title: Impact of red blood cells on choroid plexus on gene expression

status: Public on Sep 30 2025

city: Boston

first: Maria

last: Lehtinen

state: MA

address: 300 Longwood Ave, Mailcode Bch3400

country: USA

institute: Boston Children's Hospital

type: Expression profiling by high throughput sequencing

summary: Intraventricular macrophages (IVMs) reside in cerebrospinal fluid (CSF) and are considered a border-associated macrophage (BAM) population in the brain. Although they represent the first line of defense against intraventricular challenges, their developmental roles and responses to injury are poorly understood. This knowledge is relevant for conditions including neonatal intraventricular hemorrhage (IVH), where blood extravasates into brain ventricles, leading to life-long negative sequelae including cerebral palsy and hydrocephalus. Here, we show that IVMs are first responders to blood in developing brain ventricles, phagocytosing red blood cells and upregulating iron-processing machinery.

overall_design: RNA Sequencing of pooled lateral ventricle choroid plexus from CD-1 mice 24hr (E15.5) following either Saline (control) or red blood cell treatment.

first: Miriam

middle: E

last: Zawadzki

first: Christine

last: Hehnly

middle: K


title: The 7SK small nuclear ribonucleoprotein links the cell responses to transcription and replication stress by promoting replication fork reversal and homologous recombination

city: Liverpool

first: Claire

last: Wilson

address: Ashton Street

country: United Kingdom

institute: University of Liverpool

summary: Many genotoxic agents that block replication fork progression to cause DNA replication stress also block transcription, which results in transcription stress. The 7SK-small nuclear ribonucleoprotein (7SK-snRNP) regulates and promotes RNA polymerase II activity in response to transcription blocks. Individual 7SK-snRNP components HEXIM1, LARP7 and MEPCE are also reported to either facilitate or inhibit processes relevant to replication stress: conflicts between transcription and replication and homologous recombination (HR) at double-strand breaks (DSBs). Here, we investigate potential roles of 7SK-snRNP components in the response to replication stress-inducing agents such as camptothecin and hydroxyurea. We report that HEXIM1 and LARP7 promote replication fork slowing in response to agents that cause both replication- and transcription stress, in a manner consistent with their canonical 7SK-snRNP functions. Our data suggest that this role in fork slowing is mainly through facilitating RAD51-mediated replication fork reversal rather than transcription-replication conflicts. HEXIM1 and LARP7 promote RAD51 recruitment to replication-associated DSBs or post-replicative gaps under conditions of transcription stress such as induced by camptothecin or BET inhibitors, while to a lesser extent supporting HR at direct DSBs and not at all in absence of transcription stress. Our data support that LARP7 roles during replication stress are independent of its reported interaction with BRCA1 and both LARP7 and HEXIM1 promote survival of replication stress-inducing agents, especially camptothecin. 7SK-snRNP components are not recruited to stressed replication forks and RNA polymerase II inhibition phenocopies loss of these proteins. Taken together, our data support a model where 7SK-snRNP modulation of RNA polymerase II activity helps facilitate RAD51 function under transcription stress conditions, thereby linking the cell responses to transcription- and replication stress.

overall_design: To investigate the impact of camptothecin (CPT) or hydroxyurea (HU) treatment, we used chromatin RNA-Seq to quantify nascent transcripts. Sequencing was performed on human U2OS osteosarcoma cells before and after 2 hours CPT and HU treatment. Parental U2OS cells before and after DMSO treatment were used as a control. We then performed gene expression profiling analysis using data obtained from Chromatin-RNA-Seq.

first: Akhil

last: Bowry

first: Richard

middle: D

last: Kelly

first: Aditi

last: Kanhere

first: Eva

last: Petermann


title: Isoproterenol Infusion Enhances Composition and Function of G-CSF Mobilized Allogeneic Peripheral Blood Hematopoietic Cell Grafts.

city: Tucson

last: Simpson

state: AZ

address: 1501 N Campbell Avenue, CRC building Rm 5340

department: School of Nutritional Sciences & Wellness

institute: University Of Arizona

summary: Graft-versus-host disease (GvHD) and relapse remain critical challenges in allogeneic hematopoietic cell transplantation (alloHCT). Graft composition is pivotal, with naïve T cells increasing GvHD risk and NK cells improving graft-versus-leukemia (GvL) effects. Acute beta-adrenergic receptor activation mobilizes effector lymphocytes, favorably altering circulating immune cell composition. This study investigated whether infusing the non-selective beta-agonist isoproterenol (ISO) after granulocyte colony-stimulating factor (G-CSF) mobilization enhances peripheral blood hematopoietic cell (PBHC) graft composition and outcomes.

overall_design: Blood samples were collected from 10 healthy volunteers (age 27-41 yrs) after five days of G-CSF hematopoietic cell mobilization, before and after infusion with Isoproteranol (ISO). Isolated PBMCs underwent single cell RNA sequencing (scRNAseq) and gene expression analysis was performed on 26 identified clusters

first: Helena

last: Batatinha

first: Grace

middle: M

last: Niemiro

first: Nicole

middle: A

last: Pena

first: Giovannah

last: Hoskin

first: Tiffany

last: Zuniga

first: Kyle

last: Smith

first: Forrest

middle: L

last: Baker

first: Douglass

last: Diak

first: Timothy

last: Kistner

first: Preteesh

last: Mylabathula

first: Michael

last: Seckeler

first: Emmanual

last: Katsanis

middle: J


title: Gene expression of murine normal and post-lung transplant left lungs

city: Chicago

first: Blake

last: Gill

state: Illinois

address: 300 e superior st

department: Surgery

institute: Northwestern University

summary: Gene expression counts were successfully quantified through expression profiling of a total of over 800 genes in 12 separate murine left lungs.

overall_design: Murine left lung (Normal) or orthotopically transplanted allogeneic lungs were harvested at either 6 hr (6hr Control) or 24 hr (24hr Control) post-lung transplantation for nCounter gene expression pabel analysis.

first: Carl

last: Atkinson


title: Small intracellular vesicles outperform small extracellular vesicles in uptake, drug delivery, and retinal neuroprotection_LR

city: tianjin

first: hui

last: zhang

address: No. 251 Fukang Road, Nankai District

department: eye institute

country: China

institute: Tianjin Medical University Eye Hospital

summary: Small extracellular vesicles have been widely studied for their therapeutic properties and ability to deliver bioactive molecules. In addition to secretory vesicles, cells contain small intracellular vesicles involved in physiological and metabolic processes, whose therapeutic potential remains unexplored.

overall_design: Here, we developed protocols to isolate small intracellular vesicles from multiple cell types and systematically compared their molecular and functional profiles to extracellular vesicles. Intracellular vesicles are smaller, yield higher quantities, and demonstrate enhanced cellular uptake in both in vitro and in vivo models. Molecular profiling revealed that intracellular vesicles are enriched in proteins associated with the endoplasmic reticulum and Golgi apparatus, possess distinct microRNA signatures linked to intracellular membrane systems, and contain elevated levels of phospholipids such as phosphatidylcholine and phosphatidylethanolamine. Vesicles derived from umbilical cord mesenchymal stem cells showed superior therapeutic efficacy in a model of retinal degeneration by reducing endoplasmic reticulum stress and delivering neuroprotective factors. Additionally, intracellular vesicles exhibited enhanced drug-loading capacity and efficient delivery of lipophilic compounds to the retina. These findings position intracellular vesicles as promising candidates for therapeutic applications.

first: Hui

last: Zhang


title: IFNg shapes macrophage inflammatory responses by STAT1 isoform-specific epigenetic and transcriptional mechanisms

city: Wien

first: Birgit

last: Strobl

address: Veterinarplatz 1

department: TZG

country: Austria

institute: VetMedUni

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Interferon gamma (IFNg) is a pivotal cytokine that activates macrophages and shapes their response to subsequent inflammatory stimuli. Here, we investigated the distinct roles of STAT1 isoforms, STAT1alpha and STAT1beta, in IFNg-induced epigenetic remodelling and subsequent responses to lipopolysaccharide (LPS) in primary macrophages. We show that the STAT1 C-terminal TAD, which is missing in the STAT1beta isoform, is required for both H3K27 acetylation and deacetylation in response to IFNg. Notably, H3K27 deacetylation was associated with AP-1 motifs rather than STAT1 binding, suggesting indirect regulatory mechanisms. Functionally, IFNg pretreatment suppressed the induction of anti-inflammatory and virus response genes, including a subset of IFN-stimulated genes (ISGs), in response to LPS, while enhancing the expression of a distinct set of ISGs. Mechanistically, the STAT1 C-terminal TAD was critical for IFNg-mediated inhibition of LPS-induced enhancer activation at key regulatory genes, such as Il10 and Irak3, which are involved in negative feedback of toll-like receptor (TLR) signalling. Conversely, cooperative gene activation by IFNg and LPS was largely independent of the STAT1 C-terminal TAD, with notable exceptions, such as Ido1 and Tgtp1. Genome-wide analysis indicated that IRF1 and IRF8, rather than STAT1 homodimers, predominantly mediate in IFNg-induced H3K27 acetylation and transcription factor network analysis identified additional regulators integrating IFNg and LPS responses. Together, these findings reveal gene- and isoform-specific roles of STAT1 in coordinating IFNg-dependent chromatin remodelling and transcriptional cross-regulation, providing new insights into the control of inflammation and innate immunity.

overall_design: ChIP-Seq for histone marks (H3K27ac and H3K4me1) in murine bone marrow-derived macrophages at several time points and treatments

first: Mojoyinola Joanna

last: Akagha

first: Grigorios

last: Georgolopoulos

first: David

last: Martin

first: Katrin

last: Meissl

first: Lena

last: Amenitsch

first: Claus

last: Vogl

first: Matthias

last: Farlik

first: Nikolaus

last: Fortelny

first: Florian

last: Halbritter

first: Thomas

last: Decker

first: Mathias

last: Müller


title: Extracellular vesicles-mediated transfer of let-7b/7c promotes the proliferation of transition-state spermatogonia in neonatal mouse testis [miRNA-seq]

city: Shenzh

first: Tingting

last: ZHENG

state: Guangdong

address: Bulan Road

institute: Shenzhen Third People's Hospital

type: Non-coding RNA profiling by high throughput sequencing

summary: The self-renewal and differentiation of spermatogonial stem cells (SSCs) play essential roles in spermatogenesis. Extracellular vesicle (EV) is a universal strategy for intercellular communications in stem cell niches. However, the involvement of EVs in regulating the SSCs remains largely unknown. In this study, we have revealed the role of testis EVs isolated from postnatal day 7 (PND7) neonatal mouse testis in guiding spermatogonia into a transit-amplifying state with increased proliferation while retaining their differentiation potential. We profiled the repertoires of proteins and small RNAs by proteomic and small RNA transcriptomic analyses, respectively. We further showed that the EVs secreted by undifferentiated spermatogonia and the Sertoli cell lines, but not from more differentiated germ cell lines, conveyed let-7b/7c miRNA cargoes to spermatogonia, which mediates the effect of EVs on spermatognial transit amplification. Together, this study has deciphered an important intercellular communication within the spermatogonial niche mediated by let-7b/7c cargoes of EVs, providing a new insight into the regulation of SSCs and spermatogenesis.

overall_design: Small RNA sequencing analysis was performed on EVs isolated from postnatal day 7 mouse testis as the experimental group. we analyze tRNA subtypes and expression levels.

last: Zheng

first: Hoi Kei

last: Choy

first: Sze Yan

last: Chan

first: Min

first: Xiaotong

last: Luo

first: Hao

last: Chen

first: Ting

last: Xie

first: Kin Lam

last: Fok


title: Human pancreatic ductal cells from non-T1D donors respond to T1D cytokines and function as non-professional antigen presenting cells

city: Duarte

first: Hsun

middle: Teresa

last: Ku

state: CA

address: 1500 E. Duarte Road

department: Translational Research and Cellular Therapeutics

institute: City of Hope

summary: Aims/Hypothesis: Type 1 diabetes (T1D) is an autoimmune disease marked by the destruction of beta cells in the pancreatic islets, with an incomplete picture of disease pathogenesis/progression and a lack of definitive cure. A recent finding linked pancreatic ductal cells of T1D donors with elevated levels of human leukocyte antigen (HLA) Class II molecules; however, the causal relationship and functional significance of this finding remain unknown. Because HLA Class II molecules are typically expressed by professional antigen presenting cells (APCs), this raises the possibility of ductal cells functioning as non-professional APCs. In this study, we test the hypothesis that non-T1D ductal cells are responsive to T1D-associated proinflammatory cytokines, TNF-α, IL-1β, and IFN-γ, and can act as non-professional APCs. Methods: Pancreatic exocrine cells, after the removal of islets, were obtained from cadaveric donors without apparent diseases and with appropriate consent. Cells were cryopreserved, thawed into a defined culture medium tailored to support ductal cell survival in a 3D suspension culture system. Ductal cells were exposed to various doses of cytokines for 48 hours and analyzed for gene and protein expression, using qRT-PCR, bulk-RNAseq, flow cytometry and Western blot analyses. Functional ability of cytokine-treated ductal cells to present an exogenous autoantigen (glutamate decarboxylase 65kD isoform [GAD65]) to T cells was tested using a GAD65-specific autoreactive CD4+ T cell clone (named BRI4.13) isolated from a T1D donor. Results: We found that within 48 hours a combination of TNF-α, IL-1β, and IFN-γ stimulated the expression of HLA Class II, co-stimulatory, and antigen-processing molecules at mRNA and protein levels in non-T1D ductal cells. Bulk RNAseq analysis showed that cytokines most significantly upregulated biological pathways in “antigen processing and presentation” and “T1D”. When cytokine-treated ductal cells were pulsed with an exogenous GAD65 peptide and cocultured with the BRI4.13 T cells, these T cells became activated and proliferated. Unexpectedly, we also found ~1% of KRT19+ ductal cells express GAD protein endogenously. Conclusions/interpretation: These results demonstrate that non-diseased primary ductal cells are sensitive to TNF-α, IL-1β, and IFN-γ stimulation, and can upregulate APC molecules and function in antigen presentation to autoreactive CD4+ T cells. To the best of our knowledge, our results provide the first evidence demonstrating antigen presentation by non-T1D human ductal cells to T cells, which implicate ductal cells in contributing to T1D progression.

overall_design: Bulk mRNA-sequencing of human ductal cells derived from non-T1D subjects treated with "250x" (250 IU/ml TNF-α, 25 IU/ml IL-1β, and 250 IU/ml IFN-γ) and "500x" (500 IU/ml TNF-α, 50 IU/ml IL-1β, and 500 IU/ml IFN-γ) doses as well as vehicle control for 48 hrs (N=4 donors)

first: Neslihan

last: Erdem

first: Min-Hsuan

first: Hsun Teresa


title: CUT - Tag detection results for H3K9la, H4K8la, and H4K16la in tenocyte

city: Beijing

first: Tong

last: Pan

address: Northern Garden Road

institute: peking university third hospital

summary: We found that lactate and lactylation were significantly elevated in rotator cuff tears, and lactylation primarily regulates histones in tenocytes. Therefore, we screened for histone lactylation and identified that H3K9, H4K8, and H4K16 had the most prominent increases. Subsequently, we conducted CUT - Tag assays on them. The results indicated that H3K9la was enriched at the promoters of ENO3 and COL1, while H4K16la was enriched at the promoter of TNMD, which induced the transcriptional expression of these genes.     Moreover, as a glycolytic enzyme, ENO3 is further involved in the H3K9la–Eno3–lactate–H3K9la positive feedback loop to maintain a high lactate level. This feedback loop continuously drives the H3K9 - COL1 and H4K16 - TNMD regulatory axes, ultimately promoting the repair of rotator cuff tear injuries.

overall_design: Use CUT - Tag to clarify the association between histone lactylation and the regulated target genes.

first: Zhen-long

last: Liu


title: Downregulation of CD109 on melanoma cells reduces ICI efficacy by inducing TIL resistance in melanoma cells during the effector phase

city: Chiba city

first: Yuka

last: Saeki

state: Chiba

address: 1-8-1, Inohana, Chuo-ku

country: Japan

institute: Chiba university

summary: Although immune checkpoint inhibitors (ICIs) have improved the prognosis of melanoma, overcoming acquired resistance remains a challenge. The most critical mechanism is B2M mutation-mediated major histocompatibility complex (MHC) class I loss. Conversely, resistance mechanisms other than B2M mutations might be surmountable, although most of them are not yet fully understood. This study aimed to explore the novel mechanisms of acquired resistance in the absence of MHC class I loss. Previously, we established a pair of melanoma cell lines and cultured tumor-infiltrating lymphocytes (TILs) derived from an ICI-resistant melanoma patient with B2M mutation. Autologous TILs were unable to recognize the melanoma cells (MEL01), although genetic transduction of wild-type B2M (MEL01-B2M) reversed this phenomenon. To identify resistance mechanisms other than B2M mutation, we generated TIL-resistant MEL01-B2M cells by in vitro long-term co-culture (MEL01-B2M-R) and compared gene expression profiles between MEL01-B2M and MEL01-B2M-R. CD109 expression in MEL01-B2M-R cells was reduced by < 20%. Although CD109 has attracted attention as a negative regulator of transforming growth factor beta in allergic diseases, its effect on TILs, which play a central role in the efficacy of ICIs, remains unknown. Immunohistochemical analysis of 142 patients with melanoma revealed that low CD109 expression was associated with poor prognosis, regardless of MHC class I retention in melanoma tissues. In the co-culture assay, the knockout of CD109 in melanoma cells significantly impaired recognition and killing by specific TILs. These findings suggest that CD109 may serve as a predictive biomarker of ICI efficacy and as a novel therapeutic target for overcoming ICI resistance.

overall_design: Comparison of the two cell lines, HSmel-B2M(MEL01-B2M) vs HSmel-B2M-CTLR(MEL01-B2M-CTLR).

first: Takashi

last: Inozume


title: Targeting AEBP1 to mitigate pro-tumor activity of cancer-associated fibroblasts and increase therapeutic efficacy to anti-PD-1 [scRNA-Seq]

city: South San Francisco

first: Heyuan

last: Li

state: California

address: 213 E Grand Ave

institute: Merck Research Laboratories

summary: Cancer-associated fibroblasts (CAFs) are one of the components in tumor microenvironment (TME) that can facilitate tumor progression, invasion, and metastasis directly through tumor-CAF interactions, or indirectly by crosstalking with tumor infiltrating immune cells and inducing immunosuppressive TME. Indeed, high stromal signature has been associated with reduced therapeutic efficacy and resistance to Immune Checkpoint Blockade. AEBP1 is highly expressed in myofibroblast cells whose expression is further upregulated in activated fibroblasts and the extracellular matrix (ECM)-producing CAFs. AEBP1 has two alternatively spliced isoforms that the extracellular isoform binds to collagen and promotes collagen remodeling, and the intracellular isoform modulates transcription and signaling. We observed expression of both isoforms of AEBP1 in primary human CAFs.  Our data showed that combined knock out (KO) of both isoforms of AEBP1 by gene editing technology decreased CAF proliferation, collagen gel contractility and CAF-mediated tumor cell proliferation in vitro. Pan AEBP1 KO mouse fibroblasts also showed reduced activity in vitro and in vivo in the co-implantation mouse model.  We found that knocking out both isoforms of AEBP1 downregulated the collagen biosynthesis and ECM organization related pathways in both mouse fibroblasts and primary human CAFs through RNA sequencing studies. In addition, loss of AEBP1 in fibroblasts impacted tumor cell phenotypes resulting in significant decrease of tumor cells with,with epithelial-mesenchymal transition signature in the co-implantation mouse model. Furthermore, AEBP1 KO in CAFs enhanced the anti-PD-1 induced effector T cell activity and the anti-PD-1 efficacy in this co-implantation model. Altogether, our results demonstrate that AEBP1 is important in regulating CAF function in the TME.  Inhibiting AEBP1, therefore, may be a novel strategy in targeting CAF tumor-supporting activity and overcoming cancer resistance to anti-PD-1 immunotherapy.

overall_design: Single-cell RNAseq of MC38-NIH3T3 co-injected tumors 13 days after implatation. MC38 tumor cells were co-injected with wild-type or Aebp1 KO NIH3T3 cells. Whole tumor and CD45 depleted tumors are sequenced in parallel.

first: Suchitra

last: Natarajan

first: Khoa

last: Nguyen

first: Elysia

last: Saputra

first: Cindy

first: Gukhan

last: Kim

first: Yu

first: Hong

last: Sun

first: Ramli

last: Muhammad

first: Ling

first: William

last: Monis

first: Wendy

last: Blumenschein

first: Dewan

last: Hossain

first: Aleksandra

last: Olow

first: Xin

last: Yu


title: Therapeatic evaluation and single cell analysis of adipose stromal vascular fraction isolation from a commercial cell separation system

city: guangzhou

first: han

last: shunxin

address: Guangzhou North Road

institute: southern medical university

summary: In the field of regenerative therapy, the stromal vascular fraction (SVF) extracted from adipose tissue has been widely recognized for its significant benefits. However, the cellular composition and therapeutic effect of SVF products prepared via different methods are unclear.

overall_design:
SVF cells were obtained via three approaches: (1) generation of the SVF via mechanical emulsification (M-SVF), (2) generation of the SVF via laboratory enzymatic digestion (L-SVF), and (3) generation of the SVF via commercial cell separation systems (C-SVF). We evaluated their healing effects on mouse wounds. Additionally, we utilized single-nucleus RNA sequencing (snRNA-seq) technology to explore the cellular composition of the C-SVF.
Compare the regeneration effects of SVF cells obtained by one non-enzymatic and two enzymatic methods, and analyze the cell composition of ADRC produced by commercial cell isolation systems.

first: cai

last: junrong

first: lu

last: feng


title: Gene expression in Arthrobacter sp AZCC_0090 across the desiccation-rehydration continuum.

first: Paul

last: Carini

address: 1657 E Helen St

institute: University of Arizona

summary: Microbes inhabiting soils experience periodic water deprivation. The effects of desiccation on DNA, protein, and membrane integrity are well-described. However, the effects of drying and rehydration on the composition of cellular RNA and metabolites are still poorly understood. Here, we describe how slow drying and rehydration with water vapor influence the composition of RNAs and metabolites in a soil Arthrobacter. Drying reduced cultivability relative to hydrated controls, but rehydration of dried cells with water vapor restored cultivability. The fraction of 16S and 23S rRNA to the total RNA pool was constant throughout the experiment, irrespective of treatment. mRNA profiles were invariant in desiccated cells, changing only in response to drying or rehydration. Six transcriptional modules were identified that showed distinct expression patterns in desiccated-rehydrated samples, relative to hydrated controls, including desiccation-responsive and rehydration-specific profiles. Targeted metabolomics also showed a static metabolic state during desiccation. A cluster of metabolites enriched in ribonucleosides and nucleobases was responsive to desiccation and rehydration. Collectively, these results are consistent with the relative stability of mRNA and metabolite profiles in desiccated Arthrobacter. These results imply that stable mRNA in dry dormant cells and intracellular RNA recycling may obscure interpretations of RNA-based environmental analyses that use RNA as a marker of microbial activity.

overall_design: This study examines transcriptional responses to desiccation stress and recovery in Arthrobacter sp. AZCC_0090  through a 16-day time-course RNA-seq experiment. Control samples were maintained at constant 100% relative humidity throughout the experiment, while treatment samples underwent controlled desiccation: 100% RH for days 0-2, gradual drying to 65% RH between days 2-8, further drying to 25% RH between days 8-14, followed by rehydration to 100% RH between days 14-16. RNA samples were collected at four critical time points (days 2, 8, 14, and 16) from both control and treatment groups, yielding eight sample conditions that capture initial desiccation response, progressive dehydration stress, severe desiccation, and cellular recovery upon rehydration.

first: Adriana

last: Gomez-Buckley

first: Christina

middle: R

last: Guerrero

first: Melanie

last: Kridler

first: Isabella

last: Viney

first: Roya

last: Aminitabrizi

first: Malak

last: Tfaily

first: Peter

last: Moma

first: Laura

last: Meredith

first: Ryan

middle: P

last: Bartelme


title: Adipocyte- Specific FFA2 Deletion Leads to Increased Adipose Inflammation and Is Associated with Altered Intestinal Lipid Handling [jejunum_RNAseq]

first: Chioma

last: Nnyamah

address: 840 South Wood Street, Suite 1020N, MC 787

institute: University of Illinois at Chicago

summary: Obesity and related metabolic disorders are often characterized by chronic adipose tissue inflammation, driving systemic insulin resistance and general metabolic dysfunction. Free Fatty Acid Receptor 2 (FFA2) has emerged as a potential modulator of adipocyte function, inflammation, and metabolism. To investigate the role of FFA2 expressed in the adipose tissue, we generated adipose-specific FFA2 knockout mice (Adipoq-F2-KO) and assessed metabolic outcomes under standard chow and high-fat, high-sugar Western diet conditions, with and without dietary fiber supplementation. We found that adipose-specific FFA2 deletion had minimal metabolic consequences under standard dietary conditions but significantly reduced body weight and adiposity when mice were fed a fiber (fructooligosaccharide)-supplemented Western diet. Subsequent fecal analyses and transcriptomic profiling indicated impaired intestinal lipid absorption as the primary driver of reduced adiposity, suggesting disrupted adipose-intestinal communication. Unexpectedly, the lighter Adipoq-F2-KO mice also exhibited heightened adipose inflammation, characterized by increased macrophage infiltration and pro-inflammatory cytokine expression. Furthermore, in vitro loss-of-function experiments in adipocytes revealed that FFA2 knockdown impaired adipocyte maturation, lipid storage, and anti-inflammatory signaling. Additional studies using intestinal epithelial cells exposed to adipocyte-conditioned media implicated adipose-derived signals in driving intestinal dysfunction. Collectively, our findings highlight adipose-specific FFA2 as critical in regulating adipose tissue inflammation, lipid metabolism, and inter-organ communication. The data uploaded here specifically contains the comparison of mRNA from mature white adipocytes of FFA2 fl/fl mice compared to RNA from Adipoq-F2-KO mice when both are on a normal chow diet.

overall_design: This RNA sequencing dataset was generated to examine intestinal transcriptomic changes associated with adipose-specific deletion of Free Fatty Acid Receptor 2 (FFA2) in mice exposed to a Western diet supplemented with dietary fiber. Male Adipoq-F2-KO mice were generated by crossing FFA2 floxed mice (FFA2^fl/fl) with Adiponectin-Cre transgenic mice, resulting in adipocyte-specific FFA2 deletion. Littermate FFA2^fl/fl control and Adipoq-F2-KO mice were co-housed from birth and maintained on standard chow (Teklad LM-485) until 12 weeks of age. At this time point, mice were transitioned to a custom-modified high-fat/high-sugar Western diet supplemented with 10% fructooligosaccharides (FOS; D20021208, Research Diets, Inc.). After two weeks on this diet—once genotype-dependent differences in body weight were evident—mice were euthanized for tissue collection. Jejunal mucosa was isolated, and RNA was extracted for sequencing. RNA integrity was verified prior to library preparation, and bulk RNA sequencing was conducted by the UIC sequencing core facility. The resulting data were used to perform differential gene expression analysis between Adipoq-F2-KO and control mice, with the goal of identifying fiber-responsive, FFA2-regulated transcriptomic changes in the small intestine under obesogenic dietary challenge.

first: Nnyamah

last: Chioma

first: Xu

last: Kai

first: Boyett

last: James

first: Pandya

last: Nupur

first: Brian

last: Layden

first: Medha

last: Priyadarshini


title: Mechanism Study of Ganoderma Triterpenoid Extracts Inhibiting Colon Cancer Stemness and Migration Capacity

city: Fuzhou

first: Zhiyun

last: Cao

state: 福建Fujian

address: 1# Qiu Yang Road

institute: Fujian university

summary: We used RNA sequencing (RNA-Seq) to analyze gene expression in CRC cells treated with GTEA1 and GTEA7. We then validated these findings at the protein level using Western blotting and immunofluorescence. Finally, we performed migration and invasion assays for further validation.

overall_design: CRC cell line HCT116 was treated by GTE-A1 and GTE-A7 for 48 h and then performed RNA-Sequencing (RNA-Seq) by sequencing company.

first: Yuping

last: Yang

first: Chu

last: Zhang

first: Lian

last: Feng

first: Jian

last: Du

first: Ye

last: Li

first: Changhui

last: Wu


title: Branched chain amino acid sufficiency is necessary for proper luteinizing hormone response, testosterone synthesis, and motor coordination

city: New Brunswick

first: Tracy

middle: G

last: Anthony

state: NJ

address: 59 Dudley Rd

department: Nutritional Sciences

institute: Rutgers University

summary: Loss of branched-chain α-keto acid dehydrogenase kinase (BCKDK) increases branched-chain amino acid (BCAA) oxidation by disinhibiting BCKDH. We previously observed that in Bckdk knockout (KO) mice circulating BCAA levels are significantly reduced, negatively affecting neurological function, motor behavior, and male fertility. This work comparatively assessed how systemic loss of Bckdk modulates the transcriptome in testes and skeletal muscle under control diet feeding. Freely-fed adult male C57BL6/J mice and Bckdk KO mice on the C57BL6/J genetic background were euthanized by decapitation at the mid-point of the light cycle and tissues were quickly harvested and frozen in liquid nitrogen. Total RNA was extracted from frozen testes and hind-limb muscle (gastrocnemius and plantaris combined).

overall_design: Mice aged 5-6 months old carrying a mutant Bckdk allele (BckdkM) were backcrossed onto the C57BL/6J background for at least 10 generations and maintained in a conventional facility with commercial rodent diet (5001 Laboratory Rodent Diet; LabDiet) and tap water provided freely. Skeletal muscle and testis tissues were collected from freely-fed male C57BL6/J wild-type mice and BckdkM mice euthanized at the mid-point of the light cycle.

first: Yeva

last: Shamailova

first: Lingyi

last: Zhu

first: Timothy

last: Stanek

first: Elizabeth

last: Snyder


title: Small intracellular vesicles outperform small extracellular vesicles in uptake, drug delivery, and retinal neuroprotection

first: hui

last: zhang

first: Hui


title: Diagnostic Value and Clinical Significance of Potential BRAF-related Genes in Papillary Thyroid Carcinoma

first: Lan

last: Wang

address: Xinhua South Road

institute: Beijing Luhe Clinical Institute

summary: The purpose of this study was to find potential BRAF-related molecular markers to enhance the sensitivity of diagnosis of PTC.

overall_design: RNA sequencing was performed on 12 cases of four different groups, including the normal thyroid tissues, Hashimoto's thyroiditis, PTC complicated with Hashimoto's thyroiditis and PTC.The candidate genes were verified by quantitative real-time PCR and tissue microarrays.


title: Transcriptional effects of IL4 on adipocyte progenitors (APs) [RNA-seq]

city: Dresden

first: Ismini

middle: Vasileia

last: Alexaki

state: Saxony

address: Fetscherstraße 74

country: Germany

institute: IKL , Carl Gustav Carus Universitätsklinikum, TU Dresden

summary: APs isolated from subcutaneous adipose tissue (SAT) of male wild-type C57BL6J mice were cultured and treated with IL4 for 4 h. Transcriptional changes were analyzed by RNA-seq.

overall_design: SAT APs were treated with 20 ng/ml IL4 for 4 h in 1 % FBS DMEM.

first: Vasileia Ismini

first: Christine

last: Mund

first: Anupam

last: Sinha


title: ZC3H13 Loss Drives Cancer Metastatic Progression by Disrupting m6A RNA Methylation

city: Salamanca

first: Sandra

last: Blanco

address: Campus Universitario

country: Spain

institute: CSIC

summary: Aggressive metastatic cancer remains a major clinical challenge due to the unclear underlying mechanisms and the limited treatment options available. N6-methyladenosine (m6A) is a reversible modification of RNA that is frequently altered in cancer, and inhibitors targeting regulators of this process have been shown to block tumorigenesis. A better understanding of the role of m6A modifications in driving metastatic properties could help reveal potential strategies to prevent and treat metastasis. In this study, we discovered loss of the m6A writer complex component ZC3H13 as a key regulator of metastatic progression. Co-loss of ZC3H13 together with RB1 and BRCA2 occurred in patients with metastatic prostate cancer. Functional in vitro and in vivo assays demonstrated that ZC3H13 loss changes m6A writer complex activity and target specificity, leading to decreased m6A methylation and increased stability of transcripts that promote migration and invasion. Treatment with FDA-approved m6A demethylase inhibitors effectively reduced the metastatic capabilities of ZC3H13-deficient cells. Together, these findings provide insights into how the m6A writer complex selectively methylates mRNAs, highlight the pathological consequences of altered writer complex composition in cancer, and reveal therapeutic avenues for patients with metastatic cancer.

overall_design: RNA-seq and m6A MeRIP-seq profiling of wt BPH1 cells and ZC3H13 overexpressing cells (dCas and OEsg1) and control and ZC3H13 KO cells (EmpVec and ZC3KO) cells.

first: Óscar

last: Monteagudo-García

first: Paz

last: Nombela

first: Ángel C

last: Román


title: A non-canonical transcriptional regulation in natural product biosynthesis

city: Shanghai

first: Jinjin

address: 800 Dongchuan Road, Minhang District

institute: Shanghai Jiao Tong University

summary: TenA-family proteins are widespread bacterial regulators with unknown roles in natural product biosynthesis. This study aimed to functionally characterize LysR2, a TenA-family protein in Actinobacteria, and elucidate its mechanism in regulating the production of lysolipin I. We demonstrate that LysR2 represents a novel type of regulator that controls antibiotic biosynthesis not by direct DNA binding, but through protein-protein interactions, specifically by antagonizing the repressor LysR1. This work reveals an unconventional regulatory strategy, expanding the mechanistic understanding of transcriptional networks in natural product formation.

overall_design: RNA-Seq analysis was performed to identify differentially expressed genes between a lysR2 knockout mutant and the wild-type strain of the producer organism.


title: Extracellular vesicles-mediated transfer of let-7b/7c promotes the proliferation of transition-state spermatogonia in neonatal mouse testis [scRNA-seq]

first: Tingting

last: ZHENG

overall_design: single cell RNA sequencing analysis was performed on primary spermatogonial culture exposed to EVs isolated from postnatal day 7 mouse testis as the experimental group, while exposed to PBS were set as the control group. we analyze their cell clusters and explore the subtype changes.

last: Zheng

first: Hoi Kei

last: Choy

first: Sze Yan

last: Chan

first: Min

first: Xiaotong

last: Luo

first: Hao

last: Chen

first: Ting

last: Xie

first: Kin Lam

last: Fok


title: CK2-mediated DEK Phosphorylation Drives PBX3 Overexpression: A Core Event in Hematopoietic Stem Cell-to-Leukemia Stem Cell Transformation [CUT&Tag]

city: Chongqing

first: Zhe

address: 1 Yixueyuan Road, Yuzhong District

institute: Chongqing Medical University

summary: Leukemia stem cells (LSCs) possess self-renewal capacity and are largely refractory to conventional chemotherapy, thereby driving relapse and treatment failure in acute myeloid leukemia (AML). Here, we identify DEK as a crucial oncogenic factor aberrantly overexpressed in relapsed AML, with markedly increased phosphorylation by casein kinase 2 (CK2), correlating with poor patient prognosis. Using human AML cells and mouse models, we demonstrate that loss of DEK or phospho-mutants DEK, specifically at Ser306/Ser308/Ser311/Ser312 induces AML cells proliferation, differentiation, and weakened LSCs stemness. Mechanistically, phosphorylated DEK recruits GABPA to activate PBX3 transcription, thereby driving a leukemic transcriptional program. Importantly, targeting DEK or pharmacologic inhibition of CK2 using the specific inhibitor CX-4945 disrupts DEK phosphorylation and markedly sensitizes AML cells to venetoclax treatment, providing a rationale for a potential combination therapeutic strategy. Collectively, our findings uncover a unique and critical role of phosphorylated DEK as a transcriptional coactivator in AML and highlight the CK2-DEK/GABPA-PBX3 axis as a promising therapeutic target for AML.

overall_design: L-GMP(Lin-Sca-1-c-Kit+CD16/32+CD34+) from MLL-AF9-driven Wild-type (WT) and Dek-Ser306A/Ser308A/Ser311A/Ser312A(4S-A) AML mice were sorted, followed by DEK-CUT-Tag-seq. L-GMP(Lin-Sca-1-c-Kit+CD16/32+CD34+) from MLL-AF9-driven WT AML mice were sorted, followed by PBX3-CUT-Tag-seq. L-GMP(Lin-Sca-1-c-Kit+CD16/32+CD34+) from MLL-AF9-driven WT,  Dekfl/fl,MX1-Cre (KO) and 4S-A AML mice were sorted, followed by GABPA-CUT-Tag-seq.


title: IFNg shapes macrophage inflammatory responses by STAT1 isoform-specific epigenetic and transcriptional mechanisms [RNA-Seq]

first: Birgit

last: Strobl

overall_design: RNA-seq profiling of murine bone marrow-derived macrophages at several time points and treatments

first: Mojoyinola Joanna

last: Akagha

first: Grigorios

last: Georgolopoulos

first: David

last: Martin

first: Katrin

last: Meissl

first: Lena

last: Amenitsch

first: Claus

last: Vogl

first: Matthias

last: Farlik

first: Nikolaus

last: Fortelny

first: Florian

last: Halbritter

first: Thomas

last: Decker

first: Mathias

last: Müller


title: Transcriptional profiling defines unique subtypes of transit amplifying neural progenitors within the neonatal mouse subventricular zone

city: Newark

first: Rebecca

last: Zaritsky

address: 205 South Orange Ave

institute: NJMS - - Newark, NJ

summary: While significant progress has been made in understanding the heterogeneity of Neural Stem Cells (NSCs), our understanding of similar heterogeneity among the more abundant transit amplifying progenitors is lagging. Our work on the neural progenitors (NPs) of the neonatal subventricular zone (SVZ) began over a decade ago, when we used antibodies to the 4 antigens, CD133, LeX, CD140a, and NG2 to perform FACs to classify subsets of the neonatal SVZ as either multi-potential (MP1, MP2, MP3, MP4 and PFMPs), glial-restricted (GRP1, GRP2, and GRP3) or neuron-astrocyte restricted (BNAP). Using RNAseq, we have characterized the distinctive molecular fingerprints of 4 SVZ neural progenitors and compared their gene expression profiles to those of the NSCs. We performed bioinformatic analyses to provide insights into each NP type's unique interactome and the transcription factors regulating their development. Overall, we identified 1581 genes upregulated in at least one NP compared to the NSCs. Of these genes, 796 genes were upregulated in BNAP/GRP1 compared to NSCs; 653 in GRP2/MP3; 440 in GRP3; and 527 in PFMPs. One gene in particular that emerged from our analysis that can be used to distinguish the NPs from the NSCs is Etv1, also known as Er81. Also notable is that the neural stem cells downregulated cilia formation genes as they differentiated to become multipotential progenitors. Among the NPs, both PFMP and GRP3 subtypes differentially expressed genes related to neuron and oligodendrocyte development, including Matn4, Lhfpl3 and Olig2. GRP3s uniquely expressed Etv5, a transcription factor known to promote glial cell fate specification, while PFMPs uniquely expressed Lhx6, a transcription factor that regulates interneuron specification. PFMPs also expressed transcripts for olfactory receptors. Unlike the other NPs, the GRP1 and GRP2 NPs differentially expressed genes for proteins involved in immune function. The present work will serve as an important resource for investigators interested in further defining the transit amplifying progenitors of the mammalian SVZ.

overall_design: RNA sequencing of 8 populations of neural progenitors (Neural Stem cells and 7 intermediate progenitors) isolated from the perventricular zone of P5 mice after FACS.

first: Ekta

last: Kumari

first: Fernando

last: Velloso

first: Seema

last: Hussain

first: Alexander

last: Lemenze

first: Steven

middle: W

last: Levison


title: Microenvironment-Responsive Multifunctional Enzyme-Linked Hydrogel for Diabetic Bone Defects Regeneration

city: Chengdu

first: Zhenyu

last: Luo

address: No.37 Guoxue Road

institute: West China Hospital, Sichuan University

summary: Diabetes mellitus (DM) bone defects face impaired healing due to hyperglycemia, chronic inflammation, and dysregulated bone remodeling, yet existing therapies lack comprehensive strategies targeting these interconnected issues. To address this, a glucose/ROS-responsive multifunctional hydrogel (AAT-ZCG) was designed, integrating tannic acid (TA)-mediated dynamic borate ester bonds and a cascade nanozyme comprising cerium-zoledronic acid-glucose oxidase (ZCG). The hydrogel enables stimuli-responsive release of TA and ZCG within DM microenvironments, depleting glucose via glucose oxidase-mediated catalysis and mitigating inflammation through cerium-mediated ROS scavenging. Moreover, ZCG modulates macrophage polarization, stimulates angiogenesis and enhances osteogenesis. Acidic byproducts trigger ZCG degradation, releasing zoledronic acid to inhibit excessive osteoclast activation. Transcriptomic analysis revealed upregulated forkhead box O1 transcription factor, a key regulator of bone metabolism and inflammation. This all-in-one platform concurrently addresses pivotal mediators in DM bone defects, overcoming limitations of single-target approaches. By consolidating multifunctional responses, AAT-ZCG provides a concise yet effective strategy for DM bone defect regeneration.

overall_design: RNA was extracted from BMSCs used for osteogenic differentiation experiments in vitro from the control and AAT-ZCG groups. All samples underwent quality control. RNA-seq were performed by a sequencing company (Chi Biotech, Shenzhen, Guangdong, China), which also delivered the initial analysis report. Statistical significance was set at P < 0.05, with a fold change of >2 or <0.5 determining significantly differentially expressed genes (DEGs). These DEGs and different metabolites were then subjected to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses.

first: Xiaoxue

last: Fu

first: Weinan

last: Zeng

first: Zongke

last: Zhou


title: CK2-mediated DEK Phosphorylation Drives PBX3 Overexpression: A Core Event in Hematopoietic Stem Cell-to-Leukemia Stem Cell Transformation

first: Zhe

last: Chen

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

overall_design: Refer to individual Series


title: A crucial role of the malate aspartate shuttle in metabolic reprogramming in TNF-induced SIRS

city: Gent

last: Timmermans

address: Technologiepark 71

country: Belgium

institute: VIB-UGent

summary: Tumor necrosis factor (TNF) causes a lethal systemic inflammatory response syndrome (SIRS) which is characterized by significant metabolic alterations. Based on liver RNA sequencing, we found that TNF impairs the malate-aspartate shuttle (MAS), an essential redox shuttle that transfers reducing equivalents across the inner mitochondrial membrane thereby recycling cytosolic NAD+. This downregulation of MAS genes in TNF-induced SIRS likely results from loss of HNF4α function, which appears to be the key transcription factor involved. Using Slc25a13-/- mice lacking citrin – a crucial MAS component – we demonstrate that MAS dysfunction exacerbates TNF-induced metabolic dysregulations and lethality. Disruptive NAD+ regeneration leads to diminished mitochondrial β-oxidation, leading to elevated levels of circulating free fatty acids (FFAs) and to hepatic lipid accumulation. Simultaneously, MAS dysfunction promotes glycolysis coupled to lactate production and reduces lactate-mediated gluconeogenesis, culminating in severe hyperlactatemia that triggers VEGF-induced vascular leakage. Overall, MAS dysfunction contributes to metabolic failure and lethality in TNF-induced SIRS, highlighting its potential as a promising, therapeutic target.

overall_design: RNA-seq profiling of WT and Slc25a13 (Citrin) KO mice injected with PBS or TNF (8h post injection)

first: Louise

last: Nuyttens

first: Marah

last: Heyerick

first: Maxime

last: Roes

first: Elise

last: Moens

first: Céline

last: Van Dender

first: Charlotte

last: Wallaeys

first: Tino

last: Hochepied

first: Jolien

last: Vandewalle

first: Claude

last: Libert


title: CK2-mediated DEK Phosphorylation Drives PBX3 Overexpression: A Core Event in Hematopoietic Stem Cell-to-Leukemia Stem Cell Transformation [ATAC-seq]

overall_design: L-GMP(Lin-Sca-1-c-Kit+CD16/32+CD34+) from MLL-AF9-driven Dekfl/fl(FL) and Dekfl/fl,MX1-Cre (KO) AML mice were sorted, followed by ATAC-seq


title: CK2-mediated DEK Phosphorylation Drives PBX3 Overexpression: A Core Event in Hematopoietic Stem Cell-to-Leukemia Stem Cell Transformation [RNA-seq]

overall_design: L-GMP(Lin-Sca-1-c-Kit+CD16/32+CD34+) from MLL-AF9-driven Dekfl/fl(FL) and Dekfl/fl,MX1-Cre (KO) AML mice were sorted, followed by RNA-seq


title: Single-cell RNA sequencing analysis of the temporomandibular joint condyle in 3 and 4-month-old human embryos

city: nantong

first: liang

last: wang

state: chongchuan

address: nantong,jiangsu Province

institute: nantong university

summary: Background The temporomandibular joint (TMJ) is a complex joint consisting of the condyle, the temporal articu_x0002_lar surface, and the articular disc. Functions such as mastication, swallowing and articulation are accomplished by the movements of the TMJ. To date, the TMJ has been studied more extensively, but the types of TMJ cells, their differentiation, and their interrelationship during growth and development are still unclear and the study of the TMJ is limited. The aim of this study was to establish a molecular cellular atlas of the human embryonic temporomandibu_x0002_lar joint condyle (TMJC) by single-cell RNA sequencing, which will contribute to understanding and solving clinical  problems. Results Human embryos at 3 and 4 months（3M,4M） of age are an important stage of TMJC development. We performed a comprehensive transcriptome analysis of TMJC tissue from human embryos at 3 and 4 months of age using single-cell RNA sequencing. A total of 16,624 cells were captured and the gene expression profiles of 15 cell clusters in human embryonic TMJC were determined, including 14 known cell types and one previously unknown cell type, "transition state cells (TSCs)". Immunofluorescence assays confirmed that TSCs are not the same cell cluster as mesen_x0002_chymal stem cells (MSCs). Pseudotime trajectory and RNA velocity analysis revealed that MSCs transformed into TSCs, which further differentiated into osteoblasts, hypertrophic chondrocytes and tenocytes. In addition, chondrocytes (CYTL1high+ THBS1high) from secondary cartilage were detected only in 4-month-old human embryonic TMJC. Conclusions Our study provides an atlas of differentiation stages of human embryonic TMJC tissue cells, which will contribute to an in-depth understanding of the pathophysiology of the TMJC tissue repair process and ultimately help to solve clinical problems.

overall_design: This study utilized single-cell RNA sequencing (scRNA-seq) to analyze the embryonic temporomandibular joint condyle (TMJC) at different developmental stages, including 3M,4M. TMJC tissues were obtained from human embryos, preserved in a tissue preservation solution (Singleron Biotechnologies, Nanjing, China), and transported under cold chain conditions. The tissues were cut into 2–3 mm sections, rinsed with Hanks' Balanced Salt Solution (HBSS), and enzymatically digested for 15 minutes using a tissue dissociation solution (Singleron Biotechnologies, Nanjing, China). The resulting cell suspension was filtered through a 40μm sterile filter (Corning, NY, USA) and centrifuged at 150 g for 5 minutes. Erythrocytes were removed using a lysis reagent (Singleron Biotechnologies, Nanjing, China) for 10 minutes. The cells were resuspended in phosphate-buffered saline (PBS), stained with trypan blue (T6146, Sigma, Burlington, VT, USA), and assessed for viability using a TC20 automated cell counter (Bio-Rad, Hercules, CA, USA). The cell suspension was adjusted to a concentration of 1×10⁵ cells/mL, loaded into a microfluidic chip, and single-cell RNA libraries were constructed using the Single-Cell RNA Library Kit (Singleron Biotechnologies, Nanjing, China). The prepared libraries were then sequenced on an Illumina NovaSeq 6000 platform to obtain high-throughput single-cell transcriptomic data.

first: Qianqi

last: Zhu

first: Miaoying

last: Tan

first: Chengniu

last: Wang

first: Yufei

first: Chenfei

first: Junqi

last: Zhang

first: Yijun

last: Gu

first: Yuqi

last: Guo

first: Jianpeng

last: Han

first: Lei

last: Li

first: Rongrong

last: Jiang

first: Xudong

last: Fan

first: Huimin

last: Xie

first: Liang

first: Zhifeng

first: Dong

last: Liu

first: Jianwu

last: Shi

first: Xingmei

last: Feng


title: Ribosomal heterogeneity revealed by a spatial transcriptomics in the water fern Ceratopteris richardii

city: Jishou

first: Gui-Sheng

address: 120 Renmin South Street

institute: Jishou University

summary: Background and Aims: Ferns are providing insight into fundamental biological processes, and spatial transcriptomics is a potent tool in unraveling complexes of plant development. This research is targeted at leaf development in the water fern Ceratopteris richardii with the use of spatial transcriptomics. Methods: A shoot tip of sporophytes under vegetative growth was investigated using spatial transcriptomics, which conducted spot clustering, marker gene identification, and functional enrichment. Ribosomal protein genes were queried using BLAST program and categorized based on multi-alignment produced by Clustalw2 program. RNA in situ tissue hybridization was performed on three ribosomal protein genes. Key Results: Leaves were mutually different at the level of transcriptome under various developmental stages. There were unexpected complexes in tissue structure for stems. A few transcription factors were identified characteristic of leaf development. Activities associated with translation were very different between tissues, and ribosomal protein genes were heterogeneous at the level of transcription. Ribosomal protein genes were specifically expressed in the shoot apical meristem, leaf primordia, and vasculature of various organs. Conclusions: Leaves are mutually different under various developmental stages in C. richardii, with contribution of transcription factors. Stems are unexpectedly complex in tissue structure. Organs/tissues are very different in translation activity from each other, partly due to transcription heterogeneity of ribosomal protein genes. Ribosomal protein genes are specifically expressed in the shoot apical meristem, leaf primordia, and vasculature.

overall_design: The water fern Ceratopteris richardii was employed, one sporophyte under vegetative growth with three fully expanded leaves was dissected, and the central shoot tip was retained and directly immersed into the optimal cutting temperature compound (OCT, Sakura Finetek Europe B.V.) under dry ice. The specimen was sectioned with a thickness of 20 μm, and the anchored section was fixed on slides using 100% methanol. Topuidine Blue staining was applied for histological examination. RNA was trapped by poly(T)VN to the spot array, namely BMKMANU S1000 platform (BioMarker, Beijing) having a density of more than two million spots with a diameter less than 2.5 μm and 5 μm centre-to-centre distance within 6.8 mm2 area. Double-strand cDNA was synthesized to incorporate the spatial barcode and the unique molecular index (UMI), and furthermore the sample index. The fragmented DNA was obtained via enzymatic digestion, and it was sequenced using NovaSeq PE150 (Illumina). Sequencing reads were mapped to the genome assembly with the accession number of GCA_020310875.1. BSTMatrix (BioMarker) was used to construct the spot-expression matrix under a total of eight levels. The package Seurat v5 provided tools in normalizing data, identifying clusters, and determining marker genes. The threshold for the marker gene was |log2FC| ≥ 0.5 and false discovery rate < 0.05. Spot clustering was visualized using BSTViewer V1.42 (BioMarker). Genes were functionally annotated using multiple platforms such as NR, Pfam, Swiss-Prot, and TrEMBL with the help of the program BLAST, and the subsequent enrichment analysis was conducted using clusterProfiler v3.18.1.

first: Jin


title: GDF15 contributes to thyroid cancer progression and modulates thyroid cancer cell senescence in a p53-dependent manner.

city: jinan

first: jingyu

last: ma

address: Qilu Hospital of Shandong University, 107 Wenhuaxi Road, Lixia, Jinan, Shandong , P.R.China

institute: shandong university

summary: Growth differentiation factor 15（GDF15）displays aberrant expression in multiple malignancies, yet its role and underlying mechanisms in thyroid carcinoma remain unclear. This study aimed to investigate GDF15 expression and functional significance in thyroid cancer, revealing that GDF15 is significantly upregulated and participates in cellular senescence. GDF15 knockdown suppresses proliferation, migration, and invasion of thyroid cancer cells. Transcriptome sequencing demonstrates that GDF15 depletion activates the p53 pathway and induces senescence. Furthermore, our results confirm a protein-level interaction between GDF15 and p53. Given the established importance of p53 in senescence, p53 knockdown partially rescues the enhanced senescence phenotype induced by GDF15 depletion. Consequently, we identify a novel GDF15-p53 regulatory loop wherein GDF15 sustains thyroid carcinogenesis by suppressing p53-dependent senescence. Targeting this axis highlights a promising therapeutic target for thyroid carcinoma, with GDF15 inhibition representing a tumor senescence reactivation strategy.

overall_design: GDF15 expression was knocked down in thyroid cancer cell lines, and the control group was blank control. Set three repetitions for each group.


title: ZNF180 modulates tumor intrinsic immunotherapy resistance in melanoma through driving plasticity [ATAC-seq]

city: New York

first: Won-Min

last: Song

state: NY

address: 1399 Park Avenue

department: Genetics and Genomic Sciences

institute: Icahn school of medicine at Mount Sinai

summary: Through analyzing publicly available single-cell and bulk sequencing data from ICI-treated cohorts, ZNF180-regulome was predictive of ICI responses in independent bulk sequencing cohorts, and ZNF180+ tumors persisted after the therapy with immune-suppressive features such as MHC-I loss and CD155 expressions, the primary ligand to TIGIT inhibitory receptor. To investigate regulatory roles of ZNF180 to confer these immune suppressive phenotypes, we performed ZNF180 knock-down in melanoma cells in vitro with different genetic backgrounds, namely A375 (BRAF-mutant) and SKMEL147 (NRAS-mutant) cells, and performed RNA- and ATAC-sequencing. The integrative analysis revealed ZNF180 silencing promoted tumor immunogenicity through gain of accessibility on MHC-I/-II coding genes, CD155 down-regulation to avoid TIGIT/CD155 checkpoint signaling, and suppressed AP-1 transcription factor activities as the drivers of melanoma reprogramming towards MITFlowAXLhigh de-differentiated cells. Further, ZNF180 silencing increased CD4 helper T-cell infiltrations in tumors and regressed the tumors in vivo. Collectively, these results indicate ZNF180 is a tumor intrinsic regulator of melanoma plasticity to drive de-differentiated phenotypes with immune-suppressive features including loss of immunogenicity, T-cell inhibitory signals through TIGIT/CD155 checkpoint and exclusion of CD4 helper T-cells. As ZNF180-regulome manifests in non-metastatic melanoma in contrast to the current focus of standard-of-care ICI on the metastatic disease, these results establish ZNF180-regulome as a biomarker and novel therapeutic avenue for early stage melanoma to intervene ICI resistance.

overall_design: ZNF180 knock-down by shRNAs (shZ1, shZ3) was performed on A375 and SKMEL147 cells with two biological replicates per shRNA. The ATAC-seq was performed on the ZNF180 KD cells and the respective non-transfected controls.

first: Praveen

last: Agrawal

first: Sree

last: Kondapuram

first: Xianxiao

last: Zhou


title: Transcriptomic analysis of NeuroD2 CRISPant stage 47 Xenopus laevis tadpole brains

city: Dunedin

first: Caroline

last: Beck

state: Otago

address: 340 Great King Street, North Dunedin

department: Zoology

country: New Zealand

institute: University of Otago

summary: We compared transcripts from whole brains dissected from stage 47 Xenopus laevis tadpoles from F0 NeuroD2 CRISPants and Cas9 injected control sibings. NeuroD2 knockdown brains had increased expression of cell cycle associated genes and decreased expression of chromatin modifing genes. Libraries were prepared and sequenced using Illumina Nextseq P2 by the Otago Genomics Facility, University of Otago, New Zealand. Single reads of 100bp were mapped to XENLA_10.1 genome build (Xenbase, accessed November 2024)

overall_design: Tadpoles were raised to stage 47 after injection at the one cell stage with either S. pyogenes Cas9 loaded with a frame shift inducing NeuroD2 sgRNA or just Cas9. Brains were removed by dissection and total RNA extracted from pooled groups of 4 using a qiagen RNeasy mini kit with on column DNase step.  TruSeq stranded libraries were prepared. Single reads of 100bp Mapped to XENLA_10.1 genome build (Xenbase, accessed November 2024)


title: GSX2 Regulates Progenitor Maturation and Regional Identity Through Transcriptional Repression in the Developing Basal Ganglia [RNA-Seq]

city: Cincinnati

first: Brian

last: Gebelein

state: OH

address: 3333 Burnet Avenue, MLC 7007

institute: Cincinnati Children's Hospital Medical Center

summary: Transgenic mouse models have demonstrated the critical role of the homeodomain transcription factor Genetic-Screened Homeobox 2 (Gsx2)   in the developing basal ganglia. However, the technical limitations of the existing in vivo approaches, such as progenitor heterogeneity and lack of temporal resolution, have impeded the investigation of direct regulatory targets . This study engineered a Dox-inducible human embryonic stem cell (hESC) line to investigate the function of GSX2 protein in directed differentiation cultures that model developing lateral ganglionic eminence-like (LGE-like) progenitors. Transcriptomic, chromatin accessibility, and genomic binding studies revealed that GSX2: (1) binds to both high- and low-accessibility chromatin using varying binding site preferences; (2) alters chromatin accessibility largely through indirect mechanisms; (3) functions primarily as a transcriptional repressor; and (4) regulates key conserved target genes of both progenitor maturation and regional specification. These results provide insight into the key regulatory roles and targets of GSX2, thereby establishing a new tractable experimental system to investigate basal ganglia development.

overall_design: Triplicate RNA-seq profiling of transgenic H9 (WA-09) hESC line (TRE3G 2xFLAG-GSX2 WT) differentiated to LGE-like progenitors at Days 10-12 with variable transgene induction.

first: Edward

last: Farrow

first: Kenneth

last: Campbell

first: Hee-Woong

last: Lim


title: Transcriptomes of left ventricle under reverse remodeling in 4,6,8-week age mice

first: Longming

last: Huang

address: 1678 Dongfang Road

institute: Shanghai Children's Medical Center

summary: Reversible neonatal ascending aorta constriction (Rev-nAAC), neonatal ascending aorta constriction (nAAC) or sham surgery was performed in newborn mice within 24h. At the 4th, 6th and 8th week, left ventricles were collected and used for RNA sequencing (n=5 per group).

overall_design: RNA sequencing assessed gene expression changes in left ventricular samples from 4-, 6-, and 8-week-old mice that underwent either sham surgery (control group), aortic constriction (remodeling group), or reversible aortic constriction (reverse remodeling group) within 24 hours after birth.

first: Bozhong

first: Xiaomin

last: He


title: Direct contact between iPSC-derived macrophages and hepatocytes drives reciprocal acquisition of Kupffer cell identity and hepatocyte maturation

city: Singapore

first: Raman

last: Sethi

state: Singapore

address: #07-01 Matrix, 30 Biopolis Street

country: Singapore

institute: BII, A*STAR

summary: As the resident tissue macrophage of the liver, Kupffer Cells (KC) play an important role in homeostasis and tissue support. However, current in-vitro liver models often ignore the contribution of these KCs toward the proper response and function of the tissue. This is especially relevant when we consider the implications of immune-mediated drug injuries. To address this issue, we developed an isogenic co-culture system utilizing iPSC-derived macrophages (iMacs) and hepatocytes (iHeps). Directly co-culturing iHeps with iMacs improved the differentiation and maturation of the iHeps, with significant downregulation of fetal hepatocyte markers as well as upregulation of cytochrome genes. Furthermore, the co-culture also imparted stronger KC identity to the iMacs in a contact-dependent manner, with iMacs cultured in iHep conditioned media alone showing weaker expression of key KC markers. Finally, challenging the iHep-iMac co-culture system with 7 paradigm hepatotoxic compounds showed dose-dependent cytokine response in the 5 compounds associated with immune-mediated liver injuries, while no significant changes were observed in the 2 compounds with no reported immune-dependent complications. This effect was also not recapitulated when the co-culture was instead performed with human peripheral blood monocyte-derived macrophages, suggesting that iMacs are essential for liver toxicity response. Taken together, our study shows not only the importance of macrophages in tissue systems, but also that the source of macrophages is critical to the development of accurate in-vitro human models.

overall_design: IMR90-iPSCs were differentiated into iPSC-hepatocytes and iPSC-macrophages. 2 x 10^5 iMacs or monocyte-derived macrophages were added to 5 x 10^5 iHeps during a full media change (4ml) per well of a 6 well plate on Day 0. 50ng/ml of CSF-1 was added to each well. The cells were cultured for 7 days, with a half-media change (2ml) on Day 4. The cells were collected by digesting with Accutase.

first: Christopher

last: Zhe Wei Lee

first: Farah

last: Tasnim

first: Jinmiao

last: Chen

first: Hanry

last: Yu

first: Florent

last: Ginhoux


title: Distinct and convergent effects of SF3B1 mutations in human breast cancer

city: Nashville

first: Yu

last: Wang

state: TN

address: 2525 West End Ave, Ste 1020

institute: VUMC

summary: Tumor genomic profiling has uncovered many cancer drivers whose implications in terms of tumor biology and therapeutic actionability remain understudied. Hotspot mutations in SF3B1 induce widespread transcriptomic alterations and occur across multiple cancer types. Despite this, the biological and clinical consequences of SF3B1 mutations remain elusive. Characterization of the largest SF3B1 mutant breast cancer clinical cohort to date identifies SF3B1 driver mutations in approximately 2.5% of HR+ HER2- breast cancer, with strong enrichment of K700E substitutions, substantial variation in variant allele fraction, and significantly improved overall survival. In-vitro and in-vivo studies in representative cell models suggest several of the most prevalent SF3B1 mutations have deleterious effects on cell growth, leading to selective loss of the mutation over time, providing a rationale for the low frequency and low VAF of SF3B1 mutations in breast cancer. Though all introduced hotspot mutations limit growth and are reverted to wildtype over time, mutations at position R625 have a more pronounced phenotype than K700E, providing an explanation for the clinically observed skew in mutation frequencies. RNA and DNA sequencing analyses were used to identify characteristic pathway-level transcriptomic changes in SF3B1-mutant cells and identify copy number alterations as a mechanism of both improved mutation tolerability and a means to eliminate the mutation over time. These data suggest that while SF3B1 mutations are enriched in some clinical contexts, their role in breast tumorigenesis is highly complex and dependent on secondary events that overcome their deleterious effects on cell growth and survival.

overall_design: RNA-sequencing profiling of breast cancer cell lines with isogenic SF3B1 hotspot mutations.

first: Riley

last: Bergman

first: Ben

middle: H

last: Park


title: Comparative Analysis of the Transcriptome and Methylome in Distinct Trophoblast Populations During Embryo Implantation in Mares

city: Krakow

first: Tomasz

last: Szmatoła

state: Małopolskie

address: Mickiewicza 21

department: OMEI

country: Poland

institute: University of Agriculture in Krakow

summary: Background: During equine implantation, two distinct trophoblast subpopulations are identified: the invasive chorionic girdle (CG) and the non-invasive allantochorion. The invasive CG is believed to modulate the maternal immune response and facilitates embryo attachment to the endometrium, while the allantochorion contributes to placental development without breaching the endometrium. However, the mechanisms underlying differential adhesion and immune modulation by these two lineages remains poorly understood. This study aimed to investigate the regulation of biological processes underlying trophoblast attachment, development and maintenance of immune tolerance by comparing the transcriptomes and methylomes of CG and allantochorion trophoblasts before and after implantation, that is, between gestational days 33 and 42. Results: Irrespective of gestational day, allantochorion (n=4) was enriched in TGFB and its receptors TGFBR1 and TGFBR2. Across the implantation window, expression of regulatory macrophage markers such as IL33, IL4|1, PLG-RKT, and CD163 increased in the allantochorion, along with upregulation of TFEB and SERPINE1. The invasive GC (CG33, n=4) showed higher expression of NLRC5, a transcriptional regulator of MHC I, compared to the non-invasive allantochorion (ALC33, n=4). Notably, NLRC5 expression declined in the allantochorion from day 33 to 42. Furthermore, B2M, which encodes the MHC I light chain, was hypermethylated in the allantochorion. Several genes, including CAVIN1, LHB, and INSR, were both differentially expressed and methylated between the two trophoblast types, while others, such as IFNGR1, CD177, showed differential regulation across the implantation window. Gene Ontology and pathway analyses revealed that differentially expressed and methylated genes were enriched in biological processes and pathways critical for implantation, including cell migration and adhesion, TGFB signaling, fibrosis, wound healing, and leukocyte extravasation.   Conclusions: The allantochorion plays an active role in establishing the attachment to the endometrium and sustaining maternal immune tolerance during implantation. The upregulation of IL33, IL4|1, and CD163 suggests the that the allantochorion may promote the recruitment or polarization of macrophages toward a regulatory phenotype, thereby modulating the local immune environment. TFEB may contribute to the steroidogenic activity and functional maturation of the allantochorion. Spatial and temporal differences in gene methylation between CG and allantochorion suggest involvement of epigenetic regulation in trophoblast invasion and attachment to the endometrium. Finally, combined B2M hypermethylation and differential expression of NLRC5 point to epigenetic and transcriptional control of MHC I expression in the equine trophoblasts during implantation.

overall_design: Equine allantochorion (ALC) and chorionic girdle (CG) samples  were collected with non-surgical uterine lavage at gestational days 33 (N ALC =4; N CG=4) and 42 (N=4) from physiologically progressing pregnancies. RNA was isolated from each sample using PureLink™ RNA Mini Kit (Ambion) with DNAse digestion between washing. Its quality and quantity were measured on a NanoDrop2000 and a TapeStation 2200 system (RNA tapes, Agilent). Acceptable samples had an RIN over 9.5. According to the manufacturer's protocol, cDNA libraries cells were prepared using the VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina from 300 ng aliquots of purified RNA samples. The final cDNA library concentration was 10 nM. The quality and quantity of cDNA libraries was assessment using D1000 tapes on TapeStation2200 and on Quibit. The cDNA were sequenced over 150PE cycles on a HiSeq 3000 System (Illumina, San Diego, CA, USA) in outdoor facilities (Admera Health Biopharma Services).

first: Joanna

last: Jaworska

first: Dawid

last: Tobolski

first: Katarzyna

last: Ropka-Molik

last: Ząbek

first: Anne

last: Kahler

first: Shebl

last: Salem

first: Izabela

last: Wocławek - Potocka

last: Piórkowska

first: Amanda

last: De Mestre


title: Histone methyltransferase PRDM9 promotes survival of drug-tolerant persister cells in glioblastoma [RNA-Seq FPW1 DTPs]

city: Camperdown

first: George

middle: Louis

last: Joun

state: NSW

address: John Hopkins Drive

department: School of Medical Sciences

country: Australia

institute: The University of Sydney

summary: Chemotherapy often kills a large fraction of cancer cells but leaves behind a small population of drug-tolerant persister cells. These persister cells survive drug treatments through reversible, non-genetic mechanisms and cause tumour recurrence upon cessation of therapy. Here, we report a drug tolerance mechanism regulated by the germ-cell-specific H3K4 methyltransferase PRDM9. Through histone proteomic, transcriptomic, lipidomic, and ChIP-sequencing studies combined with CRISPR knockout and phenotypic drug screen, we identified that chemotherapy-induced PRDM9 upregulation promotes metabolic rewiring in glioblastoma stem cells, leading to chemotherapy tolerance. Mechanistically, PRDM9-dependent H3K4me3 at cholesterol biosynthesis genes enhances cholesterol biosynthesis, which persister cells rely on to maintain homeostasis under chemotherapy-induced oxidative stress and lipid peroxidation. PRDM9 inhibition, combined with chemotherapy, resulted in strong anti-cancer efficacy in preclinical glioblastoma models, significantly enhancing the magnitude and duration of the antitumor response by eliminating persisters. These findings demonstrate a previously unknown role of PRDM9 in promoting metabolic reprogramming that enables the survival of drug-tolerant persister cells.

overall_design: FPW1 Glioblastoma Stem Cell line were treated for fourteen days with 25uM CMPD1, to generate drug tolerant persisters (DTP). RNA sequencing was conducted on the persisters, compared to the matched, Day 0 control. N=3 experiments were conducted.

first: Loo

last: Lipin


title: Pre-encoded IFN-I sensitivity exacerbates memory T cell senescence in solid tumors

city: Hamilton

first: Yonghong

last: Wan

state: Ontario

address: 1280 Main St W

department: Medicine

country: Canada

institute: McMaster University

summary:
Solid tumors often suppress antitumor immune responses by promoting various dysfunctional CD8+ T cell states which limit the effectiveness of T-cell based immunotherapy. However, the mechanisms that promote these states have not been fully characterized. We demonstrate that spontaneous priming responses during tumor growth can produce memory T cell reservoirs that are conducive to poor proliferative responsiveness during boosting vaccination. Surprisingly, when IFN-I signaling is impeded, boosting vaccination can elicit robust proliferative responses from tumor-primed memory T cells and promote tumor control. This was observed in multiple tumor types and target antigens. In contrast to conventional memory T cells, tumor-primed memory T cells are unique in their pre-encoded responsiveness to IFN-I and show enrichment of pathways pertaining to DNA repair and cell cycle arrest. Tumor-primed memory T cells up-regulate p21 expression and blockade of either p21 or IFN-I can alleviate this effect to improve their proliferative capacity during boosting vaccination. Characterization of tumor-primed memory T cells revealed transcriptional and phenotypic features of cellular senescence, where higher senescence severity correlated with higher responsiveness to IFNAR blockade. Overall, IFN-I hyperresponsiveness may be a unique feature of senescent tumor-primed memory T cells that can exacerbate their dysfunction during cancer vaccination.
We used whole transcriptome arrays (Clariom S) to analyze the state of dysfunction when comparing VP-TM, TP-TM(B16), an TP-TM(MC38)

overall_design: C57BL/6 mice were challenged i.d. with B16-gp33/MC38-gp33 tumors in order to generate TP-TMB16/ TP-TMMC38 or acutely infected i.v. with LCMV in order to generate VP-TM. Memory T cells were isolated from secondary lymphoid tissue and sorted based on gp33H2DbTet+ CD8+ staining. RNA was extracted from purified cells for whole transcriptome analysis (ClariomS)

first: Nguyen

last: Andrew

first: Scott

last: Walsh


title: ZNF180 modulates tumor intrinsic immunotherapy resistance in melanoma through driving plasticity [RNA-Seq]

first: Won-Min

last: Song

overall_design: ZNF180 knock-down by shRNAs (shZ1, shZ3) was performed on A375 and SKMEL147 cells with two biological replicates per shRNA. The transcriptomes of the ZNF180 KD cells were compared to the respective non-transfected controls.

first: Praveen

last: Agrawal

first: Sree

last: Kondapuram

first: Xianxiao

last: Zhou


title: Functional division of insect blood cells in immunity by single-cell RNA sequencing

city: Andong-si

first: Niayesh

last: Shahmohammadi

state: Gyeongsangbuk-do

address: Songcheon 3-gil

department: Plant Medicals

country: South Korea

institute: Gyeongkuk National University

summary: This study aimed to uncover the functional diversity and differentiation pathways of hemocytes in Spodoptera exigua by applying single-cell RNA sequencing (scRNA-seq). The objective was to classify hemocyte subtypes beyond traditional morphology and identify distinct gene expression profiles associated with immune responses, differentiation, and physiological functions.

overall_design: Fifth-instar Spodoptera exigua larvae were injected with Escherichia coli, incubated for 8 h, and hemolymph was collected for single-cell preparation. Cells were captured with 10x Chromium 3 prime v2, and libraries were prepared by poly(dT) priming with cell barcodes and UMIs, followed by Illumina paired-end sequencing. This sample represents hemocyte transcriptomes following immune activation.

first: Falguni

last: Khan

first: Gahyeon

last: Jin

first: Mojtaba

last: Esmaeily

first: Shiva

last: Haraji

first: Yonggyun

last: Kim


title: Determine the effects of Wdr4 on global translation efficiency via ribosome profiling (Ribo-seq)

city: Wuhan City

first: JIe

last: Liu

state: Hubei

address: No.299 Bayi Road, Wuchang District

institute: Wuhan University

summary: Tumor-associated macrophages (TAMs) play a pivotal role in shaping the tumor microenvironment in hepatocellular carcinoma (HCC), significantly influencing disease progression and patient outcomes. WDR4, a tRNA-binding scaffold essential for N7-methylguanosine (m7G) methylation, has an undefined role in HCC-associated TAMs. Here, we found that WDR4 expression is markedly upregulated in HCC-infiltrating TAMs and correlates with poor prognosis in patients. Using HCC mouse models, we demonstrated that WDR4 depletion reprograms TAMs toward an anti-tumor phenotype and suppresses HCC progression.  To investigate the impact of WDR4 on translational efficiency, we performed ribosome profiling (Ribo-seq) on Wdr4-deficient TAMs. To ensure reproducibility and minimize potential off-target effects, we included TAMs sorted from orthotopic HCC-bearing Wdr4 conditional knockout mice, as well as immortalized bone marrow-derived macrophages (iBMDMs) with Wdr4 knocked out using two independent sgRNAs.

overall_design: An orthotopic HCC model was established in Wdr4^ff and myeloid-specific Wdr4 knockout (Wdr4^cKO) mice by inoculating Hepa1-6 cells. After tumor development, tumor tissues were harvested, and F4/80+ TAMs were isolated via flow cytometric sorting.  For in vitro experiments, monoclonal immortalized bone marrow-derived macrophage (iBMDM) lines were infected with lentiviruses expressing Wdr4-targeting sgRNAs. Following puromycin selection for at least one week, cells were collected at 70–80% confluence. This included two independent Wdr4-targeting sgRNAs and one wild-type (WT) control group.  Ribo-seq was performed on both F4/80+ TAMs and iBMDM samples. Both ribosome-protected fragments (footprint RNA) and input RNA were subjected to sequencing.

first: Jie

first: Minghe

last: Zhang

first: Peng

last: Xia

first: Yufeng

last: Yuan


title: Retinal polyunsaturated fatty acid supplementation reverses aging-related vision loss in mice

city: Irvine

first: Dorota

last: Skowronska-Krawczyk

address: Gavin Herbert Eye Institute

institute: University of California, Irvine

summary: The retina is uniquely enriched in polyunsaturated fatty acids (PUFAs), which are primarily localized in cell membranes, where they govern membrane biophysical properties such as diffusion, permeability, domain formation, and curvature generation. During aging, alterations in lipid metabolism lead to reduced content of very long-chain PUFAs (VLC-PUFAs) in the retina, and this decline is associated with normal age-related visual decline and pathological age-related macular degeneration (AMD). ELOVL2 (Elongation of very-long-chain fatty acids-like 2) encodes a transmembrane protein that produces precursors to docosahexaenoic acid (DHA) and VLC-PUFAs, and methylation level  of its promoter is currently one of the best predictors of chronological age. Here, we show that mice lacking ELOVL2-specific enzymatic activity (Elovl2C234W) have impaired contrast sensitivity and slower rod response recovery following bright light exposure. Short-term and long-term intravitreal supplementation with the direct product of ELOVL2, 24:5n-3, in aged animals improved visual function and reduced accumulation of ApoE and C3d in sub-RPE deposits. At the molecular level, the gene expression pattern observed in retinas supplemented with 24:5n-3 exhibited a partial rejuvenation profile, including decreased expression of aging-related genes and a transcriptomic signature similar to younger retinas. Finally, we present  human genetic data showing significan t association of two variants in the ELOVL2 locus with the onset of intermediate AMD, underlining the translational importance of our findings. In sum, our study identifies potential therapeutic opportunities and defines ELOVL2 as a promising target for interventions aimed at preventing age-related vision loss.

overall_design: snRNA-seq profiling of retinas from 3-month-old and 18-month-old wildtype C57BL6/J mice

first: Fangyuan

last: Gao

first: Emily

last: Tom

first: Qing

last: Nie

first: Yutong

last: Sha


title: Intestinal epigenomic alterations are associated with a dysregulated nutrient absorption phenotype in obesity [RNA-Seq]

city: Rochester

first: Aditya

last: Bhagwate

state: MN

address: 200 1st Street SW

institute: Mayo Clinic

summary: Obesity is an epidemic with myriad health effects, but little is understood regarding individual obese phenotypes and how they may respond to therapy. Epigenetic changes associated with obesity have been detected in blood, liver, pancreas, and adipose tissues. Previous work has found that dietary glucose hyperabsorption occurs in some obese subjects, but detailed transcriptional or epigenomic features of the intestine associated with this phenotype are unknown. This study evaluated differentially expressed genes and relative chromatin accessibility in intestinal organoids to characterize the obese hyperabsorptive phenotype. Methods: Intestinal organoids established from donors classified as lean, obese, or obese hyperabsorptive by body mass index and glucose transport assays were analyzed by RNA-seq, ATAC-seq, and transcription factor footprinting to characterize transcriptional and/or epigenomic features of each phenotype. Organoids from additional lean and obese hyperabsorptive donors were analyzed for specific transcripts by quantitative PCR to validate the predictive value of biomarkers associated with the hyperabsorptive phenotype. Results: Transcriptomic analysis indicated that obese hyperabsorptive subjects have significantly upregulated dietary nutrient absorption proteins and downregulated type I interferon targets. Chromatin accessibility and transcription factor footprinting suggested that enhanced binding of HNF4G promotes the obese hyperabsorption phenotype. Quantitative PCR assessment in a larger subject cohort suggested that intestinal epithelial expression of CUBN, GIP, and SLC2A5 have high correlation with hyperabsorption. Conclusions: The obese hyperabsorption phenotype is characterized by transcriptional changes that support increased nutrient uptake and appear to be driven by differentially accessible chromatin. These observations support obesogenic imprinting on intestinal stem cells (ISCs), the cell population from which organoid cultures are derived and sustained, such that absorptive, metabolic, and innate immune perturbations persist ex vivo in a controlled tissue culture environment. Recognizing that intestinal phenotypes in obesity may differ provides new perspective in considering therapeutic targets and options to manage the disease.

overall_design: Organoid cultures were established from jejunal tissue obtained during upper endoscopy procedures or tissue discarded following bariatric surgeries under approved institutional protocols. Organoids classified as Group 1 were established from lean donors (BMI ≤ 25 kg/m2) and exhibited low intestinal epithelial glucose absorption. Organoids in Group 2 were from obese donors (BMI ≥ 35 kg/m2) and showed elevated intestinal epithelial glucose absorption relative to lean donors. Organoids in Group 3 were from obese donors (BMI ≥ 35 kg/m2) with intestinal epithelial glucose absorption profiles that were similar to lean donors.

first: Badurdeen

last: Dilhana

first: Li

last: Zhen

first: Lee

last: Jeong-Heon

first: Ma

last: Tao

first: Bhagwate

last: Aditya Vijay

first: Latanich

last: Rachel

first: Dogiparthi

last: Arjit

first: Ordog

last: Tamas

first: Kovbasnjuk

last: Olga

first: Kumbhari

last: Vivek

first: Foulke-Abel

last: Jennifer


title: Targeting STING–induced immune evasion with nanoparticulate binary pharmacology improves tumor control in mice

city: Hangzhou

first: Fanchao

last: Meng

address: 79 Qingchun Road

department: NHC Key Laboratory of Combined Multi-Organ Transplantation

institute: The First Affiliated Hospital, Zhejiang University School of Medicine

summary: Harnessing the stimulator of interferon genes (STING) signaling pathway to trigger innate immune responses has shown remarkable promise in cancer immunotherapy; however, overwhelming resistance to intratumoral STING monotherapy has been witnessed in clinical trials, and the underlying mechanisms remain to be fully explored. Herein, we show that pharmacological STING activation following the intratumoral injection of a non-nucleotide STING agonist (i.e., MSA-2) results in apoptosis of the cytolytic T cells, interferon-mediated overexpression of indoleamine 2,3-dioxygenase 1 (IDO1), and evasion from immune surveillance. We leverage a noncovalent chemical strategy for developing immunomodulatory binary nanoparticles (iBINP) that include both the STING agonist and an IDO1 inhibitor for treating immune-evasive tumors. This iBINP platform developed by dual prodrug engineering and subsequent nanoparticle assembly enables tumor-restricted STING activation and IDO1 inhibition, achieving immune activation while mitigating immune tolerance. A systemic treatment of preclinical models of colorectal cancer with iBINP resulted in robust antitumor immune responses, reduced infiltration of regulatory T cells, and enhanced activity of CD8+ T cells. Importantly, this platform exhibits great therapeutic efficacy by overcoming STING–induced immune evasion and controlling the progression of multiple tumor models. This study unveils the mechanisms by which STING monotherapy induces immunosuppression in the tumor microenvironment and provides a combinatorial strategy for advancing cancer immunotherapies.

overall_design: Mice bearing  MC38 tumors received intratumoral injections of vehicle (Saline containing 10%DMSO) or MSA-2 every three days. After a total of three doses, tumors were collected, minced and dissociated (n = 3 mice or samples were pooled to control for biological variability).

first: Hangxiang

last: Wang


title: RNA-seq data of imbibed vs. mannitol- treated seeds in Arabidopsis thaliana Col - 0 and odr1 - 2 mutant

city: Shenzhen

first: Ling

last: Ding

address: No 7,Pengfei Road,Dapeng District

institute: Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences

summary: This study aims to investigate the transcriptomic differences between wild-type Arabidopsis thaliana Col-0 and the odr1-2 mutant in two experimental groups: imbibed seeds (under normal hydration conditions) and seeds subjected to 12-hour mannitol treatment (a common osmotic stress mimic).Using RNA sequencing to compare global gene expression profiles, we seek to identify differentially expressed genes (DEGs) associated with osmotic stress responses, seed imbibition, and the potential regulatory role of the ODR1 gene. Our analysis will clarify how the ODR1 mutation alters transcriptional dynamics under both normal and osmotic stress conditions, thereby providing insights into the molecular mechanisms underlying stress tolerance and seed physiology in Arabidopsis.

overall_design: Transcriptome sequencing was conducted on 12 samples (with three biological replicates per group), derived from Arabidopsis thaliana Col-0 (wild type) and odr1-2 (mutant). All samples were prepared from after-ripened seeds stratified at 4°C for 2 days (to induce dormancy break), followed by two treatments: 12 h imbibition in water or 12 h treatment with 300mM mannitol.


title: Molecular Consequences of CCN6 Variants Encoding WISP3 in Progressive Pseudorheumatoid Dysplasia

city: Istanbul

first: Eda

last: Tahir Turanli

address: Kayisdagi St.

country: Turkey

institute: Acibadem University

summary: Progressive pseudorheumatoid dysplasia (PPD) is a rare autosomal recessive cartilage disorder caused by biallelic variants in CCN6, encoding the matricellular protein WISP3. To investigate how disease-associated CCN6 variants impact chondrocytes, we overexpressed two clinically relevant variants—p.Cys52* and p.Cys114Trp—both located in the IGFBP domain, and assessed their effects on redox balance, ER stress, ECM remodeling, gene expression, and protein–protein interactions. The p.Cys52* variant led to rapid degradation of WISP3, consistent with complete loss-of-function. In contrast, p.Cys114Trp induced severe protein destabilization, mitochondrial ROS accumulation, and elevated ER stress. Proteomic analysis revealed that p.Cys114Trp established novel interactions, suggesting a gain-of-function effect. These variant-specific differences highlight how structural context influences cellular outcomes beyond variant type alone. Altogether, our findings emphasize the necessity of functional characterization to better model PPD pathogenesis and provide mechanistic insights that may guide future therapeutic strategies.

overall_design: RNA-seq profiling of human chondrocyte cell line 402-05A following plasmid-mediated overexpression of wild-type CCN6 or its variants (p.Cys52, p.Cys114Trp). Cells were harvested 48 hours post-transfection for total RNA extraction and library preparation.

first: Gulipek

last: Guven Tasbicen

first: Alper

last: Bulbul

first: Dilay Hazal

last: Ayhan

first: Yasemin

last: Alanay


title: DNA Methylation profiles of self-reported Hispanic subjects in the Northern Manhattan Study

city: Miami

first: Lily

address: 1120 NW 14th St

institute: University of Miami

type: Methylation profiling by genome tiling array

summary: The Northern Manhattan Study (NOMAS) is a community-based cohort designed to investigate the incidence and risk factors of stroke, dementia, and other vascular outcomes. DNA methylation profiles were generated using the Illumina MethylationEPIC v1.0 BeadChip, which assays about 850k CpGs, from blood samples of self-reported Hispanic adults. Eligible participants were stroke-free, aged ≥40 years, and had resided in the Northern Manhattan community for at least three months.

overall_design:
Bisulfite-converted DNA for 322 human blood samples were hybridized to the Illumina MethylationEPIC v1.0 Beadchip;
whole blood from self-reported Hispanic adults, stroke-free at enrollment, with population-level summaries provided in the associated manuscript.
*Please note that only technical sample attributes (Sample_Plate,Sentrix_ID, Batch (collection year: 2019 vs 2021)) are provided, as IRB/participant consent do not permit release of individual-level clinical variables, even in de-identified form*

first: David

last: Lukacsovich

first: Liyong

first: Tatjana

last: Rundek


title: Granulosa cell-secreted KITL is involved in maintaining zinc homeostasis in the oocytes of neonatal mouse ovaries

city: Guangzhou

first: Yan

last: Du

address: 382 Outer Ring East Road, Guangzhou Higher Education Mega Center

institute: South China University of Technology

summary: Proto-oncogenic receptor tyrosine kinase (KIT) ligand (KITL) secreted by granulosa cells and its receptor KIT on oocytes are crucial for primordial follicle formation and activation, and follicular development. In the present study, ZnSO4 decreased the number of primordial and growing follicles in cultured neonatal mouse ovaries when KITL-KIT signaling was inhibited by ISCK03. ZnSO4 also significantly increased the mRNA and protein levels of Zrt/Irt-like protein 6 (ZIP6, a zinc importer) and zinc levels in the oocytes of cultured neonatal mouse ovaries in the presence of ISCK03, suggesting that the increase of ZIP6 levels results in zinc overload in the oocytes of cultured neonatal mouse ovaries. Further experiments indicated that zinc overload resulted in oocyte apoptosis in cultured neonatal mouse ovaries via oxidative stress-driven dual mechanisms: irreversible DNA damage in the nucleus and autophagic flux blockade in the cytoplasm of oocytes. Moreover, intraperitoneal injection of ZnSO4 and ISCK03 significantly increased ZIP6 expression, DNA damage, autophagic flux blockade, and apoptosis of oocytes in neonatal mice. Taken together, these findings indicate that granulosa cell-secreted KITL is involved in maintaining zinc homeostasis in the oocytes of neonatal mouse ovaries. This study not only reveals a novel function of granulosa cells in supporting oocyte homeostasis, but also provides a theoretical basis for identifying individuals susceptible to zinc dyshomeostasis caused by the impaired KITL-KIT signaling.

overall_design: Effects of ZnSO4 and ISCK03 treatment on ovarian oocytes in neonatal mice


title: Oscillatory shear stress induced extracellular vesicles mediate valvular endothelial-interstitial cell crosstalk exacerbating aortic valve calcification [RIP-seq]

city: changsha

first: ruijiang

last: Zeng

address: No.139 Renmin Road Central

institute: The Second Xiangya Hospital of Central South University

summary: Calcific aortic valve disease (CAVD) involves pathological crosstalk between human valvular endothelial cells (hVECs) and interstitial cells (hVICs), yet the role of this communication in pathogenesis remains poorly defined. Here, we identify a novel extracellular vesicle-derived circRNA, CircILRUN, originating from hVECs and demonstrate its critical function in promoting hVIC osteogenesis and CAVD progression in vitro and in vivo. CircILRUN expression is significantly elevated in extracellular vesicles from hVECs under oscillatory shear stress. Its deletion markedly attenuates aortic valve calcification (AVC) in mice, reducing valve thickness, calcium deposition, and improving echocardiographic parameters, findings corroborated in osteogenic medium-induced hVICs. Through unbiased protein-RNA screening and biochemical validation, we identify N-acetyltransferase 10 (NAT10) as a key target of CircILRUN. Nat10 depletion also effectively reduces AVC in vivo. Mechanistically, CircILRUN acts as a molecular scaffold facilitating the interaction between NAT10 and the deubiquitinase USP11, thereby stabilizing NAT10 protein. Integrated transcriptomic and ac4C epitranscriptomic profiling reveals that CircILRUN promotes NAT10-mediated acetylation of CD36 mRNA, stabilizing CD36 and accelerating AVC progression. Collectively, our findings establish an extracellular vesicle-mediated circILRUN–NAT10–CD36 axis driving CAVD pathogenesis and identify both circILRUN and NAT10 as promising therapeutic targets

overall_design: CircRNAs expression in human valvular endothelial cell-derived exosomes (hVECs-Exos) were measured after exposure to oscillatory shear stress (OSS) and laminar shear stress (LSS), respectively. Three independent experiments were performed at each group (OSS and LSS) using different donors for each experiment.

first: Tinwen

last: Zhou


title: Intestinal epigenomic alterations are associated with a dysregulated nutrient absorption phenotype in obesity [ATAC-Seq]

first: Aditya

last: Bhagwate

overall_design: Organoid cultures were established from jejunal tissue obtained during upper endoscopy procedures or tissue discarded following bariatric surgeries under approved institutional protocols. Organoids classified as Group 1 were established from lean donors (BMI ≤ 25 kg/m2) and exhibited low intestinal epithelial glucose absorption. Organoids in Group 2 were from obese donors (BMI ≥ 35 kg/m2) and showed elevated intestinal epithelial glucose absorption relative to lean donors. Organoids in Group 3 were from obese donors (BMI ≥ 35 kg/m2) with intestinal epithelial glucose absorption profiles that were similar to lean donors

first: Badurdeen

last: Dilhana

first: Li

last: Zhen

first: Lee

last: Jeong-Heon

first: Ma

last: Tao

first: Bhagwate

last: Aditya Vijay

first: Latanich

last: Rachel

first: Dogiparthi

last: Arjit

first: Ordog

last: Tamas

first: Kovbasnjuk

first: Kumbhari


title: OSBPL3 Drives Colorectal Cancer Progression via Hippo-YAP Signaling and Modulates MEK Inhibitor Sensitivity

city: Harbin

first: yc

last: z

address: the Second Affiliated Hospital of Harbin Medical University

institute: HMU

summary: Colorectal cancer progression involves dysregulated signaling pathways such as Hippo-YAP, but upstream regulators remain poorly defined. Here we demonstrate that oxysterol-binding protein-like 3 (OSBPL3) modulates Hippo-YAP signaling to drive tumor aggressiveness. Analysis of clinical specimens and experimental models showed that elevated OSBPL3 levels in colorectal cancer tissues correlate with shortened patient survival. Depleting OSBPL3 impaired cancer cell proliferation and invasion through cell cycle arrest, while its overexpression accelerated tumor growth. Mechanistic studies revealed that OSBPL3 binds 14-3-3 proteins to promote YAP1 nuclear translocation, activating downstream oncogenic pathways. Notably, tumors with high OSBPL3 expression exhibited resistance to MEK inhibitors, but this resistance was overcome by YAP1 suppression or combined YAP/MEK inhibition in patient-derived organoids. These results establish OSBPL3 as a critical Hippo-YAP pathway regulator and propose targeting OSBPL3-mediated signaling as a therapeutic strategy for colorectal cancers with Hippo pathway alterations

overall_design: Knockdown OSBPL3 in CRC cell line.