title: Per2 deficiency in microglia alleviates motor dysfunction by inhibiting ferroptosis in spinal cord injury

city: Yinchuan

first: Hechun

last: Xia

state: Ningxia

address: No. 804 Shengli South Street, Xingqing District, Yinchuan City, Ningxia, People's Republic of China

institute: General Hospital of Ningxia Medical University

summary: Microglia play significant roles in spinal cord injury (SCI) progression. Previous studies have suggested that ferroptosis plays a crucial role in exacerbating neuronal death following SCI; however, the role of microglial ferroptosis in SCI and the underlying mechanisms remain elusive. Here, we elucidate that lipid droplets accumulate in microglia to facilitate microglial ferroptosis after SCI. Notably, microglial ferroptosis peaks at 3 days post-injury, after which it decreases. Microglial Period 2 (Per2) expression is elevated after SCI in vivo; this change is highly synchronized with the changes in microglial ferroptosis. Microglia-specific Per2 knockout promoted neurological function recovery by suppressing microglial ferroptosis. In vitro, Per2 overexpression and deficiency amplified and mitigated microglial ferroptosis, respectively. RNA-seq indicated that Gpx4 was downregulated by Per2. Coimmunoprecipitation demonstrated that Per2 directly interacted with PPARα. Overall, our results indicate that Per2 determines the susceptibility of microglial ferroptosis via the PPARα-Gpx4 axis after SCI.

overall_design: we performed transcriptomic analysis via high-throughput RNA sequencing of primary microglia transfected with a control vector or Per2-overexpression vector.

first: Pengfei

last: Bie

first: Dongpo

first: Yang

last: Gao

first: Liang

last: Wu

first: Zhanfeng

last: Niu

first: Yanbin

first: He

last: Jiang

first: Zhong

last: Zeng

first: Yaolin

last: Zhang

first: Heng

last: Fan


title: Stress-Induced Iron-Sulfur Cluster Damage as a Conserved Trigger of the Stringent Response

status: Public on Aug 20 2025

city: FRIBOURG

first: Laurent

last: Poirel

address: Ch. du Musée 18

department: Medicine

country: France

institute: Université de Fribourg

type: Expression profiling by high throughput sequencing

summary: Pathogenic bacteria rely on the stringent response to adapt to hostile environments encountered within the host. However, the mechanisms by which host-induced stress activates this response remain poorly understood. Here, we identify iron-sulfur (Fe-S) cluster damage as a conserved trigger of the stringent response in major Gram-negative pathogens, including Salmonella enterica, Enterobacter cloacae, and Klebsiella pneumoniae. We demonstrate that Fe-S cluster disruption—triggered by oxidative stress or metal imbalance—limits intracellular pools of sulfur-containing and branched-chain amino acids, thereby activating the (p)ppGpp synthetase RelA. We further show that during Fe-S cluster stress, (p)ppGpp plays a dual role: enhancing bacterial fitness and promoting virulence by upregulating the Salmonella SPI-2 type III secretion system. These findings reveal a conserved mechanism by which pathogenic bacteria integrate host-associated stresses into an adaptive transcriptional response that promotes fitness and virulence, highlighting Fe-S cluster integrity as a central hub for environmental sensing during infection.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium

overall_design: RNA-seq profiling of wild-type salmonella and their relA knockdown derivative with or without the presence of manganese

first: Eva

last: Michaud

first: Lorena

last: Ricci

first: Claire

last: Lallement

first: Lars

last: Barquist

first: Vincent

last: Cattoir

first: Charlotte

last: Michaux

first: Régis

last: Hallez

first: Severin

last: Ronneau


title: Ling-Gui-Zhu-Gan Decoction Ameliorates Heart Failure via Modulating Energy Metabolism and Lipid Homeostasis: Insights from Transcriptomics and Lipidomics

city: Jinan

first: hu

last: ying

address: No. 16369, Jingshi Road

country: China

institute: Affiliated Hospital of Shandong University of Traditional Chinese Medicine

summary: Background: Heart failure (HF) remains a global health challenge with limited therapeutic options. Ling-Gui-Zhu-Gan Decoction (LGZGD), a traditional Chinese medicine formula, has shown clinical efficacy in HF treatment, yet its molecular mechanisms remain unclear. Methods: This study investigated LGZGD's cardioprotective effects and underlying mechanisms using a doxorubicin-induced HF mouse model. Mice were divided into blank (KB), model (M), trimetazidine (QM), and LGZGD (LG) groups. Cardiac function was assessed via echocardiography, while myocardial injury and fibrosis were evaluated through histopathology. Transcriptomics and lipidomics analyses were performed to identify molecular pathways. Results: LGZGD significantly improved ejection fraction (EF) and fractional shortening (FS), alleviated myocardial vacuolization, and reduced fibrosis, outperforming trimetazidine. Transcriptomics revealed LGZGD modulated oxidative phosphorylation and ATP synthase activity, restoring energy metabolism. Lipidomics highlighted its regulation of glycerophospholipid metabolism, particularly phosphatidylethanolamine (PE) and phosphatidylcholine (PC), linked to anti-inflammatory and lipid homeostasis effects. Conclusion: Integrated omics data suggested LGZGD ameliorates HF by enhancing mitochondrial function, mitigating oxidative stress, and balancing lipid metabolism. These findings provide mechanistic insights into LGZGD's therapeutic benefits, supporting its potential as a multi-targeted intervention for HF through energy and lipid metabolic regulation.

overall_design: This study was reviewed and approved by the Animal Ethics Committee of Shandong University of Traditional Chinese Medicine (Ethics approval number: []). All procedures were conducted in strict accordance with the "Guidelines for the Use of Experimental Animals." The animals used were 8-week-old male wild-type C57BL/6JNifdc mice (weight 23–25 g), provided by Beijing Vital River Laboratory Animal Technology Co., Ltd. (Beijing, China). All mice were housed in individually ventilated cages under standard environmental conditions: a 12-hour light/dark cycle, temperature of 22±1°C, and relative humidity of 50±10%. They had free access to standard laboratory chowing and drinking water. A one-week acclimatization period was provided prior to the experiment. A total of 40 mice were randomly divided into four groups (n = 10 per group): blank group (KB), model group (M), Trimetazidine treatment group (QM), and LGZGD treatment group (LG). M, QM, and LG groups received intraperitoneal injections of doxorubicin at a dose of 2.5 mg/kg, three times per week for 2 weeks (a total of 6 injections), for a cumulative dose of 15 mg/kg. Successful model establishment was defined by a reduction of left ventricular ejection fraction by 10% from baseline, confirmed via echocardiography. Mice in the KB group were injected with an equal volume of saline. Starting on day 8, mice in the LG group were administered LGZGD (raw herbal material) via gastric gavage at a dose of 6.6 g/kg, while mice in the QM group received trimetazidine via gastric gavage at a dose of 2 mg/kg/day (equivalent to the clinical dosage). Mice in the KB and M groups were gavaged with an equal volume of distilled water. The treatment continued for two weeks. Body weight was measured before modeling, after modeling, and following drug administration.

first: Ying

last: Hu

first: Xuehan

first: Chuanhua

last: Yang

first: Yuehua


title: Peripheral Substance P induces deficits in hippocampal synaptic plasticity and memory

city: Seoul

first: Jungeun

last: Ji

address: 145 Anam-ro

department: Department of Integrated Biomedical and Life Science

country: South Korea

institute: Korea University

summary: Substance P (SP) is a neuropeptide that functions in both the central and peripheral nervous systems. Although substance P-containing neurons convey nociceptive information to the spinal cord and regulate inflammatory responses in peripheral tissues, the impact of a peripheral rise in substance P on hippocampal functions such as spatial learning and memory remains unclear. Here, we show that chronic peripheral substance P significantly impaired performance in both the object place recognition (OPR) and novel object recognition (NOR) tests compared to saline controls. Electrophysiology revealed a marked reduction in CA3‑CA1 LTP without changes in basal synaptic transmission. RNA‑Seq identified 77 differentially expressed genes (DEGs), and enrichment analysis highlighted pathways related to synaptic transmission and learning/memory.

overall_design: Male C57BL/6N mice were subcutaneously injected with substance P (10 µM, 100 µL) for 14 days. Hippocampus‑dependent behaviours (OPR, NOR) and CA3‑CA1 long-term potentiation (LTP) were assessed. RNA‑Seq was performed on hippocampal tissue, and DEGs were analysed.

first: Sunyong

last: Kim

first: Kyeong-No

last: Yoon

first: Mingyun

first: Seung Ah

last: Choi

first: Won-Woo

last: Lee

first: Jin Ho

last: Chung

first: Gunhyuk

last: Park

first: Joon-Yong

last: An

first: Dong Hun

first: Yong-Seok


title: Loss of UXS1 Selectively Depletes Pyrimidines and Induces Replication Stress in KEAP1-Mutant Lung Cancer

city: South San Francisco

first: Melat

middle: T.

last: Gebru

state: California

address: 1170 Veterans Blvd

department: Oncology

country: USA

institute: Calico Life Sciences LLC.

summary: Kelch-like ECH associated protein 1 (KEAP1) is the third most commonly mutated gene in non-small cell lung cancer (NSCLC) and is associated with poor prognosis. Here, we investigated synthetic lethal interaction genes in KEAP1-mutated cancer cells and identified a dependency on UDP xylose synthase 1 (UXS1), which converts UDP-glucuronic acid (UDP-GlcA) to UDP- xylose in the proteoglycan synthetic pathway. UDP glucose dehydrogenase (UGDH), a transcriptional target of NRF2 that converts UDP-glucose to UDP-GlcA, was highly expressed in KEAP1-mutant tumors. Upon UXS1 knockdown, depletion of UDP-xylose occurred in both KEAP1-mutant and wildtype (WT) cells, whereas UDP-GlcA accumulated to a greater extent in the KEAP1-mutant setting. The resulting shortage of available UDP and other pyrimidines slowed S-phase progression and stalled DNA replication fork marks, causing cells to undergo prolonged cell-cycle exit or apoptosis. Dependency on UXS1 was rescued by knocking out UGDH to prevent UDP-GlcA accumulation and UDP depletion. DNA replication stress in UXS1-depleted cells sensitized them to clinical cell-cycle checkpoint inhibitors. Further, CRISPR screening experiments identified genes that modulate UXS1 dependency. While liver had the highest normal tissue expression of UGDH, UXS1 knockout in the liver did not result in hepatotoxicity. Taken together, these data demonstrate that UXS1 is a selective dependency in KEAP1-mutant tumors and loss of UXS1 creates additional therapeutically exploitable vulnerabilities in KEAP1-mutant tumors.

overall_design: Human whole genome CRISPR screen using Avana library. NTC or shUXS1 expressing NCI-H460 or NCI-H2122 cells were transduced with CRISPR library and treated with dox to induce shUXS1 for 11 days.

middle: T

first: Timothy

last: Hoffman

first: David

last: Stokoe


title: OTUB2/NR4A1 restrains the development of preeclampsia by suppressing macrophage M1 polarization

city: Shenyang

first: Yan

last: Zhao

address: No.36 Sanhao Street

institute: Shengjing Hospital of China Medical University

summary: Preeclampsia is one of the most common pregnancy disorders, and characterized by insufficient trophoblast invasion and placental inflammation. RNA sequencing was performed using placental tissues collected from PE patients and control healthy pregnant women. The results showed that OTU deubiquitinase, ubiquitin aldehyde binding 2 (OTUB2) was downregulated in placenta from PE patients.

overall_design: RNA-seq profiling of placenta from preeclampsia (PE) patients and healthy pregnant women.

first: Yue

last: Wang

first: Yang

first: Fei

last: Tong

first: Qianqian

last: Gao

first: Baoxuan

last: Li


title: TET1 Functions as a Tumor Suppressor in Lung Adenocarcinoma Through Epigenetic Remodeling and Immune Modulation

city: Minneapolis

first: Abdur

last: Rahim

state: Minnesota

address: 2231 6th street SE

department: Department of Medicinal Chemistry

institute: University of Minnesota

summary: Ten-Eleven Translocation (TET1-3) dioxygenases oxidize 5-methylcytosine (5mC) in DNA to generate 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC), initiating DNA demethylation. Since their discovery in 2009, there have been contradictory reports regarding the roles of TET proteins in cancer. TET genes have been characterized as tumor suppressors because their expression levels are reduced in many human cancers including lymphoma, prostate, and pancreas, and TET2 gene mutations are common in hematological cancers. In contrast, TET1 was recently reported to be overexpressed in triple negative breast cancer and to act as a protooncogene in lung cancer. In the present study, we employed genetic approaches to directly address the function of TET1 protein in lung adenocarcinoma. We found that overexpression of TET1 in human lung adenocarcinoma (H441, H1975) cells decreased their proliferation and inhibited colony formation, cell migration, and 3D spheroid tumorigenesis. In contrast, TET1 knockout accelerated lung adenocarcinoma cell growth and promoted colony formation, cell migration, and 3D spheroid tumorigenesis. Transcriptomics and proteomics analyses revealed that TET1 overexpression was associated with increased prevalence of immune markers, primarily via activation of the TNF and NF-kB signaling pathways. Conversely, TET1 knockout in lung adenocarcinoma cells induced the expression of genes involved in cellular metabolism and cell growth. Our results are consistent with tumor suppressor role of TET1 gene in lung adenocarcinoma cells (H441, H1975) and reveal its possible role in activating antitumor immunity.

overall_design: RNA seq. profiling of wildtype H441, TET1 knock out, and TET1 overexpressed H441 cells

first: Andrew

last: Rajczewski

first: Monica

last: Kruk


title: Cerebrospinal fluid-derived extracellular vesicles: a proteomic and transcriptomics comparative analysis of enrichment protocols

city: Geneva

first: Natacha

last: Civic

address: Rue Michel-Servet 1

department: iGE3 Genomics Platform

country: Switzerland

institute: University of Geneva

summary: Proteomic and transcriptomic analyses of cerebrospinal fluid (CSF)-derived extracellular vesicles (EVs) offer unique insights into molecular changes associated with central nervous system (CNS) diseases and may result in biomarker identification. No gold standard method to enrich EVs from CSF is established and head-to-head comparisons of outputs of different protocols s’ outputs are scarce. Using a large pool of CSF, we characterized the EV preparations resulting from four enrichment protocols and compared them in terms of yield and purity. We found that particles enriched by ultracentrifugation (UC) or a combination of ultrafiltration and size exclusion chromatography (UF-SEC) bared exhibited the typical morphological and biochemical characteristics of small EVs and were highly enriched in proteins and polyadenylated transcripts associated with EV-related biological processes.  UF-SEC preparations had higher particle yields while more proteins were identified in UC preparations. Approximately 40% of the EV preparations’ proteome was not identified in unenriched CSF, among which a core proteome of 45 proteins identified in 30 EV preparations from independent experiments which may serve as CSF-derived EV markers. Enrichment scores to protein contaminants albumin and apolipoprotein E were higher in UF-SEC preparations. In conclusion, all protocols analyzed here resulted in enrichment of particles with small EVs characteristics, with EV enrichments from UF-SEC resulting in highest yield and purity.

overall_design: We used polyA RNA-seq which comprehensively quantifies messenger RNAs (mRNAs) and long non-coding RNAs (lncRNAs) to characterize and compare EV preparations’ transcriptome. RNA gel analysis showed the presence of low molecular weight bands below 200 nucleotides, also in accordance with literature.41,62 Read counts were similar in all 3 protocols  (3.3*106 for the UF-SEC35 EV preparation, 3.4*106 for the UF-SEC and UC EV preparations). Of these reads, more than 90% survived after adaptor trimming. For the UF-SEC35 and UF-SEC70 EV preparations, 59.2 % (1.9*106) and 59.7% (2.0*106) of the surviving reads were uniquely mapped to the human genome respectively, whereas this proportion was significantly higher in the UC EV preparation (86.9%, 2.9*106). Of the uniquely mapped reads, the number of genes detected with  10 counts were of 22’440 (UF-SEC35), 18’753 (UF-SEC70), and 30’171 (UC) respectively (Supplementary Table 5). Of these, 12999 genes overlapped between the 3 protocols (Figure 8A), 13092 genes (62.4%) between the UF-SEC35 and UF-SEC70 EV preparations (Figure 8B), 15070 (49.5%) between the UF-SEC35 and UC EV preparations (Figure 8C), and 17605 (56.2%) between the UF-SEC70 and UC EV preparations (Figure 8D).  For all 3 protocols, the highest proportion of uniquely mapped genes with  10 counts were protein coding, the remainder consisting of lncRNAs. As expected, RNA species (ribosomal RNA, micro RNAs) were rare, given the type of sequencing protocol chosen (Supplementary Table 5). Cellular component GO enrichment analysis of the protein coding genes with >10 counts showed that these were enriched for genes associated with EV-related biological processes (Figure 9A-C) very similar to those identified on a proteins level (Figure 5).

first: Marta

last: García-Arauzo

first: Sandrine

last: Reymond

first: Lyssia

last: Gruaz

first: Domitille

last: Schvartz

first: Mylène

last: Docquier

first: Christine

last: Deffert

first: Jean-Charles

last: Sanchez

first: Claire

last: Bridel


title: Integration of CRISPR-Cas9 Screens and Multi-Omics Profiling Reveals CHD7-ANGPT1 as a Novel Multi-Drug Resistance Axis in AML [ATAC-seq]

city: Tianjin

first: Tingting

last: Zhang

address: Tianjin,Heping district,288 Nanjing road.Institute of Hematology and Blood Diseases Hospital

type: Genome binding/occupancy profiling by high throughput sequencing

summary: To explore how the loss of function of CHD7 leads to drug resistance in acute myeloid leukemia (AML) cells, we investigated the transcriptional programs regulated by CHD7 in OCI-AML2 cells under different drug treatment conditions. This study aims to uncover the role of CHD7 in drug sensitivity and resistance, providing a theoretical basis for developing new therapeutic strategies.

overall_design: Assessment of gene expression changes in CHD7 knockdown and control sgSC cells under three different conditions:DMSO,Gilteritinib,Venetoclax.

first: Dandan

last: Yang


title: From Development to Regeneration: Insights into Flight Muscle Adaptations from Bat Muscle Cell Lines

city: Kansas City

first: Bowen

state: Missouri

department: Computational Biology

institute: Stowers Institute for Medical Research

summary: Skeletal muscle regeneration depends on muscle stem cells, which give rise to myoblasts that drive muscle growth, repair, and maintenance. In bats—the only mammals capable of powered flight—these processes must also support sustained contractile performance under extreme mechanical and metabolic stress. However, the cellular and molecular mechanisms underlying bat muscle physiology remain largely unknown. Here (Graphical Abstract), we established the first myoblast cell lines from the pectoralis muscle of Pteronotus mesoamericanus, a highly maneuverable aerial insectivore. Using spontaneous self-immortalization and exogenous hTERT/CDK4 overexpression, we generated two stable myoblast lines that retain proliferative capacity and differentiate into contractile myotubes. These cells exhibit frequent spontaneous contractions, suggesting robust functional integrity at the neuromuscular junction. Transcriptomic analysis of native pectoralis tissue revealed enriched expression of muscle metabolism, development, and regeneration, highlighting the regulation of muscle formation and tissue maintenance. Consistent with this profile, the flight muscle is triglyceride-rich, which serves as an important fuel source for energetically demanding processes, including muscle contraction and cellular regeneration. Integration of transcriptomic and metabolic data identified three key metabolic modules—glucose utilization, lipid handling, and nutrient signaling—that likely coordinate ATP production and support metabolic flexibility during the energetic demands of flight and recovery. Together, these cell lines and molecular data provide the first in vitro platform for investigating bat muscle biology and provide new tools for exploring muscle regeneration, metabolic resilience, and comparative muscle physiology.

overall_design: RNAseq profiling of wild-type Pteronotus parnellii muscle cells at timepoint 0min, 10min, 30min, and 60min post feeding

first: Jasmin

last: Camacho

first: Chongbei

last: Zhao

first: Fengyan

last: Deng

first: Valentina

last: Peña

first: Pedro

last: Morales-Sosa

first: Andrea

last: Bernal-Rivera

first: Shengping

last: Huang

first: Sonia

last: Ghosh

first: Maria

last: Katt

first: Luciana

last: Castellano

first: Cindy

last: Maddera

first: Zulin

last: Yu

first: Nicolas

last: Rhoner


title: The two histone H2AZ variant, H2AZ.1 and H2AZ.2, differentially regulate PRC1-mediated histone H2A ubiquitinatione

city: Richmond

first: Xiangyu

last: Shen

state: Virginia

address: 101N 5th street ,Apt1513,Richmond,VA2321, 1513

institute: Henan University

summary: We performed CUT&Tag experiments in mouse embryonic stem cells (mESCs) to investigate the chromatin binding of H2AZ1 and Ring1B. H2AZ1 CUT&Tag was conducted in H2AZ1KIFlag mESCs using an anti-Flag antibody. To assess how knockdown of H2AZ1 and H2AZ2 affects Ring1B occupancy on chromatin, we performed additional CUT&Tag experiments in Ring1BKIFlag mESCs under knockdown conditions. This study aims to elucidate the regulatory interplay between histone variants and Polycomb proteins in the context of pluripotent stem cell chromatin.

overall_design: CUT&Tag was performed to profile the chromatin binding of H2AZ1 and Ring1B in mouse embryonic stem cells (mESCs). H2AZ1 binding was assessed in H2AZ1KIFlag mESCs using an anti-Flag antibody. To investigate the effects of H2AZ1 and H2AZ2 knockdown on Ring1B occupancy, CUT&Tag experiments were conducted in Ring1BKIFlag mESCs under knockdown conditions for H2AZ1 and H2AZ2. Each condition included biological replicates. Sequencing libraries were prepared and sequenced as paired-end reads. Both raw  data are included in this submission.

first: Hengbin

last: Wang

first: Amanda

last: Jones


title: Nanoscale Acoustic Oscillator for Mechanoimmunology: NAOMI

city: Durham

first: Bryan

last: Pan

state: NC

address: 3 Genome Ct

institute: Duke University

summary: Mechanoimmunology provides a powerful framework for understanding how mechanical forces orchestrate immune responses, offering insights into immune cell functions and the mechanisms underlying mechanotransduction. However, a major challenge in this field is the absence of reliable platforms that deliver precise and consistent mechanical stimuli to individual cells while achieving practical and reproducible mechanobiological activation of immune cells. In this work, we introduce a highly sensitive and stable nanoscale acoustic oscillator for mechanoimmunology applications: NAOMI. NAOMI features a micropatterned substrate that promotes uniform cell monolayer formation, seamlessly integrated with an acoustic transducer system capable of generating precise nanoscale oscillations (±1 nm deviation) for up to 72 h of continuous stimulation. Unlike conventional passive mechanobiological platforms that rely on static stiffness or topographical cues, NAOMI enables programmable, uniform 3D oscillations, delivering finely tuned and reproducible mechanical stimulation for diverse experimental applications. Validation studies demonstrate that NAOMI-induced oscillations significantly amplify stress intensity and cell displacement, driving robust M1 pro-inflammatory polarization in macrophages. With its high precision, stability, and tunability, NAOMI offers a powerful and versatile platform for studying mechanoimmunology and holds strong potential to support future research and enable innovative immunotherapy applications.

overall_design: RAW264.7 cells are cultured on petri dish, acoustics-off, and acoustics-on group for 48 h. After that, cell RNA-seq data is plan to be collected to study the influence of different groups on cell behaviors. Petri dish group was served as a control.

first: Ye

last: He

first: Bo

first: Tony Jun


title: In vivo CRISPR screens identify key modifiers of human CAR T cell function [scRNA-seq]

city: Cambridge

first: Kevin

last: Bi

state: MA

address: 300 Binney Street

institute: Broad Institute

summary: Chimeric antigen receptor (CAR) T cells are highly effective in hematologic malignancies1. However, loss of CAR T cells contributes to relapse in many patients2–4. These limitations could be overcome using targeted gene editing to increase CAR T cell persistence. Here, we performed in vivo loss-of-function CRISPR screens in BCMA-targeting CAR T cells to investigate genes influencing CAR T cell persistence and function in a human multiple myeloma model. We tracked the expansion and persistence of CRISPR-library edited T cells in vitro and then at early and late timepoints in vivo to track the performance of gene modified CAR T cells from manufacturing to survival in tumors. The screens revealed several context-specific regulators of CAR T cell expansion and persistence. Ablation of RASA2 and SOCS1 enhanced T cell expansion in vitro, while loss of PTPN2, ZC3H12A, and RC3H1 conferred early selective growth advantages to CAR T cells in vivo. Strikingly, we identified cyclin-dependent kinase inhibitor 1B (CDKN1B), a cell cycle regulator, as the most important factor limiting CAR T cell fitness at late timepoints in vivo. CDKN1B ablation increased BCMA CAR T cell proliferation and effector function, significantly enhancing tumor clearance and overall survival. Thus, our findings reveal differing effects of gene-perturbation on CAR T cells over time and in different environments, highlight CDKN1B as a promising target to generate highly effective CAR T cells for multiple myeloma, and underscore the potential importance of in vivo screening as a tool for identifying genes to enhance CAR T cell efficacy.

overall_design: A small pool of CRISPR modified CAR T cells were isolated from the spine and femurs of  mice 21 days after T cell transfer. Mice had been previously engrafter with MM1.S myeloma cells for 21 days prior to CAR T cell transfer.

first: Nelson

middle: H

last: Knudsen

first: Giulia

last: Escobar

first: Felix

last: Korell

first: Celeste

last: Nobrega

first: Robert

last: Manguso

first: Marcela

middle: V

last: Maus


title: Targeting RAC1 as a novel strategy to reduce inflammation and liver damage in acute liver failure.

city: Derqui

first: Juan

last: Bayo

state: Buenos Aires

address: Av Peron 1500

department: IIMT

country: Argentina

institute: Universidad Austral-Conciet

summary:
Background & Aims:
The Rho GTPase RAC1 regulates key drivers of acute liver failure (ALF) such as oxidative stress and inflammation. The goal of this study was to determine the therapeutic potential of RAC1 pharmacological inhibition in ALF.
Methods:
The involvement of RAC1 in human ALF was explored by analyzing public transcriptome datasets. Murine models of ALF were induced by administration of either Concanavalin A, acetaminophen or D-Galactosamine/Lipopolysaccharide. In vitro assays were conducted on hepatocytes and macrophages primary cultures and cell lines. 1D-142 was used to explore the effect of RAC1 pharmacological inhibition. RNA-Seq analysis was performed and correlated with ALF human datasets to explore the therapeutic potential of RAC1 inhibition. Liver explants from patients with liver failure were treated in vitro with 1D-142.
Results:
RAC1-related pathways are upregulated in human ALF samples and correlate with immune activation and oxidative stress. Administration of 1D-142 ameliorated liver damage across all ALF murine models. 1D-142 treatment diminishes reactive oxygen species formation and reduces inflammatory cells migration and suppresses cytokine production both in vivo and in vitro. Transcriptome analysis of treated livers indicates that RAC1 pharmacological inhibition modulates dysregulated biological processes observed in ALF patients. Liver explants from ALF patients treated with 1D-142 exhibited reduced necrosis and reduced expression of pro-inflammatory genes.
Conclusions:
RAC1 plays a critical role in driving inflammation and oxidative stress in ALF. Targeted inhibition of RAC1 with 1D-142 protects against ALF in murine models; thus, RAC1 inhibition could be a potential therapeutic option for ALF.

overall_design: Transcriptomic Profiling of C57BL/6J Mouse Livers During Acute Liver Failure Induced by acetaminophen or concanavalin A and Treated with the RAC1 Inhibitor 1D-142

first: Barbara

last: Bueloni

first: Esteban

last: Fiore

first: Guillermo

last: Mazzolini


title: In vivo CRISPR screens identify key modifiers of human CAR T cell function [Bulk_RNASeq]

overall_design: T cells were isolated from the spine and femurs of intergenic control KO and CDKN1B KO BCMA CAR T cell treated mice 21 days after T cell transfer. Mice had been previously engrafter with MM1.S myeloma cells for 21 days prior to CAR T cell transfer.


title: SETD6 Mediates Selective Interaction and Genomic Occupancy of BRD4 and MITF in Melanoma [RNA-seq]

city: Be'er Sheva

first: Dan

last: Levy

address: David Ben Gurion Blvd 1

country: Israel

institute: Ben-Gurion University

summary: Aberrant transcriptional programs mediate malignant transformation of melanoma, the most aggressive form of skin cancer. The lysine methyltransferase SETD6 has been implicated in regulating transcription, cell adhesion, migration, and other processes in various cancers, however its role in melanoma remains unexplored. We recently reported that SETD6 mono-methylates the BRD4 at K99 to selectively regulate transcription of genes involved in mRNA translation. Here, we observed that BRD4 methylation at K99 by SETD6 occurs in melanoma cells. Knockout of SETD6 or a point mutation at BRD4-K99 disrupts BRD4 genomic occupancy. In addition, we show that SETD6 interacts with MITF, a master transcription factor in melanocytes and melanoma, and influences the genomic distribution of MITF. Mechanistically, we uncover a novel chromatin- localized interaction between BRD4 and MITF in melanoma. Our data suggest that BRD4 binds MITF in melanoma cells and that this interaction is dependent on both SETD6-mediated methylation of BRD4 and MITF acetylation. This chromatin complex plays a pivotal role in selective recruitment of BRD4 and MITF to different genomic loci in melanoma cells.

overall_design: RNA-Seq for SETD6 Controls and KOs in SKmel147 cells

first: Elbaz-Biton

last: Tzofit


title: CRISPR-mediated deletion of Prdm12 alters H3K9me3 landscape in CD8+ T cells: a CUT&Tag study

city: shanghai

first: guolong

last: liu

address: No. 500, Dongchuan Road, Minhang District, Shanghai

institute: East China Normal University

summary: In this study, we used magnetic bead-based separation to isolate CD8+ T cells from OTI:Cas9 transgenic mice. These cells were then transfected with Cas9 ribonucleoprotein (RNP) targeting the Prdm12 gene or non-targeting control RNP via electroporation. After 72 hours, both edited (Prdm12 knockout) and control cells were collected for chromatin profiling of histone modification H3K9me3 using CUT&Tag sequencing. The aim of this study is to investigate how Prdm12 regulates the epigenetic landscape, particularly H3K9me3 distribution, in CD8+ T cells.

overall_design: CD8+ T cells were isolated from OTI:Cas9 transgenic mice using magnetic bead separation. Cells were divided into two groups: one group was transfected with Cas9 RNP targeting Prdm12, while the other received non-targeting control RNP via electroporation. Following 72 hours of recovery, genomic editing efficiency was confirmed by T7E1 assay and/or Sanger sequencing. Both Prdm12-edited and control cells were subjected to CUT&Tag analysis using an antibody specific for H3K9me3. Libraries were prepared according to standard protocols and sequenced on an Illumina platform (e.g., NovaSeq 6000). Sequencing data were analyzed to identify genome-wide changes in H3K9me3 occupancy associated with Prdm12 loss.

first: Guolong

last: Liu

first: Xiaoling

last: Tian


title: Genome-wide chromatin accessibility profiling of Prdm12-edited CD8+ T cells by ATAC-seq

summary: This study investigates the impact of Prdm12 knockout on chromatin accessibility in CD8+ T cells. CD8+ T cells were isolated from spleens of OTI:Cas9 transgenic mice (C57BL/6 background) using magnetic bead-based negative selection. Isolated cells were subjected to CRISPR-Cas9 mediated gene editing targeting Prdm12 (Prdm12-KO group) or a non-targeting control guide RNA (Control group) via ribonucleoprotein (RNP) complex electroporation. ATAC-seq was performed to compare genome-wide chromatin accessibility between edited (treatment) and non-edited (control) cells, aiming to identify regulatory regions associated with Prdm12 function.

overall_design: Comparative analysis of chromatin accessibility in CD8+ T cells with and without Prdm12 knockout.Two experimental groups were established:Treatment group: CD8+ T cells edited with Prdm12-targeting RNP;Control group: Non-edited CD8+ T cells.Chromatin accessibility was profiled using ATAC-seq for both groups. The experiment aims to identify differentially accessible regulatory regions influenced by Prdm12 deletion.


title: Long-term engraftment and satellite cell expansion from human PSC teratoma-derived myogenic progenitors

first: Elise

last: Engquist

state: MN

address: 2231 6th St SE

department: Lillehei Heart Institute and Department of Pediatrics

summary: Myogenic progenitors were isolated by FACS using CD82, ERBB3, and NGFR from human iPSC-derived teratomas and cultured in vitro in the presence of either bFGF, EGF, NGF, or all three growth factors for 4 passages prior to RNA-sequencing.

overall_design: Bulk RNA-sequencing of human teratoma-derived myogenic progenitors cultured in four different growth factor conditons: bFGF, EGF, NGF, or all 3 growth factors.

first: Michael

last: Kyba

first: Zahra

last: Khosrowpour

middle: N


title: Human Neural Organoid Microphysiological Systems Show the Building Blocks Necessary for Basic Learning and Memory

city: Baltimore

first: Lena

last: Smirnova

address: 615 N. Wolfe St

department: Environmental Health & Engineering

institute: Johns Hopkins University

summary: Brain Microphysiological Systems including neural organoids derived from human induced pluripotent stem cells offer a unique lens to study the intricate workings of the human brain. This paper investigates the foundational elements of learning and memory in neural organoids, by quantifying immediate early gene expression in response to chemical modulation, input-specific short- and long-term synaptic plasticity, neuronal network dynamics, connectivity, and criticality to demonstrate the utility of these organoids in basic science research. Neural organoids showed synapse formation, glutamatergic and GABAergic receptor expression, immediate early gene expression basally and evoked, functional connectivity, criticality, and synaptic plasticity in response to theta-burst stimulation. In addition, pharmacological interventions on GABAergic and glutamatergic receptors, and input-specific theta-burst stimulation further shed light on the capacity of neural organoids to mirror synaptic modulation, short- and long-term potentiation and depression, demonstrating their potential as tools for studying neurophysiological and neurological processes and informing therapeutic strategies for diseases.

overall_design: RNA-seq profiling of neural organoids (Brain Microphysiological Systems) at week 8, 12, and 13 post differentiation.

first: Mary Alam El Din

last: Dowlette

first: Leah

last: Moenkemoeller

first: Alon

last: Loeffler

first: Forough

last: Habibollahi

first: Jack

last: Schenkman

first: Amitav

last: Mitra

first: Tjitse

last: van der Molen

first: Lixuan

last: Ding

first: Jason

last: Laird

first: Maren

last: Schenke

first: Erik C.

last: Johnson

first: Brett J.

last: Kagan

first: Thomas

last: Hartung


title: Single-cell RNA-seq of neutrophils from germ-free and specific-pathogen-free mice reveals gut-microbiota-driven heterogeneity and NETosis in acute pancreatitis

city: Nanchang

first: Yaoyu

last: Zou

state: Jiangxi

address: 17 Yong Waizheng Street, Donghu District

institute: The First Affiliated Hospital of Nanchang University

summary: We performed single-cell RNA sequencing (scRNA-seq) using the 10x Genomics platform to characterize pancreatic immune cell populations in germ-free (GF) and specific-pathogen-free (SPF) mice with cerulein-induced acute pancreatitis (AP). scRNA-seq analysis identified distinct neutrophil subpopulations influenced by gut microbiota presence. SPF mice showed enrichment of pro-inflammatory neutrophil clusters associated with increased neutrophil extracellular trap (NET) formation, whereas GF mice exhibited neutrophil subsets expressing reparative and protective signatures. Our data highlight the role of gut microbiota in shaping immune responses during AP.

overall_design: Following induction of AP by repeated intraperitoneal injection of cerulein (100 µg/kg hourly for 10 doses), pancreatic tissues were harvested from GF and SPF male C57BL/6 mice (7–8 weeks old). Single-cell suspensions of pancreatic immune cells were obtained by enzymatic digestion, and libraries were prepared using the 10x Genomics Chromium Single Cell 3′ v3.1 protocol. Sequencing was performed on an Illumina NovaSeq 6000 (paired-end, 2×150 bp). Raw FASTQ files and processed data (gene-cell count matrices) were deposited in GEO

first: Yin

last: Zhu

first: Jianping

last: Liu

first: Cong

last: He

first: Nianshuang

last: Li


title: Rapid generation of a sdhb loss-of-function zebrafish model for secreting pheochromocytomas and paragangliomas

city: Montréal

first: Martine

last: Tetreault

state: QC

address: 900 rue Saint-Denis

country: Canada

institute: CRCHUM

summary: Introduction: Genotype constitutes a pivotal factor in the comprehensive management of pheochromocytomas and paragangliomas (PPGLs). This underlines the need to (1) further elucidate the genetic etiology of these pathologies, (2) investigate the underlying pathogenic mechanisms, and (3) identify therapeutic targets. These goals rely on generating and studying relevant biological models, particularly in vivo. However, this has remained a disappointment using traditional animal models. In this context, there is a need to develop fast, reliable in vivo models of PPGLs which display clinically relevant biochemical hallmarks of PPGLs. Objective: Our study aims to establish zebrafish larvae as a relevant and convenient proxy for the functional characterization of PPGL-associated genetic variants. Methods: We took advantage of the genetic accessibility of zebrafish embryos to generate first-generation (F0) loss-of-function models for sdhb, a canonical PPGL-associated gene, using CRISPR/CAS9 technology. F0 zebrafish embryos were microinjected with a CRISPR/CAS9 molecular cocktail containing sdhb-specific guide RNAs and compared with control embryos injected with non-active CRISPR/CAS9. The mutagenic score of our CRISPR/CAS9 approach was validated by High-Resolution Melting analysis, and mutant zebrafish larvae were phenotyped during their first five days of development. Notably, the levels of catecholamines/metanephrines (in whole fish extract and bathing medium) and Krebs cycle metabolites were assessed by liquid chromatography-mass spectrometry. Other relevant phenotypic readouts were also performed, such as heart rate, swimming activity and overall survival. To validate the specificity of our findings, we also analyzed other zebrafish genetic mutants diseased controls (i.e. nf1 CRISPants as PPGL positive controls and scn1a-mutant as non-PPGL negative genetic controls). Finally, we performed an RNA-sequencing assay from sdhb-CRISPant and controls larvae. Results: Sdhb CRISPants exhibit increased heart rates, reduced swimming activity and premature death. In whole fish extracts, normetanephrine (NM), metanephrine (MN), and dopamine (DA) levels were about three times higher in sdhb CRISPants than in control larvae. In the bathing medium, NM and MN were also significantly elevated, along with 3-MT. We confirmed the specificity of our findings by showing that nf1-mutant larvae exhibit similar catecholamine levels but also show an adrenergic phenotype typical of cluster 2 variants of PPGLs. In contrast, scn1a-mutant larvae, despite suffering from severe epileptic encephalopathy associated with reduced lifespan, did not display elevated catecholamine levels. Complementary metabolic profiling showed that sdhb CRISPants depict a clear Complex II dysfunction signature, characterized by elevated succinate, lactate, NAD+, along with reduced aspartate and glutamate levels. Additionally, RNA-sequencing revealed downregulation of sdhb and fads2, and upregulation of genes involved in the hypoxia response, angiogenesis, stress response, and glycolysis in sdhb CRISPants compared to Cas9-control larvae. Conclusion: In this work, we validated the relevance of F0 loss-of-function zebrafish models (CRISPant) to study the pathogenicity of PPGL-causing genetic variants in vivo. We present the first in vivo model of sdhb loss-of-function with oversecretion of free catecholamines, a key clinical hallmark of PPGLs in humans. We also show that other pathological molecular hallmarks are found increased such as Krebs cycle metabolites and relevant phenotypic readouts (tachycardia, reduced lifespan, and consistent transcriptomic dysregulations). These findings suggest that zebrafish is a relevant physiopathologic model for studying PPGLs and their associated genetic etiologies and opens the door for streamlining preclinical precision medicine approaches for PPGLs.

overall_design: RNA-seq profiling of zebrafish loss-of-function model for sdhb (3 replicates) and control zebrafish (3 replicates)

first: Stefanie

last: Parisien-La Salle

first: Fanny

last: Nobilleau

first: Alexandra

last: da Silva Babinet

first: Julien

last: Lamontagne

first: Marjorie

last: Labrecque

first: Bryce

last: Rampal

first: Charline

last: Mas

first: Meijiang

last: Liao

first: Viviana Andrea

last: Barragan Torres

first: Gilles

last: Corbeil

first: Laurent

last: Chatel-Chaix

first: Margo

last: Dona

first: Isabelle

last: Bourdeau

first: Éric

last: Samarut


title: Lean breast adipocytes secrete an oxylipin that suppresses breast cancer via ferroptosis

city: Salt Lake City

first: Keren

last: Hilgendorf

state: Utah

address: 15 N Medical Drive East Rm 4100

department: Biochemistry

institute: University of Utah

summary: Obesity is predicted to become the largest modifiable risk factor for breast cancer in postmenopausal women, yet the mechanisms underlying this association are unclear. We identified a novel protective mechanism for lean adipocytes to suppress breast cancer by secreting the oxylipin 9S-HODE, which induces ferroptosis in breast cancer cells while sparing normal breast epithelial cells. Consequently, the inhibition of ferroptosis accelerates breast cancer in lean, but not obese, mice. Obese adipocytes fail to secrete 9S-HODE, suggesting that the loss of 9S-HODE significantly contributes to the acceleration of breast cancer in obesity. Further, 9S-HODE supplementation into tumors in obese mice is sufficient to reduce tumor burden and additionally can inhibit the growth of patient-derived breast cancer organoids, underscoring its potential as a therapeutic agent.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: RNA-sequencing profile of E0771, SkBr3 and NMuMG breast cancer cells were treated with control DMEM Obese inguinal adipocyte secretome or lean inguinal adipocyte secretome.

first: Meghan

middle: C

last: Curtin

first: Abigail

middle: E

last: Jackson

first: Elisabeth

middle: A

last: Brown

first: J

last: Maschek

first: David

last: Lum

first: James

last: Cox

first: Alana

middle: L

last: Wlem

middle: I


title: Spatial single-cell transcriptomics of MASLD-affected liver biopsy samples.

city: Tsu city

first: Naoto

last: Fujiwara

state: Mie

address: 2-174 Edobashi

country: Japan

institute: Mie University

summary: Metabolic dysfunction-associated steatotic liver disease (MASLD) liver biopsies were analyzed using spatial single-cell transcriptomics (CosMx Spatial Molecular Imager, NanoString) to elucidate molecular alterations associated with hepatic fibrosis morphology, as quantified by the artificial intelligence-based FibroNest algorithm (PharmaNest). This analysis identified distinct morphological fiber phenotypes (FibroPCs), among which FibroPC4, characterized by reticular fiber structures, was associated with a hepatic stellate cell (HSC) phenotype that promotes hepatocellular carcinoma (HCC). This HCC-promoting HSC phenotype was driven by insulin-like growth factor-binding protein 7 (IGFBP-7) secreted from senescent periportal endothelial cells.

overall_design: Spatial single-cell transcriptomic profiling using the NanoString CosMx Spatial Molecular Imager was performed on formalin-fixed paraffin-embedded (FFPE) liver biopsy specimens obtained from four patients with metabolic dysfunction-associated steatotic liver disease (MASLD) and fibrosis stage F2. Two biopsy sections from different patients were mounted on each slide for analysis.

first: Yuki

last: Matsushita

first: Hayato

last: Nakagawa


title: Effect of depletion of AURKB on gene expression in colorectal cancer

city: Shanghai

first: Yuyi

last: Li

address: Zhizao ju road

institute: Shanghai Jiaotong University School of Medicine

summary: We performed gene expression profiling analysis using data obtained from RNA-seq of RKO shAURKB and RKO-shNC cells. Comparative gene expression profiling analysis of RNA-seq data for RKO-shAURKB and RKO-shNC cells.

overall_design: RKO cells were infected with lentiviruses expressing shRNA targeting AURKB or control and cultured for 24 h. Total RNAs from three biological replicates were extracted for sequencing analysis.

first: Xiangjun

last: Meng


title: Influence of Pkm2-->1 isoform switching on the cardiac fibroblasts transcriptome

city: Louisville

first: Richa

last: Singhal

state: KY

address: 580 S Preston Street, Baxter II Building, Office 321B

institute: University of Louisville

summary: Cardiac fibroblasts (CFs) are essential for maintaining tissue integrity and the balance of the extracellular matrix (ECM), both of which are critical for normal heart function. Changes in metabolism can influence CF behavior, with activated fibroblasts often exhibiting distinct metabolic shifts. Pyruvate kinase, a key metabolic enzyme, has two isoforms—Pkm1 and Pkm2—produced through alternative splicing. CFs primarily express the Pkm2 variant rather than Pkm1. While Pkm2 is known to regulate gene transcription in various cell types, its role in CF gene expression is not well understood. In this study, we examined how pyruvate kinase splice variants influence CF gene transcription under baseline conditions and following activation by TGF-β or IL-1β. Our results indicate that switching from the Pkm2 to the Pkm1 variant had no significant effect on CF transcriptional regulation, regardless of ligand-induced activation.

overall_design: Isolated cardiac fibroblasts from Pkm2fl/fl mice were transduced with LacZ or iCre prior to stimulation with bFGF, IL-1b, or TGFb for 24 hours.

first: Bradford

middle: G

last: Hill

first: Collin

middle: K

last: Wells


title: Pathologic TPO-induced TPOR-CSF2RB signaling mediates Down syndrome abnormal myelopoiesis due to GATA1 mutant-dependent CSF2RB overexpression [CUT&Tag]

city: Oxford

last: Cruz

address: John Radcliffe Hospital/Headley Way

department: Radcliffe Department of Medicine

country: United Kingdom

institute: MRC Weatherall Institute of Molecular Medicine, Oxford University

summary: Transient abnormal myelopoiesis (TAM) is a human myeloid leukemia that occurs in newborns with Trisomy 21, who acquire mutations in the transcription factor GATA1. TAM originates in the fetal liver but spontaneously regresses as hemopoiesis transitions from fetal liver to postnatal bone marrow, unless clonal evolution enables transformation of the TAM clone to Myeloid Leukemia of Down Syndrome. We sought to understand the developmental tissue restriction of TAM. We show that TAM cells are marked by high expression of the cytokine receptor CSF2RB, a direct target of GATA2. Oncogenic GATA1 fails to supress CSF2RB expression. Highly expressed CSF2RB directly interacts with the thrombopoietin receptor (TPOR). Specifically at high TPO levels, activation of JAK-STAT signalling by TPOR-CSF2RB complexes is amplified and distinct from that triggered by TPOR homodimers and drives TAM cell proliferation. CSF2RB-A455D, a previously identified pathogenic gain-of function variant seen in ML-DS, requires interaction with TPOR to induce cytokine-independent cell proliferation. Together, TPOR and CSF2RB jointly exploit TPO produced by the fetal liver to sustain developmentally restricted TAM cell proliferation

overall_design: 10x Genomics Chromium Next GEM Single Cell 5′ V2 Dual Index Kit  was used to perform scRNAseq on cord blood derived  KIT+ CD34- and KIT+ CD34+ TAM (n=3), Trisomy 21 (n=3), disomic (n=3) cells. CUT&TAG was perfomed in duplicates in CMK cells to measure GATA1s and GATA2 binding as well as H3K27ac. CUT&TAG was performed to measure H3K27ac  in 7 cell lines: CMK,  HEL, SET-2, TF-1, K-562, THP-1, and JURKAT cells 48 hours post lenti delivery of the empty vector or the GATA2 coding sequence. Bulk RNA sequencing was perfomred in triplicates on TF-1 cells expressing the TPOR and empty vector or TPOR and CSF2RB 3 hours post TPO treatment.

last: Cruz Hernandez


title: The kinase inhibitor GNF-7 is synthetically lethal in topoisomerase 1 deficient Ewing Sarcoma

city: bethesda

first: Jack

last: Shern

state: MD

address: 10 Center drive

institute: NCI

summary: Relapsed Ewing sarcoma is treated with TOP1 inhibitors. Our study confirmed prior studies showing that downregulation of TOP1 is a mechanism of resistance to camptothecin. We then screened a large library of clinically relevant compounds and found that TOP1-deficient Ewing sarcoma cells are more sensitive to the kinase inhibitor GNF-7. RNA-seq results reveal that GNF-7 modulates EWS/FLI1 gene signatures in both TOP1 wild type and TOP1-deficient cells.

overall_design: RNA-seq was performed for gene expression profiling analysis in EW8 wildtype (WT) and EW8 TOP1 (TOP1 KD) knockdown cells treated with 40nM GNF-7 for 0h, 4h, 8h, 16h, 24h, 48h, and 72h.

first: Carly M

last: Sayers

first: John F


title: Transcriptomic alterations across various cell types in the PFC

city: Chongqing

first: Guo

middle: Jing

last: Ma

address: Yuzhong Road

institute: Chongqing medical university

summary: Major depressive disorder (MDD) is a prevalent mental illness that significantly impacts global health, with women showing twice the prevalence of men. This study employed the chronic social defeat stress (CSDS) model in female mice to investigate cellular and molecular changes in the prefrontal cortex (PFC) associated with depressive-like behaviors. Using single-nucleus RNA sequencing (snRNA-Seq), we examined transcriptomic alterations across various cell types in the PFC. Our results revealed that interneurons exhibited the most significant transcriptomic changes among all analyzed cell types. Notably, we identified a specific subtype of interneurons, the Sox6+ interneurons (Sox6+Int), which showed a markedly increased proportion in the CSDS group. This increase was associated with enhanced inflammatory and immune responses, as well as alterations in synaptic function and mitochondrial pathways. Furthermore, we observed significant changes in cell-cell communication patterns, particularly between Sox6+Int and oligodendrocyte precursor cells (OPCs). Weighted gene co-expression network analysis (WGCNA) identified several gene modules in Sox6+Int associated with specific depressive-like behaviors, implicating pathways related to inflammation, autophagy, and synaptic function. These findings provide novel insights into the cellular and molecular mechanisms underlying MDD in females, highlighting the potential role of Sox6+Int in stress-induced depression. Our study not only extends our understanding of the neurobiological basis of depression but also identifies potential therapeutic targets for sex-specific interventions in MDD treatment.

first: Peng

last: Zheng

first: Guojing


title: PNKP Targeting Engages the Autophagic Machinery to Enhance Ferroptosis and to Potentiate Anti-Tumor Efficacy of Doxorubicin in TNBC

city: Rehovot

first: Sima

last: Lev

address: 234 Herzl St.

department: Molecular Cell Biology

institute: Weizmann Institute of Science

summary: The polynucleotide kinase/phosphatase (PNKP) is a DNA repair enzyme possessing bifunctional DNA 3′-phosphatase and DNA 5′-kinase activities. It plays an important role in rejoining of single- and double-strand DNA breaks and is considered as a potential therapeutic target for different cancer types. Here we show that PNKP is highly expressed in triple negative breast cancer (TNBC) and associated with poor prognosis and chemoresistance. Targeting of PNKP enhanced ferroptosis in TNBC, which was associated with increased labile iron pool and ROS and concomitantly decreased in intracellular glutathione, SCD1 and GPX4 levels. Transcriptomic profiling and mechanistic data indicate that PNKP targeting robustly enhances the lysosomal and the autophagic machinery by activating STING and concurrently inhibiting STAT3, thereby increasing ferrtinophagy, intracellular iron level and modulates the expression of key ferroptosis regulators. Importantly, PNKP and STAT3 are rapidly phosphorylated, colocalize, and interact upon ferroptosis induction or doxorubicin treatment, the first line treatment for TNBC patients. Targeting of PNKP together with doxorubicin synergistically inhibited TNBC growth in animal model and TNBC-patients derived organoids. These results offer a promising therapeutic combination for TNBC and highlight the clinical potential of PNKP targeting and ferroptotic death for TNBC therapy.

overall_design: PNKP knock-down was induced in the breast cancer line MDA-MB-468 using lentiviral infection of pLKO vector harboring shRNA aimed for PNKP. Cells infected with empty pLKO served as control. Three independent repeats were carried out.

first: Avi

last: Maimon

first: Yaron

last: Vinik


title: Identification of candidate immunity biomarkers associated with age-related variations in osteoclast activity following orthodontic tooth movement

city: Wuhan

first: Rui

last: Zhang

address: 237 Luoyu Road

department: Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology

institute: School & Hospital of Stomatology, Wuhan University

summary: This study provides a comprehensive examination of the influence of age on osteoclast activity during orthodontic tooth movement, analyzed through the lens of osteoimmunology, identifying key immune molecules and cells involved in the regulation.We identified key molecules that play an important role in orthodontic bone reconstruction by analyzing the differences in immune inflammatory differential gene expression across different age groups. These molecules, which facilitate macrophage migration to the local site and their differentiation into osteoclasts, as well as directly enhance osteoclast differentiation and function, are differentially expressed in young groups, but not in adult groups.

overall_design: Gene expression profiling analysis of RNA-seq data from C57BL/6 mice of two different age groups, with each group subjected to an orthodontic tooth movement (OTM) model established between the maxillary first molar and maxillary incisors on the left side for durations of 7 and 14 days.

first: Yuhong

first: Zhen

last: Chen

first: Lulu

last: He


title: miRNA expression in family with sequence similarity 222 member B (Fam222B) knockdown B16 cells

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

summary: Using genetic functional screening, we identified Fam222B as a key molecule in the biological activity of delphinidin, a plant anthocyanidin. However, the function of Fam222B remains unclear. In this study, we evaluated the effect of silencing Fam222B expression on miRNA expression in B16 cells.

overall_design: In this study, we measured miRNA expression in B16 cells transfected with  Fam222B-siRNA or control-siRNA (n = 1, respectively).

first: Hirofumi

last: Tachibana

first: Motoki

last: Murata


title: Loss of Small Valosin-containing Protein-Interacting Protein (SVIP) in Rat Hepatoma cells Causes Increased Intracellular Retention of Very Low-Density Lipoproteins (VLDL)

city: Orlando

first: Vandana

last: Sekhar

state: Florida

address: 6900 Lake Nona Blvd, Burnett School Of Biomed Sciences

institute: University of Central Florida (UCF)

summary: In the current study we have generated a CRISPR-Cas9 mediated SVIP knockout rat hepatoma cell line with the goal to further understand the functional role of SVIP in the complex process of VLDL transport and secretion. We observed that complete absence of SVIP protein results in enhanced retention of VLDL in the hepatoma cells. This was marked by both an increased expression of apoB100 protein and neutral lipid staining detected inside SVIP knockout (SVIP KO) cells. Furthermore, RNA sequencing studies of the SVIP KO hepatoma cells revealed a significant downregulation of genes within the peroxisome proliferator- activated receptor alpha (PPAR alpha) and the nuclear factor erythroid 2-related factor 2 (Nrf2) pathways, thereby affecting hepatic fatty acid (FA) metabolism. Most importantly, we observed that cells lacking SVIP demonstrated a substantial down regulation of another very important gene associated with FA metabolism, namely the liver fatty acid-binding protein (L-FABP). Additionally, the RNAseq data also reveals that the loss of SVIP thrusts the hepatoma cells into an acute phase response (APR) like state, with an increase in the expression of protein synthesis genes.

overall_design: RNA-seq profiling of wildtype (WT) rat hepatoma cells (McARH-7777) and their CRISPR-Cas9 mediated SVIP knock out cells (KO)- untreated and treated with 0.4mM BSA-Oleic acid for 1 h and collected 24 h post treatment.

first: Thomas

last: Andl

first: Shadab

last: Siddiqi


title: Molecular characterization of cachexia in a novel head and neck cancer mouse model

city: Aurora

first: Andrew

last: Goodspeed

state: CO

address: 12801 E 17th Ave, Mail Stop 8303

institute: University of Colorado Anschutz Medical Campus

summary: Despite accounting for only ~4% of all cancers in the US, experimental and clinical observations suggest that ~40% of patients with head and neck cancer (HNC) present with ‘cachexia’, a severe comorbidity that associates with skeletal muscle defects and is responsible for decreased muscle function, worsened response to treatment, and poorer outcomes. Despite its clinical relevance, the mechanism(s) responsible for the onset of cachexia in HNC patients are not completely understood, thus leading to limited progress in diagnosis and representing a barrier to the development of treatments. Moreover, impeding the identification of viable therapies to combat HNC cachexia is also the limited availability of small animal models. Here, we characterized molecular and functional features of cachexia in a novel, preclinical model for the study of HNC, namely the mouse bearing the B0092 oral squamous cell carcinoma, transplantable in recipient C57BL/6 mice To investigate the systemic effects of HNC tumors, 10-week-old C57BL/6 male mice were implanted with B0092 cells (5x105 cells, s.c.) and monitored for up to 36 days. Growth of B0092 tumors was accompanied by skeletal muscle atrophy, loss of Extensor Digitorum Longus (EDL) muscle strength, reduced bone mineral density (BMD), measured by DEXA, and decreased trabecular bone, assessed using microCT. To identify the gene signature associated with muscle wasting caused by B0092 tumors, we performed Next Gen RNA-Sequencing of quadriceps muscle. The pathway analysis conducted using the Ingenuity Pathway Analysis (IPA) and integrated Differential Expression and Pathway (iDEP) bioinformatic tools, revealed dysfunction of mitochondria, as well as upregulation of proteasome- and translation-related pathways. In conclusion, our data suggests that B0092-bearing mice can be a useful tool to uncover novel molecular pathways and potential therapeutic targets for the treatment of HNC cachexia.

overall_design: To study the ability of B0092 head and neck squamous cell carcinoma (HNSCC) cell line to induce cahcexia, first, 8-week-old C57BL/6J mice were separated into control (n=4) and tumor bearing (n=4) groups. B0092 cells were injected s.c. near the nape of the neck with 200uL of 5x10^5 cells per mouse, while controls were injected with equal amounts of PBS vehcle. Mice were monitered for weight and muscle loss. When the mice reached ~10% weight loss from initial values (day 36), they were sacrificed and skeletal muscles and organs were collected and snap frozen in liquid nitrogen. Bulk RNASeq was performed on RNA isolated from the quadriceps muscle of both groups.

first: Patrick D

last: Livingston

first: Schuyler

last: Lee

first: Bifeng

last: Gao

first: Andrea

last: Bonetto


title: SETD6 Mediates Selective Interaction and Genomic Occupancy of BRD4 and MITF in Melanoma [CUT&Run]

city: Be'er Sheva

first: Dan

last: Levy

address: David Ben Gurion Blvd 1

institute: Ben-Gurion University

summary: Aberrant transcriptional programs mediate malignant transformation of melanoma, the most aggressive form of skin cancer. The lysine methyltransferase SETD6 has been implicated in regulating transcription, cell adhesion, migration, and other processes in various cancers, however its role in melanoma remains unexplored. We recently reported that SETD6 mono-methylates the BRD4 at K99 to selectively regulate transcription of genes involved in mRNA translation. Here, we observed that BRD4 methylation at K99 by SETD6 occurs in melanoma cells. Knockout of SETD6 or a point mutation at BRD4-K99 disrupts BRD4 genomic occupancy. In addition, we show that SETD6 interacts with MITF, a master transcription factor in melanocytes and melanoma, and influences the genomic distribution of MITF. Mechanistically, we uncover a novel chromatin- localized interaction between BRD4 and MITF in melanoma. Our data suggest that BRD4 binds MITF in melanoma cells and that this interaction is dependent on both SETD6-mediated methylation of BRD4 and MITF acetylation. This chromatin complex plays a pivotal role in selective recruitment of BRD4 and MITF to different genomic loci in melanoma cells.

overall_design: Cut&Run for Flag_BRD4_Wt and Flag_BRD4_K99R_mutant; and BRD4 and MITF in Control and SETD6 KOs cells

first: Elbaz-Biton

last: Tzofit


title: TRDMT1 methyltransferase gene knockout attenuates STING-based cell death signaling during self-extracellular RNA-mediated response in drug-induced senescent osteosarcoma cells

city: Krakow

first: Tomasz

last: Szmatoła

state: Małopolskie

address: Mickiewicza 21

department: OMEI

country: Poland

institute: University of Agriculture in Krakow

summary: Under stress conditions, endogenous biomolecules such as nucleic acids or proteins can be released from damaged cells and considered as damage-associated molecular patterns (DAMPs) activating innate immune system and context-dependent responses. In the present study, self-extracellular RNA was obtained from dying (RNA D) and senescent (RNA S) cellular models of osteosarcoma (OS), characterized by NGS, and tested against proliferating and non-proliferating (etoposide-indued senescent) OS cells (U-2 OS, SaOS-2, MG-63, 143B). RNA D and RNA S induced apoptosis, nitrooxidative stress, nucleic acid sensing pathways and cytokine production, and RNA m5C methyltransferase-based responses (TRDMT1 and NSUN2) in proliferating OS cells. In drug-induced senescent OS cells, TRDMT1 gene knockout (KO) prevented STING activation, related proinflammatory response, and cell death. Furthermore, IFNβ binding RNA partners were identified, namely NSUN2, NSUN5, NSUN6, CDKN1A, MYC, and RAD51 transcripts and these interactions were compromised in TRDMT1 KO cells and upon RNA D and RNA S treatment. TRDMT1 KO also resulted in replication stress in OS cells that was potentiated by RNA D and RNA S stimulation and associated with elevated levels of APOBEC3A and APOBEC3G, members of the cytidine deaminase protein family. In conclusion, we showed that TRDMT1 KO restricted STING-based immune and cell death response to RNA D and RNA S in nonproliferating drug resistant OS cells that might have potential therapeutic implications.

overall_design: Four cellular models of OS in vitro were used, namely U-2 OS, SaOS-2, MG-63, and 143B cells. OS cells were treated with etoposide, DNA damaging chemotherapeutic agent, at both death and senescence-inducting concentrations and RNA released to cell culture medium, RNA D and RNA S, respectively, was characterized using NGS. Proliferating and/or non-proliferating (drug-induced senescent) OS cells were then stimulated with RNA D and RNA S to reveal RNA-associated responses.

first: Gabriela

last: Betlej

first: Anna

last: Deręgowska

first: Maciej

last: Wnuk

first: Dominika

last: Błoniarz

first: Katarzyna

last: Klimczak

first: Jagoda

last: Adamczyk-Grochala

first: Julia

last: Świętoń

last: Lewińska


title: PRMT5-mediated SRSF1 methylation promotes virus-positive Merkel cell carcinoma tumorigenesis by increasing Tip60 exon inclusion

city: Durham

first: Joseph

last: Sevigny

state: NH

address: 35 Colovos Rd.

institute: Hubbard Center for Genome Studies

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

overall_design: Refer to individual Series


title: Harnessing Electroacupuncture: A Promising Strategy Against Sleep Deprivation-Exacerbated Post-Cardiac Arrest Brain Injury

city: Harbin

first: Wenchao

last: Fu

state: Chongqing

address: Second Hospital of Harbin Medical University, Xuefu Road, Nangang District, Harbin City, Heilongjiang Province, China

institute: Harbin Medical University

summary: This study investigated the mechanisms by which sleep deprivation exacerbates PCABI and evaluated the neuroprotective efficacy of electroacupuncture

overall_design: A CA model was established in SD rats, followed by RNA sequencing and molecular analyses to assess brain injury biomarkers, synaptic plasticity, and calcium signaling pathways

first: Cong

last: Hu

first: Can

last: Ma

first: Shihua

last: Lv

first: Xianzhang

last: Zeng

first: Tingting

last: Li

first: Jiahui

last: Chen

first: Xiao

last: Han

first: Xin

last: Tan

first: Xuefei

first: Wenzhi


title: Cold exposure promotes the progression of osteoarthritis through downregulating APOE in cartilage

first: Yueqi

last: Zhang

address: 150 Jimo Road, Pudong New Area,Shanghai

institute: Shanghai East Hospital, School of Medicine, Tongji University

summary: Osteoarthritis (OA) is a degenerative joint disease with limited effective therapies. Cold weathers have been shown to affect joint pain in OA patients. However, the impact of cold climate on OA progression is debated, with the underlying mechanisms not fully understood. To investigate the mechanisms by which low temperatures exacerbate OA, RNA sequencing on human chondrocytes cultured at 33 °C and 37 °C was performed. The gene expression in non-OA region chondrocytes and OA region chondrocytes at 33 °C was compared to that at 37 °C.  The Apoe gene was identified as a temperature-relevant gene associated with exacerbation of osteoarthritis. Apoe expression was downregulated in both OA and non-OA chondrocytes cultured at 33°C compared to their 37°C counterparts.

overall_design: Samples of human cartilage were taken from patients having total knee replacements.  Human chondrocytes isolated from severely damaged (OA) and healthy (non-OA) regions  of cartilage specimens (three patients) were cultured under two temperature conditions (37°C vs 33°C) for five days to investigate cold-associated OA progression. This experimental design generated four study groups (33°C-non-OA, 33°C-OA, 37°C-non-OA, 37°C-OA), each containing three biological replicates. The gene expression in non-OA region chondrocytes and OA region chondrocytes at 33 °C was compared to that at 37 °C

first: Zhe

last: Wang


title: Transcriptomic Profiling of Murine Chondrocytes Following APOE Knockout: Insights into Gene Expression Alterations

summary: We have previously demonstrated that cold stress significantly reduces APOE expression in chondrocytes, which correlates with intracellular lipid accumulation and elevated reactive oxygen species (ROS) levels. The objective of this study was to elucidate the downstream regulatory mechanisms of APOE in chondrocyte homeostasis. To achieve this, we compared genome-wide transcriptional profiles of wild-type (WT) and APOE-knockout (Apoe-KO) murine chondrocytes through RNA sequencing (RNA-seq).

overall_design: Primary chondrocytes were isolated from C57BL/6 mice, including wild-type (WT, n=3) and Apoe knockout (Apoe-KO, n=3 ) groups. Cells from each genotype were cultured under standardized conditions, followed by RNA extraction and sequencing. Genome-wide transcriptomic profiling via RNA-seq was performed to compare gene expression patterns between Apoe-KO (Case) and WT (Control) chondrocytes, aiming to identify APOE-dependent downstream targets and regulatory pathways.


title: Distinct microRNA signatures define sporadic PSP-RS and PD in patient-derived midbrain organoids

city: Catanzaro

first: Elvira

middle: Immacolata

last: Parrotta

state: Catanzaro

address: Viale Europa, 1

country: Italy

institute: University Magna Greacia of Catanzaro

type: Non-coding RNA profiling by high throughput sequencing

summary: Progressive Supranuclear Palsy–Richardson Syndrome (PSP-RS) is a rare, rapidly progressive neurodegenerative tauopathy frequently misdiagnosed as Parkinson’s Disease (PD) due to overlapping clinical features. The lack of reliable molecular biomarkers for early and differential diagnosis presents a major clinical challenge. To address this, we developed human midbrain organoids from induced pluripotent stem cells (iPSCs) derived from patients with sporadic PSP-RS, PD, and healthy controls (HCs), and profiled microRNA (miRNA) expression dynamics using small RNA sequencing. These 3D organoid models faithfully recapitulate key pathological hallmarks, including tau hyperphosphorylation in PSP-RS and Lewy body–like α-synuclein inclusions in PD. Our analysis revealed temporally dynamic, disease-specific miRNA signatures: miR-5683, miR-873-5p, miR-219b-5p, and miR-219a-2- 3p were selectively upregulated in PSP-RS, whereas PD organoids showed increased levels of miR-1-3p, miR-133b, miR-10b-5p, and miR-199a-5p. Additionally, miR-5683, miR-3085- 3p, miR-138-2-3p, and miR-124-3p emerged as key discriminators between PSP-RS and HCs. These findings highlight the utility of iPSC-derived midbrain organoids as a translationally relevant platform to uncover disease-specific regulatory networks and identify candidate miRNA biomarkers for atypical parkinsonian syndromes.

overall_design: small RNAseq was carried out to characterize dynamic changes in miRNA expression at 60, 90, and 120 days. The samples are from iPSCs-derived midbrain organoids in three conditions: sporadic Progressive Supranuclear Palsy–Richardson Syndrome (PSP-RS), parkinson disease (PD), and healthy controls (HCs). Three replicates per condition for each time point (60,90,120d) are present (total of 27).

first: Giovanni

last: Cuda

first: Elvira Immacolata

first: Desirèe

last: Valente

first: Clara

last: Zannino

first: Stefania

last: Scalise


title: Aging compromises terminal differentiation program of cytotoxic effector lineage and promotes exhaustion in CD8+ T cells responding to coronavirus infection [RNA-seq]

city: Dallas

first: Chen

last: Yao

state: Texas

address: 5901 FOREST PARK RD, NS6 218

institute: UT Southwestern Medical Center

summary: T cell aging increases the risk of viral infection-related morbidity and mortality and reduces vaccine efficacy in the elderly. A major hallmark of T cell aging is the loss of quiescence and shift towards terminal differentiation during homeostasis. However, how aging alters the differentiation program of virus-specific T cells during infection is unclear. Here, in a murine coronavirus (MHV) infection model with age-associated increased mortality, we demonstrate that aging impairs, instead of promoting, the terminal differentiation program of virus-specific CD8+ T cells. Upon infection, CD8+ and CD4+ T cells in old mice showed marked reduction in clonal expansion and upregulation of immune checkpoints associated with T cell exhaustion. Bulk and single-cell transcriptomics showed that aging upregulated T cell exhaustion transcriptional program associated with TOX in virus-specific CD8+ T cells and shift the myeloid compartment from immunostimulatory to immunosuppressive phenotype. In addition, aging downregulated the transcriptional program of terminally differentiated effector CD8+ T cells and diminished CX3CR1+ cytotoxic effector lineage. Mechanistically, virus-specific CD8+ T cells from infected aged mice displayed defects in inducing transcription factors ZEB2 and KLF2, which were required for terminal differentiation of effector CD8+ T cells. Together, our study shows that aging impairs terminal differentiation and promotes exhaustion of virus-specific CD8+ T cells responding to coronavirus infection through dysregulating expression of lineage-defining transcription factors.

overall_design: We performed bulk RNA sequencing on whole lung tissue and S598 tetramer-positive CD8 T cells isolated from the spleens of young and old mice on day 7 post-MHV infection.

first: Tuoqi

last: Wu

first: Ziang

last: Zhu

first: Guohua

last: Lou


title: Mouse model of steatohepatitis

city: Macau

last: Huang

address: Macau University of Science and Technology, Avenida Wai Long, Taipa, Macau

summary: This study aims to investigate the differences in gene expression between normal mice and mice with hepatic steatosis to reveal the molecular mechanisms underlying the development and progression of fatty liver disease and to provide potential targets for the prevention and treatment of related diseases. C57BL/6J mice were selected as the experimental subjects, and a fatty liver inflammation model was established by feeding them a high-fat, high-fructose, and high-cholesterol (FFC) diet. Specifically, the FFC diet consisted of 40 kcal% fat, 20 kcal% fructose, and 2% cholesterol, and the mice were continuously fed this diet for 24 weeks. Afterward, we monitored the total cholesterol (TC) levels in the mice, and the results showed a significant increase in total cholesterol in the model group. By comparing the gene expression profiles of normal mice and mice with fatty liver inflammation, we hope to identify key genes and signaling pathways associated with fatty liver disease, thereby deepening our understanding of the pathophysiological processes of hepatic steatosis and laying the foundation for the development of new diagnostic markers and therapeutic strategies.

overall_design: RNA-seq analysis of liver tissues of 6 normal control mice and 18 model mice

first: Qian

last: Ding

first: Rong

last: Fu

first: Xiyue

last: Chang


title: Per2 deficiency in microglia alleviates motor dysfunction by inhibiting ferroptosis in spinal cord injury [RNA-Seq]

city: Yinchuan

first: Hechun

last: Xia

state: Ningxia

address: No. 804 Shengli South Street, Xingqing District, Yinchuan City, Ningxia, People's Republic of China

institute: General Hospital of Ningxia Medical University

summary: Microglia play significant roles in spinal cord injury (SCI) progression. Previous studies have suggested that ferroptosis plays a crucial role in exacerbating neuronal death following SCI; however, the role of microglial ferroptosis in SCI and the underlying mechanisms remain elusive. Here, we elucidate that lipid droplets accumulate in microglia to facilitate microglial ferroptosis after SCI. Notably, microglial ferroptosis peaks at 3 days post-injury, after which it decreases. Microglial Period 2 (Per2) expression is elevated after SCI in vivo; this change is highly synchronized with the changes in microglial ferroptosis. Microglia-specific Per2 knockout promoted neurological function recovery by suppressing microglial ferroptosis. In vitro, Per2 overexpression and deficiency amplified and mitigated microglial ferroptosis, respectively. RNA-seq indicated that Gpx4 was downregulated by Per2. Coimmunoprecipitation demonstrated that Per2 directly interacted with PPARα. Overall, our results indicate that Per2 determines the susceptibility of microglial ferroptosis via the PPARα-Gpx4 axis after SCI.

overall_design: We induced ferroptosis in primary microglia with 1600 μM iron and 1 μM RSL3, and RNA sequencing was subsequently performed.

first: Pengfei

last: Bie

first: Dongpo

last: Su

first: Yang

last: Gao

first: Liang

first: Zhanfeng

last: Niu

first: Yanbin

last: Zhao

first: He

last: He

last: Jiang

first: Zhong

last: Zeng

first: Yaolin

first: Heng

last: Fan


title: Integration of CRISPR-Cas9 Screens and Multi-Omics Profiling Reveals CHD7-ANGPT1 as a Novel Multi-Drug Resistance Axis in AML

city: Tianjin

first: Tingting

last: Zhang

address: Tianjin,Heping district,288 Nanjing road.Institute of Hematology and Blood Diseases Hospital

summary: To explore how the loss of function of CHD7 leads to drug resistance in acute myeloid leukemia (AML) cells, we investigated the transcriptional programs regulated by CHD7 in OCI-AML2 cells under different drug treatment conditions. This study aims to uncover the role of CHD7 in drug sensitivity and resistance, providing a theoretical basis for developing new therapeutic strategies.

overall_design: Assessment of gene expression changes in CHD7 knockdown and control sgSC cells under three different conditions:DMSO,Gilteritinib,Venetoclax.

first: Dandan

last: Yang


title: Integrated biochemical and transcriptomic profiling reveals graded spleen responses to moderate versus severe hypoxia in rainbow trout (Oncorhynchus mykiss)

city: Lanzhou

first: QI

last: Wang

state: Gansu

address: Yintan Road Street

department: College of Animal Science and Technology

institute: Gansu Agricultural University

summary: Hypoxia severely threatens the survival and growth of fish, thereby greatly restricting the development of aquaculture. Rainbow trout (Oncorhynchus mykiss) is highly sensitive to hypoxia, but the regulatory mechanism of rainbow trout spleen under different levels of hypoxia is not yet clear. In this study, we analyzed the effects of moderate hypoxia (DO: 4.5 ± 0.1 mg/L) and severe hypoxia (DO: 3.0 ± 0.1 mg/L) on the biochemical parameters of rainbow trout spleen at various time points (4, 8, 12, 24 h, 1 month, and re-oxygenation for 12 and 24 h). Additionally, we comparatively analyzed the transcriptomic changes in moderate and severe hypoxia at 12 h, as well as in normoxic controls. Antioxidant enzyme activities (T-AOC, T-SOD, GOT, GPT, CAT) rose markedly under both moderate and severe hypoxia, while MDA content peaked early and then declined. Immune-related enzymes (AKP, ACP) were elevated under moderate hypoxia but suppressed under severe hypoxia. Reoxygenation gradually restored the activities of antioxidant and immune enzymes, yet MDA surged again. Transcriptomic analysis identified 5766 DEGs. These DEGs were mainly enriched in the B cell receptor signaling, Glycolysis/Gluconeogenesis, Notch, MAPK, and PI3K-Akt pathways. The analysis of dynamic expression of hypoxia-associated genes revealed that hif-1a, acly, egln2, plpp3, fn1, and cd22 were upregulated under moderate hypoxia, whereas aldoa and ldha were downregulated, with their expression levels recovering during reoxygenation. egln1, egln2, egln3, aldoa, plpp3, pk, g6pc, and eno1a were upregulated during severe hypoxia stress, and their expression returned to baseline levels following reoxygenation. These results improve our comprehension of the molecular processes involved in hypoxia stress in rainbow trout.

overall_design: Fish weighing (130 ± 5.0) g were selected and temporarily reared for two weeks in a flow-through aquaculture system with DO of 8.5 ± 0.1 mg/L, water temperature of 12 ± 0.1℃. Fish were fed a commercial pellet feed twice a day. All procedures were conducted in accordance with the approval of the Animal Ethics Committee of Gansu Agricultural University and followed the protocols approved by the institutional guidelines.Healthy rainbow trout were randomly divided into three groups, including normoxia, moderate hypoxia, and severe hypoxia groups, the oxygen levels were maintained at 8.5 ± 0.1, 4.5 ± 0.1, and 3.0 ± 0.1 mg/L, respectively, and the low oxygen environment was created by mixing oxygen and nitrogen. The reoxygenation experiment was conducted immediately after 24 h of hypoxia stress and the DO level was maintained at 8.5 ± 0.1 mg/L during the experiment. Controls were divided into C (0 h control) and CM (1 month control), and the spleens of the normoxia group were collected immediately before the start of the hypoxia experiment and 1 month after the start of the experiment. After hypoxia stress, spleen tissues were collected at 4 h, 8 h, 12 h, 24 h, TMM (moderate hypoxia for 1 month), and TMS (severe hypoxia for 1 month), as well as R12 (hypoxia for 24 h + reoxygenation for 12 h) and R24 h (hypoxia for 24 h + reoxygenation for 24 h) in each group (moderate hypoxia group and severe hypoxia group), respectively. spleen samples were collected after fish MS-222 treatment. After collection, some samples were used for histological observation, other samples were frozen immediately in liquid nitrogen, and then transferred to -80℃ refrigerator for storage for biochemical parameters, gene expression and RNA-seq assays.

first: Jingqiang

first: Kangkang

last: Liu

first: Qi


title: CFTR gene regulation in pancreatic duct, bile duct and sweat gland

city: Cleveland

first: Katreya

last: Lovrenert

address: 10900 Euclid Avenue

department: Department of Genetics and Genome Sciences

institute: Case Western Reserve University

summary: We examine cis-regulatory elements controlling expression of the cystic fibrosis transmembrane conductance regulator (CFTR) gene in ductal eptihelial cells from pancreas, bile duct and sweat gland. Mutations in CFTR are associated with the inherited disorder cystic fibrosis. We identify several novel sites in addition to multiple elements seen in in other epithelial cell types.

overall_design: ATAC-seq to examine open chromatin at the CFTR locus and genome wide in specialized epithelial cells.

first: Ayushi

last: Umrigar

first: Jenny

last: Kerschner

first: Shih-Hsing

last: Leir

first: Ann

last: Harris


title: Single cell sequencing reveals unique photoreceptor populations

city: Hamburg

first: Andreas

last: Neueder

address: Falkenried 94

department: Center for Molecular Neurobiology (ZMNH)

country: Germany

institute: University Medical Center Hamburg-Eppendorf

summary: Several ocular diseases such as retinitis pigmentosa are associated with retinal degeneration, a process during which the retina deteriorates due to the gradual death of photoreceptor cells. Although extensive research has been pursued to identify the underlying pathomechanisms, the precise molecular mechanisms that leads to photoreceptor death remains unclear. In this study, we combined the mouse model of light-induced photoreceptor degeneration with single cell RNA sequencing to decipher the transcriptional response of degenerating photoreceptor cells. We additionally performed pseudotime analysis of gene expression changes for both the control and light damaged photoreceptor clusters to analyze the extent of degeneration following a virtual trajectory of severeness. We found a transcriptional heterogeneity of rod photoreceptors in both control and degenerative conditions, and mapped several rod clusters which strongly differ in their transcriptional profile. We defined one of these clusters as the predominant disease-associated rod cluster, containing the most severely damaged rod cells. Pseudotime analysis demonstrated a strong regulation of TGFb  signaling and the RISC  complex in light damaged photoreceptors suggesting a pivotal role of these mediators in retinal degeneration.

overall_design: We used single cell RNA sequencing (scRNAseq) based on 10x Genomics libraries to study the transcriptomic response of the mouse retina under light damage and control conditions.

first: Aaron

last: Schroers

first: Isabel

last: Massoudy

first: Süleyman

last: Ergün

first: Barbara

middle: M

last: Braunger

first: Anja

last: Schlecht


title: Preclinical Model of Military Burn Pit Exposure Reveals Altered Inflammatory and Metabolic Pathways in the Rat Lung-Brain Axis

city: Minneapolis

first: Allison

middle: M.

last: Haaning

state: MN

address: 117 Pleasant St. SE

department: Minnesota Supercomputing Institute

institute: University of Minnesota

summary: Military personnel deployed to combat zones in Iraq and Afghanistan were exposed to toxic emissions from open-air burn pits, raising concerns about long-term health effects. Burn pit exposures are linked to a wide range of pulmonary and extra-pulmonary morbidities. This study aimed to model military burn pit exposure and investigate its impact on lung-brain axis signaling. Rats were exposed to carbon black nanoparticles and naphthalene (CBN) via whole body inhalation chamber for six hours to simulate burn pit exposure. Gene expression and inflammatory protein changes in lung and brain tissue were examined 24 hours post-exposure using next-generation RNA sequencing, Meso Scale Discovery biomarker assays, and western blot. Multiple inflammatory pathway proteins were significantly altered in plasma, lung and brain. Gene Set Enrichment Analysis (GSEA) in lung and brain revealed significant alterations in molecular processes in lung tissue, including increased cell cycle activity, lipid balance disruption, and enhanced inflammatory responses. Conversely, processes such as adipogenesis, oxidative phosphorylation, and epithelial to mesenchymal transition were suppressed. An elastic net penalized regression model identified a set of 104 genes in lung tissue that could indicate CBN exposure in lung. We focus on the nine genes with the greatest contribution to this model. These genes, including Tiam1, Cpsf3, and Tgfrb1, are involved in various cellular processes such as inflammation, cell signaling, and tissue remodeling. We observed significant increases in lung, brain and peripheral inflammation as well as signaling changes in lung and brain that demonstrate disruption of tissue homeostasis. Our findings demonstrate notable gene expression changes that may represent similarities to Veterans suffering from Deployment-Related Respiratory Disease (DRRD). This study provides insights into the molecular mechanisms underlying lung and brain response to burn pit-like exposures and identifies potential biomarkers for further investigation of the lung-brain axis. These results contribute to our understanding of the health impacts of military burn pit exposures and may inform future diagnostic and therapeutic strategies.

overall_design: Lung and brain tissues were harvested from male Sprague Dawley rats 24 hours after whole body inhalation of carbon black nanoparticles and naphthalene (CBN) or sham air for six hours a day for 3 consecutive days. Libraries were prepared using a TruSeq Stranded Total RNA Library Prep Kit (Illumina, San Diego, CA), and next-generation sequencing was performed using a Novaseq 6000 (Illumina) to generate 150 bp read pairs.

first: Brian

middle: J

last: Sandri

first: Henry

last: Wyneken

first: Julie

last: Tomáška

first: Grace-Divine

last: Boutouli

first: Joshua

middle: P

last: Nixon

first: Timothy

middle: R

last: Nurkiewicz

first: Chris

last: Wendt

first: Paul

last: Barach

first: Janeen

last: Trembley

first: Tammy

last: Butterick


title: Engineering chimeric PCSK9 for a vaccine against atherosclerosis

city: Ljubljana

first: Špela

last: Malenšek

address: Hajdrihova 19

department: Department of Synthetic Biology and Immunology

country: Slovenia

institute: National Institute of Chemistry

summary: Cardiovascular diseases, especially atherosclerosis, are the major cause of death in the modern era. In most cases, amelioration is achieved by decreasing the concentration of LDL cholesterol in blood, using statins or monoclonal antibodies targeting PCSK9, which are highly efficient, but are costly and requires bimonthly administration. Vaccination against PCSK9 represents an attractive alternative with potentially long-lasting efficiency, but has to overcome the challenge of autoimmune reactivity against an endogenous protein to prevent healthy tissue damage. We developed an autologous chimeric vaccine against PCSK9, which triggers a B cell immune response to produce neutralizing antibodies but avoids induction of self antigen mediated T cell cytotoxicity. We demonstrated in atherosclerosis murine model that vaccination generated an adequate humoral immune response with the effect persistent over 24°weeks, observed in lower circulating PCSK9, lower cholesterol and reduced atherosclerotic disease burden in the aortas. This is a proof of concept study for a therapeutic amelioration of atherosclerosis, which also provides a perspective on the rational design of a vaccine against endogenous proteins.

overall_design: 5 female 8-10 weeks old Apoe-/- mice (strain B6.129P2 Apoetm1Unc/J; Charles River) per experimental group were intramuscularly injected plasmid DNA (empty pCG1 vector and pCG1-chPCSK9-tox plasmid), complexed with jetPEI in vivo transfection reagent. Mice were injected 3 times with 2 weeks in-between injections. 24 weeks after beginning of the experiment animals were sacrificed and liver tissue was taken for homogenization and total RNA was extracted using TriPure Isolation Reagent (Roche) according to manufacturer's instructions. Collected RNA from animal tissue was pooled in 4 replicates and then sent for bulk RNA sequencing.

first: Duško

last: Lainšček

first: Roman

last: Jerala


title: A neonatal rat model of progressive left ventricular pressure overload induced by abdominal aortic banding microsurgery

city: Shanghai

first: Zheng

last: WANG

state: Shanghai

address: Shanghai Dongfang Road No.1678 Shanghai Children's Medical Center

institute: Shanghai Jiaotong University

summary: Objectives: Diseased animal models play a crucial role in understanding of the mechanisms and identifying therapeutic targets of human diseases. Left ventricular pressure overload (LVPO) is common in children with various types of cardiovascular diseases, such as aortic valve stenosis and hypertension. However, the current neonatal rat model of LVPO is limited in transverse aortic constriction (TAC) model, characterized by the fixed LVPO and rapid pathological progress of left ventricle, which are not in consistency with the progressive LVPO and relative slow pathological progress of left ventricle in the above pediatric cardiovascular diseases. The purpose of this study is to establish a neonatal rat model of progressive LVPO.

overall_design: RNAseq analyses of left ventricular myocardiocytes  in pressure overload, and sham-operated postnatal rats.

last: Wang

first: Debao

last: Li

first: Lincai

last: Ye


title: PRMT5-mediated SRSF1 methylation promotes virus-positive Merkel cell carcinoma tumorigenesis by increasing Tip60 exon inclusion [PacBio Sequel IIe]

first: Joseph

last: Sevigny

summary: Protein Arginine Methyltransferase 5 (PRMT5) is a key regulator of gene expression and RNA splicing, with its therapeutic potential demonstrated through synthetic lethality in MTAP-deleted cancers. Emerging evidence also suggests that MYC-driven or p53 wild-type tumors may be more sensitive to PRMT5 inhibition, though the underlying mechanisms remain unclear. Virus-positive Merkel cell carcinoma (MCC) serves as an ideal model to explore this question, as it is driven by the MYC paralog MYCL, and most virus-positive MCCs retain wild-type p53. In this study, we investigated PRMT5’s impact on the Tip60-EP400 complex, given MCC’s reliance on the interaction between MYCL and this complex. We used second-generation sequencing (Illumina) to characterize PRMT5-mediated bulk gene expression and long-read RNA sequencing (PacBio Iso-Seq) to analyze PRMT5-mediated alternative splicing. The mechanism underlying PRMT5 deficiency's selective impact on specific splice sites while leaving others unaffected remains unclear. Our findings suggest that PRMT5-mediated methylation of SRSF1 enhances its recruitment to m6A-modified RNA, ensuring proper splicing of Tip60 and maintaining Tip60-EP400 activity. In contrast, PRMT5 inhibition disrupts this recruitment, leading to widespread splicing defects, including both exon skipping and intron retention. These results provide new insights into PRMT5’s role in splicing regulation in cancer cells and may have broader implications for targeting splicing dysregulation in MYC-driven cancers.

overall_design: RNA-seq analyses of MKL-1 cells treated with DMSO or the PRMT5 inhibitor JNJ-64619178. PacBio IsoSeq Dataset.

first: Evelyn

last: Proctor

first: Heather

last: Adams

first: Kelley

last: Thomas

first: Jingwei

last: Cheng


title: Systems Biology-Based Assessment of Immune Responses to Whole Cell and Acellular Pertussis Vaccines: Rationale, Methodology and Enrollment Procedures for Omics Workflows

city: Rockville

first: Johannes

last: Goll

address: 401 N Washington St

department: Bioinformatics Service Group

institute: The Emmes Company

summary: Given the local and systemic adverse reactions associated with whole cell pertussis vaccines combined with diphtheria and tetanus toxoids (DTP), acellular pertussis vaccines combined with the same toxoids (DTaP) were developed in the 1990s. In comparison to DTP, DTaP vaccines demonstrated reduced reactogenicity and equivalent or improved immunogenicity and efficacy. However, there has been a resurgence of pertussis disease, particularly in DTaP-vaccinated children, suggesting that immunity wanes more quickly with DTaP vaccination. To elucidate the differences in immune responses to DTP and DTaP vaccines, we employed a systems biology-based strategy to compare global changes in gene expression following primary vaccination with either DTP or DTaP. We used RNA-Seq and ribosome profiling (RP) to identify transcriptional and translational signatures, respectively, in peripheral blood mononuclear cells (PBMCs) collected from 50 infant recipients of DTP or DTaP at two time-points (baseline (pre-vaccination at Day 1) and either Day 2 or 8 post-vaccination). We also used standard serologic methods to assess immunogenicity and correlated these results with the transcriptional and translational signatures. Here, we provide a detailed description of the rationale, experimental design, methodology and enrollment procedures used. Given the technical complexity of our approach, our objective is to fill knowledge gaps, describe key quality metrics, and support future publications. In brief, we recovered 4-12 million PBMCs (average 8.9 million) with 99% viability per 2.5 mL blood sample, enabling excellent nucleic acid recovery yields for preparation of high-quality sequencing libraries. In turn, these generated RNA-Seq and RP datasets with sufficient genome coverage, breadth, and depth to enable differential gene expression analyses, demonstrating the validity of our approach to study pertussis vaccine immunology specifically, and its utility to characterize mechanisms of the human immune response to vaccination generally.

overall_design:
To establish basic metrics of quality for RNA-Seq and RP workflows, as our approach had no precedent and working in the context of a vaccine study where the participants were infants presented several significant challenges.
To measure post-vaccination changes in gene expression at two different time points (24 hours and 7 days post-vaccination), and to compare changes in gene expression between vaccine groups (DTP and DTaP) following the first vaccine dose administered at ~2 months of age.
To compare the gene-expression responses measured by RNAseq and RP with those obtained using traditional immunological tools, like antibody responses, inflammatory cytokine production, cell-mediated immunity, and B-cell antibody repertoires.

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

last: Leguia

first: Antón

last: Vila-Sanjurjo

first: Diana

last: Juarez

first: Alejandra

last: Garcia-Glaessner

first: Ana

last: Gil

first: Mayita

last: Alvarez

first: Rubelio

last: Cornejo

first: Sami

last: Cherikh

first: Casey

last: Gelber

middle: B

first: Leigh

last: Howard

first: Natalia

last: Jimenez-Truque

first: Kathryn

last: Edwards

first: C

last: Creech

first: Claudio

middle: F

last: Lanata