockout mice (Wacf/f Cd19cre/+). We then performed gene expression profiling analysis using data obtained from RNA-seq of in vitro LPS activated wild-type and Wac knockout B cells.

overall_design: Splenic B cells from wild-type and Wac Cd19-cre conditional knockout mice were purified using anti-CD43 microbeads and cultured 24 hours at the concentration of 2 million cells per ml in DMEM medium supplemented with 10% FBS, 1% penicillin/streptomycin, 1% non-essential amino acids and 20 μg/ml LPS at 37℃ with 5% CO2. Total RNA of  in vitro activated B cells was extracted using RNeasy Mini Kit (Qiagen) and poly(A) mRNA was isolated with the poly(A) mRNA Magnetic Isolation Module (NEB). Libraries were prepared using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB) and sequenced on an Illumina Hiseq instrument (Illumina). Sequence reads were filtrated using Cutadapt (V1.9.1), and then mapped to the reference genome sequences (GRCm38.98) using Hisat2 (V2.0.1). Gene expression level was calculated using Htseq software (V0.6.1).

first: Xijun

last: Ou


title: Loss of FBXO11 establishes a stem cell program in acute myeloid leukemia by dysregulating LONP1 [RNA-seq]

city: Vancouver

first: Aly

last: Karsan

address: 675 West 10th Avenue

country: Canada

institute: Canada's Michael Smith Genome Sciences Centre

summary:
Purpose: The goals of this study are to compare the transcriptome profile of human cord blood derived CD34+ cells expressing shRNA targeting FBXO1, LONP1 or non-targeting shRNA, combined with or without over-expression of FLAG-FBXO11 or LONP1 by RNAseq.
Methods: mRNA profiles of CD34+ cord blood cells with combinations of FBXO11 or LONP1 knockdown or over-expression were generated by RNAseq.

overall_design: CD34+ cord blood expressing non-targeting shRNA, shRNA targeting human FBXO11, shRNA targeting human LONP1, empty vector, FLAG-FBXO11, LONP1, or a combination of one of the shRNAs with the over-expression of FLAG-FBXO11 or LONP1.

first: Hayle

last: Kincross


title: KMT5A-Mediated Methylation of IRF3 Promotes Tumor Progression through Immune Suppression

city: Wuhan

first: pengcheng

state: HUbei

address: Tongji Hospital Research Building, Wuxian East Road, Caidian District, Wuhan City, Hubei Province

institute: Tongji medical colleage

summary: Lysine methylation is a critical post-translational modification (PTM) involved in diverse physiological and pathological processes. Interferon regulatory factor 3 (IRF3) plays a pivotal role in antitumor immunity; however, the regulatory mechanisms and functional impact of IRF3 methylation within the tumor microenvironment remain incompletely understood. This study demonstrates that monomethylation of IRF3 at lysine 193 (K193) suppresses its phosphorylation-dependent activation. Mass spectrometry-based protein interactome analysis identified lysine methyltransferase 5A (KMT5A) as the key enzyme responsible for IRF3 K193 monomethylation. In colorectal cancer (CRC), aberrantly high expression of KMT5A impaired in vivo antitumor immune responses. Mechanistically, KMT5A catalyzes IRF3 monomethylation at K193, which impedes IRF3 phosphorylation and subsequent activation, thereby suppressing the production of type I interferons (IFN-I). Collectively, these findings elucidate KMT5A-mediated IRF3 K193 methylation as a critical regulatory axis promoting tumor immune evasion and progression. Furthermore, IRF3 K193 methylation represents a promising therapeutic target for CRC intervention.

overall_design: RNA-seq profiling of wildtype RNAseq analysis of wild-type RKO celLs and their knockdown derivative (shKMT5A )

first: Pengcheng


title: Transcriptomic Profiling of Wild-Type C. elegans Exhibiting High and Low Exopher Production

city: Warsaw

first: Michal

last: Turek

address: Pwinskiego 5a

country: Poland

institute: Institute of Biochemistry and Biophysics Polish Academy of Sciences

summary: We performed RNA sequencing on age-synchronized wild-type C. elegans that produced either high numbers of exophers (>20 per animal) or low numbers of exophers (<2 per animal) on adulthood day 2. This approach mirrors strategies using natural transcriptional heterogeneity within isogenic populations to uncover molecular determinants of phenotypic variation. The transcriptomes of high- and low-exopher producers differed profoundly. In total, 609 genes were significantly upregulated and 665 genes were significantly downregulated in high-exopher animals (p adj < 0.05, |log₂FC| > 1). These results demonstrate that exopher production is associated with distinct transcriptional states, indicating that variation in exopher output reflects meaningful underlying molecular differences within genetically identical populations.

overall_design: This study investigates transcriptomic differences between wild-type age-synchronized C. elegans that produce high versus low numbers of exophers. Animals were synchronized and scored on adulthood day 2 based on the number of visible exophers per worm. Two phenotypic groups were defined: (1) high-exopher producers (more than 20 exophers per animal) and (2) low-exopher producers (fewer than 2 exophers per animal). These two groups represent the main experimental conditions and constitute the variables under investigation. For each condition, independent biological samples were generated from separate populations of worms classified into the high- or low-exopher group. The design therefore consists of comparative transcriptomic profiling of high- vs low-exopher wild-type animals. No additional genetic mutants or treatment conditions are included in this submission.

first: Michał

first: Wojciech

last: Pokrzywa


title: ubH2B CHIP-seq in Wild Type and Wac Conditional Knockout Activated B Cells

summary: To investigate the function of Wac in regulatng H2B ubiquitination during B cell activation and differentiation, we used Cre-Loxp system to generate Wac conditional knockout mice (Wacf/f Cd19cre/+) and performed ubH2B chromatin immunoprecipitation coupled with high-throughput sequencing (Chip-seq) in Wac KO and WT LPS activated B cells.

overall_design: Splenic B cells from wild-type and Wac Cd19-cre conditional knockout mice were purified and cultured 24 hours with 20 ug/mL LPS. Then analyzed using ubH2B Chip-seq.


title: A targetable developmental program co-regulates angiogenesis and immune evasion [scRNAseq]

city: New York

first: Pietro

last: Berico

address: 550 1st Ave Smilow 305

department: Pathology

institute: NYU Langone Health

summary: Ultraviolet (UV)-induced DNA mutations produce genetic drivers of cutaneous melanoma initiation and numerous neoantigens that can trigger anti-tumor immune responses in the host. Consequently, melanoma cells must rapidly evolve to evade immune detection by simultaneously modulating cell-autonomous epigenetic mechanisms and tumor-microenvironment interactions. Angiogenesis has been implicated in this process; although an increase of vasculature facilitates the immune response in normal tissue, solid tumors manage to somehow enhance blood flow while preventing immune cell infiltration. By comparing the expression of transcription factors (TFs) across early-stage melanoma, naevi, and other cancer types, we found the homeodomain-containing TF HOXD13 drives a melanoblast-like developmental program, which is upregulated in melanoma and strongly correlated with angiogenesis and immune cell exclusion. Using transcriptomics, 3D chromatin profiling, and in vivo models, we demonstrate that HOXD13 upregulation promotes tumor growth in vivo by concomitantly enhancing angiogenesis and suppressing T-cell infiltration. HOXD13 orchestrates 3D chromatin contacts between distal enhancers and promoters, simultaneously activating VEGFA, SEMA3A, and CD73. VEGFA and SEMA3A remodel the tumor vasculature and CD73 elevates extracellular levels of adenosine, a vasodilator and immune suppressor that binds adenosine receptors (AdR) on endothelial and T cells. In line with these findings, HOXD13-induced growth advantage in vivo was significantly reversed by the concomitant administration of VEGFR and AdR inhibitors. By revealing a dual pro-angiogenic and immunosuppressive HOXD13-CD73/VEGF gene regulatory axis, we identify a subset of patients who might benefit from combinations of AdR and VEGFR inhibitors which are currently being tested in clinical trials.

overall_design: B16F10 tumors control or silenced for Hoxd13 were generated in syngeneic animals and CD45 positive and negative cells were processed for scRNAseq.

first: Eva

last: Hernando


title: A targetable developmental program co-regulates angiogenesis and immune evasion [Spatial Transcriptomics]

overall_design: Human acral melanoma samples were processed for Visium 10X spatial transcriptomics.

first: Markus

last: Schober

first: Iman

last: Osman

first: Robert

last: Stagnitta


title: A targetable developmental program co-regulates angiogenesis and immune evasion [RNA-Seq]

overall_design: Different human and murine melanoma cell lines upon silencing or overexpression of HOXD13 were subjected to RNA-seq.


title: Impact of CEBPβ depletion on enhancer responses to dexamethasone in Multiple Myeloma cells

city: Morgantown

first: Lei

last: Wang

state: West Virginia

address: 64 Medical Center Drive

department: Department of Microbiology, Immunology and Cell Biology

institute: west virginia university

summary: Multiple myeloma (MM) is the second most common hematological cancer. While MM is considered treatable, it remains incurable due to the eventual drug resistance in nearly all patients. A cornerstone therapeutic for MM is dexamethasone, a synthetic glucocorticoid with anti-inflammatory and anti-myeloma properties. In this study, we investigate the role of CEBPβ in modulating enhancer activities, measured by H3K27ac, in response to dexamethasone in MM cells.

overall_design: Genome-wide profile of H3K27ac by Cut&Run in multiple myeloma cell line RPMI 8226 in DMSO control cells and CEBPB knockout cells, treated with or without dexamethasone (10um) for two hours.

first: Sebastian Adam

last: Dziadowicz

first: Wang

last: Lei

first: Hu

last: Gangqing


title: A targetable developmental program co-regulates angiogenesis and immune evasion [Hi-C]

overall_design: Human melanoma cell lines with different HOXD13 expression levels were subject to HiC and H3K27ac Hi-ChIP.


title: A targetable developmental program co-regulates angiogenesis and immune evasion [ChIP-seq, ATACseq and CUT&Tag]

overall_design: Different human melanoma cell lines upon silencing or overexpression of HOXD13 were subjected to ChIP-seq, ATACseq and CUT&Tag.


title: Association of Neutrophil Gene Expression with 28-Day Ventilator Weaning in COVID-19 ARDS Patients (part 1)

first: Daisuke

last: Motooka

first: Masakazu

last: Ishikawa

first: Hiroshi

last: Ito

first: Jumpei

last: Yoshimura

first: Yuchen

last: Liu

first: Shuhei

last: Sakakibara

first: Fuminori

last: Sugihara

first: Hisatake

last: Matsumoto

first: Haruhiko

last: Hirata

last: Ogura

first: Jun

last: Oda

last: Okuzaki


title: RUNX3，a brand new NK cell infiltration biomarker mediates the metastasis of colorectal cancer

city: tianjin

first: Ming

last: Wei

address: No.94 weijin road

institute: Nankai University School of Medicine

summary: Single-cell RNA sequencing (scRNA-seq) technology enables in-depth analysis of gene expression profiles within specific immune cell populations in the TME, providing reliable insights into the molecular characteristics of infiltrating immune cell clusters and greatly facilitating biomarker identification.

overall_design: This study integrates scRNA-seq and bulk RNA-seq data to identify potential cancer biomarkers in colorectal cancer, followed by prognostic analysis to screen candidate biomarkers. Ultimately, we identified the RUNX3 molecule as a potential biomarker for colorectal cancer. We subsequently generated RUNX3-/- mice, established tumor models, and performed single-cell sequencing to further investigate the role of Runx3 in NK cell infiltration and its regulatory function in colorectal cancer.


title: A 3’UTR-derived small RNA modulates the life-cycle of the cholera toxin-encoding filamentous phage, CTXϕ [RNA-Seq]

city: Jena

first: Kai

last: Papenfort

state: Thuringia

address: Winzerlaer Straße 2

department: Faculty of Biological Sciences

institute: Friedrich-Schiller-University Jena

summary: Bacteriophages (phages) are well known to be one of the major driving forces in bacterial evolution. This is also true for virulent microorganisms, such as the major human pathogen Vibrio cholerae, whose pathogenic potential and epidemic proliferation largely depends on the interaction with environmental phages. Specifically, integration of the CTXϕ phage genome into the first chromosome of V. cholerae also involved the ctxAB genes, encoding the principle toxin responsible for the severe acute diarrheal disease, cholera. Whereas the mechanisms underlying CTXϕ-associated horizontal gene transfer and control of the ctxAB genes have been intensively studied over the past years, post-transcriptional regulation affecting the CTXϕ lifecycle has not been documented. Here, we report the discovery and characterization of the CisR small RNA (sRNA) that is produced from the 3’UTR (untranslated region) of the prtV gene and inhibits the expression of the CTXϕ-encoded cep mRNA. CisR-mediated repression of cep involves Hfq-assisted base-pairing of the two transcripts and results in reduced CTXϕ production under stress conditions. We further show that transcription of prtV-cisR requires both, the master quorum sensing transcription factor HapR, as well CRP, which coordinates global carbon metabolism. Taken together, our work provides evidence that V. cholerae employs sRNA-mediated post-transcriptional gene regulation to coordinate CTXϕ activation with both cell density and nutrient availability.

overall_design: RNA-seq expression profiling of Vibrio cholerae strain KPS14 WT grown in LB or AKI medium

first: Anne

last: Lippegaus

first: Malte

last: Siemers

first: Sebastian

last: Krautwurst


title: Mitochondrial double stranded RNA Dependent Lipid Reprogramming in Non-Small Cell Lung Cancer

city: Los Angeles

first: Sandy Che-Eun

middle: Serena

last: Lee

state: California

address: 650 Charles E Young Dr S 27-300

institute: University of California, Los Angeles

summary: Transcription of the mitochondrial genome results in the generation of double stranded RNA. Escape of mitochondrial double stranded RNA (mtdsRNA) into the cytosol is deleterious and functions as a class of damage associated molecular pathogens (DAMPs) that elicits activation of an anti-viral response in cells. To mitigate the harmful consequences of excess cytosolic mtdsRNA, mammalian cells rely on the mitochondria localized exonuclease polynucleotide phosphorylase (PNPase) to degrade excess mtdsRNA. While the regulation of mtdsRNA by PNPase has been studied in the non-cancerous cells and tissue(s), less is known about the role PNPase plays in cancer cells nor the cellular consequences that PNPase inhibition and the dysregulation of mtdsRNA degradation has on tumor cells. Here, we demonstrate that PNPase inactivation in a Kras-driven, Lkb1 mutant (KL) genetically engineered mouse model (GEMM) of lung cancer resulted in a significant extension in overall survival of mice and reduced tumor cell proliferation. PNPase loss activated a robust interferon-stimulated viral mimicry response in lung tumors that triggered reprograming of lipid metabolism and upregulation of lipid droplet biogenesis in tumor cells. Tumors that escaped PNPase loss transformed into fatty lesions characterized by a substantial accumulation of lipid droplets enriched for polyunsaturated fatty acids (PUFAs). Importantly, PNPase null KL tumors were highly sensitive to ferroptosis, which resulted in the ablation and near complete clearance of tumors from the lung of mice. Similarly, targeted pharmacological inhibition of PNPase sensitized therapy resistant human lung and pancreatic tumor cells to ferroptosis. These findings demonstrate that PNPase represents a new class of molecular target and identified that viral mimicry and lipid droplet biogenesis may be readily exploited for the treatment of therapy resistant lung and pancreatic tumors.

overall_design: Slow frozen tumours from KLluc and KLPNluc mice (90% FBS and 10% DMSO) were thawed on ice and dissociated in single cell as per 10X guidelines. Sequencing was carried out by UCLA’s genomics core.

first: Matthew

middle: R

last: Krieger

first: Aaron

last: Muscarella

first: Daniel

last: Ballard

first: Yihui

last: Cen

first: Samuel

last: Kharpatin

first: Lidoor

last: Levy

first: Hannah

last: Cessna

first: Morgan

last: Brady

first: August

middle: W

last: Brookwell

first: Bilal

last: Hamid

first: Maya

last: Cornejo

first: Connor

last: Short

first: Vanessa

last: Salvidar

first: Alyssa

last: Soeung

first: Mikayla

last: Tamboline

first: Nikole

last: Scillitani

first: Kevin

last: He

first: Chunni

last: Zhu

first: Linsey

last: Stiles

first: Cristianne

last: Beninca

last: Wiliams

first: Shili

last: Xu

first: Rushika

last: Perera

first: Brian

last: Shuch

first: Guillaume

middle: F

last: Chanfreau

first: Orian

last: Shirihai

first: Milica

last: Momcilovic

first: Jingyi Jessica

last: Li

first: Mark

middle: H

last: Ellisman

first: Michael

last: Teitell

first: Carla

middle: M

last: Koehler

first: David

middle: B

last: Shackelford


title: Transcriptome and phenotype-based epistasis analysis in Caenorhabditis elegans reveal daf-16/FoxO-dependent and independent effects of daf-2/InsR in L1 arrest and recovery

city: Durham

first: Kinsey

last: Fisher

state: NC

address: 124 Science Drive

department: Biology

institute: Duke University

summary: Reduced insulin/IGF signaling (IIS) in C. elegans increases starvation resistance in daf-16/FoxO-dependent fashion, but it is unclear whether the effects of reduced IIS are entirely dependent on daf-16/FoxO or if another effector(s) of IIS may be involved. We used RNA sequencing (RNA-seq) and phenotypic analysis of L1 starvation resistance to assess epistasis between daf-2/InsR and daf-16/FoxO. Essentially all differential gene expression caused by disruption of daf-2/InsR during starvation is daf-16-dependent. The effects of daf-2/InsR on starvation survival also appear entirely dependent on daf-16/FoxO, and the effect of daf-2/InsR on growth following starvation is largely daf-16-dependent. However, we also show daf-16-independent effects on growth and reproduction following recovery from starvation. These results support the conclusion that the effects of reduced IIS during L1 starvation are essentially daf-16/FoxO-dependent, but that reduced IIS engages one or more additional effectors during development following starvation.

overall_design: RNA-seq of fed and starved (12 hrs after hatch) wild type (N2), as well as starved daf-2(e1370), daf-16(mgDf47), and daf-16(mgDf47); daf-2(e1370) mutants

first: Rojin

last: Chitrakar

first: Ryan

last: Baugh


title: A 3’UTR-derived small RNA modulates the life-cycle of the cholera toxin-encoding filamentous phage, CTXϕ [RIL-Seq]

first: Kai

last: Papenfort

overall_design: RILseq RNA-RNA interactome profiling of Vibrio cholerae strains KPS14 and KPS995 grown in AKI medium

first: Anne

last: Lippegaus

first: Malte

last: Siemers

first: Sebastian

last: Krautwurst


title: Sensitive and unbiased genome-wide profiling of base-editor-induced off-target activity with CHANGE-seq-BE [Digenome-seq]

city: Memphis

first: Shengdar

last: Tsai

state: TN

address: 262 Danny Thomas Pl

department: Department of Hematology

institute: St Jude Children's Research Hospital

summary: To compare the sensitivity of CHANGE-seq-BE to another leading off-target discovery method, we performed Digenome-seq on the same ABE and CBE targets and evaluated them with matching analysis parameters. Many low-frequency off-target sites with editing rates were not identified by Digenome-seq and were only discovered by CHANGE-seq-BE.

overall_design: Digenome-seq applied for ABEs and CBEs targeting B2M, CBLB, CD7, CIITA, and PDCD1 in primary human T-cells

first: Rachael

last: Wood

first: Varun

last: Katta

first: Jacqueline

last: Chyr

first: Yichao


title: Runx1 Promotes Myofibroblast Cell Fate during Development and Fibrosis

city: San Diego

first: Le

last: Xu

address: 8018 Regents Road Atp. 301

department: Pediatrics

institute: University of California, San Diego

summary: Alveologenesis is the final stage of lung maturation, during which alveolar saccules are subdivided into smaller alveoli through the process of secondary septation, responsible for generating ~95% of the gas exchange surface area (1). Secondary crest myofibroblasts (SCMFs), which are transiently present in the distal alveolar regions, are required for alveolar maturation due to their ability to contract (2). By the end of alveologenesis, SCMFs are eliminated through apoptosis (3). However, the molecular drivers for the initial SCMF cell fate specification remain poorly understood. Pulmonary fibrosis is characterized by aberrant activation of lung fibroblasts into fibrotic myofibroblast, which produce excessive extracellular matrix (ECM) among other hallmarks of the disease. In the bleomycin mouse model of pulmonary fibrosis, recent lineage tracing and single-cell RNA sequencing (scRNA-seq) analyses have shown that CTHRC1+ fibrotic myofibroblasts are primarily derived from alveolar fibroblasts (4). Although several signaling pathways, including TGFβ, have been implicated in the transition of alveolar fibroblasts into fibrotic myofibroblasts (5), the downstream mediators, such as transcription factors (TFs), are not yet fully defined.

overall_design: To identify mesenchymal cell type-specific TFs through motif enrichment in addition to gene expression, we performed single-cell ATAC-seq (scATAC-seq) to profile chromatin accessibility. Mesenchymal cells (EpCAM– CD45– CD31–) were sorted from postnatal day 8 (P8) mouse lungs and subjected to scATAC-seq.

first: Rongbo

first: Xin

last: Sun


title: In situ multi-modal characterization of pancreatic cancer reveals tumor cell identity as a defining factor of the surrounding microenvironment [Nanostring CosMx]

city: Cambridge

first: Brian

last: Rabe

address: 250 Water St

institute: Bristol Myers Squibb

summary: Pancreatic ductal adenocarcinoma is heterogeneous, with low tumor purity, a prominent microenvironment, and complex architecture, which preclude the identification of shared tumor-intrinsic and stromal biology within and across patients. We overcame these challenges by achieving necessary resolution and context through the application of complimentary genomics, pathology and machine learning approaches to characterize primary untreated tumors from 39 patients. We capture 340K spatial low-bulk and 530K spatial single-cell transcriptomes and observe a spectrum of classical-to-basal tumor subtypes present within all patients. We find each subtype has distinct regulators, stromal neighborhoods, microenvironment, extracellular matrix and histology corresponding to multiple immunosuppressive and therapy resistance mechanisms. We define key tumor heterogeneity features including the presence of mixed KRAS mutations and tertiary lymphoid structures; identifying biomarkers that distinguish the latter from lymph nodes. Lastly, leveraging patient, cell and mouse data, we determine which aspects of tumor biology are recapitulated in bulk datasets and reductionist models.

overall_design: FFPE sections of treatment naïve PDAC tumor resections were characterized using the CosMx tecnology through the Nanostring technology access program (TAP, 1k universal RNA panel).

first: Anna

last: Lyubetskaya

first: Andrew

last: Kavran

first: Yulong

last: Bai

first: Alba

last: Font-Tello

last: Lewin

first: Hannah

last: Pliner

first: Yunfan

last: Fan

first: Lauren

last: Giampapa

first: Yelena

last: Cheng

first: Chao

last: Dai

first: Ruifeng

last: Hu

first: Tom

last: Lila

first: Alexandre

last: Alloy

first: Mike

last: Mason

first: Constance

last: Brett

first: Todd

first: Fayaz

last: Seifuddin

first: Steven

last: Vasquez Grinnell

first: Soren

last: Stahlschmidt

first: Yilin

last: Zhao

last: Golhar

first: Isaac

last: Neuhaus

first: Daniel

last: Carrera

first: Carlos

last: Rios

first: Pradeep

last: Kar

first: Abhishek

last: Shukla

last: Bashford-Rogers

first: Matthew

middle: J

last: Meyer

first: Enas

last: Abu Shah

first: Lara

last: Heij

first: Shivan

last: Sivakumar

first: Jimena

last: Trillo Tinoco

first: Benjamin

last: Chen

first: Konstantinos

last: Mavrakis

first: Eugene

last: Drokhlyansky


title: High PEEP activates ITGB1 inducing diaphragm fibrosis during prolonged mechanical ventilation

city: Hangzhou

first: jiahong

last: gong

address: Qingchun East Rd. 3

department: Department of Respiratory Care, Regional Medical Center for National Institute of Respiratory Diseases

institute: Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University

summary: Mechanical ventilation (MV) with high positive end-expiratory pressure (PEEP) is linked to ventilation-induced diaphragm dysfunction (VIDD), but the role of integrin beta-1 (ITGB1) in PEEP-associated diaphragm fibrosis remains unclear.

overall_design: Eighteen rabbits were divided into control (CON), MV without PEEP(MV), and MV with 8 cmH₂O PEEP (PEEP) groups. C2C12 underwent cyclic stretching (15% tension), and ITGB1 was knocked down. Fibrosis markers (TGFβ-1, α-SMA), ITGB1/ROCK1 expression, and pathway activation were analyzed via RNA sequencing, immunohistochemistry, and western blotting.

first: Jiahong

last: Gong


title: In situ multi-modal characterization of pancreatic cancer reveals tumor cell identity as a defining factor of the surrounding microenvironment

first: Brian

last: Rabe

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

overall_design: Refer to individual Series


title: Lactate as a metabolic-epigenetic signal linking high-intensity interval training (HIIT) to miRNA-Centered remodeling of the skeletal muscle methylome and transcriptome

city: Budapest

first: Zsolt

last: Radák

address: Budapest, Alkotás u. 42-48, 1123

department: Research Center for Molecular Exercise Science

country: Hungary

institute: University of sports science, Hungary

summary: Lactate, a major exercise-derived metabolite, has been proposed to couple cellular metabolism to gene regulation, yet its direct impact on skeletal muscle remains unclear. Male mice underwent six-week interventions (Control, lactate, HIIT, MCT1/2 inhibition, or HIIT+inhibition). We profiled gastrocnemius DNA methylation, mRNA-seq and miRNA-seq, and assessed signaling proteins, metabolites, and running performance. Lactate and HIIT each induced broad, site-specific remodeling of the methylome and transcriptome with substantial overlap at promoter CpGs and among DEGs. Promoter methylation changes showed weak coupling to steady-state mRNA, whereas integrative analyses revealed robust anti-directional miRNA–mRNA networks and enriched for chromatin/epigenetic regulators, identifying a lactate-driven miRNA axis as a proximate regulator of transcriptional output. At the protein level, lactate selectively increased TET2 and DNMT3A and activated PAX7, VEGF, and AKT–S6 signaling, consistent with integrative miRNA–mRNA findings. HIIT increased TET1/2 and DNMT3A with DNMT3B reduction and uniquely enhanced mitochondrial/antioxidant signaling. Blocking MCT1/2 abrogated HIIT-induced methylome and miRNA remodeling and blunted transcriptomic and protein adaptation, demonstrating that intact lactate flux is required for exercise-evoked epigenetic and transcriptomic reprogramming. Despite molecular convergence, chronic lactate did not improve running performance, indicating that lactate is necessary but not sufficient for the full physiological adaptation of training. These findings position a lactate–miRNA axis linking metabolic perturbation to epigenetic and transcriptional remodeling in skeletal muscle.

overall_design: mRNA sequencing of gastrocnemius muscle from male BALB/c mice  after 6-week interventions. Groups: Control (PBS), Lactate administration (500 mg/kg i.p.), HIIT (treadmill protocol), MCT1/2 inhibitor (AR-C155858, i.p.), and HIIT + inhibitor.

first: Lei

last: Zhou

first: Radak

last: Zsolt


title: Macrophages regulate PD-1 and CTLA-4 expression on ILC2 and their responsivity in the tumor microenvironment

city: Rome

first: Linda

last: Quatrini

address: Via San Paolo 15

department: Immunology

country: Italy

institute: IRCCS Bambino Gesù Pediatric Hospital

summary: Chronic inflammation can induce lymphocyte dysfunction, characterized by the expression of inhibitory immune checkpoints. For type 2 innate lymphoid cells (ILC2), the acquisition of a state of hypo-responsiveness associated with PD-1 expression has been reported in severe allergic inflammation. However, the regulation of ILC2 reactivity in the context of cancer is less clear. ILC2 contribution to anti-tumor immune response depends, indeed, on the type of tumor and the distinct cellular interplays within the microenvironment. Here, we show that ILC2 in malignant pleural effusions express the immune checkpoints PD-1 and CTLA-4. An in vitro model of ILC2-macrophages interaction demonstrates that this crosstalk is responsible for driving CTLA-4 expression and limiting ILC2 activation. Thus, by preventing ILC2 exhaustion, macrophages maintain ILC2 responsivity to signals from the tissue. These results reveal that, differently from PD-1, CTLA-4 expression on ILC2 is associated with the maintenance of a reactive state during chronic inflammation in the tumor microenvironment.

overall_design: RNA-sequencing was performed to compare gene expression between ILC2 sorted from co-culture with monocyte-derived-macrophages and ILC2 cultured alone.

first: Cecilia

last: Ciancaglini


title: microRNA-22 Inhibition Stimulates Mitochondrial Homeostasis and Intracellular Degradation Pathways to Prevent Muscle Wasting

city: Torino

first: Emanuele

last: Monteleone

address: Via Nizza, 52

department: Department of Life Sciences and Systems Biology

institute: Universita' di Torino

summary: MicroRNA-22 (miR-22) is a negative regulator of mitochondrial biogenesis as well as lipid and glucose metabolism in metabolically active tissues. Silencing miR-22 holds promise as a potential treatment of obesity and metabolic syndrome as it restores metabolic capacity – enhancing oxidative metabolism – and reduces ectopic fat in chronic obesity, a driver of impaired metabolic flexibility and muscle mass loss. Intramuscular adipose accumulation and defective mitochondrial function are features associated with obese-mediated muscle atrophy and hallmarks of neuromuscular disorders such as Duchenne muscular dystrophy. Therefore, miR-22 could represent a compelling molecular target to improve muscle health across various muscle-wasting conditions. This study describes a pharmacological strategy for inhibition of miR-22 in skeletal muscle by employing a mixmer antisense oligonucleotide (ASO, anti-miR-22). Administration of the ASO in a mouse model of obesity positively modulated myogenesis, while it protected dystrophic mice from muscle function decline enhancing fatigue resistance and limiting pathological fibrotic remodeling. Mechanistically, we show that anti-miR-22 treatment promotes derepression of genes involved in mitochondrial homeostasis favoring oxidative fiber content regardless of the disease model, thus promoting a more resilient phenotype. Furthermore, we suggest that miR-22 inhibition increases autophagy by transcriptional activation of multiple negative regulators of mammalian target of rapamycin (mTOR) signaling to decrease immune infiltration and fibrosis. These findings position miR-22 as a promising therapeutic target for muscle-wasting conditions and support its potential to restore muscle health.

overall_design: Bulk RNA-seq of gastrocnemius muscles from 30-week-old diet-induced obese C57BL/6J mice (high fat diet) after a 14-weeks-long treatment either with saline solution or an anti-miR-22 antisense oligonucleotide.

first: Simone

last: Tomasini

first: Anna

last: Altieri

first: Francesco

last: Margiotta

first: Fereshteh

last: Dardmeh

first: Hiva

last: Alipour

first: Anja

last: Holm

first: Sakari

last: Kappinen

first: Riccardo

last: Panella


title: Mast cell tryptase induces nuclear remodelling and reduced growth in breast cancer cells

city: Uppsala

first: Fabio

middle: Rabelo

last: Melo

address: Husargatan 3

department: Medical Biochemistry and Microbiology

country: Sweden

institute: Uppsala University

summary: Mast cells accumulate in breast cancer, but there is only limited knowledge of how they impact on breast cancer growth. Here we show that tryptase, a major compound stored in mast cell secretory granules, has profound effects on breast cancer cell morphology and growth, the latter by a combination of anti-proliferative and pro-apoptotic effects. Mechanistically, we show that tryptase is taken up by breast cancer cells, and enters their nuclei. Further, tryptase was shown to cause major effects on chromatin organization, and to induce truncation of core histone-3 (H3). H3 truncation was accompanied by reduced levels of epigenetic marks associated with H3. In vivo, tryptase-positive mast cells were found in PyMT breast cancer tumours and in human triple negative breast cancer, and a proliferation clearance zone was seen in the vicinity of tryptase-positive mast cells. It was also observed that mast cells were activated to a higher extent in breast cancer tumours than in healthy tissue. Finally, ATAC-seq analysis revealed that tryptase affected chromatin accessibility at regions of the genome associated with genes known to influence breast cancer growth. Altogether, the present study introduces a mechanism for how mast cell tryptase can regulate breast cancer cell growth.

overall_design: Hs578T (1x 105 cells) were incubated in quadruplicates in wells of a 12-well plate for 6 or 24 h, with or without 50 nM tryptase.

first: Pano

last: Filip

first: Laura

last: Bub

first: Parrine

last: Débora

first: Paivandy

last: Aida

first: Olsson

last: Anna-Karin

first: Pejler

last: Gunnar

first: Rabelo Melo

last: Fabio


title: Primary Keratinocyte Model of Actinic Keratosis Reveals UV-Induced DNA Damage Accumulation and Persistent Interferon Signaling

city: Hamburg

first: Leonardo

last: Elsbroek

address: Beiersdorfstraße 1-9

institute: Beiersdorf AG

summary: Actinic keratosis (AK) is a precancerous, UV-induced skin lesion that can progress to cutaneous squamous cell carcinoma (cSCC). While UV radiation is known to drive mutations and immunosuppression in the skin, keratinocyte-intrinsic responses to chronic, low-dose solar UV exposure have been insufficiently studied in AK. We established a patient-derived in vitro model using primary keratinocytes from AK lesions and age-matched, sun-exposed skin to investigate how repeated low-dose UV irradiation shapes keratinocyte stress responses. Integrating high-content morphological profiling, cyclobutane pyrimidine dimer (CPD) quantification and bulk RNA sequencing, we observed pronounced morphological remodeling and persistent DNA damage in AK keratinocytes despite activation of DNA repair and unfolded protein response pathways. Transcriptomic analyses revealed constitutive and UV-enhanced interferon signaling in AK cells, including upregulation of innate DNA sensing and ISGylation genes. Meta-analysis of five independent datasets confirmed interferon pathway activation as a conserved feature of AK, and IFN-α exposure further sensitized AK keratinocytes to UV-induced CPD formation. Our primary model thus uncovers sustained interferon signaling and attenuated DNA damage repair as key keratinocyte-intrinsic features of AK, suggesting that chronic interferon responses may modulate UV-induced damage and contribute to early photocarcinogenic processes.

overall_design: Primary AK and photo-exposed healthy facial epidermis keratinocytes (HEK) were irradiated with solar-simulated radiation (SSR) at 100 mJ/cm² UVB-equivalent, either once or daily for 3 days, and harvested 6 h after the final exposure for RNA-seq.


title: Metagenomic analysis of phytoplasma infected apple trees

city: Godollo

first: Eva

last: Varallyay

address: 4 Szent-Györgyi Albert Street

department: Institute of Plant Protection

institute: Hungarian University of Agriculture and Life Sciences

summary: Apple is one of the most important fruits that is propagated vegetatively, facilitating frequent transmission of viruses. The causative agent of the apple rubbery wood disease, apple rubbery wood virus 2 (ARWV2), can infect apple and pear. The branches of ARWV2-infected, symptomatic trees are flexible due to the decreased lignification of the xylem. In this research, we reanalysed our sRNA HTS datasets to survey the presence of ARWV2 in Hungary. Validation of HTS using RT-PCR revealed infection in several cultivars. The following RT-PCR-based survey revealed the infection of 15 trees, including pear and quince, without showing any rubbery wood symptoms. Analysis of the sRNA datasets allowed us to profile the sRNA pattern of ARWV2-infected and non-infected trees, and characterise the differential expression pattern of vsiRNAs and miRNAs targeting the lignin biosynthetic pathway. The results confirmed that neither the symptoms nor the gene-expression changes in the ARWV2-infected trees can be directly correlated with the presence of the virus, which can explain its frequent latent presence. Its variable concentration, sequence, and the mixed-infection status of the trees, make difficult its reliable diagnostics, which, although it would be highly needed, could be achieved as a result of further research.

overall_design: sRNA HTS based diagnostics from leaf samples of the presenting viruses in different apple cultivars infected or not with AP phytoplasma

first: Zsuzsanna

last: Nagyné Galbács

first: Almash

last: Jahan

first: Éva

last: Várallyay


title: Sulforaphane alleviates hepatocyte pyroptosis via activating Nrf2-HO-1 signaling during septic acute liver injury

city: Zhuhai

first: Shiying

last: Xie

address: No. 1439, Zhufeng Avenue, Doumen District

institute: The Fifth Affiliated Hospital of Zunyi Medical University, Zhuhai

summary: Acute liver injury (ALI) caused by sepsis is a fatal disease with a high mortality rate and poor prognosis. Sulforaphane (SFN) is a natural isothiocyanate that has robust antioxidant and anti-inflammatory properties. The aim of this study was to identify the pharmacological effects and therapeutic mechanisms  of SFN in lipopolysaccharide (LPS)-induced ALI.

overall_design: Male C57BL/6J mice (eight weeks old) were purchased from Gempharmatech (Nanjing, China) and maintained in a temperature-controlled room under a 12:12-h light–dark cycle for two weeks, with free access to tap water and standard mouse chow. The mice were randomly divided into three groups (n = 6 per group): Control, LPS and LPS + SFN. Mice were intraperitoneally administered SFN (10  mg/kg/day) for two  days before LPS (10 mg/kg) treatment. All animals were sacrificed 24 h after LPS injection, and liver samples were collected with TRIzol.

first: Huan-Wen

last: Huang

first: Shi-ying


title: Villin like suppresses nasopharyngeal carcinoma proliferation by downregulating MYC

city: Guangzhou

first: Zhongxi

state: Guangdong

address: NO.1023 Shatai South Road

institute: Southern Medical University

summary: The initial manifestations of nasopharyngeal carcinoma (NPC) are subtle and imperceptible, leading to unfavorable clinical outcomes and limited therapeutic alternatives among Southeast Asian populations. In this study, we examined the potential effects of VILL on nasopharyngeal carcinoma cells. We investigated the mRNA expression levels of VILL in HONE1 EBV cells overexpressing VILL compared to control cells. Data were analyzed to identify differential gene expression between VILL-transfected and non-transfected HONE1 EBV cells.

overall_design: We analyzed the transcriptome expression profiles (RNA-seq) in the nasopharyngeal carcinoma cell line HONE1-EBV upon overexpression of VILL.

first: Yueting

last: Wen

first: Ziying

last: Zhou

first: Yibo


title: c-di-AMP–DasR signaling axis mediates Mycobacterial acid resistance

city: Shanghai

first: Di

last: You

address: Meilong Road 130

institute: East China University of Science & Technology

summary: Genomic mapping of DasR binding sites in vivo.

overall_design: M. tuberculosis H37Ra strains grown in MB7H9 medium are subjected to ChIP-seq using a specific anti-DasR antibody

first: Yu

last: Fu

first: Xue-Qin

first: Yi-Fan

last: Liang

first: Zhan-Hui

last: Xu

first: Shi-Qi

last: Yang

first: Bang-Ce

last: Ye


title: EC359 enhances trametinib efficacy in Ras/Raf-driven ovarian cancer by suppressing LIFR signaling

city: San Antonio

first: Yidong

last: Chen

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

summary: Ovarian cancer (OCa) remains the most lethal gynecologic malignancy in the United States, with low-grade serous and mucinous subtypes frequently driven by KRAS mu-tations. These mutations activate downstream MAPK and PI3K/AKT signaling path-ways, contributing to tumor progression and resistance to therapy. Although the MEK inhibitor trametinib is used to target these pathways, its efficacy is limited in KRAS-mutant OCa due to compensatory activation of the leukemia inhibitory factor (LIF)/LIF receptor (LIFR) axis. In this study, we evaluated the therapeutic potential of combining trametinib with EC359, a selective LIFR inhibitor, in Ras/Raf-driven OCa models. EC359 significantly reduced cell viability, clonogenic survival, and induced cell death via ferroptosis in vitro. Mechanistic studies revealed that EC359 suppressed trametinib-induced activation of LIFR downstream signaling. RNA-seq analysis showed that combination therapy downregulated mitochondrial translation and MYC target genes while upregulating apoptosis-related genes. In vivo, EC359 and trametinib co-treatment significantly reduced tumor growth in Ras- and Raf-mutant xenograft models without inducing toxicity. These findings demonstrate that LIFR signaling is a critical driver in Ras/Raf-mutant OCa and that dual inhibition of the MEK and LIFR pathways offers a promising strategy to enhance therapeutic efficacy and overcome resistance in KRAS-mutant OCa.

overall_design: RNA-seq profiling of OVCAR8 cells treated with vehicle, EC359 (150 nM), trametinib (100 nM), or the combination of both agents for 7 hours. Three replicates for each condition were performed.

first: Suryavathi

last: Viswanadhapalli

first: Ratna K

last: Vadlamudi

first: Zhao

last: Lai


title: Analysis of the transcriptome response to low-nitrogen in Populus ussuriensis

city: Harbin City

first: Chenghao

last: Li

state: HeiLongJiang Province

address: No. 51 HeXing Road,Xiangfang District

department: College of Forestry

institute: Northeast Forestry University

summary: For the RNA-seq experiments, the upper three internodes were excised from 4-week-old plantlets and transferred via micro-cutting to normal nitrogen WPM(NN), which contains 10 mM NO₃⁻ and 5 mM NH₄⁺. After three weeks of rooting, the rooted plantlets were subjected to low-nitrogen (LN) treatment by transferring them to modified WPM containing 0.05 mM NO₃⁻ and 0.025 mM NH₄⁺. Root samples were collected at 0, 6, 12, 24, 48, 96, and 336 hours after LN, each process is repeated three times.

overall_design: RNA-seq of Populus ussuriensis roots

first: Feng

last: He

first: Yue

last: Chang

first: Runze

last: Liu

first: Wenlong

first: Zhiwei

first: Zhibin

last: Luo


title: TP53 Mutation is a Prognostic Biomarker for Patients with Advanced RAS Wild-Type Colorectal Adenocarcinoma Treated with Cetuximab and Pembrolizumab [dataset 1]

city: Buffalo

first: Spencer

last: Rosario

address: Elm & Carlton Sts

institute: Roswell Park Comprehensive Cancer Center

summary: Immunotherapy with checkpoint inhibitors targeting the PD1/PD-L1 and CTLA4 pathways has limited activity in patients with microsatellite stable (MSS) colorectal adenocarcinoma (CRC). In a prior study, the combination of cetuximab and pembrolizumab failed to improve outcomes for patients with advanced RAS wild-type (RASwt) CRC. In this post hoc secondary analysis, we show that patients with TP53 mutant (p53mt) tumors had significantly higher progression-free survival (PFS) and decrease in tumor burden compared to patients with TP53 wild-type (p53wt) tumors. The gene set enrichment analysis showed uniform upregulation in several metabolic gene sets and most immune gene sets including NK-mediated immunity and IL-12 pathway while the IL6 pathway was downregulated. While there were no overlapping transcriptional alterations between the p53mt and p53wt groups with treatment that remain constant despite the therapeutic intervention, we did identify functional overlap with treatment in both groups in proliferative, immune, and metabolic pathways. In the pre-treatment tumor samples, the number of PD-L1+ tumor cells was significantly higher in p53mt tumors while the number of exhausted-1 immune cells (defined as OX40-/AE1_AE3-/PD-L1- cells, positive for 1/3 exhaustion markers, LAG3 or CTLA4 or TIM3) was significantly higher in p53wt tumors. In conclusion, TP53 status was prognostic of improved disease control with cetuximab plus pembrolizumab in RASwt CRC. Future studies evaluating immune-oncology agents in patients with MSS, RASwt CRC should include TP53 as an integrated biomarker and evaluate its performance as a positive predictive biomarker (ClinicalTrials.gov NCT02713373).

overall_design:
RNA-sequencing was performed on tumor samples pre and post therapeutic intervention
Submitters state "Due to the consenting procedure for this study and NY state law, we are not allowed to release the raw FASTQ files associated with this study"

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

first: Christos

last: Fountzilas

first: Henry G

last: Withers

first: Spencer R.


title: Inhibition of Retinoic Acid Receptor Gamma Improves Bovine Embryo Development

city: Xianyang

first: Young

last: Tang

state: Shaanxi

address: #22 Xinong Road, Yangling District

department: College of Veterinary Medicine

institute: Northwest A&F University

summary: Retinoic acid receptor gamma (RARγ) plays a critical but poorly understood role in early embryo development and stem cell pluripotency. Here, we investigated the effects of the RARγ-specific inhibitor LY2955303 (LY) on in vitro-produced bovine embryos. Treatment with LY significantly increased blastocyst rates and quality, demonstrating its potential to enhance IVF outcomes in cattle. Single-embryo RNA sequencing using Smart-seq indicated that LY promotes metabolic reprogramming (upregulating glycolysis and TCA cycle activity) while suppressing apoptosis and inflammatory responses. LY- treatment starting from 16-cell stage led to enhanced glycolysis in blastocysts compared with exposure from 2-cell stage. Furthermore, LY-treatment also upregulated oxidative phosphorylation in bovine embryonic stem cells (ESCs). These findings establish RARγ as an important regulator of bovine embryo development, with its inhibition offering a novel strategy to optimize IVF embryo culture systems for livestock production.

overall_design: RNA-seq profiling of bovine embryos and cells, including LY2955303-treated and untreated bovine embryonic cells (bECs), and a small number of bovine embryonic stem cells (bESCs). Comparison of gene expression between treated and untreated groups to reveal the effects of LY2955303 on energy metabolism, cell death, and inflammation.

first: Xiangyan

last: Wang

first: Wenjing

last: Wan

last: Su

first: Shengcan

last: Xie

first: Fenfen

last: Jiang

first: Zhen

first: Shuangyi

last: Xiehe

first: Wei

last: Ma

first: Linxiu

last: Yue

first: Ningxiao

first: Ahui

first: Jintong

last: Guo

first: Xiaoting

first: Xinfeng


title: The spatial transcriptomics of EGFR-mutant non-small cell lung cancer before osimertinib treatment

city: Fukuoka

first: Satoshi

last: Nakamura

state: Fukuoka

address: 3-1-1, Maidashi, higashi-ku

department: Respiratory Medicine

institute: Kyushu University

summary: EGFR-mutant non-small cell lung cancer (NSCLC) is commonly treated with EGFR tyrosine kinase inhibitors (TKIs) such as osimertinib. However, the development of resistance remains a major clinical challenge, with various resistance mechanisms having been identified. Emerging evidence suggests that the tumor microenvironment (TME) may contribute to this resistance. In this study, we analyzed the TME of pre-treatment tumor samples from EGFR-mutant NSCLC patients using the Visium HD spatial transcriptomics platform to explore its potential role in the development of resistance.

overall_design: Spatial transcriptome of paired samples from 1 patients before and after osimertinib treatment with VisiumHD and StarDist processing

first: Ritsu

last: Ibusuki

first: Eiji

last: Iwama

first: Atsushi

last: Shimauchi

first: Hiromu

last: Kawano

first: Yui

last: Miyazaki


title: The maternal blood transcriptome reflects changes in foetal growth and is an accurate predictor of birth weight in cattle

city: Utrecht

first: Maria

middle: Belen

last: Rabaglino

address: Yalelaan 7

department: Population Health Science

country: Netherlands

institute: Utrecht University

summary: Harnessing maternal blood to predict fetal growth is an emerging area in livestock research, offering a non-invasive approach to monitor fetal development and potentially enhance reproductive management in cattle. In this study, blood samples were collected from 20 recipient cows carrying female fetuses produced via in vitro embryo transfer at 63 days of gestation. At birth, calf weights ranged from 30 to 72.5 kg, with an average of 45 kg. RNA-seq analysis of maternal blood revealed transcriptomic patterns associated with calf birth weight. Furthermore, a transcriptomic signature was identified that enables accurate prediction of calf birth weight with low error.

overall_design: Maternal blood samples (n=20) were collected via tail venipuncture using a 21-guage vacutainer needle in Tempus Tubes (Thermofisher Scientific, Waltham, MA USA) from recipients confirmed to be pregnant on day 63 of gestation with a female beef breed foetus, derived from X-sorted semen. Blood samples were kept at -20°C for 24 hours and then moved to -80°C for storage until processing for RNAseq. Birth weight was recorded at parturition for the ensuing calves.

first: Laura

last: Thompson

first: Pim

middle: G

last: van Helvoort

first: Maurice

last: Duijn

first: Daphne

middle: D

last: Reinders

first: Eliza

last: Murphy

first: Michael

last: McDonald

first: Alan

last: Crowe

first: Stephen

middle: T

last: Butler

first: Patrick

last: Lonergan


title: Spatial transcriptomics reveals dysfunctional lipid metabolism and abnormal pilosebaceous differentiation in acne vulgaris

city: Ann Arbor

first: Joseph

middle: S

last: Durgin

state: MI

address: 1500 E Medical Center Dr

department: Dermatology

institute: University of Michigan

summary: Acne vulgaris is a common skin condition involving complex interactions among lipid-secreting sebaceous glands, keratinocytes, immune cells, and microbiota. While retinoids are effective for treating acne, disease pathogenesis remains poorly understood. In particular, it remains unclear how different subtypes of acne, including inflammatory (pustular) and non-inflammatory (comedonal) lesions, vary in gene expression, signaling, and sebaceous gland involvement. Here, we performed spatial transcriptomics on healthy, non-lesional, comedonal, and pustular acne skin using a custom panel targeting sebaceous differentiation, lipid metabolism, and retinoid signaling pathways. We also designed a specialized segmentation pipeline to improve transcript assignment in the spatially complex sebaceous gland. Our analyses identified a PPARG+ transitional basal cell state in sebocytes and revealed that comedonal skin upregulates sebogenesis genes, whereas pustular skin downregulates sebogenesis. Both lesion types exhibit increased AP-1 transcription factors and elevated FABP5, a chaperone that blunts retinoic acid receptor signaling. Finally, we demonstrate that an AP-1 inhibitor, T-5224, strongly downregulates FABP5 in human keratinocytes and reduces pustule formation in a mouse model of high fat diet-induced folliculitis. Altogether, these findings indicate that altered lipogenesis, retinoid signaling, and keratinocyte differentiation are key features of acne, and nominate AP-1 and FABP5 as potential novel therapeutic targets.

overall_design: Acne donors and healthy controls were recruited by the University of Michigan’s Program for Clinical Research in Dermatology (PCRiD). Subjects were excluded if they were undergoing acne treatment or hormone regulating therapies. We collected 4 mm punch biopsies of normal skin, comedones, or pustules. Pustules were follicularly-centered papules with erythema or purulence, while comedones were non-inflamed smooth papules with follicular plugging. Specimens were fixed in 10% neutral buffered formalin overnight and processed as formalin-fixed paraffin embedded (FFPE) blocks.  For Xenium in situ analysis, 5 µm sections were mounted onto Xenium analyzer slides (10X Genomics, Pleasanton, CA) and submitted to the Advanced Genomics Core (AGC) at the University of Michigan for processing.

first: Sunny

middle: Y

last: Wong