title: Sulfatide deficiency-induced astrogliosis and myelin lipid dyshomeostasis are independent of Trem2-mediated microglial activation_Female spinal cord study

summary: This study investigates the impact of central nervous system sulfatide (ST) deficiency on gene expression in the female mouse spinal cord tissues, both in the presence and absence of Trem2, using the NanoString Neuroinflammation panel.


title: Sulfatide deficiency-induced astrogliosis and myelin lipid dyshomeostasis are independent of Trem2-mediated microglial activation_Female cerebrum study

status: Public on Sep 04 2025

city: SAN ANTONIO

first: Sijia

last: He

state: Texas

address: 7703 Floyd Curl Dr.

country: USA

institute: uthealth sa

summary: This study investigates the impact of central nervous system sulfatide (ST) deficiency on gene expression in the female mouse cerebrum tissues, both in the presence and absence of Trem2, using the NanoString Neuroinflammation panel.

overall_design: The measurment set contains 12 samples, composed of 4 genotypes (Cre-/Trem2 WT, Cre-/Trem2 KO, Cre+/Trem2 WT, and Cre+/Trem2 KO) in triplicates. Note that Cre- indicate mice with ST, Cre+ indicate mice of adult-onset ST-deficiency.

first: Namrata

last: Mittra

first: Xianlin

last: Han


title: Effect of LPS and Nicotine on gene expression in the hippocampus and PFC

city: Boulder

first: Mina

last: Griffioen

state: CO

address: 1480 30th street

department: Institute for behavioral genetics

institute: University of Colorado Boulder

type: Expression profiling by high throughput sequencing

summary: Gene expression changes have been identified in the response to immune challenges such as LPS, yet there is little information on whether there are changes in response to nicotine exposure. In order to observe whether nicotine can induce changes at the gene expression level that are consistent with other changes seen in the astrocyte activation response, we performed RNA sequencing on mice exposed to saline, LPS, or nicotine. LPS produced a robust immune response consisten with the literature, and nicotine exposure did not result in many differentially expressed genes. The changes with nicotine were consistent with GWAS data on smoking initiation, and neurotransmitter responses often seen with nicotine exposure. Taken together, this data shows that one dose of nicotine induces small changes in gene expression.

overall_design: RNAseq profiling of WT C57/BL6 mouse hippocampus and PFC in response to LPS or Nicotine

first: Griffioen

last: Mina

first: Hoeffer

last: Charles


title: A spatial transcriptomics dataset of the endometrium from repeated implantation failure patients

city: Beijing

first: Peng

last: Wang

address: No.5 Ankang Hutong, Deshengmenwai, Xicheng District

country: China

institute: Beijing Anding Hospital affiliated to Capital Medical University

summary: Repeated implantation failure (RIF) presents a significant challenge in vitro fertilization (IVF) treatment, and abnormalities in the endometrium often play a crucial role in RIF. To enhance and deepen our understanding of tissue context in the endometrium underlying RIF, we applied spatial transcriptomics (ST) sequencing using the 10x Visium platform to 8 endometrial tissues from 4 normal individuals (CTR) and 4 RIF patients during the mid-luteal phase in this study. We achieved 10131 high-quality spots, with a median detected gene number was 3156. Seven distinct cellular niches (Niche 1-7) with specific characteristics were identified in our data. Deconvolution of ST data was performed by integrating with a public single-cell RNA (scRNA) dataset, and it was found that unciliated Epithelia were the dominant components in our data. To the best of our knowledge, this is the first spatial transcriptomics atlas of endometrial tissue in normal and RIF conditions, and the spatial data can provide a valuable source for further studies investigating the RIF mechanism.

overall_design: Fresh endometrial tissues from 4 normal (named CTR) and 4 RIF samples were processed by 10x Visium Spatial Transcriptomics Sequencing. The CTR group (CTR1-CTR4) comprised non-smoking subjects aged 25, 24, 32, and 31 years, with corresponding BMIs of 18.14, 20.25, 24.37, and 20.32 kg/m². The RIF group (RIF1-RIF4) consisted of non-smoking subjects aged 31, 33, 25, and 29 years, with BMIs of 22.18, 24.47, 21.64, and 20.35 kg/m². The CTR group reported no previous embryo transfers. In the RIF group, RIF1, RIF3, and RIF4 had undergone 3 prior transfers of good-quality embryos, while RIF2 had experienced 5. Regarding obstetric history, CTR1 and CTR2 were primiparous, while CTR3 and CTR4 were multiparous. All RIF subjects were nulliparous. All participants were confirmed free of uterine pathologies (including endometriosis and adenomyosis), endocrine, metabolic, auto-immune diseases and infection. Endometrial samples were collected via Pipelle biopsy from the uterine fundus and upper cavity at 7 days after the Luteinizing Hormone (LH) surge (LH + 7).


title: Impact of Choline intake during pregnancy on maternal cognition and hippocampal gene signature in old age

city: Singapore

first: Valerie Chun Ling

last: Lin

address: 60, Nanyang Dr

department: School of Biological Sciences

country: Singapore

institute: Nanyang Technological University

summary: Women are twice as likely to have Alzheimer’s disease (AD) than men and multiparity has been suggested to be a risk factor for dementia. The present study evaluated whether the lack of certain nutrients during pregnancy influences cognition while pregnant and in old age in mouse model. Non-targeted NMR analysis revealed significantly lower levels of numerous plasma nutrients and metabolites including choline and its derivatives on gestation day 7 compared to day 1. Novel object recognition and Morris Water Maze tests revealed impaired cognition in pregnant mice compared to nonpregnant controls. Choline deprivation worsened the cognitive impairment during pregnancy and choline supplementation alleviated it. Furthermore, choline availability during pregnancy affected cognition and general health in old age, with mice given a choline-deficient diet during pregnancy performed more poorly. RNA-Seq analysis indicates lasting effect of choline intake during pregnancy on hippocampal gene signatures in old age. Choline deprivation was associated with more upregulation of proinflammatory genes, whereas choline supplementation showed upregulation of neuroprotective genes such as Prl, Gh, and hemoglobin (Hba and Hbb subunits). Together the study shows that choline supplement benefits women’s cognitive health during pregnancy and at the old age.

overall_design: RNA profiling was performed on hippocampal tissue from 15-month-old mice, including non-pregnant (nulliparous) and pregnant (multiparous) mice on a normal diet as controls, as well as pregnant mice on either a choline-supplemented or intermittent choline deprivation diet given during pregnancy. The goal was to assess the effects of pregnancy and choline diet during pregnancy on hippocampal gene expression in old age. Eight-week-old young mice were also included in the analysis.

first: Qian Yee

last: Woo

first: Bernett TK

last: Lee

first: Lim Wei

first: Jing Tao

last: Zhang

first: Ayumu

last: Tashiro

first: Pheck Khee

last: Lau

first: Guillaume

last: Thibault

first: Yulan

first: Valerie CL


title: Genome-wide homeostatic regulation of R-loops by the dual RNA-DNA topoisomerase, topoisomerase III-β (TOP3B) III

city: Bethesda

first: Anjali

last: Dhall

state: MD

address: 37 Convent Drive

department: DTB

institute: NCI

summary: We report the mapping of R-loops across the human genome in wild-type and TOP3B-KO HCT116 and HT1080 cells by performing DNA: RNA Immunoprecipitation followed by high-throughput sequencing (DRIP-seq). Cellular depletion of TOP3B globally increases the intensity of pre-existing R-loops. The enriched R-loop peaks in TOP3B-KO cells are both in intergenic and genic regions, including protein-coding and non-coding RNA genes. Long genes and genes with high exon-intron junctions accumulate more R-loops. Global transcription analyses indicate that increased R-loop signals do not significantly change transcript level in TOP3B-KO cells. However, increased R-loops in TOP3B-KO cells cause stabilization of G4-quadruplexs and increased gH2AX foci. Altogether, these results demonstrate that TOP3B is needed for the removal of deleterious R-loops that lead to genomic breaks.

overall_design: To investigate the roles of topoisomerase III-beta (TOP3B) in regulating genomic R-loop structures and global transcription process, we generated TOP3B-KO HT1080 cells using CRISPR technique and guide RNA targeting Exon 2 of topoisomerase III-beta. We took two isolated RNA from three replicates of wild type HCT116 and three replicates of E2-2 TOP3B-KO HT1080 cells and performed ribo-depleted total RNA-seq. We then performed gene expression profiling analysis using data obtained from total RNA-seq of triplicates of wild type HT1080 and E2-2 TOP3B-KO HT1080 cells.

first: Sourav

last: Saha

first: Shar-yin Naomi

last: Huang

first: Liton

first: Md Rasel

last: Al Mahmud

first: Hongliang

first: Yves

last: Pommier


title: Genome-wide homeostatic regulation of R-loops by the dual RNA-DNA topoisomerase, topoisomerase III-β (TOP3B) II

overall_design: To investigate the roles of topoisomerase III-beta (TOP3B) in regulating genomic R-loop structures and global transcription process, we generated TOP3B-KO HCT116 cells using CRISPR technique and guide RNA targeting Exon 2 of topoisomerase III-beta. We isolated RNA from two replicates of wild type HCT116 and two replicates of E2-4 TOP3B-KO HCT116 cells and performed ribo-depleted total RNA-seq. We then performed gene expression profiling analysis using data obtained from total RNA-seq of pair of replicates of wild type HCT116 and E2-4 TOP3B-KO HCT116 cells.


title: Genome-wide homeostatic regulation of R-loops by the dual RNA-DNA topoisomerase, topoisomerase III-β (TOP3B) I

overall_design: To investigate the roles of topoisomerase III-beta (TOP3B) in regulating genomic R-loop structures , we generated TOP3B-KO HT1080 and HCT116 cells using CRISPR technique and guide RNA targeting Exon 2 of topoisomerase III-beta (TOP3B) and  then performed DNA: RNA Immunoprecipitation using S9.6 antibody followed by high-throughput sequencing (DRIP-seq)  to map genomic locations of R-loops in replicates of wild type vs TOP3B-KO HCT116 (Clone E2-4) and HT1080 (Clone E2-2) cells.


title: Saikosaponin‑D triggers cancer death by targeting the PIM1/c-Myc axis to rewire oncogenic alternative splicing

city: Shanghai

first: Fuwen

last: Yuan

state: 上海

address: Cailun Road #1200, Pudong New area

institute: Shanghai University of Traditional Chinese Medicine

summary: Saikosaponins (SSs, including SSA, SSB, SSC, and SSD), the major bioactive compounds in the traditional medicine Radix Bupleuri (RB), are emerging agents exhibiting anti-tumor efficacy in several cancers. However, the respective anti-tumor efficacy of these agents and mechanisms in cancers such as gastric and prostate cancer remains unclear. In this study, we demonstrated that SSD, among SSs, possessed a significant anti-tumor role in vivo and in vitro. Transcriptome analysis revealed a down-regulation of alternative splicing factors and rewiring of oncogenic alternative splicing events such as CYP1A1, whose transcript-specific ablation with CIRSPR-Cas13 significantly abolished SSD-induced cell growth inhibition. Specifically, we showed that SSD binds to PIM1 and down-regulates its expression, thus restraining PIM1-mediated serine 62 phosphorylation of Myc, which is critical for its transcription activity. This results in decreasing the expression of Myc-governed alternative splicing factors that are responsible for the regulation of oncogenic alternative splicing events. These studies demonstrated the potent anti-tumor efficacy of SSD and exposed a PIM1/Myc pathway that drives the expression of an essential alternative splicing regulatory network that mediates SSD’s anti-tumor role in cancers.

overall_design: mRNA profiles of AGS cells treated with vehicle, SSD were generated by deep sequencing, in triplicate, using Illumina HiSeq6000

first: Xuehui

last: Li


title: Role of GPNMB in Foam Cells Formation and Atherosclerosis Progression

first: Huan

address: 38 Life Science Park Road

institute: National Center for Protein Sciences, Beijing

summary: Currently, both reliable biomarkers for disease monitoring and specific therapeutic targets are needed to combat atherosclerosis, one of the dangerous lipid metabolism disorders. We observed attenuation of atherosclerosis in a GPNMB auto-mutant (GpnmbR150X) mouse model as well as in a myeloid-specific Gpnmb-knockout mouse model. Furthermore, in GpnmbR150X BMDMs, we observed that impaired lipid droplet formation, enhanced lipid oxidative metabolism, and more robust lipid degradation by the lysosomal pathway suppressed the macrophage foaming, thereby reducing the atherosclerotic burden of excess OxLDL.

overall_design: To investigate how GPNMB affected the macrophage foaming, we performed bulk RNA-seq analysis of BMDMs from GpnmbR150X mouse or control mouse and OxLDL-treated BMDMs from GpnmbR150X mouse or control mouse.

first: Junqi

first: Xiaoping

last: Chen

first: Li

last: Tang


title: High throughput CRISPR perturbation screens identify epigenetic regulators impacting primordial germ cell development [RNA-seq]

city: Ithaca

first: Jingyi

last: Gao

state: NY

address: 618 Tower road

department: BMS

institute: Cornell University

summary: There is concern that environmental factors underlie reported declines in fertility and reproductive parameters such as the number and quality of sperm and eggs. One possible mechanism is the perturbation of epigenetic landscapes in the germline. To explore this possibility, we utilized a highly scalable in vitro platform for the differentiation of embryonic stem cells (ESCs) into primordial germ cell-like cells (PGCLCs) to conduct a CRISPRi screen of epigenetic-related genes to identify those that specifically perturb the efficiency of PGCLC formation. This platform leveraged an ESC line containing 4 inducible transcription factors (Prdm1, Prdm14, Tfap2c, and Nanog) and a PGC reporter (Stella-eGFP) that enabled highly efficient, cytokine-free differentiation and quantification en masse. A total of 701 genes with distinct sgRNAs were screened, and 53 genes were identified that decreased the efficiency of PGCLC formation. NCOR2, a transcriptional repressor that acts via recruitment of Class I and Class IIa histone deacetylases (HDACs) to gene targets, was particularly potent in suppressing PGCLC differentiation. Consistent with evidence that histone deacetylation is crucial for germline differentiation, we found that HDAC inhibitors (HDACi), including the anti-convulsive drug valproic acid (VPA) and widely-available dietary supplement sodium butyrate (SB), also suppressed ESC>PGCLC differentiation. Transcriptome analyses of HDACi-treated, differentiating ESC>PGCLC cultures revealed suppression of germline-associated pathways and enhancement of somatic pathways. Additionally, exposure of developing mouse embryos to SB or VPA caused hypospermatogenesis. This work demonstrates the feasibility of conducting large scale functional screens of genes, chemical agents and possibly genetic variants that impact germline development and epigenome.

overall_design: RNA-seq to evaluate the effect of HDACi, sodium butyrate (SB) and valproic acid (VPA), exposure on PGCLC development.

first: Liangdao

first: Dain

last: Yi

first: Alex

middle: P

last: Sheft

first: John

middle: C

last: Schimenti

first: Xinbao

last: Ding


title: Inflammatory cytokines induce novel cancer dependencies

city: Cambridge

first: Robert

middle: T

last: Manguso

state: MA

address: 75 Ames Street, Rm 7053

institute: Broad Institute of MIT & Harvard

summary: Tumor cells respond and adapt to environmental stresses, including cytokine-mediated inflammation, to facilitate growth in hostile environments. However, cytokine responses also induce transcriptional and cell state changes that may predispose tumor cells to new vulnerabilities, which remain largely unexplored. Here, we performed in vitro genome-scale CRISPR loss-of-function screens in eight cancer models exposed to IFNγ, IFNβ, or TNFα to map context-specific genetic vulnerabilities. We identified members of the GPI transamidase complex and the lipid phosphatase FITM2 as interferon-specific cancer dependencies. Tumor-specific deletion of GPI transamidase subunits or FITM2 dramatically enhanced response to immune checkpoint blockade in vivo. By integrating functional genomics, metabolomics and pharmacological blockade, we determined that loss of FITM2 predisposed cancer cells to IFNγ-driven endoplasmic reticulum and oxidative stress, culminating in a paraptosis-like cell death. Our study provides a comprehensive profiling of tumor-intrinsic dependencies governing responses to inflammatory cytokines, thereby presenting promising avenues for therapeutic intervention.

overall_design: KPC Cas9-expressing tumor cells with control or Fitm2 sgRNA were plated in a 6-well plate for 24hrs. The cells were then treated with PBS or IFNg for 36hrs before RNA was extracted.

first: Collins

middle: K

last: Cheruiyot

first: Ashwin

middle: V

last: Kammula

first: Kathleen

middle: B

last: Yates


title: Epigenetic and Transcriptional Programming of Esophageal Eosinophils by the Local Tissue Environment [ATAC-seq]

city: Cincinnati

first: Jennifer

middle: M

last: Felton

state: Ohio

address: 3333 Burnet Ave, ML7028

department: Department of Allergy and Immunology

institute: Cincinnati Children's Hospital Medical Center

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Tissue eosinophilia is a hallmark feature of allergic diseases. Eosinophils resident in different tissues have unique properties, and whether that heterogeneity is stochastic or regulated by cell-intrinsic or extrinsic factors has not been established. We profiled tissue eosinophils in the esophagus during allergic inflammation using single-cell sequencing, epigenomic mapping, and flow cytometry. Human and murine esophageal eosinophils exhibited a specialized transcriptional and epigenetic landscape, composed of metabolic, extracellular sensing, and immunomodulatory genes, and enriched for AP-1 transcription factor binding sites.  Additionally, human esophageal eosinophils were enriched for genes present within allergic disease risk loci and genes that correlated with the degree of esophageal eosinophilia. Furthermore, the esophageal eosinophil molecular signature was regulated by interactions between eosinophils and esophageal epithelial cells.  Taken together, we determined that esophageal eosinophils are programmed through interactions with epithelial cells by interplay of local tissue extrinsic factors that operate through a transcription factor complex containing AP-1.

overall_design: We performed ATAC-seq on FACS-sorted esophageal and bone marrow eosinophils (CCR3 high and CCR3 low bone marrow eosinophils) isolated from CC10-iIL13Tg mice. Experiments were performed in two to four replicates per group, each replicate was pooled from 6-10 mice.

first: Marc

middle: E

last: Rothenberg


title: Quantitative proteome and acetylome analyses uncover integrated drought resistance mechanisms in rice

first: Wei

address: 2005 Songhu Road

institute: Fudan University

summary: Drought stress significantly reduces rice productivity, necessitating efforts to understand resistance mechanisms. This study utilizes quantitative proteomic and lysine acetylomic analyses to elucidate the complex drought responses in three rice cultivars with distinct drought resistance strategies. Proteomic analysis reveals that Hanyou73, an integrated drought avoidance and drought tolerance cultivar, exhibits exceptional resistance to water deprivation compared to other cultivars. Critically, lysine acetylomic analysis underscores the pivotal role of histone acetylation, particularly H4K5ac, in modulating water management efficiency, which underpins Hanyou73's drought resilience. Leveraging this enhanced water management, Hanyou73 exhibits superior photosynthetic efficiency under drought conditions, primarily attributed to the deacetylation of ATP synthase beta subunit (AtpB) at K100, thereby augmenting ATPase catalytic activity. Additionally, deacetylation of phosphoglucomutase (PGM) at K155 indicated an adaptive metabolic response across all drought-resistant cultivars, ensuring sustained energy and metabolic intermediate supply crucial for broad adaptation mechanisms. Collectively, these findings elucidate the intricate regulatory networks in Hanyou73, highlighting its sophisticated balance between drought avoidance and tolerance strategies. This research offers valuable insights into the proteomic and lysine acetylomic dynamics underlying rice drought resistance, providing potential biomarkers for breeding towards genetic enhancement.

overall_design: ChIP-seq analysis of histone H4K5ac in rice cultivar Hanyou73 leaves under both well-watered (WW) and drought-stressed (DS) conditions.

first: Shoujun

first: Zhen

last: Wu

first: Liang

first: Qiaojun

last: Lou


title: High throughput CRISPR perturbation screens identify epigenetic regulators impacting primordial germ cell development [CRISPRi]

first: Jingyi

overall_design: Using a CRISPR inhibition (CRISPRi) screen to identify essential epigenetic regulators of PGC development.


title: Scalable and Efficient Generation of Mouse Primordial Germ Cell-like Cells

summary: Primordial germ cells (PGCs) are the founder cells of the germline. The ability to generate PGC-like cells (PGCLCs) from pluripotent stem cells has advanced our knowledge of gametogenesis and holds promise for developing infertility treatments. However, generating an ample supply of PGCLCs for demanding applications such as high-throughput genetic screens has been a limitation. Here, we demonstrated that simultaneous overexpressing 4 transcriptional factors – Nanog and three PGC master regulators Prdm1, Prdm14 and Tfap2c - in suspended mouse epiblast like cells (EpiLCs) and formative embryonic stem cells (ESCs) results in efficient and cost-effective production of PGCLCs. The overexpression of Nanog enhances the PGC regulatory network and suppresses differentiation of somatic lineages, enabling a significant improvement in the efficiency of PGCLC production. Transcriptomic analysis reveals that differentiated PGCLCs exhibit similarities to in vivo PGCs and are more advanced compared to cytokine-induced PGCLCs. These differentiated PGCLCs could be sustained over prolonged periods of culture, and could differentiate into spermatogonium-like cells in vitro. Importantly, the ability to produce PGCLC differentiation at scale enables biochemical and functional genomic screens to dissect mechanisms of germ cell development and infertility.

overall_design: RNA-seq for 4 transcriptional factor (i.e., Prdm1, Prdm14, Tfap2c and Nanog) induced PGCLC at day 2, 4 and 6, as well as EpiLC and ESC.

first: Liangdao


title: Targeting Liver Epsins Ameliorates Dyslipidemia in Atherosclerosis through Inhibition of Proprotein Convertase Subtilisin/Kexin Type 9-Mediated Low-density Lipoprotein Receptor Degradation

city: Boston

first: Krishan

last: Gupta

state: MASSACHUSETTS

address: 300 Longwood Avenu, Boston children's Hospital

institute: Boston Children's Hospital/Harvard Medical School

summary:
Background: The low-density lipoprotein receptor (LDLR) in the liver plays a crucial role in clearing low-density lipoprotein cholesterol (LDL-C) from the bloodstream. This process takes place mainly in the liver. Under atherogenic conditions, Proprotein Convertase Subtilisin/Kexin Type 9 (PCSK9), secreted by the liver, binds to LDLR on hepatocytes, preventing its recycling and enhancing its lysosomal degradation. This process reduces LDL-C clearance, promoting hypercholesterolemia. Epsins, a family of ubiquitin-binding endocytic adaptors, are key regulators of atherogenesis in lesional cells, including endothelial cells and macrophages. Given epsins' canonical role in regulating endocytosis of cell surface receptors, we aimed to determine whether and  how liver epsins contribute to PCSK9-mediated LDLR endocytosis and degradation, thereby impairing LDL-C clearance and accelerating atherosclerosis.
Methods: Liver-specific epsin knockout (Liver-DKO) atherosclerotic models were generated in ApoE-/- and PCSK9-AAV8-induced atheroprone mice fed on a Western diet. We utilized single-cell RNA sequencing, along with molecular, cellular, and biochemical analyses, to investigate the physiological role of liver epsins in PCSK9-mediated LDLR degradation. Additionally, we explored the therapeutic potential of nanoparticle-encapsulated siRNAs targeting epsins 1 and 2 in ApoE-/- mice with established atherosclerosis.
Results: Western diet (WD)-induced atherosclerosis was significantly attenuated in ApoE-/-/Liver-DKO mice compared with ApoE-/- controls, as well as in PCSK9-AAV8-induced Liver-DKO mice compared with PCSK9-AAV8-induced wild-type (WT) mice accompanied by reductions in blood cholesterol and triglyceride levels. Mechanistically, single-cell RNA sequencing of hepatocytes and aortas isolated from atherosclerotic ApoE-/- and ApoE-/-/Liver-DKO mice revealed epsin-deficient Ldlrhi hepatocytes with diminished lipogenic potential. Notably, pathway analysis of hepatocytes showed increased LDL particle clearance and enhanced LDLR-cholesterol interactions under WD treatment in ApoE-/-/Liver-DKO mice compared with ApoE-/- controls, correlating with decreased plasma LDL-C levels. Furthermore, pathway analysis of the aortas showed attenuated inflammation and endothelial activation, coupled with reduced lipid uptake, and enhanced cholesterol efflux under WD treatment in ApoE-/-/Liver-DKO mice compared with ApoE-/- controls. Moreover, the absence of liver epsins led to an upregulation of LDLR protein expression in hepatocytes. We further demonstrated that epsins bind LDLR via the ubiquitin-interacting motif (UIM), enabling PCSK9-mediated LDLR degradation. Depleting epsins abolished this degradation, thereby preventing atheroma progression. Lastly, targeting liver epsins with nanoparticle-encapsulated epsins siRNAs effectively ameliorates dyslipidemia and inhibits atherosclerosis progression. These results are consistent with findings showing an increased epsin1 and epsin2 expression in atherosclerotic cardiovascular disease patients.
Conclusions: Liver epsins drive atherogenesis by promoting PCSK9-mediated LDLR degradation, thereby elevating circulating LDL-C levels and heightening lesional inflammation. As such, targeting epsins in the liver represents a promising therapeutic strategy to mitigate atherosclerosis by preserving LDLR and enhancing LDL-C clearance in the liver.

overall_design: In this study, all animal procedures were performed in compliance with institutional guidelines and mouse protocols were approved by the Institutional Animal Care and Use Committee (IACUC) of Boston Children’s Hospital, MA, USA.

first: Gupta

last: Krishan

first: Zhu

last: Bo

first: Chen

last: Hong

last: Kaifu


title: Epigenetic and Transcriptional Programming of Esophageal Eosinophils by the Local Tissue Environment

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

overall_design: Refer to individual Series


title: Myeloid Leukemia

city: Nanjing

first: feifei

last: yang

address: Changle Road 68

institute: Nanjing first hospital,Nanjing medical university

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Next Generation Sequencing Facilitates Quantitative Analysis of  Macrophage and Leukemia Stem Cell Transcriptomes  in Mouse Iron-overload  MLL-AF9 Acute Myeloid Leukemia

summary: The goals of this study aim to reveal functional and phenotypic diversity of  Macrophage and  Leukemia Stem Cell in response to the Iron-overloaded microenvironmental cues  in mouse acute myeloid leukemia

overall_design: Anasizy the transcriptomes of Macrophage and  Leukemia Stem Celll in Mouse Iron-overload acute myeloid leukemia

first: Feifei

last: Yang


title: Urolithin A is a potent modulator of cGAS-Sting signaling pathway

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

summary: The innate immune cGAS-STING pathway has emerged as an important signaling system in the organismal defense against viral and bacterial infections, inflammatory responses to cellular damage, regulation of autophagy, as well as in tumor immunosurveillance. Such key functions of the cGAS-STING pathway make it an attractive target for pharmacological intervention in disease treatments and in controlling inflammation and immunity. Here, we show that urolithin A (UA), an ellagic acid metabolite, exerts a profound effect on the expression of STING and enhances cGAS-STING activation and STING-related autophagy in response to cytosolic DNA in human cell lines. Animal laboratory models and limited human trials have reported no obvious adverse effects of UA administration. Thus, the use of UA alone or in combination with other pharmacological compounds may present a potential therapeutic approach in the treatment of human diseases that involves aberrant activation of the cGAS-STING pathway or accumulation of cytosolic DNA and warrants further investigation in relevant transgenic animal models.

overall_design: HMC3 immortalized human microglial cells were incubated in growth medium containing either no (Control, N=3), or Urolithin A(UA, 10 μM for five days and 12.5 μM UA for 48 hours, N=3), while 500 ng double-stranded DNA (DNA) was added to cells with or without prior UA stimulation (UA+DNA and DNA, respectively, N=3 for each experiment). The NanoString human neuroinflammation panel (XT-CSO-MNROI1-12) with nCounter read-out was used to assay gene expression changes.

first: Vilhelm

middle: A

last: Bohr


title: HZL-1 CLIP-Seq in AMPK mutant and daf-2 dauer

status: Public on Sep 03 2025

city: Montreal

first: Sabih

last: Rashid

state: Quebec

address: 3611 Rue Sainte Famille, Unit 11

department: Biology

country: Canada

institute: McGill University

summary: C. elegans lacking AMPK do not exhibit reproductive defects during normal growth, but when passaged through dauer, exhibit germline hyperplasia and premature spermatogenesis, followed by complete sterility post-dauer (Narbonne and Roy, Development, 2006). Loss of a novel RNA helicase HZL-1 suppresses these phenotypes. We sought to carry out carry out a CLIP-Seq to determine what RNAs, if any, are bound by HZL-1 in the absence of AMPK in the dauer stage.

overall_design: CLIP-Seq of dauer (96 hours post-hatching at restricted temperature) in the daf-2 and daf-2; aak-1; aak-2 (aak(0)) and hzl-1 genetic background harboring a hzl-1::gfp transgene expressed under intestinal or endogenous promoter. After immunoprecipitation with anti-GFP, samples were treated with standard Trizol RNA extraction of collected samples.

first: Rashid

last: Sabih

first: Roy

last: Richard


title: Lysosomal exocytosis by macrophages as a druggable mechanism for anti-inflammatory clearance of dead adipocytes in adipose tissue

city: Leipzig

first: Raphaela

last: Wehr

state: Saxony

address: Liebigstraße

department: Institute of Anatomy

country: Germany

institute: Leipzig University

summary: The clearance of dead adipocytes in adipose tissue (AT) poses a major challenge due to their large size, which exceeds the phagocytic capacity of macrophages and prevents classical, anti-inflammatory efferocytosis. Instead, adipose tissue macrophages (ATMs) accumulate around dying adipocytes, forming crown-like structures (CLS), and engage in lysosomal exocytosis – the extracellular degradation of adipocytes. In this study, we used an ex vivo explant model of murine epididymal white AT, cultured over seven days to investigate pharmacological strategies that modulate lysosomal exocytosis. We observed a progressive increase in CLS formation, secretion of the lysosomal enzymes ß-Hexosaminidase A (HEXA) and lysosomal acid lipase (LAL), and surface abundance of LAMP1 and LAMP2, confirming ATMs as key mediators of this process. Notably, activation of lysosomal exocytosis with the mTOR inhibitor Rapamycin enhanced adipocyte clearance and significantly reduced inflammatory ATM abundance and TNF-α secretion. Bulk RNA sequencing of ATMs revealed a highly significant impact of Rapamyin on ATM proliferation.  In contrast, inhibition of lysosomal exocytosis with PIKfyve inhibitor Apilimod or targeted inhibition of LAL using Lalistat-2 disrupted lysosomal function and promoted a pro-inflammatory ATM phenotype. Our findings highlight lysosomal exocytosis as a critical pathway for the resolution of dead adipocytes and the regulation of inflammation in adipose tissue. Pharmacological enhancement of this process may represent a promising therapeutic approach to attenuate inflammation in AT and its metabolic consequences, including insulin resistance and type 2 diabetes.

overall_design: After sacrificing the mice, the rostral eWAT was dissected under sterile conditions and cut into small pieces (explants) of ≈ 1 mm3 (10 mg per explant) in PBS. Five AT explants per well were transferred to six-well plates prepared with 1 ml cell culture medium: RPMI 1640 with 10 % fetal bovine serum and 1 % antibiotics (100 U/ml penicillin and streptomycin). Explants were over casted with cell culture inserts and cultured at 37 °C with 5 % CO2 and 21 % O2 for seven days. On day one of AT explant culture, 100 µl treatment (Rapamycin 0.5 µM or Apilimod 0.5 µM or Lalistat 10 µM or DMSO-control 0.5%) solution was added in each well. Treated AT explants were digested using collagenase. SVF was resuspended in staining buffer and the Fc-receptors blocked by anti CD16/32 (1:100) for 10 min on ice. After centrifugation (300 g, 5 min, 4 °C, slow deceleration) cells were stained with labeled F4/80 antibody (1:200) on ice for 20 min, centrifugated (300 g, 5 min, 4 °C, slow deceleration), resuspended in staining buffer. Living, F4/80+ cells were sorted (~50,000 cells per sample) using a BD FACSAria SORP and frozen at −80 °C in TRIzol. RNA isolation and purification was performed using RNeasy Micro Kit by Quiagen. RNA sequencing and analysis was performed at Leipzig University’s Core Unit ‘DNA Technologien’. RNA extraction and library preparation was performed with a sequencing depth of 10 million reads/sample. Results were then analyzed using the DESeq2 package on Galaxy2. Differentially expressed genes (DEG) were considered as significant with a p-adj. value < 0.01 and a log2(fold change) > 0.5 or < -0.5. Gene set enrichment analysis was performed with datasets from the DAVID Database. For each condition, AT from 8 animals was pooled in groups of two, so that 4 samples were analyzed for each treatment.

first: Andreas

last: Lindhorst

first: Lilli

last: Arndt

first: Martin

last: Krueger

first: Nora

last: Raulien

last: Gericke


title: The Integrated Stress Response Pathway Improves Aged Murine Muscle Stem Cell Activation and in vivo Regeneration

city: San Francisco

first: Andrew

last: Brack

state: CA

address: 35 Medical Center Way

department: Orthopaedic Surgery

institute: UCSF

summary: For efficient regeneration, muscle stem cells (MuSCs) transition out of quiescence through a series of progressively more activated states. During MuSC aging, transition through the earliest steps is the slowest and delayed, with the molecular regulators that govern this transition not well characterized. Here, we found that aged MuSCs have increased baseline integrative stress response (ISR) activity in quiescence that does not increase during activation to levels observed in adult MuSCs. Rapid and transient pharmacological ISR activation in vitro was sufficient to increase aged MuSC activation rate through ISR-activator (ISR-a) and migratory behavior and also alter the transcriptional states toward an adult phenotype. ISR activation also improved aged MuSC potency and aged mouse muscle regeneration in vivo. Therefore, pharmacological activation of the ISR has therapeutic potential to improve MuSC function and skeletal muscle repair during aging.

overall_design: RNA seq profiling of adult (4 month), aged (22 month) and ISR-activator treated of activated (18h) Murin Muscle Stem Cells to investigate the effects of ISR activation on activated muscle stem cells.

first: Samiha

last: Mahin

first: Alex

last: Brown


title: Genome-wide DNA methylation analysis in prostate cancer

city: Daejeon

first: Tae Jeong

last: Oh

address: 44-6 10-ro Yuseong-gu

country: South Korea

institute: Genomictree, Inc.

type: Methylation profiling by genome tiling array

summary: Methylation profiling in prostate cancer: adjacent normal tissue vs prostate tumor tissue

overall_design: indirect comparison experiment : CRD(common reference DNA) vs Prostate tumor, CRD vs Adjacent non-tumor tissues

first: Sungwhan

last: An

first: TaeJeong

first: YangYei

last: Seo

first: Min

last: Woo


title: Deer Antler ASCs Exosomes Ameliorate Osteoarthritis via miR-140/MMP13 Axis-Mediated Dual Modulation of Inflammation and Cartilage Regeneration

city: Changchun

first: Boyin

last: Jia

state: Jilin

address: 2888 Xincheng Street

department: College of Animal Science and Technology

institute: Jilin Agricultural University

type: Non-coding RNA profiling by high throughput sequencing

summary: Osteoarthritis (OA) is a progressive degenerative joint disorder characterized by chondrocyte dysfunction and extracellular matrix degradation. While stem cell therapies have been constrained by immunological rejection risks, their derived extracellular vesicles (Exos) emerge as a promising alternative therapeutic approach. Antler, a remarkable regenerative organ with extraordinary regenerative capacity and chondrogenic potential, offers a unique biological resource. Antler Stem Cells (ASCs) provide an innovative extracellular vesicle source (ASC-Exos) that presents a compelling therapeutic strategy for addressing OA's complex pathogenesis. To investigate the therapeutic effects and mechanism of ASC-Exos in OA treatment. ASCs characteristics were confirmed through immunofluorescence and tri-lineage differentiation, while exosomes were validated using transmission electron microscopy, nanoparticle tracking analysis, and Western blot. A rat OA model was established to evaluate therapeutic effects of ASC-Exos via different administration routes. Small RNA sequencing identified key extracellular vesicle components, while dual-luciferase reporter assays confirmed regulatory interactions between miR-140 and metalloproteinase-13(MMP13). Stable miR-140 overexpressing ASCs were generated through lentiviral transduction. An IL-1β-stimulated chondrocyte OA model was employed to assess the impact of miR-140-engineered ASC-Exos (miR-140-Exos) on cellular proliferation, migration, and apoptosis. The therapeutic potential was further evaluated in in vivo animal models. We successfully isolated and characterized ASCs and ASC-Exos. Intra-articular injection of ASC-Exos demonstrated superior cartilage repair efficacy. The critical extracellular vesicle component miR-140 was identified. In vitro studies revealed that miR-140-Exos significantly enhanced chondrocyte proliferation and migration while reducing cellular apoptosis. Dual-luciferase assays confirmed miR-140 directly targets MMP13, with MMP13 overexpression partially reversing miR-140-mediated cellular effects. In vivo investigations demonstrated that miR-140-modified ASC-Exos effectively inhibited COL II degradation and suppressed NLRP3 elevation, thereby providing anti-inflammatory benefits and promoting cartilage regeneration. miR-140-Exos represent an innovative therapeutic approach for osteoarthritis, effectively promoting cartilage regeneration and alleviating inflammation through MMP13 inhibition, presenting a novel therapeutic strategy for OA treatment.

overall_design: ASC-Exos and chondrogenic-induced Chr-ASC-Exos  were collected. Total RNA pooled was collected from ASC-Exos and chondrogenic-induced Chr-ASC-Exos to construct a cDNA library. ASC-Exos and chondrogenic-induced Chr-ASC-Exos miRNAs were analyzed by Illumina NovaSeq 6000 for high-throughput deep sequenc.

first: Yuhao

last: Song

first: Xue

last: Wang

first: Xin

last: Li


title: Exogenous Delivery of Sphingomyelinase Mediates Mesenchymal Stromal Cell-Extracellular Vesicle Biogenesis, Alters Cargo Sorting, and Therapeutic Potency in vitro

city: Atlanta

first: Daniel

last: Shah

state: Ga

address: 315 Ferst Dr.

department: Biomedical Engineering

institute: Georgia Institute of Technology

summary: Mesenchymal stromal cells (MSCs) are multipotent stromal cells with regenerative, immunomodulatory, and anti-inflammatory properties, making them a promising tool in cell-based therapies. Increasing evidence suggests the therapeutic effects of MSCs are largely mediated by secreted paracrine factors and extracellular vesicles (EVs), which facilitate extracellular communication by transferring bioactive molecules such as proteins, lipids, and nucleic acids to target cells. The lipid composition of EVs is critical for their stability, uptake, and functional activity. Sphingomyelinase (SMase), an enzyme that hydrolyzes sphingomyelin into ceramide, plays a key role in EV biogenesis by influencing membrane curvature allowing for invagination and budding of multivesicular bodies (MVBs). However, the impact of SMase treatment on the characteristics and therapeutic potential of MSC-derived EVs remains largely unexplored. In this study, human MSCs were cultured with SMase for 24 hours and EVs were isolated via ultracentrifugation. EV size distribution was analyzed using nanoparticle tracking analysis (NTA), microRNA (miRNA) profile was determined using RNA-sequencing, while lipidomic and proteomic profiling were assessed using mass spectrometry. Functional assays were conducted to assess changes in bioactivity. NTA revealed a shift in EV production, with a higher vesicle concentration in SMase induced MSCs compared to untreated cells. SMase treatment significantly altered MSC-EV composition, leading to increased ceramide and glycosphingolipids. In addition, the modifications in protein and miRNA EV cargo were found to be associated with pathways involving TNF-α signaling, vesicle trafficking, wound healing, and angiogenesis. Functional assays indicated greater suppression of TNF-α in activated macrophages and greater tubular network formation in HUVECS. These findings provide new insights into distinct biophysical and biochemical changes in MSC-derived EVs following SMase stimulation, potentially enhancing their therapeutic properties and may inform strategies for optimizing future EV-based therapies.

overall_design: MSCs were treated with SMase for 24 hours and the miRNA profile of MSCs and their derived EVs was sequenced.

first: S'Dravious

last: DeVeaux

first: Hongmanlin

last: Zhang

first: Alan

middle: Y

first: Tosin

last: Adedipe

first: Nathan

middle: F

last: Chiappa

first: Krishna

last: Patel

first: Young

last: Jang

first: Steven

middle: L

last: Goudy

first: Todd

last: Sulchek

first: Krishnendu

last: Roy

first: Edward

last: Botchwey


title: Nuclear accumulation of ADAMTS1 zymogen: A novel mechanism promoting chemoresistance and metastasis in breast cancer

city: beijing

first: wang

middle: xi

last: lin

address: 10 You’anmen Outer West 1st Street

institute: capital medical univercity

summary: Chemoresistance and metastasis are the primary causes of mortality in patients with breast cancer. Here, we demonstrated that the metalloproteinase ADAMTS1 is upregulated in chemotherapy-treated and metastatic breast cancer samples. Mechanistically, the zymogen form of ADAMTS1 undergoes nuclear translocation via importin-dependent transport, where it cooperates with the SWI/SNF complex to activate a set of genes, including TBK1, STING, TRAF6, and MARCHF2, leading to STING ubiquitination and the non-classical cGAS-STING-NF-kB signaling activation, which in turn promotes chemoresistance and metastasis. Notably, long-term chemotherapy establishes a self-reinforcing loop by: (i) NF-kB/p65-mediated transcriptional induction of ADAMTS1, and (ii) MARCHF2-dependent ubiquitin-proteasomal degradation of FURIN, the protease responsible for ADAMTS1 maturation. This dual regulation results in nuclear accumulation of catalytically inactive ADAMTS1 zymogen. Clinical analyses have shown that high ADAMTS1 expression combined with low FURIN expression is strongly associated with poor patient prognosis. These results reveal a key role for the zymogen ADAMTS1 in inducing tumor chemoresistance and metastasis in response to long-term chemotherapy stimulation, supporting the use of its inhibitor melatonin as a therapeutic strategy in combination with chemotherapy for patients with breast cancer.

overall_design: we performed cleavage under targets and tagmentation (CUT&Tag) using antibodies against ADAMTS1 in MDA-MB-231BrM cells to profile genome-wide transcriptional targets of ADAMTS1.

first: Zhaohan

first: Yu

first: Xilin

first: Yaning

first: Zicheng

last: Wu

first: Minghui

last: Zhao

first: Yuchen

last: Xiang

first: Wenying

last: Zhong

first: Tingting

first: Yingqi

last: Lv

first: Wenjuan

first: Lulu

first: Jia

last: Yan

first: Hao

last: Zhuang

first: Lin

last: Shan


title: Regulatory T cell-derived TGF-β signaling governs the heterogeneity and abundance of tumor-infiltrating bystander CD8+ T cells

city: Chongqing

first: shuai

last: yue

state: Chongqing

address: Gaotanyan street

institute: army medical university

summary: ATAC-seq library was prepared using Hyperactive ATAC-seq Library Prep Kit for Illumina (Vazyme, TD711) to study bystander P14 CD8+ T cells in tumor. Here, we further demonstrate that TME-infiltrating TBYS cells subpopulations, including TCM-like, TEM-like, TRM-like ones, exhibit distinct epigenetic programs. This study gives a epigenetic profiles of bystander P14 CD8+ T cells in tumor.

overall_design: Congenic CD45.1+ P14 CD8+ T cells were adoptively transferred into naive C57BL/6 recipients (CD45.2+), which were then infected with LCMV Armstrong and engrafted with MC38 cells on Day 60 post infection. On day 15 post tumor engraftment, P14 CD8+ T cells in tumor were sorted by FACS and analyzed using ATAC-seq.

first: Yao

last: Lin

first: Junjian

last: He

first: Shuai

last: Yue

first: Ding

last: Qiu

first: Xiangyu

last: Chen


title: FGF1-FGFR2 axis regulated by nuclear receptor RORγ represents an effective strategy in intrahepatic cholangiocarcinoma

city: Guangzhou

first: Zhanfeng

last: Gu

state: Guangzhou

address: No. 183, Zhongshan Avenue West

department: Department of Hepatobiliary surgery

institute: The Third Affiliated Hospital of Southern Medical University

summary: Intrahepatic cholangiocarcinoma (iCCA) is a highly aggressive malignancy with limited therapeutic options. Although targeted therapies like pemigatinib provide partial clinical benefits, acquired resistance remains a significant challenge. Through integrative bioinformatics analysis of public datasets and immunohistochemical validation, we identified the retinoid-related orphan receptor gamma (RORγ) as markedly upregulated in iCCA. Genetic silencing and pharmacological inhibition of RORγ (GSK805/XY101) suppressed proliferation, induced apoptosis in vitro, and significantly reduced xenograft tumor growth in vivo. Mechanistically, RORγ promoted fibroblast growth factor receptor 2 (FGFR2) signaling via two complementary mechanisms: direct transcriptional activation of FGFR2 and induction of fibroblast growth factor 1 (FGF1) expression and secretion, which in turn activated FGFR2. Inhibition of RORγ markedly decreased FGF1 levels in conditioned media, whereas exogenous FGF1 restored tumor growth. Notably, RORγ antagonists synergized with pemigatinib to overcome resistance in pemigatinib-refractory models. Collectively, these findings identify the RORγ-FGF1-FGFR2 axis as a critical oncogenic driver in iCCA and highlight RORγ inhibition as a promising therapeutic strategy to suppress tumor progression and enhance sensitivity to FGFR inhibitors.

overall_design: HUCCT-1 cells were treated with vehicle, XY101 (5 µM) for 48 hours. Total RNA was extracted, and RNA-seq libraries were constructed using Illumina TruSeq Kit. RNA sequencing (RNA-seq) was performed by Beijing Genomics Institute (BGI, Shenzhen, China). Briefly, poly(A)⁺ mRNA was enriched using oligo(dT) magnetic beads. cDNA was synthesized under high-temperature conditions and purified by the kit. Sequencing was carried out on the BGISEQ platform. The resulting reads were aligned to the reference human genome assembly (GRCh37/hg19) using BWA and Bowtie 2. Gene expression levels were quantified from the RNA-seq data using RSEM, and a heatmap was subsequently generated to visualize the expression profiles.

first: Xiaojuan

last: Wang

first: Hong

first: Junhua

first: Zhaorong

last: Huang

first: Dongyue

last: Pan

first: Zhenhua

last: Zhang

first: Yechun

last: Zeng

first: Guodi

last: Cai

first: Huizi

last: Sun

first: Jun

last: Zheng

first: Yichu

last: Nie

first: Qingwen

first: Haolong

last: Li

first: Franky Leung

last: Chan

first: Jianwei

first: Yingfang

last: Fan


title: Serum Amyloid A (SAA) induces transcription affecting inflammation

first: George

middle: Henry

last: Sack

address: 725 N. Wolfe Street

department: Department of Physiology, Pharmacology and Therapeutics

institute: Johns Hopkins University School of Medicine

summary: The 104 aa protein Serum Amyloid A (SAA) is a prominent member of the acute phase response (APR) a remarkably conserved and stereotyped set of serum protein changes associated with inflammation and other stimuli. N-terminal fragments of SAA can form fibrils that can accumulate in organs (“amyloidosis”). No specific biologic function has been identified for SAA; it has been considered an inert “biomarker.” In contrast to this perception of passivity, we report that exposure to both N-terminal decapeptides and intact SAA monomers can induce multiple transcripts in both enteroids and HEK293 cells. The spectrum of transcripts prominently includes proteins related to inflammation and NF-κB control, specifically NFKB1A, TNFA1P3 and IER3. SAA thus can act directly through specific transcription to alter cellular physiology with direct effects on inflammation, likely helping explain its remarkable evolutionary conservation as part of primordial defense.

overall_design: RNA-seq profiling of HEK293 cells treated with full-length SAA protein, with corresponding vehicle controls (HOH + 0.05% BSA). Samples were harvested at specific time points to capture transcriptional changes.

middle: H

last: Sack Jr

first: Joseph

last: Yun

first: Conover

last: Talbot Jr


title: TGFβ signaling in cancer-associated fibroblasts drives a hepatic gp130-dependent pro-metastatic inflammatory program in colorectal cancer

city: Glasgow

first: Kathryn

last: Gilroy

address: Garscube

country: United Kingdom

institute: CRUK Scotland Institute

summary: The Consensus Molecular Subtype 4 (CMS4) of colorectal cancer (CRC) has the worst prognosis and  the highest frequency of hepatic metastases. It is characterized by abundant cancer-associated fibroblasts (CAFs) in the tumor microenvironment and active TGFβ signaling, but the molecular drivers of metastasis remain unclear. Here, we show that TGFβ signaling in CRC patient-derived CAFs from the primary tumor induces production of IL-6 family cytokines, particularly IL-6 and IL-11. These cytokines stimulate hepatocytes to express myeloid chemoattractants, including SAA1, through gp130-dependent JAK/STAT signaling. This promotes neutrophil recruitment to the liver, potentially creating a pro-metastatic niche. This IL-6 family-JAK/STAT stromal signaling axis is active in both a murine model of CMS4 as well as in human CRC patients in vivo. Combined, our data reveal that TGFβ-driven CAF signaling actively contributes to the formation of a neutrophil-dependent, pre-metastatic hepatic niche in the metastatic phenotype of CMS4 CRC.

overall_design: Bulk RNA seq of murine wild type colon tissue, organoid lines and colonic tumors from intracolonic transplants of these lines.

first: Mark

last: White

first: Tamsin

last: Lannagan

first: Rene

last: Jackstadt

first: Michael

last: Gillespie

first: Owen

last: Sansom


title: scRNA-seq performed in the knee joint of the DMM-induced OA mouse model versus sham-operated mice

city: NanJing

first: Chuyue

last: Pan

address: 639 Longmian Ave.

institute: China Pharmaceutical University

summary: Osteoarthritis (OA) is typically characterized by progressive cartilage breakdown, subchondral bone remodeling, osteophyte formation and low-grade joint inflammation. Accumulative evidence demonstrates that cartilage fibrosis and the resulting degradation of extracellular matrix are implicated in the late-stage pathology of OA. However, the mechanisms underlying this degenerative joint disease remain largely undefined.We isolated articular cartilage from control-sham, control-DMM and cKOAcan(chondrocyte conditional ZEB1 knockout mice)-DMM mice and performed scRNA-seq analysis.

overall_design: The cartilage from control-sham, control-DMM and cKOAcan-DMM mice was collected and stored in the sCelLiveTM Tissue Preservation Solution (Singleron) on ice within 30 mins. After being washed with Hank’s Balanced Salt Solution, the samples were cut into 1-2mm pieces and then digested with 3 mL sCelLiveTM Tissue Dissociation Solution (Singleron) by Singleron PythoN™ Tissue Dissociation System at 37°C for 15 min. The cell suspension was filtered through a 40-micron sterile strainer to remove red blood cells and stained with Trypan Blue to evaluate the cell viability. The mRNA from single cells was reversely transcribed into cDNA and the cDNA was amplified by PCR, then fragmented and ligated with sequencing adapters. The GEXSCOPE® Single Cell RNA Library Kit (Singleron) was used to construct the scRNA-seq libraries. CeleScope v1.5.2 (Singleron Biotechnologies) was used to generate gene expression profiles with default parameters and the raw data was used for further analysis.

first: Chen-Zhi

last: Zang

first: Cai-Yun

last: Xiong

first: Chu-Yue

first: Cheng

last: Tang

first: Yang

first: Stephen

middle: J

last: Weiss

first: Rong

last: Fu

first: Zhao-Qiu

last: Wu


title: Tumor nutrient stress gives rise to a drug tolerant cell state in pancreatic cancer

city: Chicago

first: Alex

last: Muir

email: amuir@berkeley.edu, amuir@uchicago.edu

state: Illinois

department: Ben May Department for Cancer Research

institute: University of Chicago

summary: Cytotoxic chemotherapy remains the standard-of-care treatment for patients with pancreatic ductal adenocarcinoma (PDAC). However, chemotherapy only has modest effects at improving overall survival due to primary or rapidly acquired chemoresistance. The biological underpinnings of PDAC therapy resistance are incompletely defined, but the tumor microenvironment is known to be a major contributor to chemoresistance. We have found chemoresistance is imprinted on PDAC cells by the tumor microenvironment and persists for a period of days after PDAC cells are removed from tumors. However, PDAC chemoresistance is lost upon long term culture in standard laboratory conditions. Interestingly, culture of PDAC cells in Tumor Interstitial Fluid Medium (TIFM), a culture medium we developed to recapitulate the nutrient availability of the tumor microenvironment, maintains PDAC cells in a chemoresistant state even after long term culture ex vivo. These findings suggest that microenvironmental metabolic stress keeps PDAC cells in a physiologically relevant, therapy resistant cell state that standard culture models fail to maintain. Using TIFM culture, we sought to understand how PDAC cells in this state resist chemotherapeutic challenge. We found that chemotherapy drugs largely retain on-target activity within TIFM medium but fail to activate cell death, enabling a “chemotolerant” cell state, which is also observed in PDAC tumors. This chemotolerant state is driven by suppression of apoptotic priming and can be overcome by targeting the anti-apoptotic regulator BCL-xL. Taken together, these findings suggest that reprogramming of cell death mechanisms by the PDAC nutrient microenvironment is a key contributor to therapy resistance in this disease.

overall_design: Murine pancreatic cancer cells (mPDAC1) were grown in RPMI-1640 or in tumor interstitial fluid medium (TIFM). Cells in each medium were treated with either vehicle or 125nM gemcitabine for 24 hours. RNA was then extracted and sent for library prep and sequencing with the University of Chicago Genomics Core.

first: Colin

last: Sheehan


title: The effect of Anaerostipes caccaei and Bifidobacterium bifidum on epithelial cells of colon

city: Chuncheon

first: Seongwon

last: Pak

address: 12-1, Bonguisan-gil 22beon-gil, Chuncheon-si, Gangwon-do, Republic of Korea

department: Biomedical science

institute: Hallym university

summary: The purpose of this study is to determine whether cross feeding relationships can contribute to the alleviation of colitis. The two strains used in this study are Anaerostipes caccae and Bifidobacterium bifidum. Both strains are clearly present in significant amounts in the intestines of healthy humans. A. caccae is a butyrate-producing bacterium that uses lactic acid and acetate to produce butyrate. On the other hand, B. bifidum is known to produce lactic acid and acetate. The purpose of this study is to confirm the effect of the ecological network between the two strains on the improvement of colitis, particularly in terms of protecting intestinal epithelial cells.

overall_design: RNA-seq profiling of colonic epilthelial cells of DSS-induced murine colitis mouse with A. caccae and B. bifidum treatment

first: Keunwook

last: Lee


title: Transcriptomic and functional responses of the cystic fibrosis airway epithelium to CFTR modulator therapy

city: Aurora

first: Austin

last: Gillen

address: 12801 East 17th Avenue

institute: University of Colorado Anschutz Medical Campus

summary: Elexacaftor/tezacaftor/ivacaftor (ETI) CFTR modulator therapy has led to rapid and substantial improvements in cystic fibrosis (CF) airway disease. Underlying molecular and cellular mechanisms, long-term efficacy, and ability to reverse airway epithelial remodeling in established disease remain unclear. Longitudinal nasal brushes from an adult CF cohort were used to evaluate gene expression, cellular composition, stem cell function, and microbiome changes at baseline and at six months and two years after ETI. The baseline to six month span showed a massive downregulation of extensive neutrophilic inflammatory gene expression programs that correlated with increased pulmonary function and decreased sinusitis. Primary airway epithelial stem cell cultures from matched donor samples showed partially improved differentiation and barrier capacity at six months. Although clinical outcomes remained stable during the six month to two year span, transcriptional changes revealed a resurgence of baseline inflammatory programs. Time course gene expression was consistent with ongoing normalization of epithelial remodeling. Relative abundance of Pseudomonas also decreased during the time course. These data suggest that ETI rectifies inflammation, epithelial remodeling, and bacterial infection in the airways, but resurgence of inflammatory gene expression may indicate ongoing inflammation, potentially presaging disease progression with long-term therapy.

overall_design: Longitudinal nasal brushes from an adult cystic fibrosis cohort were used to evaluate gene expression changes using RNA-seq at baseline and at six months and two years after Elexacaftor/tezacaftor/ivacaftor CFTR modulator therapy.

first: Eszter

last: Vladar


title: MLK4 regulates macrophage-induced gene expression changes associated with extracellular matrix remodeling, cell adhesion, and invasion

city: Warszawa

first: Krzysztof

last: Goryca

address: Banacha 2c

department: CeNT

country: Poland

institute: Uniwersytet Warszawski

summary: Tumor-associated macrophages (TAMs) are key mediators of triple-negative breast cancer (TNBC) progression, yet the molecular mechanisms by which they promote malignancy remain incompletely defined. To gain insights into the molecular mechanisms involved in macrophage-driven induction of breast cancer proliferation and the role of MLK4 signaling, we performed expression profiling using mRNA-seq. Our result highlights MLK4’s role in promoting EMT and ECM reorganization during the cross-talk between cancer cells and macrophages.

overall_design: We analyzed SUM149PT cells with and without MLK4 silencing, under co-culture conditions with THP-1-derived M2 macrophages.

first: Alicja

last: Mazan-Bury

first: Dawid

last: Mehlich

first: Anna

last: Marusiak


title: Gene expression in muscle invasive and non-muscle invasive bladder cancer cell lines exposed to hypoxia

city: Bangor

first: Tim

last: Smith

address: Dean Street Bangor LL57 1UT

institute: Bangor University

summary:
Introductionon: Hypoxic cancers are radioresistant, but biomarkers based on expression of multiple genes can identify patients who will benefit from hypoxia modification. Most studies identifying relevant genes exposed cells in culture to 1% oxygen, which activates hypoxia-inducible factor (HIF). However, oxygen concentrations in hypoxic tumours are heterogeneous ranging from <0.1%. As lower oxygen levels would likely affect transcriptional responses, we aimed to investigate how gene selection at different oxygen levels affects the genes identified and their prognostic capability.
Methods:   Four MIBC (J82, T24, UMUC3, HT1376) and two non-MIBC (RT4, RT112) bladder cancer cell lines were exposed to varying oxygen levels (20%, 1%, 0.2% and 0.1% O2) for 24 h then harvested and frozen. RNA was extracted and transcriptomes analysed using Clariom S microarrays. Differences in gene expression were investigated. Prognostic and predictive significance of a published 24-gene signature was compared with one generated from genes identified at lower oxygen levels.

overall_design: Triplicate samples for all 4 oxygen concentrations and 6 cell lines

first: Rekaya

last: Shabbir

first: Conrado

last: Guerrero Quiles

first: Leo

last: Zeef

first: Brian

last: Lane

first: Peter

last: Hoskin

first: Ananya

last: Choudhury

first: Catharine

last: West


title: CDKN2A deletion remodels immune infiltrate in Diffuse Pleural Mesothelioma

city: Reggio Emilia

first: Benedetta

last: Donati

address: Viale Risorgimento, 80

country: Italy

institute: Azienda USL- IRCCS di Reggio Emilia

summary: RNA extracted from diagnostic tumor samples of 82 patients affected by Diffuse Pleural Mesothelioma was analyzed on the nCounter system using the PanCancer Immune Profiling Panel.

overall_design: Gene expression profiles were associated to CDKN2A mutational status

first: Federica

last: Torricelli

first: Alessia

last: Ciarrocchi


title: DEAD-Box Helicase 3 Modulates the Non-Coding RNA Pool in Ribonucleoprotein Condensates During Stress Granule Formation

city: COLUMBIA

first: HAO

last: JI

state: SC

address: 715 SUMTER ST CLS RM 109

department: College of Pharmacy

institute: University of South Carolina

summary: Stress granule formation is a type of liquid–liquid phase separation in the cytoplasm, leading to RNA–protein condensates that are associated with various cellular stress responses and implicated in numerous pathologies, including cancer, neurodegeneration, inflammation, and cellular senescence. One of the key components of mammalian stress granules is the DEAD-box RNA helicase DDX3, which unwinds RNA in an ATP-dependent manner. DDX3 is involved in multiple steps of RNA metabolism, facilitating gene transcription, splicing, and nuclear export and regulating cytoplasmic translation. In this study, we investigate the role of the RNA helicase DDX3’s enzymatic activity in shaping the RNA content of ribonucleoprotein (RNP) condensates formed during arsenite-induced stress by inhibiting DDX3 activity with RK-33, a small molecule previously shown to be effective in cancer clinical studies. Using the human osteosarcoma U2OS cell line, we purified the RNP granule fraction and performed RNA sequencing to assess changes in the RNA pool. Our results reveal that RK-33 treatment alters the composition of non-coding RNAs within the RNP granule fraction. We observed a DDX3-dependent increase in circular RNA (circRNA) content and alterations in the granule-associated intronic RNAs, suggesting a novel role for DDX3 in regulating the cytoplasmic redistribution of non-coding RNAs.

overall_design: U2OS cells were maintained in high-glucose Dulbecco’s Modified Eagle Medium (ATCC, Manassas, VA, USA  ) supplemented with 10% fetal bovine serum (Mediatech Inc., Manassas, VA, USA) and 1% penicillin/streptomycin (HyClone, GE Healthcare Life Sciences, Pittsburgh, PA, USA) at 37 °C in a humidified atmosphere with 5% CO2, as previously described [21]. Cells were pre-treated with 6 μM RK-33 (MedChemExpress  Monmouth Junction, NJ, USA), stock solution 5mM DMSO (MilliporeSigma Burlington, MA, USA  D8418) for 1 h. Sodium arsenite stress was induced by treating cells with sodium arsenite, 500 µM NaAsO2 (MilliporeSigma, Burlington, MA, USA S7400), for 60 min. Basal conditions were defined as treatment with 0.12% DMSO for 2 h, corresponding to the duration and timing of RK-33 addition in treated samples.

first: Elizaveta

last: Korunova

first: Michael

last: Shtutman

first: Hao

last: Ji


title: Ouabain alleviates Mycobacterium abscessus-triggered inflammatory responses through dual regulation of NLRP3 inflammasome activity and M1 macrophage polarization

city: shenzhen

last: Li

state: guangdong

address: A16, Life Science Valley, Jinye Avenue

department: Institute of Shenzhen Respiratory Diseases

institute: Shenzhen People's Hospital

summary: Mycobacterium abscessus (M. abscessus), one of the most drug-resistant and difficult-to-treat pathogens, primarily causes chronic pulmonary inflammation in humans. The cardiac glycoside ouabain has demonstrated broad-spectrum anti-inflammatory properties in multiple disease models. However, its therapeutic potential against M. abscessus-induced pulmonary inflammation remains unexplored. In this study, we aim to investigate the role of ouabain on M. abscessus-induced inflammation. Our results demonstrated that ouabain remarkably attenuated M. abscessus-mediated inflammatory responses by decreasing the expression of pro-inflammatory cytokines TNF-α, IL-6, and IL-1β. H&E results showed that intraperitoneal administration of ouabain alleviated M. abscessus-induced pulmonary inflammation and injury. Transcriptomic analysis and qPCR results further revealed that ouabain treatment significantly suppressed the upregulation of pro-inflammatory cytokines induced by M.abscessus and downregulated NLRP3 inflammasome expression in vivo. In vitro experiments further confirmed that ouabain treatment effectively suppressed both NLRP3 inflammasome activation and M1 macrophage polarization. Collectively, these findings suggested that ouabain alleviated M. abscessus-induced pulmonary inflammation through dual mechanisms: inhibition of NLRP3 inflammasome activation and modulation of M1 macrophage polarization. This work highlights ouabain’s potential as a therapeutic candidate for combating M. abscessus infections.

overall_design: Fresh lung tissues of C57BL/6J mice with M. abscessus infected and Ouabain treatment were selected for RNA sequencing.

first: Songqiang

last: Huang

first: Xing

last: Shi

first: Kuo

last: Lu

first: Xiu

last: Yu

first: Chen

last: Qiu

first: Rongchang

last: Chen


title: Slc22a17 governs postnatal neurogenesis by maintaining the iron homeostasis in hippocampus [RNA-Seq hippocampus]

status: Public on Sep 08 2025

city: Beijing

first: Ligong

address: Shuangqing Road No.30

institute: tsinghua university

summary: Iron transporters are essential for maintaining cellular iron homeostasis. Among them, SLC22A17 mediates lipocalin-2 (LCN-2)-dependent iron transport, but its precise role in the brain remains unclear. Here, we show that Slc22a17 is critical for postnatal neurogenesis by regulating hippocampal iron balance. Conditional knockout of Slc22a17 in the murine brain causes early postnatal lethality, growth retardation, neural stem cell apoptosis, and cognitive deficits, largely due to oxidative stress from iron overload. Mechanistically, Slc22a17 interacts with p62 to modulate Nrf2 activity. Its loss aberrantly activates the Nrf2/HO-1 pathway, disrupting iron efflux and promoting accumulation of reactive oxygen species (ROS). These findings establish Slc22a17 as a key regulator of neuronal development and a potential therapeutic target for neurological disorders linked to iron dysregulation.

overall_design: RNAseq profiling of C57BL/6 mice at postnatal day 14, and total RNA was extracted for sequencing.

first: Lei

last: Tao

first: Long

last: Teng


title: Klotho deficiency promotes skeletal muscle weakness and is associated with impaired motor unit connectivity

city: Indianapolis

first: Steven

middle: S

last: Welc

state: IN

address: 635 Barnhill Dr Apt Ms-332

department: Anatomy, Cell Biology & Physiology

institute: Indiana University School of Medicine

summary: Muscle wasting and weakness are important clinical problems that limit mobility and independence, shortening health span and increasing physical disability risk. The molecular basis for this has not been fully determined. Klotho expression is downregulated in conditions associated with muscle wasting, including aging, chronic kidney disease, and myopathy. The objective of this study was to investigate a mechanistic role for Klotho in regulating muscle wasting and weakness.  Body weight, lean mass, muscle mass, and myofiber caliber were reduced in Klotho-deficient mice. In the tibialis anterior muscle of Klotho null mice, type IIa myofibers were resistant to changes in size, and muscle composition differed with a higher concentration of type IIb fibers to the detriment of type IIx fibers. Glycolytic enzymatic activity also increased. Klotho-deficient mice showed impaired muscle contractility, with reduced twitch force, torque, and contraction-relaxation rates. RNA-sequencing revealed upregulation of synaptic and fetal sarcomeric genes, prompting us to examine muscle innervation. Klotho-deficiency led to neuromuscular junction remodeling, myofiber denervation, and functional motor unit loss. Loss of motor units correlated with absolute torque. Collectively, these findings reveal a novel mechanism through which Klotho-deficiency disrupts muscle synapses and motor unit connectivity, likely influences muscle wasting and weakness.

overall_design: RNA extracted from whole tibialis anterior muscles of male wild-type and Klotho homozygous mutant littermate mice.


title: The effect of ZIKV and MBD-mutant ZIKVs infection on neonatal mouse brains

first: Rui-Ting

state: Beijing

address: No.20 Dongda Street, Fengtai District

department: State Key Laboratory of Pathogen and Biosecurity

institute: Beijing Institute of Microbiology and Epidemiology

summary: To compare the impact of WT and MBD ZIKVs on the developing brain at the molecular level, we carried out global tanscriptome analyses (RNA-seq) on one-day-old neonatal mouse brains infected with Mock, WT or MBD2 ZIKV at 3 days post-infection.

overall_design: RNA sequencing (RNA-seq)-based transcriptional profiling experiments were conducted using Mock, WT and MBD2 ZIKV infected one-day-old neonatal mouse brains at 3 days after infection.

first: Xiang


title: Integrative analysis of mRNA stability regulation uncovers a metastasis-suppressive program in breast cancer [shRBMS3_RNAseq]

city: San Francisco

first: Hani

last: Goodarzi

department: Biochemistry and Biophysics

institute: UCSF

summary: Heterogeneity in cancer gene expression is typically linked to genetic and epigenetic alterations, yet post-transcriptional regulation likely influences these patterns as well. However, the quantitative contribution of post-transcriptional mechanisms to cancer transcriptome dynamics remains unclear. Here, we systematically measured mRNA dynamics across diverse breast cancer models, revealing that mRNA stability significantly shapes gene expression variability. To decipher the regulatory grammar underlying these dynamics, we developed GreyHound, an interpretable multimodal deep-learning framework integrating RNA sequence features and RNA-binding protein (RBP) expression. GreyHound identified an extensive network of RBPs and their regulons underlying variations in mRNA stability. Among these, we uncovered a metastasis-suppressive regulatory axis centered on the RNA-binding protein RBMS3 and its post-transcriptional control of the redox regulator TXNIP. Functional and molecular analyses revealed that RBMS3 depletion resulted in targeted transcript destabilization, which was associated with poor clinical outcomes and enhanced metastatic potential in xenograft models. Using in vivo epistasis studies, we confirmed that RBMS3 regulation of TXNIP mRNA stability drives this metastasis-suppressive program. These findings position the RBMS3-TXNIP regulatory axis as a key post-transcriptional mechanism in breast cancer and illustrate how interpretable models of RNA dynamics can uncover hidden regulatory programs in disease.

overall_design: To investigate the mechanisms of RNA regulation through RBMS3 in breast cancer, we knocked down RBMS3 in MDA-MB-231 cells. With differential gene expression analysis we examined RBMS3 target transcripts.

first: Heather

last: Karner

first: Tabea

last: Mittmann


title: Integrative analysis of mRNA stability regulation uncovers a metastasis-suppressive program in breast cancer [BRCA_SLAM-seq]

overall_design: To explore the variations in RNA stability underlying heterogeneity of gene expression in breast cancer, we performed SLAM-seq on six breast cancer cell lines from different subtypes.


title: Integrative analysis of mRNA stability regulation uncovers a metastasis-suppressive program in breast cancer [MPRA_shRBMS3]

overall_design: To validate RBMS3 binding sites, we applied a dual mCherry/GFP reporter assay for 13 RBMS3 binding site sequences and respective scrambled controls. This parallel reporter library was expressed in RBMS3 knockdown and control MDA-MB-231 cells to evaluate differential stability of transcripts containing RBMS3 binding sites.

first: Vicky


title: JARID2 Inhibition Reprograms Human Hematopoietic Progenitor Cells To Enhance Bone Marrow Transplantation

city: St Louis

first: Grant

last: Challen

state: MO

address: 660 Euclid Avenue

department: Medicine

institute: Washington University School of Medicine

summary: Hematopoietic stem cell transplantation is a common treatment for many blood disorders. Umbilical cord blood (UCB) serves as a valuable source of hematopoietic stem and progenitor cells (HSPCs), particularly for patients lacking a matched donor. However, the limited number of repopulating cells in UCB units restricts its clinical utility. Here, we demonstrate that JARID2 knockdown, distinct from EZH2 loss, increases both the number and functionality of human UCB-derived HSPCs in vitro and in vivo. After ex vivo culture, these functionally enhanced HSPCs were identified as CD34⁺CD90⁺EPCR⁺CD49f⁻CD71⁻. Mechanistically, JARID2 knockdown promotes a quiescent, long-term self-renewal gene expression program by upregulating STAT1 and MHC class II. Notably, it also confers HSC-like potential to multipotent progenitors (MPPs), enhancing their regenerative capacity. These findings support JARID2 inhibition as a safe and reversible strategy to expand functional HSPCs from UCB ex vivo, potentially increasing access to this life-saving therapy for a broader patient population.

overall_design: To investigate the molecular mechanisms underlying JARID2-KD–mediated HSPC expansion and functional enhancement, we transduced enriched human CD34⁺ cells from umbilical cord blood with shRenilla, shJARID2, or shEZH2, and sorted hCD34⁺ cells for CITE-seq after 8 days of ex vivo culture. Based on CITE-seq results and other functional assays, we further sorted CD34⁺CD90⁺EPCR⁺CD49f⁻CD71⁻GFP⁺ cells after 8 days of ex vivo culture for bulk RNA-seq and CUT&Tag or CUT&RUN analysis. For scRNA-seq analysis, we transplanted CD34⁺ cells transduced with shRenilla or shJARID2 into NSG mice and collected hCD34⁺ cells from the bone marrow 20 weeks post-transplantation.

first: Wentao

last: Han

first: Hassan

last: Bjeije

first: Hamza

last: Celik

first: Michael

last: Rettig

first: Nancy

last: Issa

first: Andrew

last: Young

first: Yanan

first: Infencia

last: Xavier Raj

first: Christine

last: Zhang

first: Aishwarya

last: Krishnan

first: Tyler

last: Parsons

first: Samantha

last: Burkart

first: Jason

last: Arand

first: Wei

last: Yang

first: Jeffrey

last: Magee


title: Ubiquitin specific peptidase 7 promotes TP53 mutant malignancy by deubiquitinating and stabilizing DDR1

city: Shanghai

first: Yiying

last: Xue

address: Siping road 1239

institute: Tongji University School of Life Sciences and Technology

summary: Receptor tyrosine kinase DDR1 (Discoidin Domain Receptor 1) interacts with the extracellular matrix (ECM) to promote tumor cell proliferation through its intracellular kinase activity, while its extracellular non-enzymatic domain creates a physical barrier for immune evasion. Although DDR1 inhibitors and antibodies have been developed, targeting DDR1 kinase activity alone cannot fully block the biological effects mediated by its scaffold function. Therefore, developing DDR1 degraders presents a potentially more effective therapeutic strategy. Through screening a proprietary small-molecule ubiquitination library, we identified NSC632839, which significantly induces DDR1 protein degradation. Mechanistically, chemical proteomics and genetic studies demonstrated that NSC632839 functions by inhibiting USP7, which interacts with, stabilizes, and deubiquitinates DDR1, preventing its proteasomal degradation. Importantly, we observed that TP53 loss or mutation in tumor cells and clinical samples markedly upregulates DDR1 expression, thereby enhancing its interaction with USP7. Treatment with NSC632839 restores TP53 expression, resulting in a significant reduction in DDR1 levels. In various preclinical models, targeting USP7 with NSC632839 effectively eliminates tumor cells, offering a promising therapeutic strategy to overcome tumor relapse driven by TP53 mutations, both in vitro and in vivo. This study highlights the potential of DDR1 degradation via USP7 inhibition as a novel approach to treat TP53 mutation-enriched tumors.

overall_design: Transcriptome profiling of 60 DLBCL patient samples: Differential DDR1 mRNA expression across TP53 wild-type, mutant, and deletion subgroups

first: Jing

first: Xiu

last: Luo


title: Menin regulates YBX1 nuclear translocation to drive HKDC1 transcription and restrain glycolysis in pancreatic ductal adenocarcinoma

first: Peng

last: Chen

address: 168 Changhai Road, Shanghai, 200433,

institute: Changhai Hospital Affiliated to Navy Medical University

summary: Menin suppresses glycolysis in PDAC by binding YBX1, promoting its nuclear import, and up-regulating HKDC1 transcription. RNA-seq on PL45 cells over-expressing Menin versus vector control identified 413 DEGs; key metabolic genes GLUT1 and LDHA were down-regulated, while HKDC1 was up-regulated. Findings highlight a Menin-YBX1-HKDC1 axis as a potential therapeutic target.

overall_design: Homo sapiens PL45 PDAC cells (triplicate). Group A: pcDNA3.1-Menin over-expression (Menin-OE). Group B: empty-vector control (Vector). Total RNA isolated 48 h post-transfection, rRNA depleted, stranded paired-end (2 × 150 bp) libraries prepared with NEBNext Ultra, sequenced on Illumina NovaSeq 6000.


title: Integrative analysis of mRNA stability regulation uncovers a metastasis-suppressive program in breast cancer [CLIP-seq]

first: Hani

last: Goodarzi

overall_design: To directly uncover the binding sites of RBMS3, we employed CLIP-seq on FLAG-tagged RBMS3 expressing MDA-MB-231 cells.

first: Heather

last: Karner


title: Effects of Gestational and Lactational Exposure to Perfluorohexanoic Acid on the cerebellar transcriptome

city: Rochester

last: Stahl

state: NY

address: 601 Elmwood Ave

institute: University of Rochester Medical Center School of Medicine and Dentistry

summary: Legacy per- and polyfluoroalkyl substances (PFAS) have been associated with immune, endocrine, and neurotoxicity following gestational exposures. As a result, industries have effectively replaced them with next generation PFAS, including perfluorohexanoic acid (PFHxA). PFHxA is increasingly found in the serum of pregnant women and in breast milk, and adult human post-mortem studies indicate that PFHxA is found in the brain, with highest concentrations in the cerebellum and hypothalamus. Despite evidence of gestational, lactational, and nervous system exposure to PFHxA, developmental neurotoxicity (DNT) testing in mammals has not been conducted. For DNT evaluation, we exposed pregnant C57Bl/6J mice daily from gestational day 0 through postnatal day (P) 21 to two PFHxA exposure levels (a lower (0.32 mg/kg of body weight (bw)), or higher (50 mg/kg of bw) dose of PFHxA) or ddH20 using treat based administration. Given the high PFHxA levels in cerebellum and protracted developmental window, acute transcriptional dysregulation and cellular morphology of the cerebellum was assessed on the last day of exposure at P21. Using bulk-RNA sequencing, overall PFHxA showed subtle effects in transcripts related to neurons and glia, with females having a greater number of dysregulated transcripts than males. Using immunohistochemistry, we found that Purkinje cell linear frequency was increased in specific lobules in the higher exposure group and that microglial morphology underwent subtle changes in specific cerebellar layers in the lower exposure group in both sexes. Together these data suggest that PFHxA exposure may have lobule specific impacts on the development of both neurons and glia in the cerebellum, highlighting the importance of studying the neurotoxicity of PFHxA in both sexes.

overall_design: C57Bl6J pregnant mice were exposed to control, 0.32 mg/kg of bw (lower), or 50 mg/kg of bw (higher) exposures of PFHxA from gestational day (GD) 0 through postnatal day (P) 21 resulting in in utero and lactational exposure to PFHxA. On P21, offspring were euthanized and whole cerebella were dissected and prepared for bulk-RNA sequencing.

first: Elizabeth

last: Plunk

first: Linh

last: Le

first: Marissa

last: Sobolewski

first: Ania

last: Majewska


title: Effect of hepatocytic RKIP depletion on HFD-induced MASLD

city: Hangzhou

first: Mengjie

last: Li

address: Institute of Immunology and Bone Marrow Transplantation Center, The First 6 Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310058, 7 China.

institute: Zhejiang University

summary: High-fat diet (HFD) is a risk factor for metabolic dysfunction-associated steatotic liver disease (MASLD), yet the molecular pathways that connect dietary fats to liver dysfunction remain unclear. Hepatocyte-specific RKIP depletion in male mice exacerbates ER stress, resulting in lipid droplets accumulation and MASLD progression.

overall_design: RNA-seq profiling of liver tissues from HFD-fed RKIPf/f and Albcre-RKIPf/f mice.

first: Qiang

last: Qin

first: Xiaojian

last: Wang


title: Mutation of brain aromatase impairs behavior and neuroplasticity in adult zebrafish

city: Rennes

first: Frédéric

last: Chalmel

state: France

address: 9 avenue du Pr. Léon Bernard

department: Physiology and physiopathology of the urogenital tract

country: France

institute: Inserm U1085-Irset

summary: Brain aromatase, an enzyme responsible for the local synthesis of estrogens, plays a key role in regulating behavior and neuroplasticity in mammals. In teleost fish, brain aromatase is encoded by the cyp19a1b gene, which is strongly expressed in radial glial cells but the specific functions of this enzyme are currently unknown. To investigate its role, a cyp19a1b-mutant zebrafish line was generated using gene-editing techniques. Behavioral, neurogenic, and neurotransmission-related parameters were assessed in adult male and female zebrafish. Behavioral analysis highlighted significant alterations in mutant zebrafish including changes in swimming activity, boldness, sociability, and aggression with a stronger effect in males compared to females. Beyond these behavioral modifications, mutant zebrafish exhibited disrupted cell proliferation patterns, as assessed by PCNA immunofluorescence in key forebrain regions. Specifically, proliferation decreased in the telencephalon and in the caudal hypothalamus of mutant zebrafish while increasing in the olfactory bulbs. The number of dopaminergic and serotonergic neurons, visualized by immunofluorescence, remained unchanged. Similarly, HPLC-ED quantification of monoamines and their metabolites showed no significant differences between mutant and wild-type zebrafish. To further explore the impact of cyp19a1b mutation on gene expression, transcriptomic analysis was performed using BRBSeq technology. Gene expression analyses identified several processes affected by the mutation, including cell proliferation, apoptosis, estrogen signaling, neuroplasticity, and behavioral regulation, in a sex- and region-dependent manner. In conclusion, our results demonstrate that several behaviors, including locomotor activity, sociability, aggressiveness, and anxiety, exhibit marked sexual dimorphism. They show that cyp19a1b mutation affects locomotor activity in a context-dependent manner, increases boldness, and reduces aggressiveness. In addition, transcriptomic analyses revealed widespread dysregulation of gene expression, which likely contributes to the observed behavioral alterations. Taken together, these findings underscore the crucial role of brain aromatase in neurobiological regulation of diverse behaviors.

overall_design:
To further explore the impact of cyp19a1b mutation on gene expression, transcriptomic analysis was performed using BRBSeq technology.

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Note from submitter -  Due to constraints imposed by our funding agencies, we will be submitting  the raw data to the ENA repository.
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first: Thierry

middle: D

last: Charlier

first: Elisabeth

last: Pelligrini

first: Cassandra

last: Malleret

first: Bertrand

last: Evrard


title: Targeting of IRAK4 and GSPT1 enhances therapeutic efficacy in AML via c-Myc destabilization

city: Cincinnati

first: Kwangmin

last: Choi

state: Ohio

address: 333 Burnet Avenue

department: Experimental Hematology & Cancer Biology

institute: Cincinnati Children's Hospital Medical Center

summary: IRAK4 is a therapeutic target in myeloid malignancies, but current IRAK4 inhibitors show only modest clinical efficacy in acute myeloid leukemia (1), highlighting the need for combination strategies. To identify drugs with synergistic potential alongside IRAK4 inhibitors, we conducted a high-throughput screen of 2,803 investigational and approved drugs in isogenic IRAK4-deficient and wild-type human AML cells. The top hit from this screen was the Cereblon E3 ligase modulator (CELMoD) CC-885. Validation in vitro and in vivo confirmed that CC-885 and related CELMoDs synergize with IRAK4 inhibitors to suppress leukemic cells. Among CC-885 substrates, GSPT1 loss showed the most pronounced effects in IRAK4-inhibited leukemic cells. Transcriptional and proteomic analyses revealed that CC-885 treatment led to c-Myc suppression in IRAK4-deficient leukemic cells. GSPT1 loss reduces translation efficiency, particularly for proteins with short half-lives, such as c-Myc. Accelerated c-Myc protein loss was confirmed following GSPT1 degradation in leukemic cells, with decreased protein stability observed following inhibition of IRAK4. These effects were validated in AML patient cells, supporting the potential of IRAK4 inhibitors to modulate c-Myc activity and enhance combinatorial therapies. This study demonstrates that IRAK4 is a therapeutic target in AML, and that combination therapies, such as with certain GSPT1-targeting CELMoDs, will be necessary to achieve maximal clinical responses.

overall_design: Bulk RNAseq profiling of THP1 cells with electroporation with or without CAS9 and sgRNA targeting IRAK4 and grown through single cell cloning, treated with the CELMoD CC-885 at 50nM or equivalent amount of DMSO for 12 hours.

first: Eric

last: Vick

first: Aishlin

last: Hassan

first: Josh

last: Bennett

first: Tomoya

last: Muto

first: Courtnee

last: Clough

first: Ashley

last: Culver-Cochran

first: Kathleen

last: Hueneman

first: Lyndsey

middle: C

last: Bolanos

first: Mark

last: Wunderlich

first: Xiaohu

last: Zhang

first: Crystal

last: McKnight

first: Michele

last: Ceribelli

first: David

last: Holland

first: Carleen

last: Klumpp-Thomas

first: Kenneth

last: Greis

first: Craig

last: Thomas

first: Daniel

last: Starczynowski


title: Neutrophil-specific targeting of STAT3 impairs tumor progression via the expansion of cytotoxic CD8+ T cells

city: Münster

first: Carlos

last: Silvestre Roig

address: Von Esmarch Str. 56

institute: University of Münster

summary: Neutrophils have emerged as key players in tumor progression, often associated with poor prognosis. Despite the ongoing efforts to target neutrophil functions in cancer, therapeutic success has been limited. In this study, we addressed the possibility of blocking STAT3 signaling in neutrophils as targeted therapeutic intervention in cancer. Conditional deletion of Stat3 in neutrophil-specific manner (Ly6GcreStat3fl/fl mice) significantly impaired tumor growth and metastasis in mice. Neutrophils isolated from these mice exhibited strong antitumoral phenotype, with increased MHCII, CD80/86 and ICAM-1 expression. Immune profiling of tumors and tumor-draining lymph nodes revealed a significant enrichment of CD8+ T cells (granzymeBhi, perforinhi and IFN-γhi) with strong cytotoxic activity. To further translate these findings to human settings, we blocked STAT3 signaling in patient neutrophils using a small molecule inhibitor LLL12 and assessed their effects on patient-derived cancer explants. In agreement with in vivo mouse data, we observed the expansion and activation of cytotoxic CD8+ T cells in such explants. To test the therapeutic applicability of STAT3 targeting, we utilized myeloid cell-selective STAT3 siRNA (CpG-STAT3ASO) to target neutrophils in vivo in tumor-bearing mice. Consistent with previous results, neutrophil-specific STAT3 knockdown impaired tumor growth and enhanced cytotoxic T cell activity in tumors and tumor-draining lymph nodes of treated mice. These findings highlight STAT3 signaling as a deleterious pathway supporting protumoral activity of neutrophils and suggest neutrophil-targeted STAT3 inhibition as a promising opportunity for cancer immunotherapy, providing novel insights in targeted therapeutic avenues.

overall_design: C57BL/6JCrl mice were used as wild type (WT) strain, and neutrophil-specific STAT3 knockout mouse strain (Ly6GcreSTAT3fl/fl, referred as NStat3-/-) were used for comparison. Both NStat3-/- and WT mice were subcutaneously engrafted with mouse oropharyngeal cancer cells (MOPC) by s.c. injection of 1x106 MOPC cells in 100 μL PBS into the right flank, and tumor growth had been observed for 21 days. At the day 21 mice were sacrificed and tissues were harvested under aseptic conditions. Tumors were harvested and stored in DMEMc medium on ice maximum 30 min before processing. Tumors were digested in an enzyme solution (DMEMc medium containing dispase 0.2 μg/mL, collagenase A 0.2 μg/mL, DNase I 100 μg/mL (Merck)), 1 mL per sample for 45 min at 500 rpm and 37°C. Cells were meshed through 100 μm sterile strainers (Cell Trics, Partec, Sysmex), centrifuged at 300g and 4°C for 5 min, supernatant was discarded. The pellet was resuspended in PBS (Dulbecco’s Phosphate Buffered Saline 1x, Gibco) containing Mouse BD Fc Block (BD Biosciences, Clone: 2.4G2, RRID:AB_394656) and incubated for 10 min at 20°C. The cells then stained for 30 min at 4°C with PE-anti-mouse Ly6G, Pacific Blue-anti-CD11b antibodies and APC/Cy7-viability dye for FACS of tumor-associated neutrophils (TANs). Cells were sorted using BD FACS Aria III Cell Sorter with the purity >95%.

first: Irem

last: Ozel

last: Silvestre-Roig

first: Jadwiga

last: Jablonska


title: Atypical chemokine receptor CCRL2 shapes tumor spheroid 2 structure and immune signaling in melanoma

city: Jette

first: Diana

last: Al Delbany

address: Laarbeeklaan 103

country: Belgium

institute: Vrije universiteit Brussel

summary: C-C motif chemokine receptor-like 2 (CCRL2) is an atypical chemokine receptor (ACKR) 15 that binds chemerin with high affinity but lacks classical G protein-coupled signaling. In-16 stead, it functions as a non-signaling presenter of chemerin to CMKLR1-expressing cells, 17 modulating antitumor immunity. CCRL2 is highly expressed in the tumor microenviron-18 ment and various human cancers, and its expression has been linked to delayed tumor 19 growth in mouse models, primarily through the chemerin/CMKLR1 axis. While CCRL2’s 20 role in immune surveillance is well established, its tumor cell-intrinsic functions remain 21 less clear. Here, we investigated the impact of CCRL2 overexpression and knockout on 22 tumor cell behavior in vitro. Although CCRL2 did not affect proliferation, migration, or 23 clonogenicity in B16F0 melanoma and LLC carcinoma cells, it significantly influenced 24 spheroid morphology in B16F0 cells. Transcriptomic analysis revealed that CCRL2 modu-25 lates innate immune signaling pathways, including TLR4 and IFN-γ/STAT1, with context-26 dependent downstream effects. These findings suggest that CCRL2 shapes tumor archi-27 tecture by rewiring inflammatory signaling networks in a cell-intrinsic manner. Further 28 studies in other cancer types and cell models are needed to determine whether CCRL2’s 29 regulatory role is broadly conserved and to explore its potential as a therapeutic target in 30 solid tumors.

overall_design: RNAseq on Control B16 melanoma, B16-CCRL2 overexpression and B16-CCRL2 knockout spheroids collected at day

first: Mai Chi

last: Duong

first: Marius

last: Regin

first: Ayoub

last: Radi

first: Anne

last: Lefort

first: Frederic

last: Libert

first: Marc

last: Parmentier

first: Claudia

last: Spits


title: The transgenerational impact of high fat diet and diabetic preg-nancy on embryonic transcriptomics and mitochondrial health

city: Sioux Falls

first: Michael

last: Kareta

state: SD

address: 2301 East 60th Street North

department: Genetics & Genomics

institute: Sanford Research

summary: Overnutrition increases comorbidities such as gestational diabetes during pregnancy that can have detrimental consequences for both parent and progeny. We previously reported that high fat (HF) diet and late-gestation diabetes (DM) incite mitochondrial dysfunction, oxidative stress, and cardiometabolic disease in first generation (F1) rat offspring, partially through epigenomic and transcriptomic programming. Oogonia, which become the second generation (F2), are also exposed which could incite generational risk. This study aimed to determine whether the F2 transcriptome already has genomic variation at the preimplantation embryo stage, and whether variations normalize, persist or compound in the third generation (F3). F0 female rats were fed a control or HF diet, then DM was induced in HF-fed dams on embryonic day (E) 14 exposing F1 offspring and F2 gametogonia to hyperlipidemia, hyperglycemia and fetal hyperinsulinemia during the last third of pregnancy. F1 pups were reared by healthy dams and bred to produce F2 embryos (F2e) and F2 pups. F2 offspring were bred to produce F3 embryos (F3e). Embryos were assessed by a novel grading method, live cell imaging, and single-cell RNA sequencing. Embryo grades were not different, but HF+DM F2e had more cells while F3e had fewer cells and overall fewer embryos. HF+DM F2e had similar mitochondria quantity but a down regulation of genes involved in lipid metabolism and more oxidative stress, consistent with mitochondrial dysfunction. They also had an upregulation of chromatin remodeling genes. The predicted developmental effect is accelerated embryo ageing and epigenetic drift. In contrast, HF+DM F3e had an adaptive stress response leading to increased mitochondria quantity and an up regulation of genes involved in mitochondrial respiration, metabolism, and genomic repair that led to a predicted developmental effect of delayed embryo maturation. Although pathways vary, both generations have metabolically linked differentially expressed genes that influence cell fate and developmental pathways. In conclusion, HF+DM pregnancy can program the early embryonic transcriptome for three generations, despite an intergenerational healthy diet.

overall_design: scRNAseq of F2 and F3 generation rat blastomeres from F0 controls or HF fed dams with late-gestation diabetes

first: Abigail

last: Klein

first: Benjamin

middle: P

last: Derenge

first: Malini

last: Mukherjee

first: Michelle

last: Baack