title: Aging-induced Suppression of Cirbp Compromises DHODH-Mediated Ferroptosis Defense and Attenuates Hypothermic Cardioprotection during Heart Transplantation [ChIP-seq]

city: Shanghai

first: Yifan

last: Zhu

state: Shanghai

address: No.1678, Road Dongfang, Pudong district

institute: shanghai children’s medical center

summary: The purpose of this study was to explore the potential mechanism of attenuated hypothermic cardioprotection in the aging donor heart during transplantation and investigate its translational values. We performed chromatin occupancy of Sp1 profiling analysis using data obtained from chromatin immunoprecipitation-sequencing (ChIP-seq) of LV myocardium from the wild-type rat

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for SP1 in left ventricular myocardium in WT Sprague-Dawley (SD) rat

first: Chenyu

last: Jiang

first: Yiwei

last: Liu

first: Hao

last: Zhang


title: Comparative analysis of nuclei isolation protocols for transcriptomic profiling of brain tissue

status: Public on Mar 05 2026

city: Indianapolis

first: Holly

last: Kersey

state: Indiana

address: 320 West 15th Street | NB 103

department: Medical & Molecular Genetics

country: USA

institute: Indiana University

type: Expression profiling by high throughput sequencing

summary: Single-nucleus RNA sequencing (snRNA-seq) enables gene expression analysis at the single-cell level in complex tissues like the brain. The technique's effectiveness depends on obtaining high-quality nuclei suspensions, characterized by high yield, minimal cell-type biases, low contamination, and accurate gene expression profiles. This study compares three nuclei isolation methods using mouse brain tissue: sucrose gradient centrifugation, a spin column-based method, and a machine-assisted platform. Sucrose gradient centrifugation yielded the highest nuclei recovery with minimal doublets. The machine-assisted platform produced the highest viability with the lowest mitochondrial and RNA contamination. The column-based method had the lowest nuclei yield and highest ambient RNA contamination. These findings highlight the impact of isolation techniques on snRNA-seq data quality, with implications for optimizing neuroscience research and improving the study of brain cell-type diversity and disease mechanisms at the single-nucleus level.

overall_design: Mouse cortex was used to prepare nuclei isolation methods using three differing methods, (1) sucrose gradient centrifugation-based, (2) spin column-based, and (3) and a machine assisted platform, for snRNA-seq (N=2/condition)

middle: N

first: Dominic

middle: J

last: Acri

first: Luke

middle: C

last: Dabin

first: Kelly

last: Hartigan

first: Jung Hyun

last: Park

first: Jungsu

last: Kim


title: Aging-induced Suppression of Cirbp Compromises DHODH-Mediated Ferroptosis Defense and Attenuates Hypothermic Cardioprotection during Heart Transplantation [RNA-seq]

country: China

summary: The purpose of this study was to explore the potential mechanism of attenuated hypothermic cardioprotection in the aging donor heart during transplantation and investigate its translational values.

overall_design: By using aging donors in the rat model of heart transplantation, we attempted to identify the most relevant protein in the process by using RNA sequencing.


title: Loss of BAP1 cooperates with TP53 deficiency to transform a common myelo-erythroid progenitor (RNA-seq - mus musculus)

city: Washington

first: Alexandros

last: Tzatsos

state: DC

address: 800 22nd St NW SEH 8850

department: GW Cancer Center

institute: George Washington University

summary: We performed RNA-seq and ChIP-seq in lineage depleted bone marrow cells isolated from single and double Bap1 and Trp53 knockout mice to identify transcirptional and epigenetic programs that drive erythroleukemia.

overall_design: RNA-seq in single and double Bap1 and Tp53 lineage depleted murine bone marrow cells


title: Gene expression profiles of CBPWTp53-floxed, CBPAAp53-floxed,CBPWTp53ΔIEC and  CBPAAp53ΔIEC  intestinal cyrpts

city: Taipei

first: Yi-Ting

last: Lin

address: No. 1, Jen-Ai Road, 1st Section

department: Department of Pharmacology

country: Taiwan

institute: College of Medicine, National Taiwan University

summary: CREB-binding protein (CBP) is a coactivator modulating DNA accessibility for transcription factors.CBP phosphorylation at Ser1382/1386 enhanced NF-𝜅B- while suppressed p53-mediated gene expression to promote cell growth, suggesting that post-translational modification of CBP regulates cell fate. Here we report that CBP knock-in mice (CBPAA), in which Ser1383/1387 are replaced with alanines, develop a phenotype resembling ulcerative colitis (UC) driven by non-hematopoietic cells. These mice exhibit reduced organoid formation, intestinal epithelial cell (IEC) proliferation, accompanied by increased CBP/p53 binding. All findings are reversed in CBPAA mice with IEC-specific p53 deletion (CBPAAp53ΔIEC) mice. To investigate how impaired CBP phosphorylation results in dampened IEC stemness, RNA-seq was performed to profile the transcriptome of colonic crypt.

overall_design: Crypts were disaggregated from intestinal epithelium of CBPWTp53-floxed, CBPAAp53-floxed,CBPWTp53ΔIEC and CBPAAp53ΔIEC mice. Total RNAs were extracted from colonic crypts, and sequenced by Illumina NovaSeq 6000.


title: Loss of BAP1 cooperates with TP53 deficiency to transform a common myelo-erythroid progenitor (ChIP-seq - mus musculus)

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We performed RNA-seq and ChIP-seq in lineage depleted bone marrow cells isolated from single and double Bap1 and Trp53 knockout mice to identify transcriptional and epigenetic programs that drive erythroleukemia.

overall_design: ChIP-seq for H3K4me3, H3K27me3, and H2AK119Ub in single and double Bap1 and Tp53 knockout lineage depleted murine bone marrow cells.


title: Aging-induced Suppression of Cirbp Compromises DHODH-Mediated Ferroptosis Defense and Attenuates Hypothermic Cardioprotection during Heart Transplantation

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

overall_design: Refer to individual Series


title: Targeting CDC42 for acute kidney injury therapy via orchestrating KLF2/HIF-1α/PINK1-mediated mitophagy

city: Chongqing

first: Xue

last: Zhou

address: 重庆医科大学

institute: College of Pharmacy

summary: Acute kidney injury (AKI) is an unsolved global public health problem, requiring new effective therapies. Cytokinesis cycle 42 (CDC42) is a potent therapeutic target for multiple diseases, whereas its function in AKI remains unknown. Here we report that inhibition of CDC42 protects against AKI via orchestrating kruppel-like factor 2 (KLF2)/HIF-1α/PINK1-mediated mitophagy. We showed Cdc42 was not only abundantly expressed in murine renal tubular epithelial cells (RTECs) but also up-regulated in human and murine RTECs post cisplatin exposure, respectively. Then, administration of a CDC42 inhibitor in vivo and in vitro, conditional knockdown of Cdc42 in murine RTECs, and knockout of CDC42 in human RTECs abated cisplatin-caused mitochondrial dysfunction and kidney injury. Furthermore, by integratively using transcriptome sequencing, bioinformatics analysis, dual luciferase reporter assay, and chromatin immunoprecipitation, we found CDC42 inhibition alleviated mitochondrial dysfunction via KLF2/HIF-1α/PINK1-mediated mitophagy, during which CDC42 inhibition enhanced the promoter activity of KLF2, while KLF2 transcriptionally up-regulated HIF-1α, and HIF-1α subsequently transcriptionally up-regulated PINK1, the crucial regulator of mitophagy. Moreover, the function of KLF2 and HIF-1α in CDC42-mediated RTECs damage and mitochondrial dysfunction was verified. In conclusion, we uncovered the role and underlying mechanism of CDC42 in AKI, providing AKI patients with new therapeutic strategies.

overall_design: To elucidate the molecular mechanism underlying the protective effect of CDC42 against AKI, we performed RNA sequencing of CDC42 KO cells and NC cells to discover the potential downstream target gene.


title: 2026_Warmuth_Doetsch_affinity-combined-CAR-T_cell-products_scRNAseq

status: Public on Mar 04 2026

city: Munich

first: Linda

last: Warmuth

address: Trogerstr. 30

country: Germany

institute: Technical University Munich

summary: Adoptive cell therapy with genetically engineered T cells expressing Chimeric Antigen Receptors (CARs) of high binding affinity has proven to be remarkably successful in refractory and relapsed B-cell malignancies. However, its broader clinical potential remains underexploited by the development of side effects due to intense CAR-T cell activation, as well as tumor relapse due to antigen-escape and limited persistence of CAR-T cells during sustained activation via high-affinity receptors. These challenges highlight the critical need for strategies that maximize the safety and efficacy of CAR-T cell therapies. Recent studies suggest that optimal adjustments of the CAR binding affinity to its ligand offers promising opportunities. In this study, we characterized a broad range of CARs with varying affinities for the same target epitope down to physiological TCR-like binding interactions. While CAR affinity had minimal impact on in vitro functionality across a broad range, it strongly correlated with tumor control in vivo, which was significantly compromised for low-affinity binders. On the other hand, CARs with lower affinity induced only mild cytokine release syndrome (CRS) in humanized mouse models. Based on these findings, we implemented an affinity-combination approach to leverage the strong anti-tumor efficacy of high-affinity CARs alongside the enhanced safety profile of lower-affinity CARs. We observed strong synergistic effects in combined products, like lower monocyte-induced cytokine production as compared to high-affinity CAR-T cells alone, while preserving efficacy. High-affinity CARs maintained strong functionality in mixtures with low-affinity CARs going along with strongly reduced signs of exhaustion when applied in combination. In long-term in vitro and in vivo settings, low-affinity CAR-T cells dominated over time proving more resilience to chronic antigen exposure, comparable to physiological T cell responses. Overall, our findings demonstrate that affinity-combination might be an attractive strategy to generate more effective CAR-T cell products with an improved therapeutic index.

overall_design:
RNA sequencing profile of primary human T cells isolated fromn bone marrow of tumor bearing NSGS mice engineered to express JCAR017 or JCAR021 after 30 days, from individual and affinity combined treatment strategies
Please note that Sample 1 and Sample 2 correspond to two separate chips/lanes that were used for the experiment. Each lane was loaded with the extracted sample from seven mice, and both lanes possess data from JCAR017 and JCAR021. The multiplexed samples with corresponding barcodes are annotated in the feature_README.txt   file.

first: Sarah

last: Doetsch

first: Adrian

last: Straub

first: Mateusz

last: Poltorak

first: Elvira

last: D'Ippolito

first: Dirk

last: Busch

first: Sabrina

last: Wagner


title: tRNA-seq profiling of RKO colorectal cancer cells under arginine restriction

city: Pittsburgh

first: Parham

last: Habibzadeh

state: PA

address: 200 Lothrop Street

department: Department of Medicine

institute: University of Pittsburgh Medical Center

type: Non-coding RNA profiling by high throughput sequencing

summary: Here, we investigate how arginine limitation leads to changes in the cell tRNA pool using a YAMAT-seq-adapted protocol, the library was contructed based on illumina truseq small RNAseq library protocol for the adaptors and barcodes

overall_design: 4 biological replicates of arginine-replete (400 uM, "Feed") and 4 of arginine-restricted (12.5 uM) RKO cells treated for 24 hours. Paired-end 150 bp sequencing was subsequently performed on Illumina platform.

first: Qiushuang

last: Wu

first: Sohail

last: Tavazoie

first: Dennis

last: Hsu


title: Neddylation E2 enzyme UBE2F promotes colitis and colon tumorigenesis by targeting the PTPRN-pSTAT5 axis

city: Hangzhou

first: Zhijian

last: Li

address: Kaixuan street number 86

institute: Zhejiang university

summary: The inflammatory bowel diseases (IBDs) and colitis-associated colon cancers are common human diseases. Whether and how neddylation enzyme mechanistically regulates the process of these diseases are largely elusive. Here we report that UBE2F, a neddylation conjugation enzyme, plays a promoting role. UBE2F expression is significantly upregulated in IBDs, and mice with Ube2f deletion in colon epithelial cells are significantly more resistant to DSS-induced colitis and AOM-DSS induced colon tumorigenesis. Mechanistically, Ube2f deletion inactivates Cullin-RING ligase-5 (CRL5) E3, leading to accumulation of protein tyrosine phosphatase receptor type N (PTPRN), a new substrate of CRL5, and a stabilizer of p-STAT5, to promote differentiation of ISCs into secretory lineages for epithelial integrity against colitis, which is abrogated by a STAT5 PROTAC degrader. Ube2f deletion also reduces tumor incidence in the ApcMin/+ mouse model. An inverse correlation between UBE2F and PTPRN levels is found in human colon cancer tissues. Collectively, the UBE2F-CRL5-PTPRN-STAT5 axis plays a key role in colitis and colon tumorigenesis, and UBE2F serves as an attractive therapeutic target for IBD and colon cancer.

overall_design: Transcriptome assembly and annotation protocols were provided by LC Bio-Technology Co., Ltd (Hangzhou, China). Briefly, total RNA was extracted from freshly collected mouse intestinal tissues using TRIzol reagent (15596018, Invitrogen) following the manufacturer’s instructions. All the experiments were conducted in triplicate. mRNA was purified from total RNA using Dynabeads Oligo (dT), and the cleaved RNA fragments were reverse-transcribed to generate cDNA libraries with an average insert size of 300±50 bp. The 2×150 bp paired-end sequencing (PE150) was performed on an Illumina Novaseq™ X Plus platform. And bioinformatic analysis was performed using the OmicStudio tools (https://www.omicstudio.cn/tool).

first: Yi

last: Sun


title: RNA-seq analysis of carbon framework-mediated metabolic reprogramming in senescent cells: effects of C3N nanosheets and photoactivation

first: xuelian

last: wang

address: Ruijin er road No.197

institute: Ruijin hospital

summary: This RNA-seq dataset investigates the senolytic effects of carbon nitride quantum dots (C3N QDs) combined with irradiation on senescent human umbilical vein endothelial cells (HUVECs). The study compares three experimental conditions: senescence alone (S), senescence treated with C3N QDs (S+C), and senescence treated with C3N QDs followed by irradiation (S+C+I). Transcriptomic profiling revealed that the combined treatment (S+C+I) significantly reprogrammed gene expression patterns associated with aging and inflammation. Specifically, the S+C+I group showed a notable upregulation of genes such as MAPT, FOXO4, and PTEN, while markedly downregulating key senescence-associated secretory phenotype (SASP) factors including IL6, CXCL8, SERPINE1, and TERT compared to the S group. These data provide comprehensive insights into the molecular mechanisms by which C3N QDs-mediated photoactivation alleviates cellular senescence and suppresses pro-inflammatory pathways.

overall_design: The study comprises three experimental conditions: 1. S group: Senescent cells (control) 2. S+C group: Senescent cells treated with C3N QDs 3. S+C+I group: Senescent cells treated with C3N QDs followed by irradiation

first: Xuelian

last: Wang

first: Hanyu

last: Ma

first: Zhen


title: Myofibroblast programming blocks differentiation of TLS-organizing fibroblastic reticular cells in pancreatic cancer

city: Columbus

first: Andrew

last: Gunderson

state: OH

address: 460 W. 10th Avenue

department: Department of Surgery

institute: The Ohio State University

summary: Pancreatic ductal adenocarcinoma (PDAC) is considered an immunologically cold cancer type. This perception is due to its rapid progression, strong presence of immunosuppressive cells and lack of response to current immunotherapies. However, we and others have shown that many patient PDAC tumors contain robust lymphocyte infiltration, aggregated in the form of tertiary lymphoid structures (TLS). The presence of TLS in PDAC is prognostic for long-term survival and in other cancer types, predictive of response to immunotherapy. Despite the clinical benefit to generating TLS in tumors, why they form in some PDAC patients but not others, remains unknown. The desmoplastic stroma in PDAC contributes to defective anti-tumor immunity largely due to myofibroblastic cancer associated fibroblasts (myCAF) induced by transforming growth factor-beta (TGF). Other groups have demonstrated that mesenchymal cell phenotypes with lymphoid tissue organizing properties regulate TLS formation in tumors. In order to restore effective anti-tumor immunity for PDAC patients, CAF phenotypes must be reprogrammed to support rather than restrict intratumoral immune activity. Using a lymphotoxin beta receptor (LTBR) agonist we observed induction of TLS-like aggregates in some murine PDAC tumor models, but not others. The CAF phenotypes of TLS-resistant models were predominantly myCAF while the TLS-permissive models were enriched for a VCAM1+ICAM1+ reticular-CAF (rCAF) subset. Induction of myCAF differentiation in vitro with TGF1 silenced LTBR/TNFR mediated upregulation of rCAF chemokine expression and attenuated B and T cell migration towards fibroblasts. Therapeutic TGFR1 inhibition ameliorated these effects thereby allowing LTBR agonism to repolarize rCAF phenotypic programming associated with improved lymphocyte recruitment and T cell-dependent tumor control. In patient PDAC tumors, rCAF resided next to TLS while myCAF were distally located. These data indicate that the myCAF-regulated PDAC stroma antagonizes acquisition of rCAF subsets critical for TLS formation but can be therapeutically remodeled to promote beneficial immune responses in immunosuppressive PDAC tumors.

overall_design:
This is a retrospective analysis of patients who were diagnosed with pancreatic ductal adenocarcinoma cancer (PDAC) and who received surgical resection of their primary tumors. Included individuals were adults of 18years or older and diagnosed with pancreatic ductal adenocarcinoma, preferebly without neoadjuvant therapy. Selected FFPE blocks were sectioned and libraries prepared using a 10x genomics 11mmx11mm FFPE Visium Cytassist Kit. Libraries were sequenced using NovaSeq X Plus or NovaSeq-6000 for 100 cycles. Sequences were further processed using SpaceRanger v2.1.1. Raw and SCTransformed counts are aggregated with H&E image alignment in Seurat (v5) objects, with relevant spot metadata, and saved as .RDS files.

***************************************************************
Raw sequencing files are being deposited in dbGAP accession (phs004521.v1)
***************************************************************

first: Gunderson

last: Andrew

first: Kirschstein

last: Elijah

first: Harder

last: Olivia

first: Krull

last: Jordan

first: Ma

last: Qin


title: Dural scRNA-seq in two organoids derived from malignant ascites of the same gastric cancer patient before (Primary) and after (Resistance) resistant to paclitaxel

first: Guo

last: Leilei

address: 800 Dong Chuan Road

department: Shanghai Center for Systems Biomedicine

institute: Shanghai Jiao Tong University

summary: We have employed a single sequencing(scRNA-seq) approach using 10× Genomics scRNAseq of organoids to study paclitaxel resistance in gastric cancer(GC). Patient-derived organoids (PDOs) can recapitulate majority aspects of tissue where they are derived from, in terms of specific molecular profiles, divergent phenotypes, concerning growth pattern, response to classical chemotherapy. This study represents the dural scRNA-seq in two organoids derived from malignant ascites of the same GC patient before (Primary) and after (Resistance) resistant to paclitaxel.

overall_design: Organoids were established using malignant ascites of the same GC patient before (Primary) and after (Resistance) resistant to paclitaxel.The organoids were digested into single cells and analyzed using scRNA-seq.

first: Leilei

last: Guo

first: Wenshuai

last: Liu


title: SP1 as a Potential Therapeutic Target in Hypoxia-Associated Osteoporosis: Evidence from Multi-Omics [RNA-seq]

city: Chengdu

first: Hao

last: Jiang

state: Sichuan

address: 37 Guoxue Alley, Wuhou District

department: National Clinical Research Center for Geriatrics

institute: West China Hospital, Sichuan University

summary: Primary rat BMSCs were cultured under 1% O₂, and osteogenic/adipogenic differentiation was assessed by ALP activity, staining, immunofluorescence, and qRT-PCR. ATAC-seq and RNA-seq were integrated to characterize hypoxia-induced chromatin and transcriptional changes.

overall_design: Primary rat BMSCs were cultured under 1% O₂ or normal for 7 Days，then ATAC-seq and RNA-seq were integrated to characterize hypoxia-induced chromatin and transcriptional changes

first: Maolin

last: Yuan

first: Ting

last: Qiao

first: Rui

last: Ou

first: Yunhong

last: Wu


title: SP1 as a Potential Therapeutic Target in Hypoxia-Associated Osteoporosis: Evidence from Multi-Omics [ATAC-seq]


title: Female iPSC X-chromosome inactivation (XCI) erosion and its transcriptomic effects during CRISPR gene editing and neural differentiation

city: Evanston

first: Christina

last: Thapa

state: Illinois

address: 1001 University Place

department: Center for Psychiatric Genetics (CPG)

institute: Endeavor Health

summary: Human induced pluripotent stem cells (hiPSC) and iPSC-differentiated neural cells, in combination with CRISPR editing, are commonly used for studying neurodevelopmental and other brain disorders. Female iPSCs undergo random X-chromosome inactivation (XCI) via epigenetic silencing by noncoding X inactive specific transcript (XIST). It is known that female iPSCs may lose XIST expression, leading to XCI erosion that affects both X-linked and autosomal gene expression. However, the effects of CRSIPR editing and neural differentiation on XCI erosion in iPSC-derived neurons and how this may confound a real-world transcriptomic analysis of differentially expressed genes (DEGs) are poorly understood. Here, leveraging bulk RNA-seq of hundreds of CRISPR-edited female iPSC lines from four donor lines for 66 genes and single-cell RNA-seq of iPSC-derived neurons of a subset of 42 edited genes, we investigated the effects of XCI erosion during CRISPR editing and in iPSC-derived neurons. We found that XCI erosion was variable in CRISPR-edited female iPSCs and largely preserved in iPSC-derived neurons. Like in iPSCs, XIST in neurons predominately influenced the expression of X-linked genes; however, its effect on autosomal genes was more pronounced in single neurons. Mechanistically, XIST epigenetically causes allelic imbalance of both X-linked and autosomal genes, with the former showing stronger allele-specific expression (ASE) bias. Notably, XIST-induced ASE bias exhibited a conserved positional pattern at loci affecting neurodevelopmental genes across different female lines and cell types. Finally, we demonstrated a confounding effect of XCI erosion on DEG analyses in iPSC-derived neurons. These results have significant implications in hiPSC modeling of neurodevelopmental and other brain disorders.

overall_design: As part of the SSPsyGene Consortium, our Assay and Data Generation Center (ADGC) for the Model of iPSC-derived Neurons for neurodevelopmental and psychiatric disorders (NPD) (MiNND) aims to generate isogenic hiPSC lines carrying (Loss-of-function) LoF alleles for about 150-200 NPD genes on multiple donor genetic backgrounds. Here, we generated 297 iPSC lines from 6 donor lines (4 females and 2 males) for 66 LoF genes across multiple batches. Transcriptional effect of LoF was assayed using bulk RNA-seq.

first: Jubao

last: Duan

first: Zhiping

last: Pang

first: Hanwen

last: Zhang


title: M2 Macrophage-Derived Exosomes Ameliorate BPD by Inhibiting Ferroptosis via Suppression of the ZAKα-p38 Signaling Pathway

city: Wuxi

first: Yahui

last: Zhou

state: Jiangsu

address: No. 299-1 Qingyang Road, Liangxi District, Wuxi, Jiangsu, China

department: Department of Neonatology

institute: Affiliated Children’s Hospital of Jiangnan University

summary: Background: Bronchopulmonary dysplasia (BPD) is a common lung disease in premature infants. Hyperoxia-induced oxidative stress and ferroptosis are key pathological mech-anisms leading to alveolar epithelial (AT) cell injury and impaired alveolar development. M2 macrophage-derived exosomes (M2-Exo), as intercellular communication carriers, have potential protective effects in regulating oxidative stress-related diseases, but the molecular mechanism by which they exert effects by regulating ferroptosis in BPD re-mains unclear. Objective: To explore the protective effect of M2-Exo on hyperoxia or inflammation-induced BPD models and clarify its antioxidant mechanism. Method: In vitro AT cell injury models and in vivo BPD models were constructed by hyperoxia or LPS induction. M2-Exo were isolated, identified, and used to intervene in models. Oxidative stress and ferroptosis-related indicators (ROS, MDA, iron accumulation, GPX4), AT cell functional markers (AQP5, SPC), and ZAKα-p38 pathway activation contents were de-tected. ZAKα overexpression was used to verify pathway dependence. Results: M2-Exo intervention significantly enhanced AT cell viability, upregulated the expression of AQP5 and SPC, and reversed alveolar simplification. Concurrently, it effectively sup-pressed hyperoxia or LPS-induced oxidative stress and ferroptosis, as evidenced by re-duced contents of ROS and MDA, diminished iron accumulation, and GPX4 expression. Mechanistically, M2-Exo significantly inhibited the activation of the ZAKα-p38 pathway, and ZAKα overexpression could antagonize the antioxidant, anti-ferroptotic, and AT cell protective effects of M2-Exo. Conclusions: M2-Exo alleviate AT cell oxidative stress and ferroptosis by inhibiting the ZAKα-p38 pathway, thereby improving hyperoxia or in-flammation-induced BPD and providing a new strategy and molecular target for the antioxidant treatment of BPD.

overall_design: The experiment was carried out as follows: LPS-induced BPD model: Neonatal rats were randomly assigned to three groups: Con: Rats were raised in room air (21% O2) for seven days. LPS: Rats received daily intraperitoneal injections of LPS (500 μg/kg, 50 μL) under ambient air conditions. LPS + M2-Exo: Rats were treated with LPS (500 μg/kg) + M2-Exo (50 μg/kg) in a total volume of 50 μL daily. Hyperoxia-induced BPD model: Neonatal rats were randomly assigned to the following groups: Con: Rats were raised in room air (21% O2) for seven days. Hyperoxia (Hyp): Rats were exposed to 85% O2 in alternating cycles of 12 h hyperoxia and 12 h normoxia (21% O2). Hyp + M2-Exo: Rats received daily intra-peritoneal injections of M2-Exo (50 μg/kg, 50 μL) during exposure to hyperoxia. At the end of the experiment, rats were euthanized by cervical dislocation.

first: Yahan

last: Pu

first: Mingyue

last: Lv

first: Ru

last: Yan

first: Honglian

first: Lihui

last: Yu

first: Weilai

last: Jin

first: Le

first: Zhiwei


title: Epigenetic Activation of SIRT6 Protects the Aging Intervertebral Disc [scRNA-Seq]

city: Philadelphia

first: Makarand

middle: V

last: Risbud

address: 1025 Walnut St.

institute: Thomas Jefferson University

summary: Aging is one of the important risk factors for Intervertebral disc degeneration, a major contributor to chronic low back and neck pain. Our recent work has demonstrated a promising role for SIRT6, a nuclear NAD⁺- dependent deacetylase and defatty acylase, in maintaining intervertebral disc health with aging. We therefore investigated whether SIRT6 activation improves outcomes of disc health by studying the spinal phenotype of 24-month-old mice treated with a well-studied agonist, MDL-800, for 6 months. Histological studies revealed healthy disc tissue morphology, enhanced cell viability, and lower degeneration scores in mice treated with MDL-800. Further mechanistic insights revealed that SIRT6 activation decreased H3K9ac levels, improved cell phenotype and matrix quality, and reduced the SASP burden in the disc, characterized by decreased abundance of p21, IL-6 and TGF-b. Tissue RNA-Seq, in vitro measurements of histone 3 modifications, and multi-omics ATAC-seq/RNA-seq analyses revealed that SIRT6 activation altered the epigenetic status (decreased H3K9ac, H3K36me3, and H3K79me2) and transcriptomic landscape of disc cells. Notably, MDL-800 treatment increased LC3II levels, indicating enhanced autophagic flux in nucleus pulposus cells. Furthermore, plasma LC-MS and NMR analyses revealed minimal systemic metabolic changes. ScRNA sequencing of splenocytes and bone marrow cells showed a decrease in the proportions of B cells, T cells, and granulocytes, without an altered systemic cytokine profile, indicating good tolerance and the absence of systemic inflammation following MDL-800 treatment. Our study demonstrates that SIRT6 activation modulates autophagy and cell senescence in the disc, underscoring the feasibility of targeting SIRT6 activation as a promising pharmacological strategy to maintain disc health in the aging spine.

overall_design: Spleen and Bone marrow cells were isolated from 24 month old BL/6 mice using standard cells isolation protocols. Single cell RNA seq was performed using 10x genomics platform. Samples were multiplexed.

first: Pranay

last: Ramteke

first: Olivia

last: Ottone


title: Epigenetic Activation of SIRT6 Protects the Aging Intervertebral Disc

overall_design: Nucleus pulposus and annulus firosus cells were isolated from 24 month old BL6 mice intervertebral discs tissues via standard isolation protocol and RNA-seq was performed


title: Vasculogenic Tissue Nano-Transfection Enhances Functional Recovery Following Nerve Reconstruction Surgery in a Mouse Model of Segmental Nerve Defect - Sciatic nerve tissue

first: Ana

middle: Isabel

last: Salazar Puerta

address: 140 W 19th Ave Building 151

summary: Peripheral nerve injuries (PNI) often result in persistent sensory, motor, and functional deficits, even after surgical reconstruction. While gene and cell therapies offer promise for enhancing regenerative outcomes, effective and targeted delivery remains a significant challenge. Here, we explored vasculogenic Tissue Nano-Transfection (TNT) as a novel, non-viral, reprogramming-based cell therapy to improve outcomes following graft reconstruction surgery. TNT aims to improve nerve regeneration by inducing vasculogenic reprogramming and promoting neovascularization to support axonal growth. Through a combination of in vitro screening and in vivo testing in a nerve crush model, we identified an optimal formulation of the vasculogenic genes, Etv2, Fli1, and Foxc2 (EFF), for enhancing reprogramming and axonal repair. TNT-based deployment EFF in a long segmental nerve defect reconstructed with isografts resulted in significant improvements in functional recovery, including grip strength and muscle contractility. Histological analyses demonstrated increased vascular density and myelinated axon counts. These findings support the therapeutic potential of TNT-mediated vasculogenic reprogramming as an adjunct to surgical repair of complex PNI offering a promising strategy to improve nerve regeneration and functional outcomes.

overall_design: RNAseq profiling of Sciatic nerve tissue. Mice were subjected to crush injury followed by electrotransfected with TFs Etv2, Fli1, Foxc2 (111 and 112 ratios) using TNT. Sciatic nerve tissue was collected 7 days post-transfection, compared to sham-transfected tissue and healthy tissue.

middle: I

last: Salazar-Puerta

first: Sara

last: Kheirkhah

first: Jonathan

middle: P

last: Stranan

first: Hallie

last: Harris

first: Nada

last: Khattab

first: Megumi

last: Fukuda

first: Grant

last: Barringer

first: Carlos

middle: A

last: Vasquez-Martinez

first: Samuel

last: Cortes

first: Neil

last: Ott

first: William

middle: R

last: Lawrence

first: Devleena

last: Das

first: Jordan

middle: T

last: Moore

first: Tiam

middle: M

last: Saffari

first: Juan

middle: D

last: Salazar-Gil

first: Diego

last: Alzate-Correa

first: Junyan

first: Kavya

last: Dathathreya

first: Natalia

last: Higuita-Castro

first: Tatiana

middle: Z

last: Cuellar-Gaviria

last: Arnold

first: Amy

first: Daniel

last: Gallego Perez


title: A Comprehensive Adenoid Cystic Carcinomas-Derived Organoid Platform for Disease Modeling and Drug Screening Captures Interpatient Heterogeneity

city: Beijing

first: Zhigang

last: Cai

address: No.22 Zhongguancun South Avenue, Haidian Disrict

institute: Peking University

summary: Salivary adenoid cystic carcinoma (ACC) is a highly aggressive salivary gland malig-nancy characterized by infiltrative growth patterns that hinder complete resection. Lacking effective chemotherapy, recurrent or metastatic ACC remains clinically incur-able. This research aimed to develop an efficient culture system for ACC organoids, which can preserve tumor heterogeneity and establish a reliable drug screening plat-form. Under our optimized culture conditions, ACC organoids grew rapidly and suc-cessfully recapitulated three characteristic histopathological patterns. Whole-genome sequencing (WGS) further confirmed they mirrored the genomic features of their pa-rental tumors, including significantly mutated genes, non-coding regulatory region mutations, copy number variation, and minor allele frequency. RNA sequencing con-firmed ACC organoids recapitulated the MYB-NFIB fusion gene. At the protein level, these organoids contained multiple cellular components, including epithelial cells, mesenchymal cells, K7+ duct cells, a-SMA+ myoepithelial cells, K5+ basement mem-brane cells, and CD44+ tumor stem cells, with proper spatial distribution patterns. With an 88% success rate, the first ACC organoids platform, incorporating normal sal-ivary gland (SG) organoids as toxicity controls, enabled high-throughput drug testing within two weeks. In conclusion, we develop an efficient culture system for ACC or-ganoids that can preserve tumor heterogeneity and establish a reliable drug screening platform for mechanistic studies and personalized precision therapy research.

overall_design: Fresh tumor and adjacent normal salivary gland (SMG) tissues were obtained from ACC patients undergoing surgical resection. One portion was used to establish organoids, while the other was used for RNA-seq to verify the transcriptional similarity between the organoids and their parental tissues.

first: Yingyue

last: Chai

first: Yi

last: Sui

first: Xinyuan

last: Zhang

first: Shang

last: Xie

first: Xiaofeng

last: Shan

first: Yanrui

last: Feng

first: Yifan

last: Kang


title: Metastasis-associated wound repair promotes reciprocal lung epithelium activation and breast cancer metastatic outgrowth

city: Aurora

first: Jessica

last: Christenson

state: CO

department: Pathology

institute: University of Colorado Anschutz Medical Campus

summary: When tumor cells colonize distant organs during metastasis, they interact extensively with surrounding cells. These interactions often change the behavior of surrounding cell populations which collectively induce a pro-tumor microenvironment that permits tumor cell outgrowth into overt, clinically detectable metastatic disease. The lung is one of the most common sites of breast cancer (BC) metastasis. A chronic wound repair-related phenotype developed within the lung microenvironment during metastatic outgrowth in immunocompetent preclinical mouse models of BC. This phenotype was characterized by an increased number and activation of lung type II alveolar epithelial (AT2) cells surrounding growing metastases. Metastatic outgrowth significantly changed AT2 gene expression, resulting in a modified secretome. AT2-derived secreted factors also promote triple-negative breast cancer (TNBC) growth. AT2 secreted factors are regulated by the cyclic adenosine monophosphate (cAMP) response element-binding protein (CREB). Targeting CREB signaling with the phosphodiesterase 4 (PDE4) inhibitor roflumilast reduced AT2-BC reciprocal interactions in vitro and metastatic outgrowth in vivo. Finally, AT2 cells adjacent to metastases in lungs from patients with metastatic BC express higher PDE4B compared to AT2 cells in normal lungs.  Alveolar epithelial cells are the most common cell type in the lung. Our studies demonstrate the potential for targeting metastasis-associated wound repair and lung epithelial cell activation during metastatic outgrowth with FDA-approved PDE4 inhibitors. This strategy may be an effective way to treat and manage progression of established metastatic BC within the lung.

overall_design: To study the latter stages of lung metastasis, such as metastatic outgrowth, 5x105 Met-1 mouse mammary carcinoma cells in 100µL 1X PBS were intravenously (IV) injected into the tail veins of 10-week-old female FVB/NJ mice (The Jackson Laboratory, No. 001800, RRID:IMSR_JAX:001800). Alternatively, 3x105 66Cl4 mouse mammary carcinoma cells in 100uL 1X PBS were IV injected into the tail veins of 10-week-old female BALB/cJ mice (The Jackson Laboratory, No. 000651, RRID:IMSR_JAX:001026). To examine how the metastatic microenvironment is altered during outgrowth, lungs with a low versus high metastatic burden were compared. Lungs were collected 1 week following IV injection as a model for low metastatic burden and 3 weeks post-injection as a model for high metastatic burden.

middle: L

first: Nicole

middle: S

last: Spoelstra

first: Michelle

last: Williams

first: Linda

last: Logan

first: Kathleen

last: O'Neill

first: David

last: Orlicky

first: Nolan

last: Baker

first: Jennifer

last: Wagner

first: Alyse

middle: W

last: Staley

first: Adrie

last: van Bokhoven

first: Andrew

last: Goodspeed

first: Li Wei

last: Kuo

first: Lyndsey

last: Crump

last: Diamond

middle: K

last: Richer


title: House dust mite extract primes Drosophila melanogaster host defense against microbial infections through two distinct mechanisms

city: Guangzhou

first: Rui

last: Xu

address: No. 1023-1063 Shatai South Road

institute: Southern Medical University

summary: Allergen immunotherapy directly addresses the biological cause of allergies like those causing asthma. For perennial allergies, the treatment involves exposure to house dust mite (HDM) extracts that aim to block T helper 2 responses. Here, we investigate whether exposure to HDM extracts affects other aspects of innate host defenses against infection using the Drosophila genetic model organism. We find that pre-treatment of flies with HDM extract injection provides a degree of protection against several types of microbial infections, namely Gram-negative and Gram-positive bacterial infections as well as fungal infections. Interestingly, this protection appears to be achieved through distinct mechanisms. The priming afforded by HDM extracts against Gram-negative bacteria is mediated via a mild induction of the Immune deficiency pathway. In contrast, the protection against a Gram-positive bacterium, Staphylococcus aureus, and some Aspergillus fumigatus mycotoxins may involve the induction of host anti-oxidant defenses. We conclude that HDM extract appears to stimulate distinct host defenses that are differentially relevant according to the nature of the subsequent immune challenge. Future studies on the role of the host anti-oxidant responses in the Drosophila model will reveal how the host is able to cope with deleterious reactive oxygen species that may be generated during infections.

overall_design: RNA-seq profiling of wild-type Drosophila melanogaster after HDM extract injection and its vehicle control.

first: Yingyi

last: Pan

first: Zihang

last: Yuan

first: Wang

last: Liao

first: Xiao

last: Yu

first: Dominique

last: Ferrandon

first: Jun

last: Bai


title: Effects of High Flow Velocity Stress on Energy Metabolism and Transcription Level of Triplophysa orientalis

city: WUxi

first: Xin

last: Gao

institute: Nanjing Agricultural University

summary: This study aims to investigate flow velocity-regulated genes associated with oxidative stress and energy metabolism.

overall_design: A total of 640 healthy T. orientalis of comparable body size (0.4 ± 0.1 g; 3.5 ± 0.7 cm) (Figure 1C) were randomly assigned to 24 annular raceway system (20 fish per system). The total sample size of 640 fish corresponds to the full design of eight flow-velocity treatments with four system-level replicates per treatment and 20 fish per system (8 × 4 × 20), and because only 24 systems were available, the 32 system replicates were completed in sequential experimental blocks. Based on shi et al, who reported that 1-3 body lengths per second (BL/s) is a commonly suitable flow range for Triplophysa [43], eight flow treatments were established to examine flow effects: 3, 6, 9, 15, 21, 27, 33 and 39 BL/s. Each treatment included four system-level replicates and the trial lasted 3 days. Throughout the experiment, water quality and feeding regimes in all system were maintained consistent with those during acclimation. For downstream molecular analyses, skeletal muscle was sampled from individual fish without pooling, with five individuals from the 3 BL/s group and four individuals from the 33 BL/s group used for RNA-seq, and the same biological replicates and RNA samples used for qPCR validation. During the experiment, we observed the behavioural states of T. orientalis across all flow rate treatment groups. At 3 and 6 BL/s, the fish predominantly maintained a staction holding posture; at 9, 15 and 21 BL/s, they frequently adopted a sculling posture; while at 27 and 33 BL/s, the fish sustained an upstream swimming posture. However, when flow velocity reached 39 BL/s, T. orientalis could no longer sustain upstream swimming and exhibited signs of exhaustion (Figure 1D). After 3 days, all T. orientalis were netted and anesthetized with tricaine methanesulfonate (MS-222; Sigma-Aldrich) at 100 mg/L. Skeletal muscle was dissected, Each RNA-seq and qPCR sample represents skeletal muscle from a single individual fish; libraries and qPCR reactions were prepared independently for each individual, so A_1–A_5 and G_1–G_4 are true biological replicates rather than technical replicates. The annular raceway system was the experimental unit for velocity exposure, and for molecular sampling we selected fish across independent system-level replicates, with no more than one fish taken from any single system to avoid pseudoreplication. snap-frozen in liquid nitrogen, and stored at −80 °C until analysis. Although eight flow treatments were established and all groups were assessed under the same experimental conditions, we focused the transcriptomic comparison on 3 BL/s and 33 BL/s because they represent a suitable velocity and a high, yet sustainable strong-current endpoint over 3 days; 39 BL/s induced clear exhaustion and was therefore not used for transcriptomic profiling. This endpoint selection maximizes contrast for detecting flow-responsive pathways while remaining biologically and ethically appropriate.

first: Hui

last: Wan

first: Yuxuan

last: Jiang

first: Liping

last: Qiu

first: Zhongquan

first: Shunlong

last: Meng

first: Chao

last: Song


title: Profiling the transient gastrulation inducing property of amnion-like cells.

city: Cincinnati

first: Aryeh

last: Warmflash

state: Ohio

address: 3333 Burnet Avenue

department: Developmental Biology

institute: Cincinnati Children's Hospital

summary: Studies in the mouse have established that communication between the trophectoderm and the epiblast is crucial for initiating gastrulation. In the primate embryo, the amnion rather than the trophectoderm is directly juxtaposed to the epiblast and may play this role. To model the interactions between the amnion and epiblast, we differentiated human pluripotent stem cells (hPSCs) to amnion-like cells (AMLCs) and juxtaposed them in a controlled manner with undifferentiated hPSCs, which represent the epiblast. We found that juxtaposition between these cell types is sufficient to initiate a range of cell behaviors associated with gastrulation including organized differentiation to primitive streak and downstream mesendodermal cell fates and directed cell migration out of the primitive streak region. Performing knockout experiments specifically in either the epiblast or amnion compartment revealed intricate crosstalk that is required to properly initiate gastrulation. In particularly, using knockouts of NODAL we show that Nodal signaling in both the amnion and epiblast is required for gastrulation patterning. Finally, we show that inductive ability is a transient property acquired during amnion differentiation, and that cells that differentiate from this inductive state acquire an extraembryonic mesenchyme identity. This study establishes a system to study epiblast-amnion communication and shows that this communication is sufficient to initiate gastrulation in the epiblast.

overall_design:
RNAseq profiling of ESI017 human emrbyonic stem cells undergo AMLC treatment (BMP4 50ng/ml, SB431542 10 µM) for 2 days and 4 days. An experiment investigating Wnt activation dynamic is run in parallel with the experiment mentioned above. Wnt3a and Chir treated. ESI017 is collected 18 hours or 6 hours after the treatment. Reanalysis of control GSM7834978 from GSE245027 was performed for this study.

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The table below lists GEO accessions reused/reanalyzed for this study.
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first: Xiangyu

last: Kong

first: Siqi

last: Du


title: Mechanisms of the antiproliferative effects of SIRT6 inhibition in melanoma: A multi-omics analysis [RNA-Seq A375]

city: Madison

first: Karla

middle: Beatriz

last: Anaya Aldrete

state: Wisconsin

address: 1111 highland ave. WIMR2 room 7418

department: Dermatology

institute: University of Wisconsin Madison

summary: Melanoma is one of the deadliest types of skin cancer due to its ability to metastasize if not treated early. While targeted- and immune- therapies have significantly improved melanoma treatment outcomes, acquired drug resistance even with combined therapeutics remain prevalent. SIRT6 is a nuclear histone deacetylase that regulates DNA repair, metabolism, and chromatin remodeling. It is overexpressed in melanoma and its inhibition in melanoma is known to have anti-proliferative response, and alterations in pathways related to cell cycle, senescence, and metastasis.In this study we utilized RNA sequencing, proteomics, and Ingenuity Pathway Analysis on genetically modified human melanoma cells to determine the downstream mechanism of SIRT6 in melanoma.

overall_design: Total RNA (biological triplicates) from A375 melanoma cells was isolated using an RNeasy plus Mini Kit (QIAGEN,CA) from SIRT6 KD and control groups. RNA was submitted to Novogene for quality control, library preparation and bulk RNA sequencing.

middle: B

first: Durdana

last: Muntaqua

first: Liz

last: Garcia-Peterson

first: Mary

last: Ndiaye

first: Jeong

middle: H

last: Nam

first: Nihal

last: Ahmad


title: Synthetic lethality between RB-loss and E2F3 inhibition in small cell cancers targeted by pyrimidine synthesis blockade

city: Los Angeles

first: Evan

middle: Robert

last: Abt

state: CA

address: 650 Charles E. Young Drive, South

department: Molecular and Medical Pharmacology

institute: University of California Los Angeles

summary: Small cell carcinoma, often found with neuroendocrine features, is a lethal cancer variant, as seen for small cell lung cancer and treatment-resistant late-stage small cell neuroendocrine prostate cancer (SCPC). A genome-wide CRISPR dependency screen using SCPC models generated through human prostate cell transformation identifies a requirement for the transcription factor E2F3 in this cancer subtype. E2F3 dependency is linked to RB inactivation, an event that occurs nearly universally across small cell cancers. The requirement for E2F3 is shared by RB-deficient cells originating from the prostate, lung and adnexa (ovary and fallopian tube). In RB-deficient cancer cells, E2F3 inhibition restrains cell cycle progression, proliferation, and tumor growth in vivo. Inhibition of de novo pyrimidine synthesis limits E2F3 expression and suppresses small cell cancer proliferation in culture. Directly or indirectly targeting E2F3 to leverage a pan-cancer synthetic lethality resulting from RB inactivation represents a potential treatment strategy.

overall_design: Comparative sgRNA abundance profiling analysis of pooled CRISPR–Cas9 screening data in three PARCB cell lines transduced with the GeCKO sgRNA library, assessing sgRNA enrichment and depletion after 2 weeks of culture.

first: Owen

middle: N

last: Witte

first: Thomas

middle: G

last: Graeber

first: Jack

last: Freeland

first: Liang

last: Wang


title: Vasculogenic Tissue Nano-Transfection Enhances Functional Recovery Following Nerve Reconstruction Surgery in a Mouse Model of Segmental Nerve Defect.

first: Ana

middle: Isabel

last: Salazar Puerta

overall_design: RNAseq profiling of sciatic nerve tissue electrotransfected with TFs Etv2, Fli1, Foxc2 using TNT. A segmental nerve isograft was transected into the nerve gap of mice following TNT. Sciatic nerve tissue was collected 13 weeks post-transfection and grafting, compared to sham-transfected nerve, healthy nerve and cut and no repair nerves as a negative control.

middle: I

last: Salazar-Puerta

first: Sara

last: Kheirkhah

first: Jonathan

middle: P

last: Stranan

first: Hallie

last: Harris

first: Nada

last: Khattab

first: Megumi

last: Fukuda

first: Grant

last: Barringer

first: Carlos

last: Vasquez-Martinez

first: Samuel

last: Cortes

first: Neil

last: Ott

first: William

last: Lawrence

first: Devleena

last: Das

first: Jordan

last: Moore

first: Tiam

last: Saffari

first: Juan

last: Salazar-Gil

first: Diego

last: Alzate-Correa

first: Junyan

last: Yu

first: Kavya

last: Dathathreya

first: Natalia

last: Higuita-Castro

first: Tatiana

last: Cuellar-Gaviria

last: Arnold

first: Amy

first: Daniel

last: Gallego Perez


title: TGF beta mediates crosstalk between CD8 Positive T cells and CD39 Positive induced Treg cells in autoimmune inflammation

first: ye

last: chen

state: Guangdong

address: Tianhe Center, Tianhe District

institute: sun yat-sen university

summary: Autoimmune inflammation results from dysregulated immune responses, in which dysfunction of regulatory T cells (Tregs) is recognized as a key contributing factor due to their essential role in maintaining immune homeostasis and preventing autoimmunity. The stability and functionality of Tregs are heavily influenced by their immune microenvironment, including inflammatory and tumor contexts. Tregs comprise diverse subsets, but the distinctions and interactions among these populations remain poorly understood. Although CD8+ T cells have been implicated in autoimmune disease pathogenesis, their interactions with CD4+ Foxp3+ Tregs and the underlying regulatory mechanisms are not well characterized. In this study, we identified CD8+ T cells as crucial enhancers of CD4+ induced Treg (iTreg) differentiation, function, and stability. CD8+ T cells markedly upregulated the expression of CD39, Helios, CTLA-4, and CD103 in iTregs, enhancing their immunosuppressive capacity. In a naive CD4+ T cell transfer colitis model, co-transfer of naive CD8+ T cells ameliorated colitis by boosting iTreg-mediated suppression of Th1 and Th17 responses. Mechanistically, we found that CD8+ T cells regulate iTreg phenotypes through a ROS/TGF-beta signaling axis, with IRF4 in CD8+ T cells playing a central role. Furthermore, CD8+ T cell-primed iTregs exhibited superior therapeutic efficacy in an autoimmune arthritis model by suppressing Th1/Th17 responses and preserving endogenous Treg populations. These findings reveal a novel role for CD8+ T cells in supporting iTreg-mediated immune regulation and suggest a promising approach for enhancing Treg-based therapies in autoimmune diseases.

overall_design: RNA-seq was performed on flow-sorted CD4⁺Foxp3⁺ iTregs generated either from CD4⁺ T cells cultured alone or co-cultured with CD8⁺ T cells during iTreg differentiation.

first: Chen

last: Ye

first: Zheng

last: Songguo


title: The Role of EGL-6 Expression in FLP-17 Mediated Signaling

city: Bethesda

first: Ashley

last: Frakes

state: MD

address: 9000 Rockville Pike, 10N219

department: NIDDK, Genetics & Biochemistry Branch

institute: National Institutes of Health

summary: Our work seeks to understand the role of neuropeptide signaling in the regulation of metabolism and cellular stress. The goal of this sequencing experiment was to determine how loss of function of the GPCR EGL-6 changes transcriptional profiles in adult C. elegans in the context of overexpression of the neuropeptide FLP-17.

overall_design: 500-600 animals were isolated per sample and 5 sample replicates were taken per genotype. Five strains were included for comparison: AEF243 (flp-17 (n4894)IV), AEF236 (egl-6 (n4537)X), AEF148 (flp-17oe; SSR1463 6x), AEF237 (egl-6 (n4537)X;SSR1463 6x), and N2 (background control). All experimental strains were outcrossed 6x into N2 before the start of the experiment.

first: Carrie

last: Sheeler


title: Mechanisms of the antiproliferative effects of SIRT6 inhibition in melanoma: A multi-omics analysis

first: Karla

last: Anaya Aldrete

overall_design: Total RNA (biological triplicates) from G361 melanoma cells was isolated using an RNeasy plus Mini Kit (QIAGEN,CA) from SIRT6 KD and control groups. RNA was submitted to Novogene for quality control, library preparation and bulk RNA sequencing.

first: Durdana

last: Muntaqua

first: Liz

last: Garcia-Peterson

first: Mary

middle: A

last: Ndiaye

first: Jeong

last: Nam

first: Nihal

last: Ahmad


title: Upregulation of the lncRNA MEG3 in Metastatic Hepatoblastoma

city: Birmingham

first: Morgan

middle: Louise

last: Brown

state: Alabama

address: 1670 University Blvd.

institute: University of Alabama at Birmingham

summary: Hepatoblastoma is the most common primary liver malignancy in children, and outcomes remain poor for patients with metastatic disease. Long non-coding RNAs (lncRNAs) regulate tumor behavior, but their role in metastatic hepatoblastoma is not well defined. This study investigated the expression and functional significance of the lncRNA, maternally expressed gene 3 (MEG3), in a metastatic model of hepatoblastoma. RNA sequencing compared the metastatic hepatoblastoma cell line HLM_2 with its parental HuH6 cell line to identify differentially expressed lncRNAs. MEG3 expression was examined using hepatoblastoma patient datasets and validated using qPCR in cell lines, orthotopic tumors, and COA67 patient-derived xenografts. Functional effects of MEG3 knockdown in HLM_2 cells were evaluated with siRNA to evaluate clonogenicity, tumorsphere formation, migration, and invasion. The effects of MEG3 overexpression on clonogenicity, migration, and invasion were assessed in HuH6 cells. MEG3 was significantly upregulated in metastatic cells and orthotopic tumors compared with controls. MEG3 silencing reduced clonogenicity, tumorsphere formation, migration, and invasion. MEG3 overexpression increased clonogenicity, migration, and invasion. These findings indicate that MEG3 is upregulated in metastatic hepatoblastoma and may contribute to aggressive tumor phenotype, warranting further examination of the mechanistic role of MEG3 in hepatoblastoma, and its relevance as a biomarker or therapeutic target.

overall_design: Total cellular RNA from parent HuH6 hepatoblastoma cells and the metastatic HLM_2 hepatoblastoma cells was extracted using the miRNeasy kit using the manufacturer's protocol. RNA seq was utilized to compare the cell lines.

first: Maryam

last: Shaikh

first: Nazia

last: Nazam

first: Ali

middle: M

last: Eakes

first: Pranava

last: Nande

first: Abdulraheem

last: Kaimari

first: Joel

middle: C

last: Opara

first: Jamie

last: Aye

first: Karina

middle: J

last: Yoon

first: Elizabeth

last: Beierle


title: Diagnostic performance comparison of SE-SPTM-PCR and miRNA deep sequencing using 2-fold gradient dilutions of simulated HCMV viral infection samples

city: Xiamen

first: Weida

last: Huang

state: Fujian

address: Xiangshan Street

department: School of Public Health

institute: Xiamen University

summary: MicroRNAs are promising liquid biopsy biomarkers, but their clinical translation is hindered by detection challenges, including low abundance, high sequence similarity, and background interference. We developed SE-SPTM-PCR, a detection platform integrating selective miRNA enrichment using locked nucleic acid probes with specific probe terminal-mediated RT-qPCR. To evaluate the ability of the SE-SPTM-PCR platform to discriminate samples with only slight differences in load, we tested simulated specimens with two-fold serial dilutions using both SE-SPTM-PCR and miRNA sequencing. These simulated specimens were prepared by spiking HCMV viral culture supernatant (propagated in MRC5 cells) into plasma samples obtained from three groups of age- and sex-matched healthy donors (n=10 per group). The results demonstrated that the diagnostic performance of the SE-SPTM-PCR platform significantly outperformed that of miRNA sequencing.

overall_design: Simulated specimens were prepared in three groups (n=10 per group) at volume ratios of plasma to HCMV supernatant to PBS of 90:10:0, 90:5:5, and 90:2.5:7.5, respectively.Nucleic acid extraction was performed from 600 μL of each simulated specimen using the miRNeasy Serum/Plasma Kit (Qiagen). Small RNA libraries were constructed using the VAHTS Small RNA Library Prep Kit for Illumina V2 (Vazyme).

first: Zecheng

last: Zhong

first: Shiyin

last: Zhang


title: Regulation of Downstream Processing by Different Expression Levels of FLP-17

first: Ashley

last: Frakes

summary: Our work seeks to understand the role of neuropeptide signaling in the regulation of metabolism and cellular stress. The primary goal of this sequencing experiment was to determine how whole animal expression of FLP-17 changes in the context of different extrachromasomal arrays and how this corresponds to hsp-4p::gfp reporter expression. As a secondary goal, we sought to determine how increasing FLP-17 expression modulates downstream transcriptional pathways.

overall_design: 200-500 animals were isolated per sample and 5-6 sample replicates were taken per genotype. Five strains were included for comparison: AEF276 (flp-17(n4894)IV; zcls4[hsp-4p::GFP]V), AEF231 (zcls4[hsp-4p::GFP]V), AEF378 (ashEx67[gcy-31p::flp-17::GFP; coel::RFP]; zcls4[hsp-4p::GFP]V), AEF373 (zcls4[hsp-4p::GFP]V; Ex[flp17p::FLP-17::flp-17 3’UTR + unc-122p::mCherry]), and AEF149 (ssrEx1193[flp-17p::flp-17::GFP, myo-3p:mCherry]; zcls4[hsp-4p::GFP]V). AEF231 is a 6x outcross of SJ4005 into an N2 background. AEF276, AEF373, and AEF378 are within the AEF231 background. AEF149 is in the SJ4005 background.

first: Carrie

last: Sheeler


title: Decoding transcriptional, metabolic and cell death signatures in osteoarthritis and endemic osteoarthritis at single-cell resolution

city: Xi'an

first: Xuzhao

last: Bian

state: Shaan'xi

address: No.28 Xianning West Road

institute: xi'an jiaotong university

summary: The molecular differences between osteoarthritis (OA) and endemic OA (Kashin-Beck disease, KBD), have been investigated at bulk-level, inherently masking cellular heterogeneity and critical discriminative markers.We conducted single-cell RNA sequencing (scRNA-seq) on a total of 139,943 chondrocytes isolated from 17 human cartilage samples, including 3 healthy controls, 8 patients with OA, and 6 patients with KBD. Chondrocyte populations were identified and compared. Differentially expressed gene, functional enrichment, metabolic activity, and cell death signature analyses were performed, with validation by immunohistochemistry staining and quantitative real-time PCR. We found that the preHTC, FC, preInfC, and InfC populations were enriched in OA, whereas ProC and HomC populations predominated in KBD. The HTC population, located in the deep cartilage zone, showed no major differences between the two diseases. Although cell population–specific functions were largely conserved across 11 chondrocyte subtypes, disease-specific transcriptional signatures were evident. OA cartilage displayed upregulation of extracellular matrix (ECM) remodeling and immune activation pathways, particularly within preInfC and InfC populations. In contrast, KBD chondrocytes exhibited marked activation of endoplasmic reticulum (ER) stress and oxidative stress responses, especially in ProC-2, ProC-3, and HomC-2 populations. Ferroptosis activity was significantly higher in KBD cartilage compared with OA and controls, with the strongest enrichment observed in ProC and HomC populations. These findings deepen our understanding of chondrocyte heterogeneity and highlight the InfC population in OA, as well as ProC and HomC populations in KBD, as potential target cell populations for therapeutic intervention.

overall_design: Six cartilage samples were collected from patients with Kashin-Beck diseases.

first: Yue

last: Fan

first: Di

first: Yan

last: Wen

first: Shiqiang

last: Cheng

first: Xuena

last: Yang

first: Dalong

last: Gao

first: Mikko

last: Lammi

first: Feng

first: Xiong

last: Guo

first: Shiquan

last: Sun


title: Temporal dynamics and functional annotation of transcriptome rhythmicity in HEK293T cells

city: Suzhou

first: Tao

address: No.28 Kehua Road

institute: Suzhou Vocational Health College

summary: HEK293T cells are a widely used experimental model in cell biology. However, the presence and robustness of intrinsic circadian rhythmicity in HEK293T cells remain controversial. To address this issue, we synchronized HEK293T cells with dexamethasone and initiated sample collection 24 hours after synchronization. Cells were harvested every 4 hours over a 48-hour period, followed by transcriptomic (RNA-seq) analysis.

first: Songbai

last: Liu

first: Fei

last: Ge

first: Yuling

first: Ying

last: Zhao


title: Lupus-Associated Immune Complexes Induce Shared Proinflammatory Transcriptional Programs in Human Monocytes

first: Minhyung

last: Kim

address: 8700 Beverly Blvd

department: Urology

institute: Cedars-Sinai Medical Center

summary: Lupus-associated immune complexes (ICs) activate monocytes and contribute to disease pathogenesis. Here, we performed microarray analysis of monocytes stimulated with dsDNA ICs, Ro60/anti-Ro60 (Ro) ICs, or snRNP ICs to characterize IC-induced transcriptional responses. All three IC types induced overlapping sets of differentially expressed genes compared with unstimulated monocytes. Pathway enrichment analysis of upregulated genes revealed common activation of immune-related pathways, including NOD-like receptor, NF-κB, TNF, and Toll-like receptor signaling pathways. These results indicate that distinct lupus-associated ICs trigger shared inflammatory programs in monocytes, supporting a common mechanism of IC-driven innate immune activation.

overall_design: Untouched CD14⁺CD16⁻ monocytes freshly isolated from the peripheral blood of healthy adult donors (N = 6) were incubated for 2 hours either unstimulated or stimulated with lupus-associated immune complexes (ICs).

first: Insoo

last: Kang

first: Min Sun

last: Shin

first: Sungyong

last: You


title: Endophytic Beauveria bassiana Blastospores Enhance Susceptibility of Ostrinia furnacalis to Chlorantraniliprole via Regulation of ABCC4 and HSP70

city: Changchun

first: Xiaohui

last: Dong

address: No. 1363, Shengtai Street, Jingyue High-tech Industrial Development Zone

department: Institute of Plant Protection

institute: Jilin Academy of Agricultural Sciences

summary: Endophytic colonization by entomopathogenic fungi represents a promising sustainable pest management strategy. This study investigated the physiological and molecular effects of maize endophytically colonized by Beauveria bassiana (strain BbOFDH1-5) conidia and blastospores on the Asian corn borer, Ostrinia furnacalis.

overall_design: We evaluated larval development, protective enzyme activities, and subsequent susceptibility to the insecticide chlorantraniliprole, utilizing gut transcriptomic analysis to elucidate the underlying mechanism. Results demonstrated that larvae fed on maize colonized by either spore type, particularly blastospores, exhibited significantly reduced food consumption, body weight, and survival rates. Additionally, the activities of protective enzymes (SOD, POD, CAT) were markedly suppressed. Feeding on blastospore-colonized maize significantly increased larval susceptibility to chlorantraniliprole. Transcriptomic analysis revealed that this enhanced sensitivity is linked to the downregulation of detoxification-related genes, ABCC4, and the upregulation of stress-response genes such as HSP70. These findings confirm that B. bassiana blastospores can synergistically enhance the efficacy of chemical insecticides by impairing larval physiology and suppressing gut-associated resistance mechanisms, providing a novel basis for integrated pest management.


title: CRISP3, a potential tumor suppressor, inhibits the progression of high-grade serous ovarian carcinoma by modulating the PI3K/AKT pathway

city: shanghai

first: Ma

last: mingjun

address: Shanghai First Maternity and Infant Hospital一妇婴保健院

institute: Tongji University

summary: Background: Ovarian cancer (OC) remains the most common cause of gynecological cancer-related death, and about 70% of the deaths are from advanced high-grade serous ovarian cancer (HGSOC). Cysteine-rich secretory protein 3 (CRISP3) is related to various human diseases, however, the roles and mechanisms of CRISP3 in HGSOC remain unclear. Methods: The clinical significance of CRISP3 in patients with OC was analyzed using The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus databases. CRISP3 ex-pression in OC tissues was validated by RNA-sequencing (RNA-seq), quantitative PCR, and immuno-histochemistry. Furthermore, we explored the effect of CRISP3 expression modulation on the biological be-havior of HGSOC through CCK-8, EdU, and transwell assays in vitro and the differences of CRISP3 during the progression of HGSOC in vivo. We utilized RNA-seq, GSEA and Western blotting to detect CRISP3's regulatory mechanisms. Finally, we employed data from the IMvigor210 cohort and TCGA to assess the correlation of CRISP3 with clinical response to immunotherapy, and the landscape of immune cell infiltra-tion. Results: CRISP3 expression was markedly reduced in HGSOC. In vitro studies demonstrated that CRISP3 knockdown significantly enhanced proliferation, migration, and invasion of HGSOC cells, whereas its overexpression suppressed these malignant phenotypes. Moreover, CRISP3 expression was found to be downregulated during OC progression in vivo. Mechanistically, CRISP3 acted as a tumor suppressor through the PI3K/AKT signaling pathway to inhibit the progression and metastasis of HGSOC. Addition-ally, we observed an association between CRISP3 expression and CD8⁺ T cells, macrophages, neutrophil and Th1 cells infiltration. Conclusions: We demonstrate that CRISP3 suppresses tumorigenesis in HGSOC by regulating the PI3K/AKT pathway, and that its expression alterations correlate with disease progression, supporting its utility as a biomarker.

overall_design: RNA-seq profiling of  OENC-CRISP3 (control) and OE-CRISP3 (overexpression) .

first: Mingjun

last: Ma

first: Xiu

last: Tian

first: Weiwei

last: Cao

first: Chao

last: Wang

first: Yue

last: Zhang

first: Jiani

first: Shanshan

first: Sijia

last: Gu

first: Jianxiao

last: Li

first: Yaqian

first: Yaodi

last: Shao

last: Huang

first: Shuo

last: Shi

first: Renhao

last: Xue

first: Chen

last: Chu

first: Jindan

last: Sheng

first: Yu


title: Functional Analysis of Hepatocyte Host Factor A1BG in Antiviral and Antitumor Effects

city: Yoshida-gun

first: Juan

last: Lyu

state: Fukui

address: 23-3 Matsuoka, Eiheiji-cho

department: Second Department of Internal Medicine

country: Japan

institute: University of Fukui

summary: To investigate the biological function of A1BG in HepG2 cells, we employed siRNA-mediated knockdown and plasmid-based overexpression approaches to modulate A1BG expression. Global gene expression changes associated with altered A1BG expression were subsequently examined using RNA microarray analysis.  We found that differentially expressed genes associated with A1BG overexpression were predominantly enriched in pathways related to antiviral and antitumor responses, including the Th1/Th2 signaling pathway, FGFR1 ligand binding and activation, and activation of matrix metalloproteinases.

overall_design: RNA microarray analysis was performed in HepG2 cells to evaluate the effects of A1BG knockdown and overexpression. HepG2 cells were transfected with si-Nontarget or A1BG siRNA, or with empty vector or A1BG vector, and harvested 72 h after transfection. The comparison combinations used in this analysis were 1) si-Nontarget–treated HepG2 cells versus si-A1BG–treated HepG2 cells, and 2) empty vector–transfected HepG2 cells versus A1BG vector–transfected HepG2 cells.

first: Takuto

last: Nosaka

first: Yosuke

last: Murata

last: Akazawa

first: Tomoko

last: Tanaka

first: Kazuto

last: Takahashi

first: Tatsushi

last: Naito

first: Masahiro

last: Ohtani

first: Lihong

first: Yasunari

last: Nakamoto


title: Vasculogenic Tissue Nano-Transfection Enhances Functional Recovery Following Nerve Reconstruction Surgery in a Mouse Model of Segmental Nerve Defect

city: Columbus

first: Ana

last: Salazar Puerta

institute: The Ohio State University

summary: Peripheral nerve injuries (PNI) often result in persistent sensory, motor, and functional deficits, even after surgical reconstruction. While gene and cell therapies offer promise for enhancing regenerative outcomes, effective and targeted delivery remains a significant challenge. Here, we explored vasculogenic Tissue Nano-Transfection (TNT) as a novel, non-viral, reprogramming-based cell therapy to improve outcomes following graft reconstruction surgery. TNT aims to improve nerve regeneration by inducing vasculogenic reprogramming and promoting neovascularization to support axonal growth. Through a combination of in vitro screening and in vivo testing in a nerve crush model, we identified an optimal formulation of the vasculogenic genes, Etv2, Fli1, and Foxc2 (EFF), for enhancing reprogramming and axonal repair. TNT-based deployment EFF in a long segmental nerve defect reconstructed with isografts resulted in significant improvements in functional recovery, including grip strength and muscle contractility. Histological analyses demonstrated increased vascular density and myelinated axon counts. These findings support the therapeutic potential of TNT-mediated vasculogenic reprogramming as an adjunct to surgical repair of complex PNI offering a promising strategy to improve nerve regeneration and functional outcomes.

overall_design: RNAseq profiling of fibroblasts cultures electrotransfected with TFs Etv2, Fli1, Foxc2 24 hours post-transfection, compared to sham-transfected cells and naïve cells.

last: Salazar-Puerta

first: Sara

last: Kheirkhah

first: Jonathan

last: Stranan

first: Hallie

last: Harris

first: Nada

last: Khattab

first: Megumi

last: Fukuda

first: Grant

last: Barringer

first: Carlos

last: Vasquez-Martinez

first: Samuel

last: Cortes

first: Neil

last: Ott

first: William

middle: R

last: Lawrence

first: Devleena

last: Das

first: Jordan

middle: T

last: Moore

first: Tiam

last: Saffari

middle: D

last: Salazar-Gil

first: Diego

last: Alzate-Correa

first: Junyan

last: Yu

first: Kavya

last: Dathathreya

first: Natalia

last: Higuita-Castro

first: Tatiana

middle: Z

last: Cuellar-Gaviria

last: Arnold

first: Amy

first: Daniel

last: Gallego Perez


title: Integrative analysis of DNA methylation and inflammatory protein biomarkers in hypertension

city: Shanghai

first: Yan

last: Wang

address: 197 Ruijin 2nd Road, Shanghai

institute: Shanghai Institute of Hypertension, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine

type: Methylation profiling by genome tiling array

summary: Abstract Background and objective: To investigate the relationship between inflammation and hypertension by comparing epigenetic and serum biomarkers of inflammation and their association with target organ damage (TOD). Methods: The epigenome-wide methylation profiles of peripheral leukocyte DNA from 176 patients with hypertension were analyzed using Illumina Infinium Methylation EPIC BeadChips. The commercially available Olink® Target 96 Inflammation panels were utilized to evaluate markers associated with inflammation. We identified CpG-protein association protein quantitative trait methylation loci (pQTMs) using mixed linear regression, adjusting for potential confounders. The possible roles of the discovered pQTMs were ascertained by Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) pathway analyses. The association between pQTMs and TOD was also analyzed. Results: In our analysis, we found 771 significant associations across 11 biomarkers, with a false discovery rate (FDR) of less than 0.05. Lambda estimates ranged from 0.847 to 1.202. Among these, 39 pQTMs showed an association with urine albumin-creatinine ratio, while 82 pQTMs showed an association with carotid intima-media thickness. Conclusion: Our findings contribute to the understanding of inflammatory biomarkers associated with alterations in DNA methylation in hypertension. However, these results will need to be validated in future studies.

overall_design: We aimed to investigate the associations of inflammatory biomarkers with DNA methylation in patients with hypertension using an epigenomic approach.   Leukocyte DNA was analyzed using the Illumina Infinium Methylation EPIC BeadChip in   176 hypertensive patients and the commercially available Olink® Target 96 Inflammation panels were utilized to evaluate markers associated with inflammation.


title: Primary human fibroblasts and keratinocytes stimulated with IL-17A and/or TNF

city: Aarhus

first: Hakim

last: Ben Abdallah

state: Denmark

address: Palle Juul-Jensens Boulevard 45

department: Dermatology and Venerology

country: Denmark

institute: Aarhus University Hospital

summary: This study investigated the transcriptional responses of fibroblasts and keratinocytes to IL-17A, TNF and their combined stimulation.

overall_design: Skin samples obtained from healthy adults undergoing plastic surgery were used to isolate both primary human dermal fibroblasts (n = 4) and keratinocytes (n= 4). The cells were stimulated for 24 hours with a vehicle (PBS with 0.15% bovine serum albumin) as a control, 100 ng/ml IL-17A (R&D Systems, Bio-Techne, Minneapolis, Minnesota, USA), and 10 ng/ml  TNFα (R&D Systems).  Total RNA was isolated and underwent bulk RNA sequencing.


title: Hypoxia-mimicked mitochondrial stress triggers APOBEC3A-mediated DNA damage via non-canonical innate immune activation

city: Paris

first: Beibhinn

last: O'Hora

address: 25-28 Rue du Dr Roux

country: France

institute: Institut Pasteur

summary: Hypoxia is a hallmark of the tumour microenvironment, driving metabolic reprogramming, immune activation, and genome instability. Here, we showed that cobalt chloride (CoCl2), a hypoxia-mimetic agent, potently induces the expression of the DNA cytidine deaminase APOBEC3A (A3A) in human THP-1 monocytic cells. A3A upregulation occurred in a dose-dependent manner, independently of type I interferon signalling, and was accompanied by increased double-strand DNA breaks. Transcriptomic profiling revealed broad hypoxia-driven reprogramming, characterized by activation of the stress response and downregulation of mitochondrial signalling pathways. Mechanistically, cobalt chloride induced mitochondrial dysfunction, metabolic reprogramming, and cytosolic release of mitochondrial DNA (mtDNA). Cytosolic mtDNA was transcribed by RNA polymerase III into immunostimulatory RNA, which activated the RIG-I/TRAF6/NF-κB axis to drive A3A expression. Inhibition or knockdown of RNA polymerase III markedly reduced both A3A levels and DNA damage, highlighting the central role of this pathway. All together, our findings reveal a novel interferon-independent signalling route through which hypoxia-induced mitochondrial stress activates A3A, directly linking metabolic dysfunction to genome instability. This mechanism implicates mitochondrial perturbation as a key driver of APOBEC3-mediated mutagenesis in hypoxic tumours and other diseases associated with mitochondrial stress.

overall_design: For the experimental setup, THP-1 cells (ATCC TIB-202) were cultured in RPMI 1640 medium supplemented with 10% heat-inactivated fetal calf serum, 50 U/mL penicillin, 50 μg/mL streptomycin, and 0.05 mM β-mercaptoethanol, and maintained in 150-cm² flasks under standard conditions. Low-passage cells were used to ensure consistent responses across experiments. To investigate the effects of cobalt chloride (CoCl₂), cells were divided into two groups: untreated controls and treated samples. Three biological replicates were prepared for each condition. Treated samples were exposed to 200 μM CoCl₂ for 20 hours, while untreated samples were cultured under identical conditions without CoCl₂


title: Hypoxia coordinates adipocyte hypertrophy andhyperplasia through HlF1aa-ATGL-PPARy pathway enablesrapid and healthy energy storage in grass carp

city: yangling

first: Jian

last: Sun

address: xinong road

institute: Northwest Agriculture & Forestry University

summary: Animals often face food scarcity in nature. In order to survive, some animals store substantial fat when food is available. However, the physiological mechanism by which they store substantial fat and maintain metabolic health in the short term is poorly understood. Here, using the grass carp (Ctenopharyngodon idellus) as a model, which exhibits remarkable fat storage capacity, we found that adipose tissue responded to energy overload first and expanded through adipocyte hypertrophy and hyperplasia. Mechanistically, hypoxia inducible factor-1αa (hif-1αa) was activated in mature adipocytes after short-term high-energy intake, thereby bidirectionally regulating adipose triglyceride lipase (atgl) to drive healthy expansion of adipose tissue in grass carp: (1) Hif-1αa downregulates atgl protein levels via the ubiquitin-proteasome pathway, promoting adipocyte hypertrophy; (2) Hif-1αa upregulates atgl transcription to sustain basal lipolysis, releasing free fatty acids that activate peroxisome proliferator-activated receptor γ (pparγ) in preadipocytes to promote adipocyte hyperplasia. This crosstalk-mediated rapid adipocyte hyperplasia prevents detrimental excessive hypertrophy and significantly boosts the overall energy storage capacity. Taken together, our study reveals how grass carp utilize hypoxia signals (a signal often associated with metabolic disorders in mammals) to coordinate the pattern of adipose tissue expansion, achieving rapid and healthy lipid storage. Our findings redefine hypoxia's role as a metabolic orchestrator rather than a stress indicator, suggesting potential implications for a theoretical basis for addressing obesity-related diseases in humans and farmed animals caused by excessive energy intake.

overall_design: Terminally differentiated adipocytes were treated with CoCl2, and then co-cultured with grass carp preadipocytes for 48h. ChIP-seq of PPARγ in grass carp preadipocytes was performed.


title: Doxorubicin induces immediate transcriptional change and apoptosis in spermatogonia from prepubertal rats.

city: Laval

first: Geraldine

last: Delbes

state: QC

address: 531 boulevard des Prairies

country: Canada

institute: Institut national de la recherche scientifique

summary: Chemotherapy can compromise the fertility of boys with cancer, yet no standard protocols exist to preserve their reproductive potential. Before puberty, germ cells are almost exclusively spermatogonia that can be the target of anticancer drugs. Doxorubicin (DXO), a widely used anthracycline in pediatric oncology, has been associated with infertility in adulthood, but its immediate effects on prepubertal germ cells remain poorly understood. In the present study, a preclinical rat model of prepubertal DXO exposure was developed to characterize the mechanisms underlying immediate DXO-induced germ cell damage. Six-day-old pups, received a single intraperitoneal injection of DXO (5 mg/kg) and effects were measure after 24 or 48 h. DXO exposure significantly reduced relative testis weight from 24 h and significantly increased apoptosis and germ cell loss at 48 h, while circulating testosterone remained unchanged, suggesting a selective germline effect. RNA-seq was done on GFP-positive germ cells purified at 24 h. Transcriptomic analysis confirmed the enrichment in spermatogonial stem cells (SSCs) in the GFP-sorted population. Moreover, DXO induced 51 differentially expressed genes (49 upregulated, 2 down regulated) that were mostly related the p53-dependant apoptosis pathway. Pro-apoptotic genes (Cdkn1a, Bbc3/Puma, Tp53inp1, Fas) and oxidative stress regulators (Sesn2, Eda2r, Abhd4) were induced, whereas DNA repair genes (Mgmt, Xrcc1, Polh, Gadd45α, ...) were not activated. Our data revealed the DXO-induced immediate transcriptomic response after 24h, leading to germ cell death observed by histology at 48h. These findings suggest that SSCs respond to DXO by favoring apoptosis and stress regulation, a strategy that may preserve germline integrity and reduce the risk of transmitting genetic damage to the next generation.

overall_design: RNA-seq profiling of GFP-positive germ cells isolated from prepubertal rats 24 h after in vivo exposure to doxorubicin (5 mg/kg) or vehicle control at PND6.

first: Hermance

last: Beaud

first: Elisa

last: Hug

first: Marie-Pier

last: Scott-Boyer

first: Arlette

last: Rwigemera

first: Amélie

last: Tremblay

first: Arnaud

last: Droit

first: Géraldine

last: Delbès


title: Transient SUMOylation Inhibition In Human Pre-adipocytes Stably Imprints a Transcriptional Beiging Fate

city: Oslo

first: Pierre

last: Chymkowitch

address: Blindernveien 31

department: Biosciences

country: Norway

institute: University of Oslo

summary: Assess chromatin opening in response to TAK981 treatment in human pre-adipocytes.

overall_design: Chromatin accessiblity sequencing of differentiated immortalized human white adipocytes that have been treated transiently with TAK-981 or DMSO as vehicle control and collected at different timepoints during differentiation

first: Patrizia

last: Nothnagel

first: Paul-Arthur

last: Meslin

first: Jonas

last: Wik

first: Yunna

middle: E

last: Strøm

first: Magnar

last: Bjørås

first: Jorrit

last: Enserink

first: Bjørn

middle: S

last: Skålhegg

first: Nolwenn

last: Briand

first: Anthony

last: Mathelier


title: Context-dependent effect of glucocorticoid receptor activity shapes ovarian cancer cell plasticity and therapy response

city: Baronissi

first: Giovanna

middle: Maria

last: Ventola

state: Salerno

address: Via S. Allende, 43L

country: Italy

institute: Genomix4life s.r.l.

summary: The phenotypic plasticity of cancer cells, i.e. their adaptability to a variable/ stressful environment, is fundamental for disease progression/aggressiveness. Here we revealed that the glucocorticoid receptor (GR, NR3C1), a key player in the human response to stress, controls proliferation, morphology, motility/invasion, and the gene expression profile of high-grade serous ovarian carcinoma (hereafter OC) cells. By modulating glucose metabolism, GR acts as a tumor suppressor delaying ovarian cancer growth under 3D-settings. Conversely, under 2D conditions GR acts as a tumor promoter, driving cell mesenchymalization, increasing cell motility and chemoresistance. Strikingly, modulators of glucose metabolism as metformin and 2-deoxyglucose, are alone sufficient to induce similar cell behavioural changes. So, in ovarian cancer a GR-glucose metabolism axis modulates a escaping signalling response triggered by stressful (3D overgrowth, starvation) condition.

overall_design: SKVO3 cells were infected with lentiviral particles carrying a short hairpin RNAs (shRNA) targeting NR3C1 gene (shNR3C1), and a resistance to puromycin and  an empty vector (shEmpty) used as a control.  RNAseq was performed using (shNR3C1) vs (shEmpty) grown in 2D setting and in spheroids generated by (shNR3C1) vs (shEmpty) grown in 3D setting.

first: Micaela

last: De Girolamo

first: Eduardo

last: Ibello

first: Teresa

last: Improda

first: Ilaria

last: Tedesco

first: Carmela

last: Dell’Aversana

first: Silvia

last: Buonaiuto

first: Salvatore

last: Arbucci

first: Cristina

last: D’Aniello

first: Dario

last: De Cesare

first: Renato

last: Franco

first: Concetta

last: Ambrosino

first: Lucia

last: Altucci

first: Luigi

last: Cobellis

last: Patriarca

first: Gabriella

last: Minchiotti

first: Gilda


title: Ablation of PKCα phosphorylation cascades by CRISPR-Cas9 Base Editing Rescues Heart Failure [RNA-Seq]

city: Dallas

first: Lei

last: Guo

state: TX

address: 5323 Harry Hines Blvd

department: Department of Population and Data Sciences

institute: University of Texas Southwestern Medical Center

summary: BACKGROUND: The global prevalence of heart failure is increasing significantly, and the prognosis for patients with heart failure remains poor, highlighting the urgent need for novel therapeutic strategies. Protein kinase C alpha (PKCα) plays a central role in heart failure progression. Phosphorylation of PRKCA at T497 triggers a series of phosphorylation cascades, leading to its activation. Ablation of T497 phosphorylation leads to reduced protein stability and activity. However, there is no therapeutic strategy for heart failure targeting PKCα T497. METHODS: We employed CRISPR-Cas9 adenine base editing to ablate the phosphorylation site T497 of PKCα. We generated mice harboring a PKCα phosphoresistant T497A mutation in the germline and administered adeno-associated virus 9 (AAV9) harboring base editor of PrkcaT497A to postnatal wild-type (WT) mice to explore its clinical feasibility. To model for heart failure, mice were subjected to transverse aortic constriction (TAC). Cardiac function, hypertrophy, fibrosis, and transcriptional changes were evaluated by echocardiography, wheat germ agglutinin staining, Masson’s trichrome staining, and RNA sequencing, respectively. The editing efficiency of PrkcaT497A was assessed using Sanger sequencing and deep amplicon sequencing. Cellular Ca2+ homeostasis was analyzed using epifluorescence microscopy in Fura-2–loaded human induced pluripotent stem cells-derived cardiomyocytes (iPSC-CMs) carrying the PRKCAT497A mutation under chronic angiotensin II (AngII) stimulation. RESULTS: The T497A mutation in PKCα prevented subsequent phosphorylation and led to PKCα degradation. Four weeks after TAC surgery, WT mice showed dramatically impaired cardiac function, cardiac remodeling, and increased lung weight, whereas PKCα phosphoresistant mice were protected from these effects. PKCα phosphoresistant mice also showed protection against heart failure-related aberrant changes in cardiac gene expression, cardiac hypertrophy, and fibrosis. Likewise, mice administrated with AAV9-base editors exhibited similar cardioprotective effects against TAC-induced heart failure. In vitro, PKCα-edited iPSC-CMs were protected from AngII-induced impairments in contractility and Ca2+ transients observed in WT iPSC-CMs. CONCLUSIONS: The editing of PRKCAT497A through adenine base editing may potentially provide a promising therapeutic approach for human cardiac diseases.

overall_design: RNA-seq profiling of hearts from 10-week-old wild-type and Prkca T497A mutant mice subjected to Sham or TAC surgery. Tissue was collected 1 weeks post-surgery.

first: Tomonori

last: Tadokoro

first: Hui

last: Li

first: Yoon-Jung

last: Kim

first: Lin

last: Xu


title: Granzyme A-Producing Type 1 Innate Lymphoid Cells Restore Salivary Secretion in the Aged Submandibular Gland

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

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

summary: Salivary gland function declines with age, contributing to oral and respiratory diseases, yet the mechanisms maintaining secretion remain unclear. We analyzed mice across aging stages, measuring saliva output and histology, and performed site-specific single-cell RNA sequencing around lymphoid clusters to infer immune–epithelial interactions, validated in coculture and in vivo depletion models. Saliva production was preserved or slightly increased in early aging, coinciding with lymphoid cluster formation enriched in Gzma⁺ ILC1s predicted to interact with epithelial cells via the Gzma–Pard3 axis, which enhanced Aqp5 expression in vitro. Depletion of ILC1s in aged mice reduced saliva output, demonstrating that ILC1-derived GZMA supports epithelial secretory capacity. Thus, aging salivary glands accumulate ILC1s that sustain epithelial function through a GZMA-dependent pathway, maintaining secretion and identifying the GZMA–Pard3 axis as a potential target to preserve gland function and prevent xerostomia-related disorders.

overall_design: single-cell RNA-sequencing from lymphoid cluster region and non-lymphoid cluster region

first: Hiroaki

last: Abe

first: Erika

last: Yamashita

last: Okuzaki

first: Masaru

last: Ishii


title: Treg cells retain stable lineage commitment during pregnancy in mice after late gestation inflammatory challenge

city: Adelaide

first: Sarah

last: Robertson

state: South Australia

address: 4 North Terrace

department: Discipline of Obstetrics and Gynaecology

country: Australia

institute: The University of Adelaide

summary: Inflammation is a major driver of preterm birth, a common pregnancy disorder and the leading cause of childhood death. T regulatory (Treg) cells are essential mediators of maternal fetal tolerance and are critical for constraining uterine inflammation. In some tissue settings, loss of Foxp3 expression can cause instability in Treg cell lineage commitment, elevated production of proinflammatory cytokines, and compromised suppressive function. Whether preterm birth susceptibility is associated with loss of lineage fidelity and adoption of pro-inflammatory phenotypes in Treg cells is unknown. In this study, we investigated the lineage stability of Treg cells in vivo in mice using a Foxp3 fate-mapping system and models of preterm birth induced by late-gestation inflammatory challenge with lipopolysaccharide (LPS) or interleukin-1β (IL-1β). Ex-Foxp3-expressing (exFoxp3) cells were observed in the uterus-draining lymph nodes (udLNs) in non-pregnant mice and in similar abundance across normal gestation, and a proportion expressed pro-inflammatory cytokines IFNγ and/or IL-17A. Bulk RNA-sequencing of sorted Treg and exFoxp3 cells from late-gestation udLNs revealed substantial loss of the Treg cell lineage program in exFoxp3 cells, characterised by reversal in expression of canonical Treg cell genes and pathways. Late gestation LPS or IL-1β administration to induce preterm birth did not expand the exFoxp3 cell population. We conclude that uterine Treg cells exhibit a high level of lineage stability in pregnancy regardless of proinflammatory challenge. Whether there is any biological or pathophysiological significance of exFoxp3 cells in gestational tissues remains to be defined.

overall_design: RNAseq of Treg cells and CD4+ exFoxp3 cells isolated from gestation day 18.5 uterus-draining lymph nodes of Foxp3 fate-reporter mice (Foxp3GFPCre.Rosa26RFP) using fluorescence-activated cell sorting (FACS).

first: Kerrie

middle: L

last: Foyle

first: Ella

last: Green

first: Jessie

last: Walker-Rogers

first: Ha

last: Tran

first: David

last: Olson

first: Lachlan

last: Moldenhauer


title: RNA-seq of human THP-1 macrophages infected with adherent-invasive E. coli (AIEC) strains

first: Olivier

last: Espeli

address: 11 place Marcelin Berthelot

department: CIRB

institute: College de France

summary: Adherent-invasive Escherichia coli (AIEC) are associated with Crohn’s disease through their ability to invade, survive, and replicate within intestinal macrophages. To characterize the host response, we performed RNA-seq profiling of THP-1–derived macrophages infected for 24 h with five distinct AIEC strains, compared to uninfected controls. Transcriptomic analysis revealed extensive reprogramming of macrophage gene expression, marked by activation of pro-inflammatory signaling pathways (NF-κB, JAK–STAT, TNF) and concomitant suppression of lysosome-, phagosome-, and peroxisome-associated programs. Although pro-death signals were induced, execution modules of apoptosis and ferroptosis remained restrained, consistent with macrophage survival and thus permissive for bacterial replication. A conserved transcriptional signature emerged across strains, characterized by sustained inflammation coupled with diminished antimicrobial capacity. In parallel, we observed strain-specific differences in cytokine expression, lysosomal function, and lipid metabolism, highlighting that macrophage responses vary depending on the infecting AIEC strain. Overall, these data reveal that AIEC sustain macrophage inflammatory responses yet restrain cell death and antimicrobial mechanisms, establishing conditions that favor their replication and long-term survival within the host.

overall_design: RNA-seq profiling was performed on THP-1–derived macrophages infected with five different AIEC strains for 24 hours, alongside uninfected control macrophages. Each condition included two biological replicates. This design allows comparison of transcriptomic responses between infected and control macrophages and among the different AIEC strains to identify both conserved and strain-specific host responses.

first: Emma

last: Bruder

first: Hosni

last: Nedjar

first: Emilie

last: Vazeille

first: Caroline

last: Chevarin

first: Anthony

last: Buisson

first: Nicolas

last: Barnich

last: Espéli


title: Oncogenic Role of Aberrant EZH2 in Hepatoblastoma Development

city: Cincinnati

first: Erica

last: DePasquale

state: OH

address: 3333 Burnet Ave.

department: Gastroenterology

institute: Cincinnati Children's Hospital

summary: Hepatoblastoma (HB) is the most common pediatric liver malignancy, yet its cellular origins and molecular drivers remain poorly defined. Using single-nuclear RNA sequencing (snRNA-seq), we identified a proliferative, hepatocyte-derived tumor cell population (cycling HepT) enriched for EZH2 expression, particularly in the aggressive embryonal subtype. Integrative genomic and transcriptomic profiling confirmed EZH2 overexpression. Disruption of the PRC2 complex was evident through mislocalization and reduced expression of SUZ12, a core component. EZH2 overexpression correlated with upregulation of mitotic regulators such as AURKB and Ki67 in human HB gene expression analysis as compared to background liver. Targeted sequencing identified variants of uncertain significance in EZH2 and SUZ12 in 11 of 11 patient tumors. Pharmacologic inhibition of EZH2 with EPZ-6438 reduced proliferation and sensitized HB cells to cisplatin through gene regulation, potentially modulating platinum accumulation both in vitro and in vivo. In summary, EZH2 promotes HB progression through both epigenetic silencing and noncanonical signaling pathways. These findings support EZH2’s contribution to HB pathogenesis, therefore identifying it as a novel therapeutic target.

overall_design: 10X Genomics single-nuclear sequencing was performed on hepatoblastoma liver biopsies and adjacent non-tumor tissue controls.

first: Kathryn

last: Glaser

first: Lara

last: Berklite

first: Brian

last: Hickner

first: Priyanka

last: Rao

first: Roma

middle: H

last: Patel

first: Andrew

last: Badachhape

first: Somak

last: Roy

first: Emily

last: Schepers

first: Nikolai

last: Timchenko

first: James

last: Geller

first: Sarangarajan

last: Ranganathan

first: Gregory

last: Tiao

first: Bruce

last: Aronow

first: Takanori

last: Takebe

last: Woodfield

first: Sanjeev

last: Vasudevan

first: Alexander

last: Bondoc


title: Rapamycin ameliorates cognitive impairment by activating microglial amyloid-β degradation in mouse models of amyloidosis

city: Chongqing

first: Kai

last: Guo

address: 1 Youyi Road, Yuzhong District

institute: Chongqing Medical University

summary: Alzheimer's disease (AD) lacks effective treatments despite being the most prevalent dementia. This study examines whether rapamycin, an mTOR inhibitor with immunomodulatory properties, alleviates AD pathology by regulating microglia (the brain's resident immune cells).Rapamycin was administered orally to 2-month-old 5×FAD and hAPPNL-G-F mice, two amyloid plaque-dominant AD models. Behavioral and AD-pathological assessments were performed at approximately 5 months of age. Primary microglia exposed to rapamycin and fluorescently labeled amyloid-β (Aβ) oligomers were analyzed for phagocytic and degradative functions. The BV2 microglial cell line received rapamycin, oleic acid, and autophagy inhibitors to investigate mechanisms underlying rapamycin-regulated microglial degradation capacity. Oral rapamycin administration significantly reduced cerebral Aβ plaque burden, diminished dystrophic neurites, suppressed glial hyperactivation, and increased plaque-proximal microglial density in both 5×FAD and hAPPNL-G-F mice, ultimately mitigating memory deficits. Mechanistic investigations revealed rapamycin-activated microglial lysosomal degradation pathways, stimulated lipid droplet clearance in BV2 microglia, and enhanced Aβ phagocytic clearance in primary microglia. Our findings provide compelling evidence that rapamycin enhances Aβ clearance by targeting microglial lysosomal function, thereby establishing a novel glia-directed therapeutic strategy for AD.

overall_design: RNA-seq of cortical tissues from 5-month-old male and female 5×FAD mice treated with rapamycin or vehicle control from 2 to 5 months of age. Four biological replicates per group [Female Control(FC), Female Rapamycin(FR), Male Control(MC), Male Rapamycin(MR)].

first: Shihui

first: Weishan

last: Fu

first: Yating

last: Wang

first: Qi

last: Liu

first: Jiaxin

last: Li

first: Hongsheng

last: Zhang