title: Transcriptome sequencing of liver injury models

status: Public on Jun 30 2025

city: 郑州

first: yucheng

last: li

state: 河南省

address: 河南省郑州市金水区博学路街道金水东路156号

country: China

institute: Henan University of Chinese Medicine

type: Expression profiling by high throughput sequencing

summary: The liver is the largest solid organ and digestive gland in the human body. It plays a key role in the metabolism, transformation and detoxification of the three major organic substances. Therefore, the liver occupies an important place in the body's metabolism of substances. Crizotinib is a new type of drug with high efficiency for the treatment of lung cancer, but it has a large toxic effect, so this paper studies the acute effect of crizotinib on the liver, and studies its key targets for toxic effects through high-throughput transcriptome sequencing, which is divided into normal group and administration group, each group n=3, and the samples are mouse tissue samples.

overall_design: CITE-seg: ICR mice were randomly divided into dosing and normal groups. After 7 days of adaptation, the normal group was given 300mg/kg of crizotinib based on the same dose of normal saline, and three mice from each group were randomly selected for high-throughput transcriptome sequencing based on the same dose of normal saline, and samples were collected one week after administration.


title: Serotonin through serotonylation impact on gene expresion on human purified trophoblast after 48h in culture

city: New Haven

first: Nolwenn

middle: Sue

last: Morris

address: 333 Cedar Street

department: OBGYN

country: USA

institute: Yale University

summary: Serotonin (5-hydroxytryptamine) plays a critical role in human development in utero. Recent evidence suggests that it is taken up from the maternal circulation and gets concentrated in trophoblasts (Kliman et al., 2018). A novel mechanism involving serotonin has been described: serotonylation, a covalent linkage of 5-HT with protein glutamines mediated by a tissue transglutaminase (Farelly et al., 2019). Our objective was to understand the role of serotonin, through serotonylation, in protein, gene and phenotype expression in human placenta. Trophoblast puriScation and culture, western blot (WB), immunochemistry (IHC), and RNAseq (with IPA) were performed. Experiments were repeated at least 3 times, and corresponding statistical analysis was done. Through WB and IHC, we found that serotonylation seems to be present in human placenta and cytotrophoblasts. Moreover, through IHC and RNAseq/IPA, serotonylation seems to have consequences on gene and phenotype expression; especially on fusion, proliferation and invasion, which leads to implantation and placental structure, initial steps of pregnancy. Through IPA analysis, those phenotype and serotonylation impacted-genes were also found to be involved in embryonic, organismal, tissue and organ development, and especially the brain and behavior, foreshadowing central role in human body physiological development. Lastly, IPA results also showed that those same genes were also involved in many different pathologies, especially ones like Alzheimer, Parkinson, ALS, depression, ASD or cancer (EMT). To conclude, these Sndings seem to show that the human placenta, through the cytotrophoblast, is an essential organ to understand the origin of human life and pathophysiological development. Serotonin, through serotonylation, seems to be central by regulating original embryonic genes involved in different processes during life, especially in initiation of pregnancy (invasion and placentation), development of the human body, behavior, and different pathologies, leading to potential diagnostic or therapeutic options for patients.

overall_design: RNAseq profiling of purified trophoblast (CTB) with different inhibitors with or without 5-HT at 48h (serotonylation and serotonin transport inhibitor).

middle: S

first: Seth

middle: M

last: Guller

first: Zhonghua

last: Tang

first: Yuan-Wei

last: Zhang

first: Erin

middle: C

last: Siegman

first: Kristin

last: Milano

first: Gary

last: Rudnick

first: Harvey

middle: J

last: Kliman


title: Effect of FL-Fc-DM1 drug on gene expression of THP-1 cells

city: Shenzhen

first: Dengyang

state: Guangdong

address: Zhenmei road, guangming district

institute: Seventh affiliated hospital, Sun Yat-sen University

summary: To eliminate  cell-cycle arrested AML cells, we developed a FL-Fc-DM1 drug by conjugating FLT3 liangd Fc fusion protein and mertansine. We used the THP-1 cells as a AML model. The total mRNA of THP-1 cells treated with different concentration of FL-Fc-DM1 were sequenced.

overall_design: THP-1 cells were cultured in RPMI 1640 medium supplemented with 10% FBS. In the control group, THP-1 cells were cultured for 1 day. In the FL-Fc-DM1 treatment groups, THP-1 cells were treated with FL-Fc-DM1 (1 and 3 nM) for 24 hours. We than analyze the transcriptome differences between different groups.

last: zhang

first: Yun

last: Chen


title: Effect of FL-Fc-DM1 drug on gene expression of Molm-13 cells

summary: To eliminate  cell-cycle arrested AML cells, we developed a FL-Fc-DM1 drug by conjugating FLT3 liangd Fc fusion protein and mertansine. We used the Molm-13 cells as a AML model. The total mRNA of Molm-13 cells treated with different concentration of FL-Fc-DM1 were sequenced.

overall_design: Molm-13 cells were cultured in RPMI 1640 medium supplemented with 10% FBS. In the control group, Molm-13 cells were cultured for 1 day. In the FL-Fc-DM1 treatment groups, Molm-13 cells were treated with FL-Fc-DM1 (1 and 3 nM) for 24 hours. We than analyze the transcriptome differences between different groups.


title: Selective targeting of mutant huntingtin intron-1 improves rescue provided by antisense oligonucleotides in HTT.Q111/+ mice

city: Seattle

first: Robert

last: Bragg

state: Washington

address: 300 9th Ave

institute: University of Washington

summary: Huntington’s disease (HD) arises from the toxic gain of function caused by a CAG expansion in the coding region of the HTT gene. HD is increasingly appreciated to emerge from multiple pathogenic processes, including somatic instability in mutant HTT’s (mHTT) CAG repeat tract, which leads to diverse deleterious consequences. These include the alternative processing of HTT pre-mRNA to generate the HTT1a transcript that encodes the very toxic, mHTT isoform referred to as HTT1a. We set out to compare the efficacy and safety of allele-selective lowering of mHTT compared to non-allele-selective lowering using antisense oligonucleotides (ASOs) in heterozygous HttQ111 (Q111) mice. We developed a mutant specific ASO (MutASO) targeting Htt intron-1 that selectively reduced mutant full-length HTT, as well as HTT1a, in the brains of Q111 mice. Compared to the rescue provided by a pan-allele-targeting ASO (PanASO) that lowers wild-type HTT and full-length mHTT (sparing HTT1a), the MutASO essentially eliminated aggregate formation, and provided marked protection from transcriptional dysregulation in HD knock-in mice. Thus, by targeting the ASO to the region upstream of the cryptic polyadenylation sites required to generate the HTT1a transcript, our allele-selective MutASO potently reduced HTT1a protein levels. Here, our findings advocate that HTT1a may have a disproportionate impact on aggregate formation and transcriptional dysregulation and that lowering the levels of HTT1a should be included in the design of HTT-lowering based therapeutic strategies for HD.

overall_design: Mice were treated with ASO from 3 to 9 months of age. We sequenced n=5 per genotype (WT or HTT.Q111/+) treated with Saline, PanASO, or MutASO. Total N=30

first: Yuanjing

last: Liu

first: Christian

last: Landles

first: Edward

last: Smith

first: Georgina

last: Osborne

first: Anthony

last: Lamattina

first: Naoki

last: Iwamoto

first: Michael

last: Byrne

first: Chandra

last: Vargeese

first: Gillian

last: Bates

first: Jeffrey

last: Carroll


title: Transcriptomic Changes in Human Pulmonary Fibroblasts Following Microplastics Exposure

city: Krakow

first: Tomasz

last: Szmatoła

state: Małopolskie

address: Mickiewicza 21

department: OMEI

country: Poland

institute: University of Agriculture in Krakow

summary: To assess the cellular effects of polystyrene (PS) micro- and nanoparticles, human pulmonary fibroblasts (HPFs) were exposed to spherical PS particles of two diameters (100 nm and 1 µm) across multiple concentrations. For 100 nm particles, the concentrations were 0.1 g/L (A), 0.01 g/L (B), and 0.001 g/L (C); for 1 µm particles, 0.1 g/L (A), 0.05 g/L (D), 0.01 g/L (B), and 0.001 g/L (C) were tested. In summary, our data show that both particle size and concentration critically influence the cellular response to microplastics. At low concentrations (0.001 g/L), smaller particles (100 nm) induced transcriptional activation of mitochondrial and biosynthetic genes, suggesting early metabolic adaptation. In contrast, high concentrations (0.1 g/L), particularly of larger particles (1 µm), led to suppression of metabolic, mitochondrial, and proteostatic pathways, indicating functional impairment and potential cellular stress.

overall_design: HPFs were obtained from PromoCell GmbH (cat. no.: C-12360; Germany) and cultured in Dulbecco’s Modified Eagle Medium (DMEM, High Glucose; Thermo Fisher Scientific, USA), supplemented with 10% fetal bovine serum (FBS; Thermo Fisher Scientific, USA) and an antibiotic-antimycotic solution containing penicillin (10,000 U/mL), streptomycin (10,000 µg/mL), and amphotericin B (25 µg/mL; Thermo Fisher Scientific, USA). Cells were maintained at 37°C in an atmosphere containing 5% CO₂. To assess the cellular effects of PS micro- and nanoparticles, HPFs were exposed to spherical PS particles of two different diameters.  For the 100 nm particles, three concentrations were selected: 0.1 g/L (A), 0.01 g/L (B), and 0.001 g/L (C). For the 1 µm particles, four concentrations were included: 0.1 g/L (A), 0.01 g/L (B), 0.001 g/L (C) and 0.05 g/L (D) .

first: Joanna

last: Chwiej

first: Ewa

last: Ocłoń

first: Magdalena

last: Wytrwał

first: Karolina

last: Papacz

first: Igor

last: Jasielczuk

first: Artur

last: Gurgul

first: Aleksandra

last: Wilk


title: RNA-seq Analysis of Hinokitiol-Treated LUAD Cells

city: 上海

first: 港

last: 郭

address: 上海市闵行区浦江镇联航路1188号25号楼

institute: 上海欧易生物医学科技有限公司

summary: A549 and HCC827 cells were treated with Hinokitiol (20 μM) or DMSO for 24 hours and subjected to RNA-seq analysis.

overall_design: Group A549C: Control group, A549 cells treated with DMSO for 24 hours.Group A549H: A549 cells treated with Hinokitiol (20 μM) for 24 hours.Group HCC827C: Control group, HCC827 cells treated with DMSO for 24 hours.Group HCC827H: HCC827 cells treated with Hinokitiol (20 μM) for 24 hours.

first: Yanbin

last: Kuang

first: Yuqing

last: Lou


title: Inhibiting EZH2 Alleviates Osteoarthritis and Pain in an Experimental Murine Model Through Modulating Synovial and Macrophage Inflammation, Axon Guidance, and Osteoclastogenesis

city: Caen

first: Catherine

last: Baugé

address: Esplanade de la paix

country: France

institute: Université de Caen Normandie

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Enhancer of zeste homolog 2 (EZH2), a histone methyltransferase, has gained attention as a promising therapeutic target in osteoarthritis (OA) due to its central role in modulating inflammation, catabolism, and hypertrophy within chondrocytes. Previous studies have further demonstrated that EZH2 inhibition can slow OA progression in surgically induced mouse models, highlighting its potential in reducing joint degradation. However, the precise mechanisms by which EZH2 influences other key cell types in OA pathology remain poorly understood. In this study, we aimed to evaluate the effects of EZH2 inhibition in an alternative OA model and investigate its broader impact on cellular and molecular pathways across various tissues involved in OA progression and joint pain.  OA was induced in mice via intra-articular injection of monosodium iodoacetate (MIA), with disease progression evaluated by histological and behavioral assessments. In parallel, human synoviocytes and bone marrow-derived cells were isolated from OA patients. Synoviocytes were stimulated with interleukin-1β (IL-1β) in the presence or absence of the EZH2 inhibitor EPZ-6438 (Tazemetostat), and ChIP-Seq and proteomic analyses were conducted to identify genomic and proteomic targets of EZH2. Additionally, the effects of EZH2 inhibition on M1 macrophage polarization and osteoclast differentiation were analyzed.  Results revealed that EZH2 inhibition attenuated both OA progression and joint pain in the MIA-induced mouse model. IL-1β stimulation significantly upregulated EZH2 expression in synoviocytes, and treatment with the EZH2 inhibitor reduced the expression of genes linked to inflammation, pain, and catabolism while promoting autophagy. Proteomic analysis highlighted significant alterations in pathways related to IL-1β signaling, matrix metalloproteinase (MMP) activation, and autophagy, as well as changes in proteins associated with metabolic regulation and axon guidance. Importantly, EZH2 inhibition decreased M1 macrophage polarization and osteoclast formation, cellular processes that contribute to OA pain and inflammation.  In conclusion, this study underscores the pivotal role of the histone methyltransferase EZH2 in the pathophysiology of osteoarthritis and associated joint pain. Our findings reveal that EZH2 inhibition not only attenuates inflammation in synovial cells and macrophages but also modulates axon guidance and osteoclastogenesis, both critical in OA progression and pain. These insights position EZH2 inhibition as a promising, multi-targeted therapeutic approach for addressing the complex cellular interactions underlying osteoarthritis, offering new hope for effective treatment strategies in this debilitating condition.

overall_design: ChIP-seq of EZH2 in fibroblast-like synoviocytes stimulated or not with IL-1b. Cells were collected from 2 different patients.

first: Sybille

last: Brochard

first: Juliette

last: Aury-Landas

first: Karim

last: Boumédiene


title: Macrophage-derived KIF13B acts as a potential therapeutic target in atherosclerosis by enhancing MERTK-mediated efferocytosis [scRNA-Seq]

city: 海淀区

first: YiRan

last: Liu

state: 北京市

department: Department of Biomedical Informatics, State Key Laboratory of Vascular Homeostasis and Remodeling, School of Basic Medical Sciences, Peking University, Beijing, China

institute: PKU

summary: Atherosclerosis is a chronic inflammatory disorder with high morbidity and mortality rates worldwide. Emerging evidence has reported that Kinesin family member 13b (KIF13B), a crucial motor protein, integrates hepatic lipid metabolism and inflammatory response to protect liver disease. However, the relationship between KIF13B and atherosclerosis remains unknown. The present study aimed to elucidate the specific role of KIF13B in atherosclerosis and its potential therapeutic significance.

overall_design: RNA-seq profiling of primary bone marrow-derived macrophages(BMDMs) extracted form WT(WT) and Kif13b-/-(KO) mice. For in vitro efferocytosis assessment, BMDMs were then co-cultured with apoptotic Jurkat cells(BMDMs with AC) at a 1:5 ratio (macrophages:apoptotic cells) for 90 minutes and also have WT(WA) and Kif13b-/- (KA)phenotype.

first: Yitong

last: Xu

first: Yiran


title: PPARγ loss in colonic CD8⁺ T cells disrupts the epithelial barrier in people with HIV

city: CAMBRIDGE

first: Qiming

last: Zhang

state: MA

address: 88 Ames Street

institute: Koch institute

summary: A hallmark of HIV infection is disruption of intestinal barrier integrity that persists in people with HIV (PWH) despite treatment with antiretroviral therapy (ART). This disruption is central to HIV disease progression, yet the causes remain incompletely understood. We report a novel mechanism by which immunometabolic defects in colon resident CD8+ T cells in PWH lead to intestinal epithelial apoptosis and disruption of intestinal barrier integrity. We show that in PWH, these cells downregulate the lipid sensor peroxisome proliferator-activated receptor-g (PPARg), which results in reduced intracellular lipid droplets, impaired fatty acid oxidation, and acquisition of lipids by CD8+ T cells from intestinal epithelial cells, which then contributes to epithelial cell death. Our findings indicate that HIV-associated immunometabolic dysregulation of colon CD8+ T cell leads to loss of intestinal epithelial homeostasis. These results identify potential new strategies to reduce comorbidities in PWH and other disorders with disrupted intestinal barrier integrity.

overall_design: To investigate the functional differences of colon resident CD8+ T cells between people with HIV (PWH) on ART and uninfected individuals, we sorted colon resident CD8+ T cells ( CD3+ CD103+ CD69+ CD8+) from colon biopsies of PWH on ART and uninfected snd performed bulk RNA seq.

first: Das Adhikari

last: Upasana


title: Effect of FL-Fc-DM1 drug on gene expression of Molm-13 cells pretreated with cytarabine.

first: Dengyang

summary: Cytarabine is one of the first line chemo drugs to treat acute myeloid leukemia (AML). However, cytarabine can induce AML cell cell cycle arrest at G0/G1 phase. These cell-cycle-arrested AML cells resist cytarabine, show a senescence-like phenotype or stem-cell like phenotype. To eliminate these cell-cycle arrested cells, we developed a FL-Fc-DM1 drug by conjugating FLT3 liangd Fc fusion protein and mertansine. We used the Molm-13 cells as a AML model. The total mRNA of Molm-13 cells treated with different drugs (cytarabine, FL-Fc-DM1) were sequenced.

overall_design: Molm-13 cells were cultured in RPMI 1640 medium supplemented with 10% FBS. In the control group, Molm-13 cells were cultured for 4 days. In the cytarabine group, Molm-13 cells were treated with 0.5/1 µM cytarabine for 4 days. In the FL-Fc-DM1 treatment group, Molm-13 cells were treated by cytarabine (0.5/1 µM) for 3 days and then treated with FL-Fc-DM1 (1 nM) for another 24 hours in the absence of cytarabine. We than analyze the transcriptome differences between different groups.

first: Yun

last: Chen


title: Targeting steroid receptor RNA activator as a novel therapeutic strategy for myocardial hypertrophy

city: Nanjing

first: Wen

address: No. 101 Longmian Avenue, Jiangning District, Nanjing, China

institute: Nanjing Medical University

summary: Myocardial hypertrophy develops when the heart is subjected to biomechanical stress, neurohormonal or hemodynamic stimuli. Isoprenaline-induced myocardial hypertrophy in mice exhibited abnormally elevated steroid receptor RNA activator (SRA) level in hypertrophic myocardium, suggesting SRA’s potential functions in hypertrophic pathogenesis. SRA knockout or cardiac-specific knockdown attenuated cardiac remodeling without impairing baseline cardiac function. RNA sequencing and mechanistic studies identified SRA as a transcriptional coactivator that enhances GR-mediated upregulation of HSP70, which in turn activates pro-hypertrophic Akt signaling. Adenoviral SRA overexpression in H9C2 cardiomyocytes amplified isoprenaline-triggered hypertrophic gene expression via this GR-HSP70-Akt axis. Those findings establish SRA as a stress-responsive regulator of maladaptive cardiac growth and propose SRA inhibition as a targeted therapeutic strategy for hypertrophy-related cardiomyopathy. This work bridges noncoding RNA biology with metabolic signaling in heart disease, offering both mechanistic insights and translational potential.

overall_design: WT and SRAKO mice were treated with isoproterenol for 4 weeks.


title: Plasma extracellular vesicle-derived miR-296-5p is a maturation-dependent rejuvenation factor that downregulates inflammation and improves survival after sepsis

city: Augusta

first: Sang Ho

last: Kwon

state: Georgia

address: 1120 15th Street

department: Cellular Biology and Anatomy

institute: Augusta Univeristy

type: Non-coding RNA profiling by high throughput sequencing

summary: There is a progressive decline in physiological function with age, and aging is associated with increased susceptibility to injury and infection. However, several reports have indicated that the agility of youth is characterized by transferable rejuvenating molecular factors, as was observed previously in heterochronic parabiosis experiments. These experiments demonstrated a rejuvenating effect of young blood in old animals. There have been several efforts to characterize these youthful or maturation-associated factors in the young blood. In this report, we demonstrate the resilience of young mice, at or before puberty, to polymicrobial sepsis and show an age-dependent effect of plasma extracellular vesicles on the outcome following sepsis. The EVs from the young mice were cytoprotective, anti-inflammatory, and reduced cellular senescence markers. MicroRNA sequencing of the extracellular vesicles showed an age-associated signature and identified miR-296-5p and miR-541-5p to progressively reduce their levels in the blood plasma with increasing age. We further show that the levels of these miRNAs decline with age in multiple organs. The miRNAs miR-296-5p and miR-541-5p showed a reparatory effect in an in vitro wound healing model and the miR-296-5p, when given intraperitoneally, reduced mortality in the mouse model of sepsis. In summary, our studies demonstrate that EVs from very young mice have a reparative effect on sepsis, and the reparative factors are likely maturation-dependent. Our observation that miR-296-5p and miR-541-5p are plasma EV constituents that significantly reduce with age and can reduce inflammation suggests a therapeutic potential for these miRNAs in inflammation and age-associated diseases.

overall_design: Total RNA from young, mature, 1year and 2 year old mice EVs was extracted using the Total Exosome RNA Isolation Kit (Invitrogen, 4478545). miRNA Library was prepared by using Illumina TruSeq stranded mRNA kit and sequencing was carried out at Novogene

first: Lun

last: Cai

first: Parmita

last: Kar

first: Yutao

first: Xiaogang

last: Chu

first: Ashok

last: Sharma

first: Tae Jin

last: Lee

first: Raghavan

middle: P

last: Raju

first: Ali

last: Arbab


title: Effect of FL-Fc-DM1 drug on gene expression of MV-4-11 cells pretreated with cytarabine.

summary: Cytarabine is one of the first line chemo drugs to treat acute myeloid leukemia (AML). However, cytarabine can induce AML cell cell cycle arrest at G0/G1 phase. These cell-cycle-arrested AML cells resist cytarabine, show a senescence-like phenotype or stem-cell like phenotype. To eliminate these cell-cycle arrested cells, we developed a FL-Fc-DM1 drug by conjugating FLT3 liangd Fc fusion protein and mertansine. We used the MV-4-11 cells as a AML model. The total mRNA of MV-4-11 cells treated with different drugs (cytarabine, FL-Fc-DM1) were sequenced.

overall_design: MV-4-11 cells were cultured in IMDM medium supplemented with 10% FBS. In the control group, MV-4-11 cells were cultured for 4 days. In the cytarabine group, MV-4-11 cells were treated with 2/5 µM cytarabine for 4 days. In the FL-Fc-DM1 treatment group, MV-4-11 cells were treated by cytarabine (2/5 µM) for 3 days and then treated with FL-Fc-DM1 (1 nM) for another 24 hours in the absence of cytarabine. We than analyze the transcriptome differences between different groups.


title: Cell Cycle Reprogramming Mediates Acquired Oxaliplatin Resistance in Pancreatic Cancer [cell lines]

city: Houston

first: Sung Wook

last: Kang

state: TX

address: one plaza

department: Surgery

institute: Baylor college of medicine

summary: Purpose: Pancreatic ductal adenocarcinoma (PDAC) remains a lethal malignancy with limited treatment options. While oxaliplatin-based (Oxa) therapy, such as FOLFIRINOX, has improved outcomes in select patients, Oxa resistance significantly limits its efficacy. This study investigates cell cycle mechanisms driving Oxa resistance and explores targeting these pathways as a therapeutic strategy.  Experimental Design: Murine KPC and human Panc1 oxaliplatin-resistant (Oxa-R) cell lines were established. RNA sequencing, Western blotting, and flow cytometry were used to analyze DNA damage and cell cycle regulators. Viability assays and a murine orthotopic PDAC model were employed to evaluate the therapeutic potential of CDK4/6 inhibition with Oxa.  Results: Oxa-R cell lines exhibited slower proliferation rates, reduced response to Oxa treatment, and significant upregulation of G2/M and E2F1 signaling pathways, findings that correlated with poor survival outcomes in human clinical datasets. In Oxa-sensitive PDAC cells, Oxa treatment activated the ATR-Chk1 pathway, leading to cyclin D1 suppression and apoptosis. In contrast, Oxa resistance was characterized by compensatory upregulation of CDK4/6 signaling, which enabled cells to bypass DNA damage-induced cell cycle arrest. Notably, the addition of CDK4/6 inhibitors restored Oxa sensitivity in resistant cell lines, resulting in enhanced apoptosis in vitro and significantly reduced tumor growth in vivo.  Conclusion: Oxa resistance in PDAC is mediated by cell cycle dysregulation involving cyclin D1 and CDK4/6. Targeting CDK4/6 with Abemaciclib reverses resistance and enhances Oxa efficacy, offering a promising therapeutic strategy for resistant PDAC.

overall_design: Murine KPC and human Panc-1 cells were cultured in DMEM complete medium. To establish a stable pancreatic cell line resistant to Oxa, KPC cells or Panc-1 cells were cultured at a starting concentration of 5 μM/mL Oxa for 48 and 96h respectively. When the surviving population of KPC and Panc-1 cells reached 80% confluency, the cells were sub-cultured twice. The concentration of Oxa in the surviving KPC and Panc-1 cells were exposed to 5 μM/mL increments in the same manner and up to a final concentration of 40 μM/mL for KPC cell and 15 μM/mL for Panc-1 cells. The surviving Oxa resistant (Oxa-R) KPC and Panc-1 cells were cultured in 5 μM/mL Oxa. The sensitivity of parental and Oxa-R cell lines to Oxa was determined by cell viability assay analyzed by treatment for 48h (KPC) and 96h (Panc-1) with different concentrations of Oxa.

first: Hyun-sung


title: The Crucial Role of Renal FOXO1 in Gluconeogenesis During Starvation and Its Implications in Kidney Disease

city: Busan

first: Haeseung

address: 63 Beon-gil 2, Busandaehag-ro, Geumjeong-gu

department: College of Pharmacy

country: South Korea

institute: Pusan National University

summary: Renal gluconeogenesis accounts for half of systemic gluconeogenesis during starvation, but its regulatory mechanisms and implications in chronic kidney disease (CKD) remain unknown. In this study, using single-cell RNA sequencing of starved kidneys and various animal models, we aimed to identify key pathways involved in renal gluconeogenesis and their role in the development of hypoglycemia during starvation in diseased kidneys. Under the starvation condition, renal gluconeogenesis was highly induced in proximal tubule cells with FOXO1 activation. In renal tubular epithelial cells, starvation-induced FOXO1 activation was required to stimulate gluconeogenesis and promote glucose production. We further analyzed whether renal FOXO1-mediated gluconeogenesis is impaired in CKD. In CKD animal models, the kidneys exhibited reduced FOXO1 and gluconeogenic protein expression; however, serum glucose levels remained unchanged, suggesting that diminished renal gluconeogenesis does not significantly impact circulating glucose levels. When CKD mice were subjected to starvation, serum glucose levels were significantly reduced after 72 hours. In the CKD model, FOXO1 activation failed, accompanied by a lower induction of gluconeogenic protein expression. Similar to diseased condition, aged mice exposed to starvation also showed impaired gluconeogenic response in the kidney, contributing to reduced circulating glucose levels. Under the in vitro condition, we found that profibrotic TGFβ1 inhibits starvation-induced gluconeogenesis by directly suppressing the FOXO1 signaling pathway in tubular cells. Finally, we generated tubule-specific FOXO1 knockout (KO) mice by crossing FOXO1 floxed mice with Ksp-cre mice. These tubule-specific FOXO1 KO mice exhibited reduced expression of gluconeogenic genes in the kidney, leading to hypoglycemia during starvation. Collectively, we demonstrated crucial role of renal FOXO1 in gluconeogenesis during starvation, and its implication in kidney disease.

overall_design: This study aims to investigate the effects of starvation on the mouse kidney, both with and without kidney damage. Control mice and folic acid-treated mice (250 mg/kg, IP injection) were subjected to starvation, after which their kidneys were collected for analysis.

first: KiWung

last: Chung


title: In Vivo Tumor Growth Control by General Control Nonderepressible 2 (GCN2) Targeting Agents Results from Kinase Activation

city: Cambridge

first: Eric

middle: Scott

last: Lightcap

address: 40 Landsdowne Street

institute: Takeda Pharmaceuticals

summary:
The objective of this study was to determine the therapeutic effect and PK/PD relationship of Hibercell compound HC-7366 after 3 days continuous BID dosing (7 administrations) in the MOLM-16 subcutaneous leukemia xenograft model. Single point plasma concentrations were determined 1 h post dose on day 4.
HC-7366 at dose levels of 0.3 mg/kg, 1 mg/kg, 3 mg/kg, 10 mg/kg and 30 mg/kg BID dosing all exhibited significant antitumor activities with TGI% values of 74.8%, 91.5%, 93.6%, 82.0%, and 62.0% (P values < 0.05 vs. vehicle control group), respectively. The maximum antitumor effects were achieved at 3 mg/kg which resulted in Partial Response (PR, ≥50% tumor regression) in 100% of animals.
The plasma concentrations of HC-7366 at 1 h post dose on day 4 provided a single point determination of systemic exposure.  The concentrations increased in approximate proportion to dose level across the range 0.3 – 30 mg/kg.
These data indicate that HC-7366 treatment exhibits a ‘U-shaped’ dose/exposure-response relationship in this model when dosed at 0.3, 1, 3, 10 or 30 mg/kg, orally (PO), twice per day (BID).
Regarding the safety profile, most animals treated with HC-7366 at dose level of 1 mg/kg and 3 mg/kg showed minor to moderate BW loss during the study period. IHC on these samples demonstrated maximal induction of the ATF4 targets ASNS, PSAT1 and PHGDH at 1 and 3 mg/kg doses, with 0.3, 10 and 30 have smaller increases over vehicle. RNA-Seq confirmed that the ASNS, PSAT1 and PHGDH effects were regulated at the mRNA level in the U-shaped manner. DDIT3, BBC3, and ATF4 mRNA also demonstrated a U-shaped upregulation, with maximal effect at 3 mg/kg. Notably, PPP1R15A, MCL1, PPP1R15B, EIF2AK4, CASP3, and EIF2S1 mRNA showed much more modest regulation. These data strongly suggest that HC-7366 is having its maximal efficacy in MOLM-16 when it is behaving as a GCN2 activator (i.e., at 1 and 3 mg/kg), where higher concentrations begin to inhibit this effect (at 10 and 30 mg/kg).

overall_design: RNA-Seq profiling of subcutaneous MOLM-16 xenograft tumor samples from mice treated for 4 days with vehicle as control or 0.3, 1, 3, 10 or 30 mg/kg HC-7366. 9 replicates per treatment arm. Tumor from untreated mice was also collected and profiled (n=5).

first: Feven

last: Tameire

first: Paulina

last: Wojnarowicz

first: David

last: Surguladze

first: Sho

last: Fujisawa


title: AMPK mutant dauer transcriptome

city: Montreal

first: Sabih

last: Rashid

state: Quebec

address: 3611 Rue Sainte Famille, Unit 11

department: Biology

country: Canada

institute: McGill University

summary: C. elegans lacking AMPK do not exhibit reproductive defects during normal growth, but when passaged through dauer, exhibit germline hyperplasia and premature spermatogenesis, followed by complete sterility post-dauer (Narbonne and Roy, Development, 2006). Loss of RNAi pathway  components suppresses several of these phenotypes (Kadekar and Roy, PLoS Biol, 2019). We sought to carry out a transcriptomic analysis of control and AMPK mutant animals in the dauer and post-dauer stage to understand what gene expression changes occur due to the absence of AMPK, and how RNAi pathway components may be affected. The daf-2 mutation was used to induce dauer by a temperature shift to 25 °C.

overall_design: RNA-Seq of dauer (96 hours post-hatching at restricted temperature) and post-dauer (96 hours after shift to permissive temperature) in the daf-2 and daf-2; aak-1; aak-2 (aak(0)) genetic background. Standard Trizol RNA extraction of collected samples.

first: Richard

last: Roy


title: IFN-γ-induced PD-L1+ and MHC II+ macrophages and Tim-3+ tumor-reactive CD8+ T cells predict a positive response to anti-PD-1 therapy in tumor-bearing mice

city: GOSSELIES

first: Abdulkader

last: AZOUZ

address: Rue Adrienne Bolland, 8

country: Belgium

institute: Université Libre de Bruxelles

summary: While immune checkpoint inhibitors have demonstrated durable responses in various cancer types, a significant proportion of patients do not exhibit favourable responses to these interventions. To uncover potential factors associated with a positive response to immunotherapy, we established a bilateral tumor model using P815 mastocytoma implanted in DBA/2 mice. In this model, only a fraction of tumor-bearing mice responds favourably to anti-PD-1 treatment, thus providing a valuable model to explore the influence of the tumor microenvironment (TME) in determining the efficacy of immune checkpoint blockade (ICB)-based immunotherapies. Moreover, this model allows for the analysis of a pretreatment tumor and inference of its treatment outcome based on the response observed in the contralateral tumor. Here, we demonstrated that tumor-reactive CD8+ T cell clones expressing high levels of Tim-3 were associated to a positive anti-tumor response following anti-PD-1 administration. Our study also revealed distinct differentiation dynamics in tumor-infiltrating myeloid cells in responding and non-responding mice. An IFNγ-enriched TME appeared to promote the differentiation of monocytes into PD-L1pos MHC IIhigh cells in mice responding to immunotherapy. Monocytes present in the TME of non-responding mice failed to reach the same final stage of differentiation trajectory, suggesting that an altered monocyte to macrophage route may hamper the response to ICB. These insights will direct future research towards a temporal analysis of tumor-associated macrophages (TAMs), aiming to identify factors responsible for transitions between differentiation states within the TME. This approach may potentially pave the way to novel strategies to enhance the efficacy of PD-1 blockade.

overall_design: DBA/2 Ola Hsd mice were injected subcutaneously (s.c.) in one flank with 2 x 106 P815 mastocytoma cells or bilaterally (in both flanks) with either 1 x 106 P815 cells or P1A KO cells. Only mice harbouring well-established tumors, as determined by a tumor volume falling within the range of 100 to 200 mm3, and with similarly sized tumors on each flank, were enrolled in the experiment. Mice were treated intraperitoneally (i.p) with anti-PD-1 anti-mouse monoclonal antibody

first: Jelena

last: Gabrilo

first: Sylvie

last: Vande Velde

first: Coralie

last: Henin

first: Sébastien

last: Denanglaire

last: Azouz

first: Louis

last: Boon

first: Benoit

last: J. Van den Eynde

first: Muriel

last: Moser

first: Stanislas

last: Goriely

first: Oberdan

last: Leo


title: Transcriptomic analysis explore the molecular mechanism of enhancement of Ponceau 2R decolorization by Trametes hirsuta X-13 after addition of sinapic acid

city: Chang Sha

first: Yang

last: Han

address: No. 498, Shaoshan South Road

institute: Central South University of Forestry&Technology

summary: To investigate the molecular mechanism underlying the effect of sinapic acid on the decolorization of Ponceau 2R by T. hirsuta X-13, comparative transcriptomic analyses were conducted across four groups: the strain cultured on basic medium (CK), basic medium containing Ponceau 2R (P2R), basic medium containing sinapic acid (SA), and basic medium containing both Ponceau 2R and sinapic acid (P2R+SA).

overall_design: Comparative transcriptomic analysis of strain X-13 was conducted by generating four mRNA sequencing libraries based on: the strain cultured on basic medium (CK), basic medium containing Ponceau 2R (P2R), basic medium containing sinapic acid (SA), and basic medium containing both Ponceau 2R and sinapic acid (P2R+SA) at 48 h.

first: Jiangshan

last: Ma

first: Han

last: Yang

first: Rui

last: Feng

first: Yujiang

last: Qin

first: Haoling

last: Hu

first: Gao-Qiang

last: Liu


title: GATA2 deficiency drives a profibrotic program and metabolic dysfunction in alveolar macrophages

city: Pittsburgh

first: Rachel

last: Gottschalk

state: PA

address: 200 Lothrop St., W1047 BST

department: Center for System Immunology

institute: University of Pittsburgh

summary: Alveolar macrophages (AMs) have homeostatic, anti-inflammatory programming to limit tissue damage in response to minor challenge and the distinct, lung-specific function of catabolizing lipid-rich pulmonary surfactant to support gas exchange. GATA transcription factors (TFs) have been well established to cooperate with and antagonize other TFs to shape immune cell fates and GATA2 is expressed in a lung-specific manner in macrophages. Both mutations and lung macrophage downregulation of GATA2 have been associated with chronic pulmonary pathologies in humans, but the role of GATA2 in shaping AM function is not well defined. Using mice with myeloid-specific deletion of the GATA2 DNA binding C-terminal zinc finger domain, we show that GATA2 deficiency promotes a profibrotic state and metabolic dysfunction in AMs in response to type 2 stimuli. While homeostatic functions of AMs remained largely intact, GATA2 deficiency increased expression of genes associated with pulmonary fibrosis in response to IL-33-induced inflammation. Coincident with GATA2-dependent expression of genes in metabolic pathways, seahorse metabolic flux analysis suggests that AM metabolism is compromised, likely due to mitochondrial dysregulation, in the absence of GATA2. AM GATA2-dependent gene networks are enriched for targets of TFs previously demonstrated to interact with GATA2 in other cellular contexts, including PU.1, PPARγ, and other TFs that regulate AM homeostatic and inflammatory function. Thus, GATA2 mediates AM metabolic and transcriptomic programming to limit responses that support the development pulmonary fibrosis.

overall_design: To investigate the role of GATA2 in alveolar macrophages, we generated a myeloid-specific Gata2 deficient mice, designed so that the DNA binding C-terminal zinc finger domain (exon 5) is deleted in the presence of myeloid-specific Cre recombinase. RNA-seq profiling was performed on sorted murine alvolar macrophages 24 hours after intranasal exposure to PBS or IL-33.

first: Morgan

last: Jackson-Strong

first: Satarupa

last: Ganguly

first: Aaron

last: Francis


title: Kimchi intake promotes antigen-presenting cell signaling and CD4⁺ T cell remodeling without inducing systemic immune activation: A single-cell RNA-seq substudy of a randomized, double-blind, placebo-controlled clinical trial

city: Gwangju

first: Wooje

last: Lee

email: wjlee@wikim.re.kr, ntinamu001@gmail.com

address: 86, Kimchi-ro, Nam-gu

institute: World Institute of Kimchi

summary: This study aimed to investigate the systemic immunological effects of kimchi consumption in humans. We conducted a 12-week randomized, double-blind, placebo-controlled clinical trial involving thirteen overweight but otherwise healthy adults who consumed either placebo, spontaneously fermented kimchi (S-K), or starter kimchi fermented with Leuconostoc mesenteroides KCKM0828 (LMS-K). Peripheral blood mononuclear cells (PBMCs) were collected before and after the intervention and subjected to single-cell RNA sequencing (scRNA-seq) to profile immune responses at single-cell resolution.

overall_design: Thirteen overweight but otherwise healthy adults (BMI 23–30 kg/m²) were enrolled in a 12-week randomized, double-blind, placebo-controlled trial of kimchi consumption (ClinicalTrials.gov: NCT05898802). Participants were randomized to placebo (n = 4), spontaneously fermented kimchi powder (S-K; n = 5), or starter-fermented kimchi powder prepared with Leuconostoc mesenteroides KCKM0828 (LMS-K; n = 4). Peripheral blood mononuclear cells (PBMCs) were collected at two time points per subject—baseline (pre-intervention) and post-intervention (week 12)—yielding 26 samples.  Cryopreserved PBMCs were thawed, washed, and counted, then multiplexed via antibody-conjugated poly(A) DNA barcodes. Single cells were captured and barcoded on the BD Rhapsody HT Xpress system, followed by cDNA synthesis on mRNA-capture beads. Whole-transcriptome and sample-tag libraries were constructed using the BD Rhapsody WTA amplification kit and sequenced on an Illumina NovaSeq X Plus (2 × 100 bp, paired-end). Raw FASTQ files were processed with the BD Rhapsody WTA Analysis Pipeline v2.2.1 and aligned to GRCh38 for downstream single-cell analyses.

first: Sung Wook

last: Hong


title: Tumor-infiltrating natural killer cell profiling for therapeutic stratification in smokers with resectable non-small cell lung cancer

last: Kang

summary: Objective: Neoadjuvant chemoimmunotherapy has improved outcomes in resectable non-small cell lung cancer (NSCLC), yet its real-world implementation is often challenged by surgical delays, cancellations, immune-related fibrosis, and increased postoperative complications. Smokers with NSCLC, despite being at higher risk for postoperative complications, have enhanced responses to neoadjuvant chemoimmunotherapy. This study aimed to identify smoking-associated immune cell determinants that could inform treatment strategies. Methods: Single-cell RNA sequencing was performed on 61 lung samples from non-smokers, smokers, and patients with chronic obstructive pulmonary disease (COPD), as well as 8 invasive lung adenocarcinomas, to define smoking-related immune signatures. Using RNA sequencing data from 102 resected NSCLC and 24 NSCLC patients treated with neoadjuvant chemoimmunotherapy, we conducted in silico deconvolution to evaluate associations between cellular composition and clinical outcomes. Results: Among 140 lung cellular phenotypes, two natural killer (NK) cell subsets were strongly associated with smoking and COPD severity. “Stress-responsive NK (NKSR)” cells exhibited immature features and cytokine-responsive signatures. “Exhausted NK (NKExh)” cells showed mature features and elevated multiple immune checkpoint expression (PDCD1, TIGIT, and LAG3). Abundant intratumoral NKSR cells were associated with significantly improved survival after surgery, particularly in current smokers. Conversely, tumors with low NKSR and high NKExh cell profiles were associated with better responses to neoadjuvant chemoimmunotherapy. Conclusions: Tumor-infiltrating NK cell phenotyping may aid in therapeutic stratification in smokers with NSCLC. NKSR cell preservation predicts favorable outcomes with upfront surgery, while NKExh cell enrichment indicates greater benefit from neoadjuvant chemoimmunotherapy. These profiles may help optimize treatment by balancing therapeutic benefit and risk.

overall_design: This study was conducted under protocols approved by the Institutional Review Board at Baylor College of Medicine (BCM) (H-35782) and the University of Arizona (UA) (1811124026). Written informed consent was obtained from all participants for the collection of clinical data and biospecimens. At BCM, a prospectively maintained, single-institution database was reviewed retrospectively. The BCM cohort included 102 patients with histologically confirmed NSCLC who underwent complete pulmonary resection and mediastinal lymph node dissection. Staging was determined according to the 8th edition of the TNM classification. At UA (by Dr. Polverino), lung tissue samples were obtained from patients undergoing lung volume reduction surgery or lung transplantation for severe emphysema, or from patients undergoing lung resection for a solitary peripheral nodule, with sampled tissue taken from a region at least 10 cm away from the nodule. The UA cohort included 13 non-smokers, 21 ever-smoker control subjects, 15 patients with mild chronic obstructive pulmonary disease (COPD)(GOLD stage 1-2), and 12 patients with severe COPD (GOLD stage 3-4). COPD was defined as pre-bronchodilator forced expiratory volume in 1 second (FEV1)/forced vital capacity (FVC) ratio of less than 0.7 (70%). Disease severity was classified according to the GOLD criteria as follows: GOLD 1 (FEV1 ≥ 80%), GOLD 2 (50% ≤ FEV1 < 80%), GOLD 3 (30% ≤ FEV1 < 50%), and GOLD 4 (FEV1 < 30%).

first: Hyun-sung


title: Polyploid cisplatin-resistant cancer cells have altered nuclear organization and epigenomic status

city: Baltimore

first: Anna

last: Gonye

state: Maryland

address: 733 N. Broadway

institute: Johns Hopkins University School of Medicine

summary: Chemotherapy resistance remains a critical barrier in cancer treatment, partly driven by polyploid cells that survive therapy and contribute to tumor recurrence. Here, we investigated epigenomic and transcriptional changes associated with cisplatin-surviving polyploid cells compared to parental cancer cells in prostate cancer (PC3) and triple-negative breast cancer (MDA-MB-231) cell lines. We observed persistent dysregulation of chromatin compaction and altered nuclear structure in polyploid cells following cisplatin treatment. Genome-wide chromatin accessibility profiling via ATAC-seq revealed significant remodeling, notably decreased promoter accessibility at proliferation-associated loci and increased accessibility of distal regulatory elements linked to inflammation and stress response. RNA-seq analyses demonstrated a coordinated transcriptional shift away from proliferative signatures toward inflammatory and survival pathways, including activation of NFκB, interferon response, and integrated stress response pathways. Importantly, we identified subsets of genes showing concordant changes in promoter accessibility and transcriptional activity, directly linking chromatin remodeling to transcriptional reprogramming. These integrated findings highlight the role of chromatin dynamics and epigenetic plasticity in chemotherapy resistance, demonstrating that widespread chromatin accessibility changes facilitate the transition to a stress-adapted, polyploid cell state. This study provides new insights into the molecular mechanisms supporting cancer cell persistence after chemotherapy.

overall_design: MDA-MB-231 (breast cancer cell line) and PC3 (prostate cancer cell line) were treated with cisplatin. Surviving cells were analyzed 1 and 10 days post-treatment removal (PTR). Bulk ATAC-sequencing was performed on untreated cell lines and surviving cells 1 and 10 days PTR in biological triplicate.


title: Effect of FL-Fc-DM1 drug on gene expression of MV-4-11 cells.

city: Shenzhen

first: Dengyang

last: Zhang

institute: Seventh affiliated hospital, Sun Yat-sen University

summary: To eliminate  cell-cycle arrested AML cells, we developed a FL-Fc-DM1 drug by conjugating FLT3 liangd Fc fusion protein and mertansine. We used the MV-4-11 cells as a AML model. The total mRNA of MV-4-11 cells treated with different concentration of FL-Fc-DM1 were sequenced.

overall_design: MV-4-11 cells were cultured in IMDM medium supplemented with 10% FBS. In the control group, MV-4-11 cells were cultured for 1 day. In the FL-Fc-DM1 treatment groups, MV-4-11 cells were treated with FL-Fc-DM1 (0.5 and 1.5 nM) for 1 day. We than analyze the transcriptome differences between different groups.

first: Yun

last: Chen


title: Effect of DRP1 mutations on synaptic development during iPSC-derived cortical neuron maturation

city: Nashville

first: Vivian

last: Gama

address: 465 21st Ave South

institute: Vanderbilt University

summary: With the advent of exome sequencing, a growing number of children are being identified with de novo loss of function mutations in the large GTPase essential for mitochondrial fission - Dynamin Related Protein 1 (DRP1); these mutations result in severe neurodevelopmental phenotypes such as developmental delay, optic atrophy, and epileptic encephalopathies. Though it is established that mitochondrial fission is an essential precursor to the rapidly changing metabolic needs of the developing cortex, it is not understood how identified mutations in different domains of DRP1 uniquely disrupt cortical development and synaptic maturation. We leveraged the power of both high-resolution imaging and induced pluripotent stem cells (iPSCs) harboring DRP1 mutations in either the GTPase or stalk domains to model early stages of cortical development. Transcriptional profiling of mutant DRP1 cortical neurons during maturation, as well as imaging of organelle dynamics and neuronal synapses, strongly suggests that altered mitochondrial morphology of DRP1 mutant neurons affect synaptic development leading to pathogenic dysregulation of synaptic activity.

overall_design: iPSC-derived cortical neurons harboring DRP1 mutations differentiation over 100 DIV and profiled for transcription changes, synaptic markers, mitochondrial motility, and calcium dysregulation

first: Baum

last: Tierney

first: Gama

last: Vivian


title: REGION-SPECIFIC GENE EXPRESSION AND SEX INFORM ABOUT  DISEASE SUSCEPTIBILITY IN THE AORTA  - MCAM Knockdown

city: Los Angeles

first: Feiyang

last: Ma

state: CA

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

institute: UCLA

summary: Pathology in large vessels frequently develops at specific locations, implying that local stressors and spatially restricted gene expression are likely contributors to disease susceptibility. To identify site- and sex-specific differences that could inform about vulnerability, we performed single-cell transcriptomics in the carotids, aortic arch, thoracic, and abdominal aorta. Our findings revealed: (1) regionally defined transcriptional profiles, (2) signatures associated with embryonic origins, and (3) differential contributions of sex-specific effectors. Sex differences were predominantly observed in the thoracic and abdominal aorta. MCAM/CD146, a transcript with sex-skewed expression in vSMC of the abdominal aorta showed a 2.5-fold lower expression in males when compared to females. siRNA knockdown was performed to identify downstream targets of MCAM in vascular smooth muscle cells and to assess if sex affected number and biological function of genes modulated by changes in MCAM expression. MCAM was found to be further downregulated in vSMC associated with aortic aneurysms in humans. The findings reveal underlying diversity within vSMC populations with relevance to understanding site-specific and sex-specific variation of vascular pathologies.

overall_design:
Gene expression profiling analysis of RNA-seq data from vascular smooth muscle cell lines 40 hours following transfection with either control or MCAM siRNA. All samples prepared in duplicate, with six distinct vSMC donors (3M/3F). A subset of samples were used as non-transfected controls
PCZ16,G88 and LN983 are female Samples. T79, R88 and G82 are male Samples.

first: Milagros

last: Romay

first: Maria-Luisa

last: Iruela-Arispe


title: Macrophage-derived KIF13B acts as a potential therapeutic target in atherosclerosis by enhancing MERTK-mediated efferocytosis [RNA-Seq]

first: YiRan

last: Liu

summary: Atherosclerosis is a chronic inflammatory disorder with high morbidity and mortality rates worldwide. Emerging evidence has reported that Kinesin family member 13b (KIF13B), a crucial motor protein, integrates hepatic lipid metabolism and inflammatory response to protect liver disease. However, the relationship between KIF13B and atherosclerosis remains unknown. The present study aimed to elucidate the specific role of KIF13B in atherosclerosis and its potential therapeutic significance.

overall_design: RNA-seq profiling of primary bone marrow-derived macrophages(BMDMs) extracted form WT(WT) and Kif13b-/-(KO) mice. For in vitro efferocytosis assessment, BMDMs were then co-cultured with apoptotic Jurkat cells(BMDMs with AC) at a 1:5 ratio (macrophages:apoptotic cells) for 90 minutes and also have WT(WA) and Kif13b-/- (KA)phenotype.

first: Yitong

last: Xu

first: Yiran


title: CAMK1D activates PINK1/Parkin-dependent mitophagy to promote enzalutamide resistance in prostate cancer

city: Jinan

first: Fei

middle: fei

last: Sun

state: Shandong

address: WENHUAXI road

institute: Department of Pathology, Qilu Hospital, Shandong University

summary: Although AR-targeted therapies (e.g., enzalutamide) initially improve outcomes of prostate cancer (PCa) patients, resistance inevitably develops, driven in part by prostate cancer stem-like cells (PCSCs). However, the molecular mechanisms linking PCSCs maintenance to enzalutamide resistance (ENZR) remain incompletely characterized. The emergence and reversal of ENZR represent critical clinical challenges in PCa therapeutics. Cancer stem-like cells (CSCs) have been implicated in contributing to ENZR through multiple pathways. Here, we demonstrated that CAMK1D, a Ca²⁺/calmodulin-dependent kinase, is consistently upregulated in PCa with ENZR and contributes to resistance by enhancing mitophagy in PCa cells both in vitro and in vivo. Mechanistically, CAMK1D promotes the expansion of PCSCs by enhancing mitophagy through activation of the AMPK-PINK1 signaling pathway, thereby facilitating cellular adaptation. We reveal that CAMK1D interacts with AMPK, triggering lysosomal AMPK activation via metabolic stress–induced PINK1 phosphorylation. This AMPK-PINK1 cascade reprogramsmitochondrial metabolism to fuel PCSCs expansion. In patient-derived xenograft chimeras, targeting mitophagy or CAMK1D-AMPK signaling pathway suppresses tumor growth and depletes the PCSCs population. Our findings establish mitochondrial hemostasis as an important nexus between ENZR and AMPK-mediated PCSCs enrichment in PCa. CAMK1D emerges as a key regulator of ENZR by orchestrating mitophagy-dependent stemness maintenance. Therapeutically, we developed an Enz-siCAM/HNA nanoformulation that potently reverses ENZR and improves treatment responses.

overall_design: In this research, We established an orthotopic PCa model in mice using RM-1 cells exclusively and collected tumor tissues from both control and enzalutamide-treated groups. These tissues were then subjected to scRNA-seq for further analysis.

first: Lin

last: Gao

first: Bo

last: Han


title: Immune cells and compensatory renal hypertrophy after unilateral nephrectomy

first: Hyun Jun

last: Jung

state: MD

address: 720 Rutland Ave, Ross Research Building 1165B

department: Medicine (Nephrology)

summary: Background: The underlying mechanisms of compensatory renal hypertrophy (CRH) after unilateral nephrectomy (UNX) are complex and incompletely understood. Most studies have examined hemodynamic and tubular epithelial factors.  We studied immune cells in CRH after UNx in mice.  Methods: Following UNx of the left kidney of C57BL/6J WT mice, GFR measurements, flow cytometry, single-cell RNA sequencing, and measurements of remnant kidney were performed over 8-weeks period. Rag1-/- mice lacking T and B cells were studied to begin to study the role of direct role of adaptive immune cells in CRH.  Results: The largest increase in GFR and increase in kidney weight-to-body weight ratio (KW:BW) in WT mice was at 24 hours, after which GFR remained relatively constant while KW:BW steadily increased.  Immune cell populations exhibited dynamic and time-dependent fluctuations following UNx. Early responses (4 and 72 hours) were characterized by significant changes in CD4+ T cells, CD8+ T cells, macrophages, neutrophils, and dendritic cells. Later time points (1 to 8 weeks) showed increased effector memory T cells and B cells, with decline in naïve T cells and macrophages.  GFR was significantly higher at 1 week and 4 weeks in Rag1-/- mice compared to controls. Conclusions: Immune cells undergo significant changes in numbers, phenotype and transcriptional programming during CRH after UNx, and could have a direct role in modifying GFR adaptations.

overall_design: Flow-sorted CD45+ kidney cells from nephrectomized mice were partitioned and barcoded using the 10X Chromium Controller, with approximately 10,000 cells loaded onto the NovaSeq 6000 S4 200-cycle flow cell. The library was constructed using the Chromium Next GEM Single Cell 5' HT v2 Kit and sequenced on the Illumina NovaSeq 6000 system

first: Shishir Kumar

last: Patel

first: Qisen

last: Guo

first: Mahta

last: Gooya

first: Sanjeev

last: Noel

first: Hamid

last: Rabb


title: Culture Media Strongly Influences Primary Human Bronchial Epithelial Cells' Transcriptomic Response to Ozone Exposure

city: Chapel Hill

first: Sarah

middle: A

last: Lester

state: North Carolina

address: 120 Mason Farm Rd

department: Department of Genetics

institute: University of North Carolina at Chapel Hill

summary: Exposure to the ambient air pollutant ozone induces acute and chronic respiratory health effects in part by causing inflammation of the airways. Several aspects of the inflammatory response to ozone can be modeled in vitro using primary human bronchial epithelial cells (HBECs) cultured at an air-liquid interface. We tested two commonly used HBEC culture media systems, one proprietary and one non-proprietary, to identify which system yielded the most in vivo-like pro-inflammatory response to acute ozone exposure as indicated by gene expression. Cells from six donors were grown in each culture system in parallel followed by examination of epithelial morphology and cell type proportions prior to ozone exposure. Cultures grown in the proprietary system were notably thicker and contained more ciliated and secretory cells, as well as internal cyst-like structures. The transcriptomic response to acute ozone exposure (0.5 parts per million ozone x 2 hours) was strongly affected by media. HBECs grown in the proprietary system exhibited minimal changes after ozone, with only  only 7 differentially expressed genes (DEGs). In contrast,  HBECs grown in the non-proprietary system exhibited a more dynamic response with 128 DEGs, including hallmark response genes indicative of inflammation (CXCL8) and oxidative stress (HMOX1). Gene set enrichment analysis using the 128 DEGs further corroborated upregulation of oxidative stress and inflammation pathways. In total, our results indicate that the choice of HBEC culture media should be carefully considered to best model the in vivo response to ozone.

overall_design: RNA-seq profiling of well-differentiated primary human bronchial epithelial cells grown in PneumaCult or UNC media systems, collected 2hr after ozone or filtered air exposure.

first: Sabri

middle: H

last: Abdelwahab

first: Scott

last: Randell

first: Samir

middle: N

last: Kelada


title: RNA-seq of xenograft  tumor in control group and C26 group

city: Beijing

first: Yi

last: Zhang

address: Beijing

institute: Peking University

summary: We performed RNA-sequencing (RNA-seq) with tumor tissues of mice MC38 xenograft models treated with C26.

overall_design: Tumor tissues of mice MC38 xenograft models were utilized for total RNA extraction employing the RNeasy plus mini kit (Qiagen, #74134). Post-extraction, the RNA samples underwent evaluation of purity and concentration via 4200 TapeStation analysis. Subsequently, RNA-Seq samples were pooled and subjected to sequencing on NextSeq2000 using Illumina TruSeq Stranded mRNA Library Prep, employing paired-end sequencing services provided by the National Cancer Institute Core Sequencing Facility. Reads from the samples underwent adapter and low-quality base trimming using Cutadapt prior to alignment against the reference genome (mm10) and annotated transcripts using STAR. Mapping statistics were computed using Picard software, while library complexity was assessed based on unique fragments in the mapped reads using Picard’s MarkDuplicate utility. Furthermore, gene expression quantification analysis was conducted for all samples using STAR/RSEM tools. Raw counts were subsequently uploaded for gene expression and KEGG pathway analysis with online NetworkAnalyst platform (https://www.networkanalyst.ca).

first: Ruize

last: QU


title: IR DC-CM treated BMSCs

city: Shanghai

first: MENGTING

last: ZHENG

address: Jumen Road

institute: Shanghai Jiaotong University

summary: The BMSCs were cultured with unirradaited/irradiated DC-CM for 3 days. Total RNA was extracted and sent to DIATRE biological technology company (China) for library preparation, RNA-seq, and data analysis. DESeq2 package was carried out to perform differential expression analysis, and differentially expressed genes (DEGs) were determined by a P value <0.05. Gene ontology (GO) analysis and Kyoto encyclopedia of genes and genomes (KEGG) pathway enrichment analysis were utilized to detect the molecular and biological processes as well as signaling pathways.

overall_design: RNA-seq profiling of BMSCs induced by unirradiated/irradiated mDC-CM (ctrl, mDC-0Gy, mDC-8Gy) at Day3.


title: RNA-seq identification of herpes simplex virus type 1 transcription in Neuro-2a cells overexpressing FOXK1 and FOXF1

city: Hangzhou

first: Xiang

last: Yuhang

address: Yuhang Tang street

summary: We used inducible Neuro-2a cell lines with stable expression of FOXK1 and FOXF1. The cells were induced to express FOX protein under doxycycline for 36 hours and then infected with HSV-1 for five hours. The cells were collected and cleaved, and total RNA was extracted for RNAseq analysis

overall_design: Through RNAseq analysis, we mainly focused on the changes in the number of viral reads under the condition of FOX protein overexpression. P stands for wild-type Neuro-2a cells, K stands for Neuro-2a cells that overexpress FOXK1, and F stands for Neuro-2a cells that overexpress FOXF1.

first: Dongli

last: Pan

first: Yuhang

last: Xiang


title: ZmEMF1a is required for the maintenance of H2Aub and H3K27me3 modifications in maize kernel development [ChIP-Seq]

first: Zhijia

last: Yang

address: No.2 Yuanmingyuan West Road, Haidian

department: College of Agronomy and Biotechnology

institute: China Agricultural University

summary: Polycomb group (PcG) proteins are known to silence gene expression by modifying histones, such as H2Aub and H3K27me3, which is essential for maintaining cell type and tissue-specific gene expression patterns. However, the impact of PcG proteins on gene regulation through H2Aub and H3K27me3 during maize kernel development remains poorly understood. Here, we characterized a maize miniature seed mutant, mn8, and identified the underlying gene through map-based cloning. We found that Mn8 encodes ZmEMF1a, a plant-specific PcG protein. Mutation in ZmEMF1a leads to significantly reduced kernel size and weight. Molecular analyses showed that ZmEMF1a interacts with PRC1 component ZmRING1 and PRC2 subunit ZmMSI1, which are crucial for the establishment of H2Aub and H3K27me3 modifications.  The deficiency of ZmEMF1a resulted in significant reduction in genomic levels of H2Aub and H3K27me3. Combined ChIP-seq and RNA-seq analyses showed that H2Aub is negatively correlated with gene expression in maize, contrasting with the positive correlation observed in Arabidopsis. Compared with wild-type (WT) endosperms, mn8 endosperms exhibited elevated expressions of homology genes of cell proliferation repressors, such as ZmDA1, ZmBB1, ZmES22, ZmMADS8, and ZmMADS14, accompanied with decreased levels of 3K27me3 or H2Aub at these loci. These findings indicate that lack of ZmEMF1a impairs the deposition of H3K27me3 and H2Aub marks at cell division repressor genes. Taken together, our results demonstrate that ZmEMF1a plays a crucial role in regulating maize kernel development by maintaining the levels of H2Aub and H3K27me3 modifications.

overall_design: Two biological replicates of mn8 and B73 endosperm tissues were obtained from two independent F2 ears at 12 DAP. ChIP-seq with Anti-H2Aub and anti-H3K27me3.


title: ZmEMF1a is required for the maintenance of H2Aub and H3K27me3 modifications in maize kernel development [RNA-Seq]


title: Extracellular Vesicles Derived from Mesenchymal Stromal Cells Reduce Pseudomonas aeruginosa Burden and the Inflammatory Response in Cystic Fibrosis Mouse Lung

city: Hanover

first: Sharanya

last: Sarkar

state: NH

address: Dewey Field Road, HB 7550

department: Microbiology and Immunology

institute: Geisel School of Medicine at Dartmouth

summary: Chronic lung infections and presistent inflammation are a leading cause of morbidity and mortality in people with cystic fibrosis and therefore there is a need for therapies that can simultaneously eliminate infection and the hyperinflammatory lung environment in CF. Mesenchymal stromal cell-derived extracellular vesicles (MSC EVs) represent a promising solution, offering potent anti-inflammatory, immunomodulatory, and antimicrobial properties while being safe and non-toxic. This study demonstrates the efficacy of MSC EVs in a CF mouse model of acute Pseudomonas aeruginosa lung infection. MSC EVs reduced Pseudomonas burden, immune cell infiltration, and pro-inflammatory cytokine levels in the lungs.

overall_design: MSCs were transfected with either 1) a mimic miRNA (negative control) with no known targets in P. aeruginosa or mice or 2) miRNA let-7b-5p. EVs were isolated from the MSCs and inoculated into the lungs of CF mice with an acute P. aeruginosa infection. These smRNA-seq data are from the MSC EVs and their parent MSCs.

first: Lily

last: Taub

first: Bruce

last: Stanton

first: Barnaby

last: Roxanna


title: Identification of the binding DNA of FOXF1 by ChIP in Neuro-2a cells

summary: Neuro-2a cells were transfected with pFOXF1 for 42 hours then infected with herpes simple virus1 for 5 hours. Samples infected for 5 hours were sequenced by ChIP for binding DNAs of the FOXF1 in Neuro-2a cells.

overall_design: Input represents unenriched cell samples, and IP represents cell samples after FOXF1 enrichment. We explored the binding pattern of FOXF1 on the viral genome by comparing the differences between the post-IP samples and the Input samples.


title: Effects of the FOXF1 on herpes simplex virus 1 and host chromatin accessibility in Neuro-2a cells

summary: This is a part of the study that shows that a host gene,FOXF1, promote herpes simplex virus 1 (HSV-1) genome accessibility. These ATAC analyses viral and host genome accessibility in Neuro-2a cells. Neuro-2a cells were transfected with pFOXF1 and pcDNA plasmids for 42 hours then infected with herpes simple virus1 for 3 hours.

overall_design: P represents cell samples transfected with pcDNA plasmid as control group. F represents cell samples transfected with pFOXF1 plasmid as the experimental group.Comparison of cells overexpressing FOXF1 with control cells. Infect the cells for viral and host genome accessibility identification


title: Alteration in the transcriptome of lung basal epithelial cells isolated from IPF lungs upon genetic knockdown of  SOX9

city: Cincinnati

first: Satish

middle: Kumar

last: Madala

state: Ohio

address: 3235 Eden Ave

department: Internal Medicine

institute: University of Cincinnati

summary: Pulmonary fibrosis (PF) is associated with various chronic lung diseases such as idiopathic pulmonary fibrosis (IPF), systemic sclerosis (SSc), and cystic fibrosis (CF). It is characterized by the progressive accumulation of mesenchymal cells and excessive extracellular matrix production (ECM), resulting in scar tissue formation. PF arises from a dysregulated response to alveolar injury, leading to a progressive decline in lung function that remains largely unresponsive to current pharmacological therapies. Both airway and alveolar epithelial cells, along with mesenchymal cells, contribute to PF, but the cell-specific pathways and gene networks driving the pathophysiology remain poorly understood. Our recent  findings indicate abnormal activation of SOX9 in lung basal epithelial cells from IPF lung biopsies and in a mouse model of repetitive bleomycin-induced fibrosis. In this study, we aimed to determine the role of SOX9 in regulating transcriptomic changes in basal epithelial cells during pulmonary fibrosis. Our results show that SOX9 governs the transcriptional programs involved in basal epithelial cell differentiation to mucus producing goblet cells, and inflammation. In conclusion, this study demonstrates that SOX9 is a critical regulator of basal cell dysfunction in IPF and represents a potential target for therapeutic intervention.

overall_design: mRNA profiles of cultured fibrotic lung resident distal basal epithelial cells isolated from IPF lungs and treated with either Control or SOX9-specific siRNA

first: Priyanka

last: Singh

first: Pratibha

middle: R

last: Gajjala

first: Steven

middle: K

last: Huang

first: Anil

middle: G

last: Jegga


title: Role of Rad18 in glioblastoma proliferation

city: Montpellier

first: Domenico

last: Maiorano

address: 141, rue de la cardonille

institute: CNRS

summary: The Rad18 E3 ubiquitin ligase, a key regulator of DNA damage tolerance,also functions in repair of DNA double strand breaks. Rad18 is overexpressed in the  brain cancer glioblastoma (GBM) and its downregulation sensitizes GBM cells to DNA damaging agents. Here we show that Rad18 has an essential role in GBM cells proliferation in the absence of external damage, surprisingly independent of its catalytic activity. Rad18 downregulation leads to cell cycle arrest in the G1 phase with no apparent increase in DNA damage. We also founbd that Rad18 sustains GBM stem cells self-renewal and survival, as well as the growth of GBM orthotropic xenografts in mice. We also show that increased Rad18 expression enhances the growth of non-transformed cells and induces features of oncogenic transformation. Mechanistically, we show that Rad18  downregulation negatively regulates the Hippo pathway by interfering with the nuclear retention of the YAP1 transcription factor. Altogether, these data show that Rad18 has an essential, non-catalytic function, in GBM proliferation, and propose Rad18 as a key target to sensitize GBM to therapy.

overall_design: U87 cells treated with a control siRNA (siCTRL), with an siRNA targeting Rad18 expression (siRad18), with a control shRNA or with a shRNA targeting Rad18.


title: Effects of overexpression of GFP-TDP-43, GFP-TDP-43(86-414) or GFP in human H4 cells, in the presence or absence of the EIF2B activator DNL343.

city: South San Francisco

first: Thomas

last: Sandmann

email: genomics@dnli.com, sandmann@dnli.com

state: California

address: 161 Oyster Point Blvd

institute: Denali Therapeutics

summary: Neuronal TDP-43 aggregates are a hallmark ALS pathology. The integrated stress response (ISR) occurs downstream of TDP-43 pathology and may exacerbate TDP-43 aggregation and neurodegeneration. Here we tested the effects of overexpression of GFP-taggted TDP-43 proteins in H4 cells, in the presence or ascence of the EIF2B activiting small molecule DNL343. Cytoplasmic TDP-43 expression caused upregulation of ISR gene transcripts, including MTHFD2, GDF15, SLC7A11, and ATF3, relative to the GFP expressing sample. Transcript level changes induced by GFP-TDP-43(86-414) were prevented by DNL343 treatment, with significant downregulation of ISR genes, including CHAC1, ATF4, and DDIT3.

overall_design: H4 cells were engineered to overexpress either GTF-TDP-43 (full length), GFP-TDP-43 (cytomplasmic domain) or GFP alone. After inducing protein expression for either 8 or 24 hours, cells were treated with either DMSO or 1 uM DNL343 for 2.5 hours before harvesting total RNA. The experiment was performed in 4 replicates, e.g. cells were treated independently on 4 different days. One sample failed quality control, leaving 47 samples in total for 3-tag RNA-sequencing to quantify transcriptome-wide gene expression levels.

first: Brittany

last: Flores

first: Joseph

middle: W

last: Lewcock

first: Gilbert

last: Di Paolo


title: SMXL7 nuclear condensates regulate transcription and chromatin architecture in Arabidopsis [RNA-seq]

city: Changsha

first: Ruifeng

last: Yao

state: Hunan

address: TianMa Road #27

department: College of Biology

institute: Hunan University

summary: This study investigates the role of SMXL7 protein condensates in regulating gene expression and chromatin organization in the model plant Arabidopsis thaliana. The researchers found that SMXL7 forms phase-separated nuclear condensates that sequester transcription factors and histone demethylases, thereby repressing gene expression. These condensates also associate with and modulate levels of the repressive histone mark H3K27me3, influencing higher-order chromatin structure. The findings reveal a novel mechanism linking plant hormone signaling to epigenetic regulation and nuclear architecture, with implications for understanding how plants control development in response to environmental cues. This work provides new insights into the functions of biomolecular condensates in transcriptional control and hormone signaling in plants.

overall_design: To identify genes regulated by SMXL7, RNA-seq was performed using 3-week-old whole seedlings of wild-type Col-0, s678 mutants and SMXL7d53 plants. Three independent biological samples were collected for each genotype.

first: Li

last: Chen

first: Jindong

last: Li

first: Gang

last: Xu


title: SMXL7 nuclear condensates regulate transcription and chromatin architecture in Arabidopsis [DAP-seq]

overall_design: To explore the in vivo binding pattern of SMXL7, DAP-seq was performed using gDNA extracted from 3-week-old wild-type seedlings. HaloTag-fused SMXL7 protein was expressed in a TnT SP6 High-Yield Wheat Germ Protein Expression System and purified using Magne HaloTag Beads.


title: SMXL7 nuclear condensates regulate transcription and chromatin architecture in Arabidopsis [Hi-C]

overall_design: Three genotypes: wild-type (Col-0), smxl678 mutant, and SMXL7d53 Two biological replicates per genotype Samples from seedlings


title: Effects of overexpression of a C9orf72 repeat expansion linked to GFP, or a GFP control in human HEK293 cells, in the presence or absence of the EIF2B activator DNL343.

summary: Neuronal TDP-43 aggregates are a hallmark ALS pathology. The integrated stress response (ISR) occurs downstream of TDP-43 pathology and may exacerbate TDP-43 aggregation and neurodegeneration. Here we assessed the effects of overexpression of a GFP-taggted C9orf72 repeat expansion in HEK293 cells on the transcriptome, in the presence or ascence of the EIF2B activiting small molecule DNL343. Expression of (G4C2)71-GFP upregulated most of the pre-defined ISR genes compared to GFP expression alone. These transcriptional changes were largely corrected by DNL343 treatment.

overall_design: HEK293 cells were engineered to overexpress either GFP-taggted C9orf72 repeat expansion (e.g.(G4C2)71-GFP) or GFP alone. After inducing protein expression for24 hours, cells were treated with either DMSO or 1 uM DNL343 for 2.5 hours before harvesting total RNA. The experiment was performed in 6 replicates, e.g. cells were treated independently on 6 different days. One sample failed quality control, leaving 23 samples in total for 3-tag RNA-sequencing to quantify transcriptome-wide gene expression levels.


title: SMXL7 nuclear condensates regulate transcription and chromatin architecture in Arabidopsis [ChIP-seq]

overall_design: To investigate genome-wide H3K27me3 levels, ChIP-seq was performed using 3-week-old seedlings of wild-type Col-0, s678 mutants and SMXL7d53 plants. ChIP was conducted with antibodies against H3 (Abcam) and H3K27me3 (Abcam).


title: SMXL7 nuclear condensates regulate transcription and chromatin architecture in Arabidopsis [ATAC-seq]

overall_design: To investigate changes in chromatin accessibility, ATAC-seq was performed on 3-week-old seedlings of wild-type Col-0, s678 mutants and SMXL7d53 plants. The quality of the libraries was assessed by DNA-based fluorometric assay and electrophoresis before sequencing with Illumina HiSeq 4000 paired-end reads of 2 × 50 bp.


title: Identification of RNAs regulated by ZMAT3 and p53

city: Bethesda

first: Javed

last: Khan

address: 37 Convent Dr.

department: Genetics Branch

institute: NCI, NIH

summary: Identify the transcriptome regulated by p53 and ZMAT3 in HCT116 colorectal cancer cell line. The hypothsis of this study is that ZMAT3 regulates the expression of a subset of RNAs that are also regulated by p53 to mediate its biological functions.

overall_design: To identify the RNAs regulated by p53, mRNA-seq was performed from total RNA isolated from HCT116 cells transfected with a control (CTRL) siRNA or p53 siRNAs (SMART pool of 4 siRNAs) in biological duplicates for 72 hours. To identify the RNAs regulated by ZMAT3, mRNA-seq was performed from total RNA isolated from a ZMAT3-wild type clone and a ZMAT3 knockout clone in biological triplicates.

first: Ashish

last: Lal

first: Xinyu

last: Wen


title: The regulatory effect and mechanism of F-actin gene on the response of cadmium toxicity in farmland Pardosa pseudoannulata

city: changsha

first: Huilin

middle: huilin

last: Yang

state: huannan

address: Donghu Street

institute: Hunan Agricultural University

summary: Reveal the sequence characteristics of key genes of F-actin; RNAi technology was used to investigate the regulatory effect of F-actin gene on cadmium contamination of Pardosa pseudoannulata, and to elucidate the response mechanism of F-actin in regulating spiders to cadmium pollution.

overall_design: Cloning, sequencing and expression profiling of F-actin gene in Pardosa pseudoannulata, phenotypic analysis and transcriptomic analysis of cadmium-contaminated spiders after RNA interference, and candidate target analysis of F-actin regulating Hippo signaling pathway.


title: Investigational eIF2B activator DNL343 modulates the Integrated Stress Response in Preclinical Models of TDP-43 Pathology.

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

overall_design: Refer to individual Series


title: KRT20 suppresses the exosomal secretion of PRDX2 to mitigate ferroptosis in acute kidney injury

first: Lijun

last: Yin

address: No. 139 Renmin Middle Road

institute: The Second Xiangya Hospital of Central South University

summary: Acute kidney injury (AKI) is a commonly observed but poorly understood clinical syndrome. Keratin 20 (KRT20), a key component of intermediate filaments, is generally known as a biomarker of renal tubular injury, but its role in kidney disease remains unclear. By bioinformatics analysis and further laboratory validation, we confirmed that expression of KRT20 was highly upregulated in the renal proximal tubular cells (RPTC) during the early phase of AKI prior to the rise of KIM1 gene expression. We reported here that KRT20 was upregulated via Fosb in the kidneys of ischemia/reperfusion injury and cisplatin-nephrotoxic AKI mice. Knockout of KRT20 specifically in RPTC aggravated AKI. Mechanistically, KRT20 protected against AKI by sequestering peroxiredoxin 2 (PRDX2), an antioxidant protein, to prevent renal tubular cell ferroptosis. Specifically, KRT20 bound to PRDX2 to suppress its exosomal secretion from kidney tubular cells. We further found that ALG-2-interacting protein X (Alix) interacts with PRDX2 to mediate its exosomal secretion and KRT20 competed with Alix to interact with PRDX2 at its N terminal domain and thereby inhibiting its exosomal secretion. Finally, we showed that the expression of KRT20 and PRDX2 correlated with kidney injury and decline of renal function in AKI patients. In conclusion, KRT20 is upregulated in early AKI to protect kidney tubule cells by sequestering PRDX2 and inhibiting ferroptosis. KRT20 could be an early biomarker for AKI and a potential drug target for AKI prevention and therapy.

overall_design: To investigate the function of KRT20 in AKI, we constructed a renal proximal tubular cell specific Krt20 knockout mouse model.

first: Zebin

last: Deng

first: Jiachen

last: Liu

first: Lin

last: Ye

first: Jun

first: Yingbo

last: Dai

first: Yinhuai

last: Wang

first: Yu

first: Xuejing

last: Zhu

last: Lu

first: Dongshan

last: Zhang

first: Shaobin

last: Duan

first: Zheng

last: Dong

first: Fei

first: Anqun


title: Uncovering altered neural molecular mechanisms in metabolic disorders induced psychiatric disorders

city: Hyderabad

first: Arvind

last: Kumar

state: Telangana

address: CSIR-CCMB, Habsiguda, Near habsiguda metro station

country: India

institute: Center for Cellular and Molecular Biology

summary: Lifestyle changes involving high caloric diet, sedentary life, and/or persistent stress appear to play a role in the onset of metabolic syndrome (MetS), which is characterized by hyperglycemia, hyperinsulinemia, dyslipidemia, obesity, and type-2 diabetes. MetS in the long run appears to have cerebrovascular consequences, resulting in neuropsychiatric disorders. However, there is a paucity of molecular studies using relevant animal models of metabolic disorder-induced neuropsychiatric disorders. Here, we tried to model the clinical conditions of MetS by feeding C57bl/6 Ncrl mice a high fructose diet (Hfr) for almost 12 months. Random glucose, fasting glucose, glucose tolerance, and triglycerides did not differ significantly between the Hfr diet and Control diet (Cont) groups even after a year on the Hfr diet, except for the accelerated aging-like phenotype in coat color and shiny texture. However, exposure to chronic stress for a week induced metabolic disorder as reflected in high post-prandial blood glucose in the Hfr group, and subsequently mood disorder (depression and anxiety) (p<0.01) and cognitive disorder (p<0.01) as indicated by the behavioral tests.  To uncover the underlying molecular mechanisms in the prefrontal cortex, a transcriptomic study was performed. The data analysis revealed hundreds of differentially expressed genes (DEGs) between the groups (i.e., HfrUST vs CoUST = 348 genes; CoST vs CoUST  = 496 genes; HfrST vs HfrUST =226 genes and HfrST vs CoST= 18 genes). The pattern of gene expression was strikingly different in the HfrST group compared to the Ctrl group, thus correlating the phenotype, i.e. MetS induced mood and cognitive disorders. Pathway analysis of the DEGs indicated perturbations in cellular metabolism, inflammation, innate immunity, neurogenesis, vasculogenesis, ion channels, and neuronal signaling. In addition, altered epigenetic regulators appear to mediate the stress-induced precipitation of metabolic and neuropsychiatric disorders. The outcome of our study supports the hypothesis of disease susceptibility due to lifestyle changes involving a high-calorie diet and chronic stress.

overall_design: Our study uses systems nutrigenomics to unveil the complex molecular interactions influenced by fructose. We aim to demonstrate the potential molecular mechanisms by examining the effects of fructose diets on pathogenesis. This will provide insights into the novel molecular mechanisms underlying fructose-induced metabolic syndrome (MeS)-mediated neuropsychiatric disorders. Such research could pave the way for developing effective strategies to alleviate common human diseases.


title: Epigenetically mediated drug resistance in myeloma is coordinated by a myeloma-associated long non-coding RNA PLUM [ChIP]

city: Singapore

first: Yinghui

last: Li

state: Singapore

address: 60 Nanyang Drive

department: School of Biological Sciences

country: Singapore

institute: Nanyang Technological University

summary: Multiple myeloma (MM) is the second most prevalent hematological malignancy that carries a poor prognosis. Despite significant advances in new treatments, most patients relapse due to the high genetic heterogeneity leading to treatment resistance. Recurrent mutations causing hyperactivation of the non-canonical NF-ĸB pathway are frequently enriched in relapsed, refractory MM patients, contributing to disease severity and drug resistance. Here, to identify NF-ĸB targets involved in chemoresistance, we combined multi-modal analysis of the NF-ĸB/p52 regulated myeloma epigenome with patient transcriptomics and uncovered a long non-coding RNA (lncRNA) linked to treatment resistant MM patients. The lncRNA termed PLUM is overexpressed in NF-ĸB+ high-risk MM subtypes and patients who are refractory to VRd (Bortezomib-Lenalidomide-Dexamethasone) treatment regimen. We reveal that PLUM interacts with Polycomb repressive complex 2 (PRC2) to regulate its stability and histone methyltransferase activity. Notably, PLUM binds to the disordered region of PRC2 subunit EZH2, modulating the expression of tumor suppressor genes, FOXO3 and ZFP36, to activate the unfolded protein response (UPR). Disruption of PLUM-EZH2 interaction using steric antisense oligonucleotides re-sensitized myeloma tumor cells to drug treatment, correlating with the loss of PRC2 stability and EZH2 H3K27 trimethylation activity. These findings indicate NF-ĸB/p52 regulated lncRNA, PLUM, modulates the myeloma epigenome by facilitating formation of PRC2 complex and EZH2 activity to mediate chemoresistance. Targeting specific PLUM-EZH2 interactions may represent a clinically important strategy for the treatment of relapsed, refractory MM.

overall_design: KMS-11 PLUM knock-down followed by RNA-seq (control/treated triplicates), H3K27me3 ChIP-seq (control/treated triplicates) and EZH2 ChIP-seq (endogenous triplicates)

first: Kamalakshi

last: Deka

first: Jean-Michel

last: Carter

first: Daniel

last: Ang

first: Akash

last: Bahai

first: Nicholas

last: Sim

first: Hooi

middle: Y

last: Chong

first: Guan

last: Lee

first: Suet

last: Tan

first: Wee

last: Chng

first: Dennis

last: Kappei


title: The role of adaptor protein PINCH mediated signaling pathway in morphogenesis of vasculature

first: Chunxiao

last: Wang

address: Siping road

institute: Tongji university

summary: In order to investigate the underlying molecular mechanisms of the integrin-PINCH signaling pathways in angiogenesis, arterial samples from E14.5 mice were obtained for RNA extraction and RNA-seq sequencing. RNA-seq analysis showed that the enriched regulated genes were associated with various biological processes, including the ERK1/2 cascade, collagen biosynthetic process, and multiple cell behaviors , cell adhesion, migration, extracellular matrix remodeling, muscle contraction, etc. The results suggest that the PINCHs play an essential role in angiogenesis by modulating gene expression and signaling pathways as well as regulating cell behaviors of vascular wall, and deletion of PINCHs lead to altered biological processes, influencing the development and functionality of blood vessels, which are associated with cell adhesion, proliferation, apoptosis, and migration.

overall_design: In order to investigate the functional roles of PINCHs in the development of vascular medial layer cells and angiogenesis, we used vascular medial layer cell specific mouse model (Pdgfrb Cre/+; PINCH1f/+; PINCH2-/- mice and PINCH1f/f; PINCH2-/-, dmut).  Then we performed RNA-seq analysis of the aortic smooth muscle tissue at E14.5/18.5 and comparative gene expression profiling analysis of RNA-seq data for control and PINCH-null (mut) mice.

first: Xingqun

last: Liang

first: Yunfu

last: Sun

first: Zeyue

last: Zhu

first: Yao

last: Jin

first: Qicheng

last: Zou


title: Epigenetically mediated drug resistance in myeloma is coordinated by a myeloma-associated long non-coding RNA PLUM [RNA]

first: Yinghui

last: Li

overall_design: KMS-11 PLUM knock-down followed by RNA-seq (control/treated triplicates), H3K27me3 ChIP-seq (control/treated triplicates) and EZH2 ChIP-seq (endogenous duplicates)


title: Lysosomes cell autonomously regulate myeloid cell states and immune responses

first: Leon

last: Tejwani

address: 161 Oyster Point Blv.

summary: Myeloid cells maintain tissue homeostasis via the recognition, engulfment, and lysosomal clearance of dying cells and cellular debris, which is often accompanied by changes from homeostatic to reactive states. While a role for phagocytic receptors in gating these transitions has been described, less is known about if and how lysosomes can contribute to transcriptional and functional plasticity. To determine how lysosomal health impacts myeloid cell states, we evaluated microglia and macrophages deficient for progranulin (encoded by Grn), a lysosomal protein with pleiotropic functions whose loss is associated with several neurodegenerative diseases. Single-cell RNA-sequencing of the aged mouse brain identified a Grn knockout (KO)-specific microglial subpopulation marked by high GPNMB expression that displays hallmarks of lysosomal dysfunction, including lipofuscin accumulation. Epigenetic analysis of aged microglia revealed MITF/TFE transcription factors as key mediators of the transcriptional states associated with Grn deficiency. In addition to identifying a core myeloid cell transcriptional response to diverse lysosomal stressors, targeted perturbations of various lysosomal properties in vitro uncovered a cell autonomous, TREM2-independent, response to lysosomal deacidification (via v-ATPase or VPS34 loss of function) that overlaps with Grn KO microglia phenotypes, including the induction of a lysosomal gene program, increased proliferation, and secretion of pro-inflammatory cytokines. Compound loss-of-function approaches established GPNMB upregulation upon lysosomal stress is required for the compensatory response to enhance lysosomal function via promoting acidification. Finally, pharmacological endolysosomal reacidification through sodium/proton exchanger inhibition partially rescued Grn KO microglia phenotypes. Overall, these data establish a fundamental link between lysosomal health and myeloid cell epigenetic, transcriptional, and functional states observed in neurodegeneration models.

overall_design: Two year old mice were anesthetized, transcardially perfused with PBS, and brains were removed for scRNA-seq or microglial H3K27ac analyses (see below). Hemibrains were separated and one half was frozen for nuclei isolation for H3K27ac ChIP-seq. Microglial nuclei sorted from two mice were pooled for each individual replicate, and analyses were performed with duplicates for each genotype.

first: Christopher

middle: D

last: Balak

first: Lukas

middle: L

last: Skuja

first: David

last: Tatarakis

first: Anil

last: Rana

first: Gabriel

last: Fitzgerald

first: Connie

last: Ha

first: Gabrielly

last: Lunkes de Melo

first: Elizabeth

first: Catherine

last: Heffner

first: Matthew

last: Simon

first: Jason

last: Dugas

first: Lily

last: Sarrafha

first: Eric

first: Thomas

last: Sandmann

last: Glass

first: Gilbert

last: Di Paolo


title: Epigenetically mediated drug resistance in myeloma is coordinated by a myeloma-associated long non-coding RNA PLUM

first: Yinghui


title: Upstream open reading frame translation enhances immunogenic peptide presentation in mitotically arrested cancer cells

city: Heidelberg

first: Fabricio

last: Loayza-Puch

state: non-US Resident

address: Im Neuenheimer Feld 280

country: Germany

institute: German Cancer Research Center (DKFZ)

summary: Mitosis is a critical phase of the cell cycle and a vulnerable point where cancer cells can be effectively disrupted, leading to cell death and inhibition of tumor growth. However, challenges such as drug resistance remain significant in clinical applications. During mitosis, mRNA translation is generally downregulated, while non-canonical translation of specific transcripts proceeds. Here, we demonstrate that mitotic cancer cells redistribute ribosomes toward the 5' untranslated region (5' UTR) and the start of the coding sequence (CDS), enhancing the translation of thousands of upstream open reading frames (uORFs) and upstream overlapping open reading frames (uoORFs). This mitotic induction of uORF/uoORF enriches the presentation of immunopeptides at the surface of cancer cells following treatment with mitotic inhibitors. Functional assays indicate the potential of such neoepitopes to provoke cancer-cell killing by T cells. Altogether, our findings highlight the therapeutic potential of targeting uORF/uoORF-derived neoepitopes in combination with mitotic inhibitors to enhance immune recognition and tumor cell elimination.

overall_design: We performed ribosome profiling in  mitotically arrested U2OS. Cells were treated with  Nocodazole (0.5 µM)  for 16 hours.

first: Alexander

last: Kowar

first: Jonas

last: Becker

first: Rossella

last: Del Pizzo

first: Zhiwei

last: Tang

first: Julien

last: Champagne

first: Jasmine

last: Montenegro-Navarro

first: Fiona

last: Tilghman

first: Hanan

last: Sakeer

first: Angelika

last: Riemer

first: Reuven

last: Agami


title: SMXL7 nuclear condensates regulate transcription and chromatin architecture in Arabidopsis

first: Ruifeng

last: Yao

summary: This study investigates SMXL7's role in transcriptional repression and chromatin organization in Arabidopsis. SMXL7 forms nuclear condensates that sequester transcription factors and associate with H3K27me3 heterochromatin, thereby modulating chromatin accessibility and genome architecture. These findings uncover a link between hormone signaling and epigenetic regulation in plant development.

overall_design: This study investigates the role of SMXL7 in transcriptional repression and chromatin architecture using five data groups. Arabidopsis thaliana wild-type and mutant lines (s678 mutants and S7d53 overexpression lines) were analyzed. Techniques included ATAC-seq, Hi-C, RNA-seq, DAP-seq, and ChIP-seq to assess SMXL7 effects on chromatin accessibility, genome interactions, transcriptome changes, and H3K27me3 deposition. Data comparisons were made between mutants and controls to discern SMXL7-specific impacts on chromatin structure and gene regulation.

first: Li

last: Chen

first: Jindong

last: Li

first: Gang

last: Xu


title: The role of adaptor protein PINCH mediated signaling pathway in morphogenesis of vasculature [CUT&Tag]

first: Chunxiao

last: Wang

summary: To uncover direct targets of PINCH that could account for its role in vasculature, we performed cut tag analysis on wild type aortic smooth muscle using PINCH1 antibody at E18.5. Our analyses uncovered 50789 significant binding peaks for PINCH, mainly located at intergenic or intronic regions.

overall_design: CUT&Tag analyses were performed using the aortic smooth muscle tissue of ctrl mice at E18.5. Tissue samples were dissected under fluorescence microscope.

first: Xingqun

last: Liang

first: Yunfu

last: Sun

first: Zeyue

last: Zhu

first: Yao

last: Jin

first: Qicheng

last: Zou