title: Comparative mutant analyses reveal a novel mechanism of ARF regulation in land plants [RNA-seq]

status: Public on Apr 11 2025

city: Edinburgh

first: Annis

middle: Elizabeth

last: Richardson

address: Max Borne Crescent, Kings Buildings

department: Institute of Molecular Plant Sciences, School of Biological Sciences

country: United Kingdom

institute: University of Edinburgh

summary: The plant hormone auxin regulates a wide variety of transcriptional responses depending on the cell type, environment, and species. How this diversity is achieved may be related to the specific complement of auxin signalling components in each cell. The levels of activators (class-A AUXIN RESPONSE FACTORS) and repressors (class-B ARFs) are particularly important. Tight regulation of ARF protein levels is likely key in determining this balance. Through comparative analysis of novel, dominant mutants in maize and the moss Physcomitrium patens, we have discovered a ~500-million-year-old (myo) mechanism of class-B ARF protein level regulation mediated by proteasome degradation, important in determining cell fate decisions across land plants. Thus, our results add a key piece to the puzzle of how auxin regulates plant development.

overall_design: A segregating population of heterozygous dominant Truffula (Trf) and homozygous normal (N) siblings (in W22 backcross background) were grown under greenhouse conditions until 5-weeks old. Plants were cut at the root-shoot node and submerged 10cm deep in either 100µM IAA/1%EtOH or 1% EtOH control. Shoot apices were harvested at 30 minutes post treatment, and snap frozen in 2 replicate pools (3 individuals per pool), for Trf and N. Total RNA was extracted and sent for sequencing. Read data was quality checked, and used to carry out differential gene expression analysis between control and IAA treated groups for Trf and N genotypes to identify trasncriptional changes associated with auxin response in Trf and N plants.

first: Heather

last: Jones

first: Sarah

last: Hake


title: Comparative mutant analyses reveal a novel mechanism of ARF regulation in land plants [WGS]

overall_design: Bulk-segregant whole genome sequencing experiment to identify potential causal variants between Trf and normal siblings. Leaf discs from 80 individuals for Trf and N siblings from a W22-backcross population were harvested, and sequenced to 10x depth, aligned to the Zea mays NAM5.0 genome, and the variants extracted to identify potential causal EMS-type variants in the mapping interval.

first: Amber

last: de Neve

first: Kjel

last: Johnson


title: In vitro molecular hallmarks of human gingiva fibroblasts

status: Public on Apr 12 2025

city: London

first: Paul

last: Sharpe

address: Guy's Hospital

department: Centre for Craniofacial and Regenerative Biology

institute: King's College London

type: Expression profiling by high throughput sequencing

summary: To deconstruct in vitro cell identity and improve efficiency and reliability of culture systems, we carried out gene-expression analysis between in vivo and in vitro gingival mesenchymal cells

overall_design: We performed gene expression profiling analysis using data obtained from RNA-seq of 4 different patient samples.

first: Ana

last: Caetano

last: Volponi

first: Veronica

last: Booth

first: Eleanor

last: D'Agostino


title: Selective NSD2 Inhibition Reveals an Epigenetic Vulnerability of KRAS-Driven Cancers [CUT&Run]

city: Stanford

first: Or

last: Gozani

state: CA

address: 327 Campus Drive

department: Biology

country: USA

institute: Stanford University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: NSD2, through generation of the epigenetic modification histone H3 di-methylated at lysine 36 (H3K36me2), is a candidate convergent downstream effector of oncogenic KRAS-signaling. However, whether NSD2 targeting represents a therapeutic vulnerability of KRAS-driven cancers is unknown. Here, we characterize a first-in-class, clinical grade small molecule catalyticNSD2inhibitor (NSD2i) series and find pharmacological targeting of NSD2 constitutes an epigenetic dependency with broad therapeutic efficacy in KRAS-driven pre-clinical cancer models. NSD2i inhibits NSD2 potently, with single digit nM IC50values, and shows high selectively for NSD2 versus NSD1, NSD3, and other similar enzymes. Structural analyses reveal the molecular basis of NSD2i specificity for NSD2, which includesS-adenosylmethionine (SAM)-competitive binding and catalytic disruption via a dual-channel obstruction mechanism. Proteo-epigenomic and single cell strategies in pancreatic ductal adenocarcinoma (PDAC) and lung adenocarcinoma (LUAD) samples support a model in which durable NSD2i exposure reverses H3K36me2-driven pathologic chromatin plasticity, re-establishing silencing at H3K27me3-legacy loci to curtail KRAS-regulated and oncogenic-associated gene expression programs. Accordingly, NSD2i treatment inhibits PDAC and LUAD cell viability and patient-derived xenograft tumor growth. Further, NSD2 inhibition, which is well toleratedin vivo, is equally effective as KRAS inhibition (sotorasib) treatment in prolonging survival in advanced stage autochthonous KRASG12C-driven PDAC and LUAD mouse tumor models. Moreover, in these models, NSD2 inhibition and sotorasib co-treatment synergize to confer sustained survival with extensive tumor nodule regression and elimination.Together, our work uncovers targeting of the NSD2-H3K36me2 axis as an actionable vulnerability in KRAS-driven cancers and provides a mechanistic rationale for testing NSD2i-KRAS inhibition combination therapies in the clinic.

overall_design: To investigate how NSDi affects epigenomic profile in PDAC cell line, we treated MIA-PaCa2 cell line with either vehicle(DMSO) or NSD2i. We collected cells at day1, day5, day9. We performed CUT&Run for H3K4me1, H3K4me3, H3K27AC, H3K27me, H3K36me1, H3K36me2, H3K36me3, H3K9me3, NSD2 and IgG.

first: Jinho

last: Jeong

first: Eric

last: Bareke

first: Jacek

last: Majewski


title: Exploring the inhibitory mechanism ofgastric cancer by Banxia Xiexin Decoctionthrough the combination of serumpharmacochemistry, networkpharmacology, and transcriptomics

status: Public on Apr 13 2025

city: Fuzhou

first: xiuli

last: Zhang

address: No. 1 Qiuyang Road, Minhou Street, Fuzhou City, Fujian Province

country: China

institute: Fujian University of Chinese Medicine

summary: The objective of this research is to identify differentially expressed genes (DEGs) in AGS and SUN cell samples treated with BXD-0 (0 mg/mL), BXD-L (0.5 mg/mL), and BXD-M (1 mg/mL) (n=3 per group). DEGs were analyzed both between treatment groups (e.g., BXD-L vs. BXD-0) and between cell lines (AGS vs. SUN).

overall_design: RNA sequencing was performed on AGS and SUN cell samples divided into three groups: BXD-0 (0 mg/mL), BXD-L (0.5 mg/mL), and BXD-M (1 mg/mL) to identify differentially expressed genes (DEGs) and related pathways.

first: Yao

last: Lin

first: Jia

first: Fang

middle: Q

last: Xue

first: Xiu

middle: L


title: LDL-stimulated  microglial activation exacerbates white matter damage

city: Wuhan, Hubei

first: Minghao

last: Dong

address: No. 1095, Jiefang Avenue

institute: Tongji Hospital

summary: The role of microglia in triggering the blood-brain barrier (BBB) impairment and white matter damage after chronic cerebral hypoperfusion are unclear. Here we show that the vessel-adjacent microglia, that being specifically activated by plasma low-density lipoprotein (LDL) leakage during white matter damage, could induce demyelination and attenuate BBB integrity. We further show that LDL stimulation enhance microglial phagocytosis, resulting in over-engulfment of myelin debris, and overwhelming lipid metabolism balance in microglia. Unexpectedly, LDL-stimulated lipid-laden microglia exhibit a total suppressed profile of inflammatory responses, and compromised pro-regenerative properties. Overall, our study demonstrates that LDL-stimulated perivascular microglia show a particular disease-related molecular signature, characterized by suppressed regenerative properties, that is associated with the propagation of demyelination during white matter ischemia.

overall_design: Transcriptional profiles of naive microglia and microglia under myelin debris stimulation with or without LDL supplementation. Transcriptional profiles of OPCs co-cultured with naive microglia and microglia under myelin debris stimulation with or without LDL. Transcriptional profiles of endothelial cells co-cultured with naive microglia and microglia under myelin debris stimulation with or without LDL supplementation supplementation

first: Luoqi

last: Zhou

first: Yunhui

last: Chu

first: Daishi

last: Tian

first: Chuan

last: Qin


title: Oncogenic role of the DNMT1 in diffuse large B-cell lymphomas [RNA-seq]

city: huaian

first: Liang

last: Yu

address: 1 Huanghe West Road, Huai 'an City, Jiangsu Province

institute: The Affiliated Huaian No.1 People's Hospital of Nanjing Medical University

summary: Diffuse large B-cell lymphoma (DLBCL), the most common aggressive non-Hodgkin lymphoma, demonstrates significant molecular heterogeneity and suboptimal clinical outcomes. Notably, 10%-15% of patients develop primary refractory disease following first-line R-CHOP (rituximab, cyclophosphamide, doxorubicin, vincristine, prednisone) regimen. While epigenetic modulators have emerged as potential therapeutic options for these high-risk cases, clinical application of broad-spectrum DNA methyltransferase inhibitors such as decitabine and azacitidine remains limited by their multi-target toxicity profiles. In this study, we demonstrated that DNA methyltransferase 1 (DNMT1) plays a critical oncogenic role in DLBCL pathogenesis.

overall_design: RNA sequencing (RNA-seq) were performed in SU-DHL-8 cell treated with DMSO or GSK3685032

first: Jingjing

last: Ma

first: Dongnan

last: Li

first: Yifan

last: Wang

first: Chunling

last: wang

first: Linag


title: Loss of Tbx4 Affects Postnatal Lung Development and Predisposes to Pulmonary Hypertension

city: Indianapolis

first: Micheala

last: Aldred

state: IN

address: 980 W Walnut St

institute: Indiana University

summary: Pulmonary arterial hypertension (PAH) is a progressive vascular disease characterized by remodeling of the precapillary pulmonary arteries. Genomic variation within the T-box 4 (TBX4) transcription factor is the second most common genetic cause of PAH, and can also cause severe lung developmental disorders with neonatal PH. Currently, the effect of TBX4 loss-of-function on later stages of lung development and predisposition to lung disease, including PH, is not well understood. Therefore, we have generated Tbx4 conditional knockout (Tbx4-CKO) mice in which Cre recombinase deletes exon 5 of Tbx4 within the embryonic lung mesenchyme to create a null allele. We harvested lungs from these mice at various timepoints to examine alveologenesis, vascularization, vascular remodeling, lung cellular composition, and disruption of transcriptional activity compared with control lungs. Right ventricular systolic pressure (RVSP) was measured in six-month-old mice to evaluate for PH. Tbx4-CKO lungs show enlargement of airspaces, as confirmed by an increase in mean linear intercept at P14 (24.9%), P36 (31.5%), and P180 (49.6%). These lungs also show a 39.3% decrease in von Willebrand Factor-positive vessels and a 14.2% increase in vessel wall thickness. Consistent with these results, Tbx4-CKO mice show a statistically significant increase of 15.7% in RVSP and 16.3% in the Fulton index. Bulk-RNA sequencing analysis revealed enrichment of pathways and genes relevant to lung alveologenesis, angiogenesis, and PH. Our results show that disruption of Tbx4 expression during early lung development is sufficient to disrupt postnatal lung development and circulation.

overall_design: RNAseq profiling of lungs from control (Tbx4fl/fl)  and TBX4 conditional knockout (TBX4-CKO) mice at postnatal days 14 and 36 (P14, P36).


title: Effect of Grx2 gene knockout on the transcriptomic profile of BMSCs.

city: Nanjing

first: muzhe

last: li

address: Qixia District

institute: Nanjing University of Chinese Medicine

summary: To investigate the gene expression changes after Grx2 knockout, we isolated primary BMSCs from Grx2+/+ and Grx2-/- mice and passaged them to the 7th generation. Then, we performed gene expression analysis using RNA-seq data from six cell samples (three replicates per group).

overall_design: Comparative gene expression profiling analysis of RNA-seq data was performed for Grx2+/+ O-BMSCs and Grx2-/- O-BMSCs (3 replicates per group).

first: Muzhe

first: Yong


title: Transcriptomic Profile of TLR7-Induced B Cell Development in Lupus Mouse Spleen In Vivo, with and without IL-4 Interference

city: Birmingham

first: Min

last: Gao

state: AL

address: 1900 University Blvd, THT Building Suite #130G

institute: University of Alabama at Birmingham

summary: We investigated how IL-4 affects age-related B cell development in the context of TLR7 activation. Using single-cell RNA sequencing (scRNA-seq), we analyzed the transcriptomic profiles of autoimmune mice administered R848 with or without IL-4 treatment in vivo. Our results reveal that the differentiation of B cells into DN2 or DN4 stages is established early during the naive phase. IL-4 appears to redirect B cell development towards the transitional stage 2 (T2) and follicular (FO) pathways, while simultaneously inhibiting the formation of T3, marginal zone precursor, and marginal zone B cells in response to R848 stimulation. The transcriptomic data indicate that IL-4 promotes a T-dependent developmental program and suppresses a TLR/BCR-dependent program.  IL-4 favors the differentiation of B cells into the precursor of DN4 lineage over the DN2 lineage.

overall_design: B cells were isolated from mice that have been treated in vivo with or without IL-4 (3 mice per group).  All mice received in vivo R848 ip injection (2 days apart).  scRNA-seq analysis was carried out using B cells from the spleen of these mice two days after the 2nd dose of injection.

first: Changming

last: Lu

first: Shanrun

last: Liu

first: Hui-Chen

last: Hu

first: John

last: Mountz


title: IL-17 enhanced the susceptibility to fluoxetine resistance in depression via the JAK1-STAT6 signaling pathway

city: Hangzhou

first: Wumin

address: 548 Binwen Road, Binjiang District, Hangzhou City, Zhejiang Province

department: School of basic medicine

institute: Zhejiang Chinese Medicine University

summary: This study aims at investigating the role of IL-17 in fluoxetine resistance in depression.The WGCNA analysis was utilized to analyze differentially expressed genes between response to antidepressant (GRA) group and resistance to antidepressant (AR)group. Furthermore, the treatment resistance model of depression was established inChronic unpredictable mild stress (CUMS) mice administrated with fluoxetine (widely used clinical medication for the treatment of depression) according to sucrose preference rate. Depression-like behaviors in mice were detected in Control group, CUMS group, GRA group, AR group, SR1001 (Th17 differentiation inhibitor) group. Subsequently, HT22 cells were exposed to IL-17 secreted by Th17 differentiation. Transcriptome sequencing from the Control and IL-17 group was used to screen differential genes. And then HT22 cells were transfected with si-JAK1 or si-STAT6. Th17 differentiation, the integrity of the blood-brain barrier (BBB), JAK1-STAT6 signaling pathway related proteins were detected by western blot, immunocytochemistry, flow cytometric analysis, ELISA experiments, immunofluorescence, and PCR. The inhibition of Th17 differentiation and the reduction of peripheral IL-17 release could increase their sensitivity to fluoxetine resistance and relieve the depression-like behavior. This process may be associated with the JAK1-STAT6 pathway.

overall_design: The HT22 cells were obtained from the Chinese Academy of Sciences (Shanghai, China).  These cells were cultured in DMEM complete medium supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin.  HT22 cells were cultured at 37°C in a constant temperature incubator with a 5% CO2 atmosphere.  Next, the cells were exposed to IL-17. The main purpose was to validate the potential relationship between the JAK1-STAT6 signaling pathway and IL-17.

first: Mingjia

last: Zhang

first: Yaonan

last: Hong


title: Oncogenic role of the DNMT1 in diffuse large B-cell lymphomas [BSRR]

first: Liang

type: Methylation profiling by high throughput sequencing

overall_design: Bisulfite-Seq (reduced representation) were performed in SU-DHL-8 cell treated with DMSO or GSK3685032

first: Jingjing


title: Liver-specific inactivation of Cideb improves metabolic profiles and ameliorates steatohepatitis and fibrosis in animal models for MASH

city: SHANGHAI

first: XIAN

last: JIN

state: SHANGHAI

address: Cailun Road 720, 2-404

institute: ENNOVABIO

summary:
Background and Aims: Germline mutations in CIDEB, a lipid droplet (LD)-associated protein, confer protection against various liver diseases in humans. Whether liver-specific inhibition of CIDEB will bring clinical benefits remains to be determined. We aim to establish preclinical proof of concept by testing GalNac-conjugated Cideb siRNAs in animal models for obesity and MASH and to develop siRNA drug candidates for clinical investigations.
Method: Surrogate siRNAs targeting mouse Cideb were designed and evaluated via a panel of assays. In vivo administration of the surrogate siRNAs was conducted in diet-induced obesity model and CDAA-HFD model for MASH. Plasma and liver lipid levels were measured, and liver histopathological features were analyzed. RNA-Seq analysis of liver tissues was performed to gain a comprehensive mechanistic understanding of Cideb target biology. Concurrently, humanized CIDEB knock-in mice were generated as a research tool to aid human therapeutic siRNAs discovery and development.
Results: Single administration of a potent surrogate siRNA resulted in more than 80% target knockdown up to two weeks. In the DIO model, Cideb knockdown led to significant reductions of plasma total cholesterol (TC) and triglyceride (TG) levels, a significant decrease in hepatic macro-steatosis and notable body weight loss. In the CDAA-HFD model, Cideb siRNA treatment significantly reduced liver weight as well as liver TC and TG levels. Furthermore, remarkable reductions of hepatic steatosis and total NAS score were observed with a concomitant amelioration of liver fibrosis. Transcriptome analyses revealed key mechanisms upon Cideb inactivation beyond lipid metabolism.
Conclusion: CIDEB exhibits significant potential as a therapeutic target for the treatment of MASH. Liver-targeting siRNA candidates are being developed to test the therapeutic hypothesis in humans.

overall_design: To study the mechanism of action of the Cideb knockdown in MASH, the CDAA-HFD mouse model was utilized. The model was treated with the saline as vehicle, GFT505 as a positive control, a siRNA with scramble sequence as a negative control, and the surrogate siRNA targeting mouse Cideb. Gene expression profiling was conducted using RNA-seq on liver samples from the various groups.


title: Loss of polarity by CDC42 depletion and oncogenic Kras activation in the intestine lead to a necrotizing enterocolitis (NEC)-like disease

city: Cincinnati

first: Zheng

state: OH

address: 8760 Sturbridge Dr

department: Division of Experimental Hematology and Cancer Biology

institute: Cincinnati Children's Hospital Medical Center

summary: Cdc42 is a key regulator of cell polarity that modulates cytoskeletal dynamics, morphology, and directional movement and plays a important role in maintaining epithelial integrity. Loss of Cdc42 in the small intestine causes disrupted polarity, hyperplasia, and mislocalization and expansion of transit-amplifying (TA) cells at the expense of intestinal stem cells (ISCs). KRAS, on the other hand, is essential for intestinal cell proliferation and differentiation, and oncogenic KRAS mutations can lead to disrupted epithelial homeostasis and contribute to gastrointestinal transformation. A human cancer database analysis suggests that loss of polarity mutations and oncogenic KRAS mutations are mutually exclusive in colon cancer patients. We found that intestinal epithelium-specific deletion of Cdc42 combined with oncogenic Kras expression in inducible Villin-CreER mice causes severe defects in the small intestine leading to lethality. Mice with Cdc42 deletion and oncogenic Kras expression in the intestinal epithelium exhibited reduced weight, disrupted villous mucosal structure, altered tight junction protein expression, reduced proliferation, loss of ISCs, inflammation, and enterocyte necrosis. These defects resemble Necrotizing Enterocolitis (NEC), a severe gastrointestinal disorder affecting preterm infants characterized by inflammation and necrosis of the small intestine epithelial cells. Single cell RNAseq analyses revealed that Cdc42 loss combined with oncogenic Kras expression resulted in disrupted intestinal polarity machinery with altered hippo signaling, exacerbated inflammation highlighted with elevated IL1 expression, and necroptosis. Targeted inhibition of necroptosis, IL-1 receptor, or YAP signaling rescues NEC-like defects. Additionally, ISCs-specific deletion of Cdc42 and oncogenic Kras expression induced by an intestinal stem cell driver, Omlf4-CreER, led to similar NEC-like defects in the mouse intestinal epithelium. These findings present a mechanism involving YAP-IL1-necroptosis signaling by combined disruption of polarity and oncogenic cues such as Kras in intestine function and provide insights into the effects of hyperactivation of these pathways in disrupting intestinal epithelia.

overall_design: intestinal epithelium-specific deletion of Cdc42 combined with oncogenic Kras expression in inducible Villin-CreER mice to generate CDC42KO/Kras sample, while WT, CDC42 KO, and Kras are used as control. After harvesting using described methods (Barker et al., 2007), villi/crypts were resuspended in mixed medium comprised of 30% 10x TrypLE and 70% Advanced DMEM/F12 , incubated at 37 degree for 30-45 min. Mixing and passaging through a glass pipette was preformed every 10 min and suspensions were monitored with a microscope. After disruption of the cell aggregates, cells were filtered through a 40 um filter and then pelleted by centrifugation (5 min at 300–400g), washed once with Advanced DMEM/F12, and resuspended in the same medium for 10x genomics sc-RNA seq.

first: Cuiqing

last: Fan

first: Ryan

last: Jorgensen

first: Mike

last: Adam

first: Yi

last: Zheng


title: Loss of ADAR1 in tumor cells activates cDC1s and sensitizes pancreatic cancer to immunotherapy

city: Shanghai

first: Botai

last: Li

address: No. 25/Ln 2200 Xie-Tu Road

institute: Shanghai Jiao Tong University

summary: Pancreatic cancer is notoriously resistant to immunotherapy, primarily due to inadequate antigen presentation and the exclusion of immunogenic cells from the tumor microenvironment. Strategies to enhance antigen presentation and promote the infiltration of cytotoxic CD8+ T cells may improve the efficacy of immunotherapy in pancreatic cancer. In this study, we show that ADAR1 is overexpressed in pancreatic cancer, and higher ADAR1 expression correlates with poorer survival outcomes in patients. Depletion of ADAR1 in tumor cells leads to an accumulation of endogenous double-stranded RNA (dsRNA), which triggers the MDA5-mediated type I interferon (IFN) response and results in excessive IFNβ production. Tumor-derived IFNβ then promotes the recruitment and activation of cDC1s, thereby enhancing CD8+ T cell infiltration and activation, and ultimately sensitizing pancreatic cancer to CD8+ T cell-based immunotherapy. These findings suggest that combining ADAR1 inhibition with immunotherapy may offer a promising therapeutic strategy for pancreatic cancer.

overall_design: For RNA-seq analysis of FC1199 cells, control, Adar1-null or ADAR1/STAT1 DKO FC1199 cells were stimulated with IFNγ (10 ng/ml, Peprotech) for 24 hours. RNA was extracted from cell pellets using Trizol (Takara). Poly(A) RNA was isolated from 1 μg of total RNA to generate cDNA libraries following the TruSeq™ RNA Sample Prep Kit protocol. The libraries were then sequenced using the Illumina NovaSeq 6000 platform. For RNA-seq data analysis, paired-end clean reads were aligned to the mouse reference genome (GRCm39) using Hisat2. Aligned reads were quantified for mRNA expression using featureCounts. Differential expression analysis and data normalization were performed with DESeq2.

first: Xiaoshuang

first: Bowen

last: Xie

first: Xuan

last: Zhong

first: Peng

last: Wei

first: Ting

first: Chen

last: Dong


title: microRNA landscape in extracellular vesicles/exosomes derived from bioglass-primed human adipose tissue-derived MSCs

city: Taipei

first: Chien-Wei

last: Lee

address: No.155, Sec.2, Linong Street

country: Taiwan

institute: National Yang-Ming University

type: Non-coding RNA profiling by high throughput sequencing

summary: To compare the expression profile of extracellular vesicles/exosomes derived from naïve and bioglass-primed human adipose tissue-derived MSCs

overall_design: Examination of small RNA expression in EVs derived from bioglass-primed human adipost tissue-derived MSCs

first: Hongtao

last: XU


title: Effect of Alisol B on gene expression in GT1-7 cells

first: Yating

last: Lin

address: Minhang District

institute: Children’s Hospital of Fudan University

summary: Based on previous experiments showing that Alisol B could regulate GnRH secretion from GT1-7 cells, cellular transcriptome sequencing was used to investigate the potential mechanism by which Alisol B regulates GnRH secretion from GT1-7 cells.

overall_design:
To investigate the effect of Alisol B on gene expression in GT1-7 cells,  when the cells reached 70-80% confluence, they were starved in serum-free medium for 12 hours. Afterward, they were incubated for 24 hours with or without 0.125μM Alisol B.
We then performed gene expression profiling analysis using data obtained from RNA-seq of the Alisol B intervention group and the control group cells with three replicates each.
Differential gene expressions analysis of RNA-seq data of the Alisol B intervention group and the control group cells with three replicates each.


title: Selective NSD2 Inhibition Reveals an Epigenetic Vulnerability of KRAS-Driven Cancers [RNA-Seq]

first: Or

last: Gozani

summary: NSD2, through generation of the epigenetic modification histone H3 di-methylated at lysine 36 (H3K36me2) is a candidate convergent downstream effector of oncogenic signaling. However, whether selective inhibition of NSD2 enzymatic activity at chromatin can serve as an effective cancer therapy is unknown. Here, we characterize a first-in-class, clinical grade small molecule catalytic NSD2 inhibitor (NSD2i) series and find that pharmacological targeting of NSD2 constitutes an epigenetic dependency with broad therapeutic efficacy in KRAS-driven pre-clinical cancer models. NSD2i potently inhibits NSD2 with single digit nM IC50 values and high selectivity over NSD1, NSD3, and other methyltransferases. Structural analyses reveal the molecular basis of NSD2i specificity for NSD2 includes S-adenosylmethionine (SAM)-competitive binding and catalytic disruption via a binary-channel obstruction mechanism. Proteo-epigenomic and single-cell strategies in pancreatic ductal adenocarcinoma (PDAC) and lung adenocarcinoma (LUAD) samples support a model in which sustained NSD2i exposure reverses H3K36me2-driven pathologic chromatin plasticity, re-establishing silencing at H3K27me3-legacy loci to curtail KRAS-regulated and oncogenic-associated gene expression programs. Accordingly, NSD2i inhibits PDAC and LUAD cell viability and patient-derived xenograft tumor growth. Further, NSD2i, which is well-tolerated in vivo, prolongs survival in advanced-stage autochthonous KRASG12C-driven PDAC and LUAD mouse tumor models nearly as effectively as KRAS inhibition with sotorasib. Moreover, in these models, NSD2i synergizes with sotorasib to confer sustained survival with extensive tumor nodule regression and elimination. Together, our work uncovers targeting of the NSD2-H3K36me2 axis as an actionable vulnerability in KRAS-driven cancers and provides a mechanistic rationale for testing NSD2i-KRAS inhibitor combination therapies in the clinic.

overall_design: To investigate how NSD2i affects gene expression in PDAC cell line, we treated MIA-PaCa2 cell line with either vehicle(DMSO) or NSD2i. We collected cells at day1, day5, day9 and extracted total RNA from cells. We performed gene expression profiling analysis from RNA-seq. We additionally investigated how NSD2i affects gene expression in NCI-H1373(LUAD), KP2(PDAC) cell lines. We treated cell lines with either vehicle(DMSO) or NSD2i. We collected cells at day5 and extracted total RNA from cells.

first: Jinho

last: Jeong

first: Eric

last: Bareke

first: Jacek

last: Majewski


title: Ontogeny Dictates Oncogenic Potential, Lineage Hierarchy, and Therapy Response in Pediatric Leukemia [scRNA-seq]

city: New York

first: BiNGS

last: Core

address: 1470 Madison Ave

institute: Icahn School of Medicine at Mount Sinai

summary: Pediatric cancers are increasingly linked to transformation events before birth, yet how ontogeny influences oncogenesis remains poorly understood. Using a humanized model of NUP98-NSD1-driven pediatric acute myeloid leukemia, particularly aggressive when accompanied by WT1 mutations, we investigated how the developmental stage of hematopoietic stem cells impacts leukemic transformation, disease progression and therapy response. Fetal-derived hematopoietic stem cells readily transform into leukemia, with WT1 mutations enhancing stemness and alter lineage hierarchy, while stem cells from later developmental stages progressively withstand transformation. Single-cell analyses revealed that fetal-origin versus postnatal leukemic stem cells exhibit greater quiescence and metabolic reliance on oxidative phosphorylation. Notably, therapeutic responses markedly differed between fetal- and postnatal-origin leukemias, even when driven by the same oncogenic mutations. In patients, onco-fetal transcriptional programs were associated with worse outcomes. We identified tailored combination therapies that specifically diminished aggressive fetal-origin leukemia, underscoring the need to consider ontogeny in treatment of pediatric cancers.

overall_design: Human CD34+ HSPCs were edited with control, WT1ko, NUP98-NSD1, NUP98-NSD1/WT1ko, and then xenotransplanted into NSG mice. Human CD45+ cells were flow cytometry sorted from primary, secondary, or post-treated xenografts and submitted to scRNA-seq. Additionally, human CD45+ cells were sorted from PDX model and submitted to scRNA-seq.

first: Ke

last: Wang

first: Shayan

last: Saniei

first: Nikita

last: Poddar

first: Subrina

last: Autar

first: Saul

last: Carcamo

first: Meghana

last: Sreenath

first: Jack

middle: H

last: Peplinski

first: Rhonda

middle: E

last: Ries

first: Isabella

middle: G

last: Martinez

first: Clifford

last: Chao

first: Anna Huo-Chang

last: Mei

first: Noshin

last: Rahman

first: Levan

last: Mekerishvili

first: Miguel

last: Quijada-Álamo

first: Grace

last: Freed

first: Mimi

last: Zhang

first: Katherine

last: Lachman

first: Jing

first: Giang

last: Pham

first: Dan

last: Filipescu

first: Mirela

last: Berisa

first: Tommaso

last: Balestra

first: Julie

middle: R

last: Haines

first: Angelo

last: D’Alessandro

first: Daniel

middle: J

last: Puleston

first: Emily

last: Bernstein

first: Jerry

last: Chipuk

first: Mark

last: Wunderlich

first: Sarah

middle: K

last: Tasian

first: Bridget

last: Marcellino

first: Ian

middle: A

last: Glass

first: Christopher

middle: M

last: Sturgeon

last: Landau

first: Zhihong

last: Cheng

first: Eirini

middle: P

last: Papapetrou

first: Franco

last: Izzo

first: Soheil

last: Meshinchi

last: Hasson

first: Elvin

last: Wagenblast


title: A germline ETV6 mutation disrupts hematopoiesis via de novo creation of a nuclear export signal

city: Dallas

first: Glen

last: Liszczak

state: TX

address: 5323 Harry Hines Blvd, Building L3.104

institute: University of Texas Southwestern Medical Center

summary: Germline mutations in the transcriptional regulator ETV6 are a root cause of familial inherited thrombocytopenia and predispose carriers to myelodysplastic syndromes and acute leukemias. Here, we report that the ETV6 P214L mutation creates an XPO1-dependent nuclear export signal to cause protein mislocalization. Strategies to disrupt XPO1 nuclear export activity fully restore ETV6 P214L protein nuclear localization and transcription regulation activity, establishing XPO1-dependent mislocalization as a critical mechanism underscoring ETV6 P214L dysfunction. Mechanistic insight inspired the design of ‘humanized’ ETV6 mice in which the germline P214L mutation is sufficient to elicit severe defects in thrombopoiesis and hematopoietic stem cell maintenance and survival in animals. These studies define a unique mechanism by which the ETV6 P214L mutation exerts a dominant negative effect on protein function and reveal critical mutation-dependent disruptions to hematopoiesis that underlie disease phenotypes.

overall_design: RNA-seq profiling of Ba/F3 cells expressing NRAS G12D and one of ZsGreen (control), ETV6-IRES-ZsGreen, ETV6 P214L-IRES-ZsGreen, or ETV6 I209S P214L-IRES-ZsGreen on day 3 after removal of IL-3 from media conditions. The purpose of this experiment is to determining if breaking the nuclear export sequence created by the ETV6 P214L mutation with a secondary I209S mutation would result in ETV6 I209S P214L samples transcriptionally phenocopying wild-type ETV6 samples.

first: Michael

last: McConville

first: Toby

last: Thomas

first: Ryan

last: Beckner

first: Benjamin

last: Kroger

first: Catherine

last: Valadez

first: Yuh Min

last: Chook

first: Stephen

last: Chung


title: GRHL and PGR control WNT4 expression in the mammary gland via 3D 2 looping of conserved and species-specific enhancers [BC44 HC11 C57MG RNA-seq]

city: Amsterdam

first: Renee

last: van Amerongen

address: Science Park 904

department: Swammerdam Institute for Life Sciences

country: Netherlands

institute: University of Amsterdam

summary: This dataset belongs to a study in which we functionally dissect the cis-acting enhancer network and spatiotemporal transcriptional mechanisms that regulate WNT4 expression in the mouse mammary gland and the human breast. As part of these efforts, we performed transcriptional profiling of BC44 and HC11,  which differentially express Wnt4. This bulk RNAseq dataset also includes a third mouse mammary epithelial cell line, C57MG and should serve as a reference atlas for differential gene expression between these three cell lines.

overall_design: Bulk RNA sequencing of untreated BC44, HC11 and C57MG mouse mammary epithelial cell lines.

first: Katrin

last: Wiese

first: Nika

last: Heijmans

first: Renée


title: GRHL and PGR control WNT4 expression in the mammary gland via 3D 2 looping of conserved and species-specific enhancers [T47DS RNA-seq]

summary: This dataset belongs to a study in which we functionally dissect the cis-acting enhancer network and spatiotemporal transcriptional mechanisms that regulate WNT4 expression in the mouse mammary gland and the human breast. As part of these efforts, we identified GRHL as a luminal lineage transcription factor. In follow up work, we studied the interplay between GRHL2 and PGR in the presence and absence of progesterone signaling. This bulk RNAseq dataset allows investigation of the PGR signaling response in human T47DS breast cancer cells in either the presence or absence of GRHL2 gene expression.

overall_design: Bulk RNA sequencing of control (wildtype T47DS) or GRHL2 knockdown (polyclonal shGRHL2) T47DS cells treated with the progesterone analogue R5020 for either 4 or 24 hours.

first: Marleen

last: Aarts

first: Anthonius

last: van Boxtel


title: Ontogeny Dictates Oncogenic Potential, Lineage Hierarchy, and Therapy Response in Pediatric Leukemia [GoT-ChA]

first: BiNGS

last: Core

overall_design: Primary FL- and CB-derived CD34+ HSPCs were sorted and cultured in X-VIVO 10 medium supplied with 1% BSA and FLT3L, G-CSF, SCF, TPO and IL-6. After 48h cells were edited with control or NUP98-NSD1/WT1ko, and then cultured and expanded for 4 weeks, then cells were harvested, washed with PBS once and submited for GoT-Cha.

first: Ke

last: Wang

first: Shayan

last: Saniei

first: Nikita

last: Poddar

first: Subrina

last: Autar

first: Saul

last: Carcamo

first: Meghana

last: Sreenath

first: Jack

last: Peplinski

first: Rhonda

last: Ries

first: Isabella

last: Martinez

first: Clifford

last: Chao

first: Anna Huo-Chang

last: Mei

first: Noshin

last: Rahman

first: Levan

last: Mekerishvili

first: Miguel

last: Quijada-Álamo

first: Grace

last: Freed

first: Mimi

last: Zhang

first: Katherine

last: Lachman

first: Jing

first: Giang

last: Pham

first: Dan

last: Filipescu

first: Mirela

last: Berisa

first: Tommaso

last: Balestra

first: Julie

last: Haines

first: Angelo

last: D’Alessandro

first: Daniel

last: Puleston

first: Emily

last: Bernstein

first: Jerry

last: Chipuk

first: Mark

last: Wunderlich

first: Sarah

last: Tasian

first: Bridget

last: Marcellino

first: Ian

last: Glass

first: Christopher

last: Sturgeon

last: Landau

first: Zhihong

last: Cheng

first: Eirini

last: Papapetrou

first: Franco

last: Izzo


title: Ontogeny Dictates Oncogenic Potential, Lineage Hierarchy, and Therapy Response in Pediatric Leukemia [ChIP-Seq]

first: BiNGS

last: Core

overall_design: NUP98-NSD1/WT1ko leukemic cells derived from the xenograft model were in vitro cultured and expanded in X-VIVO 10 medium, supplemented with 1% BSA and FLT3L, G-CSF, SCF, TPO and IL-6. Chromatin immunoprecipitation (ChIP) was performed using RPDM16 and H3K27ac antibodies. Following immunoprecipitation, DNA fragments were purified and assessed for quality control. High-quality DNA was used to prepare sequencing libraries, which were subsequently subjected to next-generation sequencing.

first: Ke

last: Wang

first: Shayan

last: Saniei

first: Nikita

last: Poddar

first: Subrina

last: Autar

first: Saul

last: Carcamo

first: Meghana

last: Sreenath

first: Jack

last: Peplinski

first: Rhonda

last: Ries

first: Isabella

last: Martinez

first: Clifford

last: Chao

first: Anna Huo-Chang

last: Mei

first: Noshin

last: Rahman

first: Levan

last: Mekerishvili

first: Miguel

last: Quijada-Álamo

first: Grace

last: Freed

first: Mimi

last: Zhang

first: Katherine

last: Lachman

first: Jing

first: Giang

last: Pham

last: Filipescu

first: Soheil

last: Meshinchi

last: Hasson

first: Elvin

last: Wagenblast


title: Ontogeny Dictates Oncogenic Potential, Lineage Hierarchy, and Therapy Response in Pediatric Leukemia [scATAC-seq]

first: BiNGS

last: Core

overall_design: Human CD34+ HSPCs were edited with control, NUP98-NSD1, NUP98-NSD1/WT1ko, and then xenotransplanted into NSG mice . Human CD45+ cells were flow cytometry sorted from primary or secondary xenografts and submitted to scATAC-seq.

first: Ke

last: Wang

first: Shayan

last: Saniei

first: Nikita

last: Poddar

first: Subrina

last: Autar

first: Saul

last: Carcamo

last: Sreenath

first: Dan

first: Mirela

last: Berisa

first: Tommaso

last: Balestra

first: Julie

last: Haines

first: Angelo

last: D’Alessandro

first: Daniel

last: Puleston

first: Emily

last: Bernstein

first: Jerry

last: Chipuk

first: Mark

last: Wunderlich

first: Sarah

last: Tasian

first: Bridget

last: Marcellino

first: Ian

last: Glass

first: Christopher

last: Sturgeon

last: Landau

first: Zhihong

last: Cheng

first: Eirini

last: Papapetrou

first: Franco

last: Izzo


title: Pin4 Links Post-transcriptional and Transcriptional Responses to Glucose Starvation in Yeast

city: Edinburgh

first: Michaela

last: Ristova

address: Old College, South Bridge

institute: University of Edinburgh

summary: Adaptation to environmental change is essential in all organisms, with RNA-binding proteins (RBPs) playing critical roles in rapid cellular responses. We analyzed the largely uncharacterized yeast RBP Pin4, and its involvement in adaptation to glucose depletion. A UV crosslinking technique to identify protein-RNA interactions (reCRAC) revealed that in glucose conditions Pin4 selectively binds a specific motif in 3' UTRs of mRNAs involved in glycolysis, amino acid, and mitochondrial metabolism. Following glucose withdrawal, Pin4-RNA binding was greatly reduced, with residual binding favoring transcripts associated with protein translation. Cells lacking Pin4 were greatly impaired in recovery from nutrient starvation and hypersensitive to oxidative stress, consistent with the mRNA targets. RNAseq and reporter assays indicated that loss of Pin4 caused increased target mRNA abundance. In wildtype yeast, glucose depletion induces diauxic shift, with massive changes in transcription patterns. Very unexpectedly, this response was almost entirely abolished in cells lacking Pin4, or carrying a point mutation in its RNA-recognition motif. We conclude that Pin4 contributes to energy homeostasis by regulating post-transcriptional and transcriptional responses, and postulate that this key stress response pathway is riboregulated.

overall_design: To investigate the role of yeast RNA binding protein Pin4, we created N-terminal FLAG-Ala4-His8 (FH) tagged Pin4 strain in BY4741 background  to identify by reCRAC the RNAs bound by Pin4 during growth in 2% glucose medium (glucose) and following transfer to 2% glycerol plus ethanol (Gly/EtOH) medium for 16 min (stress). We also deleted PIN4 and did RNAseq in glucose conditions and in shifting the cells to 2% Gly/EtOH for 16 min to determine whether the loss of Pin4 affects target mRNA abundance.

first: Ristová

last: Michaela

first: Tollervey

last: David


title: Comparative mutant analyses reveal a novel mechanism of ARF regulation in land plants

first: Annis

last: Richardson

address: Max Borne Crescent, Kings Buildings

summary: The plant hormone auxin regulates a wide variety of transcriptional responses depending on the cell type, environment, and species. How this diversity is achieved may be related to the specific complement of auxin signalling components in each cell. The levels of activators (class-A AUXIN RESPONSE FACTORS) and repressors (class-B ARFs) are particularly important. Tight regulation of ARF protein levels is likely key in determining this balance. Through comparative analysis of novel, dominant mutants in maize and the moss Physcomitrium patens, we have discovered a ~500-million-year-old (myo) mechanism of class-B ARF protein level regulation mediated by proteasome degradation, important in determining cell fate decisions across land plants. Thus, our results add a key piece to the puzzle of how auxin regulates plant development.

overall_design: A segregating population of heterozygous dominant Truffula (Trf) and homozygous normal (N) siblings (in W22 backcross background) were grown under greenhouse conditions until 3-weeks old. Shoot apices were harvested and snap frozen in 3 replicate pools (10 individuals per pool), for Trf and N. Total RNA was extracted and sent for sequencing. Read data was quality checked, and used to carry out differential gene expression analysis between Trf and N siblings to identify trasncriptional changes associated with the vegetative Trf phenotypes.

first: Amber

last: de Neve

last: Hake


title: RNA-seq of Col-0, h2a, h2a.z and h2a.w

first: Xiang

last: Li

state: Shanghai

address: Songhu Road 2005

institute: Fudan University

summary: RNA-seq of Col-0, h2a, h2a.z and h2a.w

overall_design: To investigate the effect of substitution between histone H2A and its variants on gene expression in Arabidopsis thaliana, we analyzed the RNA-seq data in Col-0 and the indicated mutants.

first: Aiwu

last: Dong

first: Jiabing

last: Wu

first: Shuoming

last: Yang

first: Jiachen

last: Wang


title: Single-Cell Profiling Reveals Global Immune Responses during the Progression of Murine Epidermal Neoplasms

city: Aurora

first: Xiying

last: Fan

state: CO

department: Dermatology

institute: University of Colorado Anschutz Medical Campus

summary: Immune cells are critical components of the tumor microenvironment, playing an immportant role in tumor growth and progression. We used single cell RNA sequencing (scRNA-seq) to analyze the global immune response during cSCC progression.

overall_design: CD45+ immune cells from C57 control and 2323 skin tumors were isolated by fluorescence-activated cell sorting (FACS) and analyzed using scRNAseq

first: Tonya

last: M. Brunetti

first: Kelsey

last: Jackson

first: Dennis

last: R. Roop


title: The roles of glioma-associated macrophages/microglia in human GBM

city: Kyoto

first: Akira

last: Watanabe

state: Kyoto

address: Rm504, Miyako Bldg, 233, Isa-cho, kamigyo-ku

country: Japan

institute: CyberomiX Inc

summary: The tumor microenvironment of glioblastoma (GBM) is characterized by a high proportion of glioma-associated macrophages/microglia (GAMs). We performed spatial analysis (Visium) to profile GAMs in human GBM.

overall_design: Three GBM cancer patient-derived FFPE tumor tissue (4 samples) were used for the analysis. Expression of each GAM markers were analyzed using 10x Genomics Visium.


title: Expanded chromatin accessibility mapping explains genetic variation associated with complex traits in liver

city: Philadelphia

first: Brandon

last: Wenz

state: PA

address: 3400 Civic Center Boulevard

institute: University of Pennsylvania

summary: Genome-wide association studies (GWAS) have identified thousands of genomic loci associated with a variety of common, complex human traits. The contribution of genetic variants to gene expression regulation has been well studied, supporting the idea that gene expression plays a causal role at some complex trait-associated loci. However, many current studies have not comprehensively investigated the impact of genetic variation on chromatin accessibility at a large scale within a single tissue. Genetic variants associated with differences in chromatin accessibility, known as chromatin accessibility quantitative trait loci (caQTLs), are major contributors to gene expression differences and GWAS signals. We assessed chromatin accessibility in 189 human liver tissue samples using ATAC-seq and identified over two million accessible chromatin regions enriched for gene regulatory characteristics. We integrated chromatin accessibility and genotype data from 175 samples and identified 14,076 caQTLs. Using publicly available blood lipid GWAS data, we found 157 loci where the colocalization of caQTLs, expression quantitative trait loci (eQTLs), and GWAS signals generated specific molecular hypotheses about causal regulatory elements, affected genes, and, in some cases, transcription factors, resolving these associations to single-nucleotide resolution. We performed a comprehensive analysis of the GWAS signals that remain without a proposed mechanism beyond liver caQTLs and eQTLs. After incorporating additional potential regulatory mechanism data, we found that approximately 26% of blood lipid GWAS signals remain without a proposed mechanism. Overall, our results demonstrate the benefits of integrating multiple datasets to improve our understanding of GWAS signals while emphasizing the need for additional experiments to fully characterize them.

overall_design: ATAC-seq was performed on biopsies from normal human liver samples and consensus peaks were called across all samples.

first: Benjamin

middle: F

last: Voight


title: ConSeqUMI, an error-free nanopore sequencing pipeline to identify and extract individual nucleic acid molecules from heterogenous samples.

city: Salt Lake City

first: Justin

last: English

state: UT

address: 15 N Medical Drive East RM 4100

department: Biochemistry

institute: University of Utah

summary: Nanopore sequencing has revolutionized genetic analysis by offering linkage information across megabase-scale genomes. However, the high intrinsic error rate of nanopore sequencing impedes the analysis of complex heterogeneous samples, such as viruses, bacteria, and edited cell lines. Achieving high accuracy in single-molecule sequence identification would significantly advance the study of quasi-species genomic populations, crucial for fields like immunology, pathology, epidemiology, and synthetic biology, where clonal isolation is traditionally employed for complete genomic frequency analysis. Here, we introduce ConSeqUMI, an innovative experimental and analytical pipeline designed to address long-read sequencing error rates using unique molecular indices for precise consensus sequence determination. ConSeqUMI processes nanopore sequencing data without the need for reference sequences, enabling accurate assembly of individual molecular sequences from complex mixtures. We establish robust benchmarking criteria for this platform’s performance and demonstrate its utility across diverse experimental contexts, including mixed plasmid pools, recombinant adeno-associated virus genome integrity, and CRISPR/Cas9-induced genomic alterations. Furthermore, ConSeqUMI enables detailed profiling of human pathogenic infections, as shown by our analysis of SARS-CoV-2 spike protein variants, revealing substantial intra-patient genetic heterogeneity. Lastly, we demonstrate how individual clonal isolates can be extracted directly from sequencing libraries at low cost, allowing for post-sequencing identification validation of observed variants. Our findings highlight the robustness of ConSeqUMI in processing sequencing data from degenerate UMI-labeled molecules, offering a critical tool for advancing genomic research.

sample_organism: Severe acute respiratory syndrome coronavirus 2

overall_design: Unique molecular index (UMI)-labeled DNA molecules derived from various source materials including plasmids, AAV genomes, SARS-CoV-2 spike protein CDS, and PCR products were sequenced on the MinION platform from Oxford Nanopore Technologies and analyzed using a novel pipeline, ConSeqUMI.

first: Adam

last: Zahm


title: Effect of deletion of NELL2 on gene expression in calvarial preosteoblasts

city: Tianjin

first: Hairui

last: Yuan

state: Tianjin

address: 6 Huan-Rui-Bei Road

department: Chu Hsien-I Memorial Hospital & Institute of Endocrinology

institute: Tianjin medical university

summary: Neural EGFL-like 2 (NELL2) is a secreted protein known for its regulatory functions in the nervous and reproductive systems, yet its role in bone biology remains unexplored. In this study, we observed that the NELL2 levels were diminished in the serum of osteoporosis patients, as well as in the bone of aged and ovariectomized (OVX) mice. In vitro loss-of-function and gain-of-function studies revealed that NELL2 facilitated osteoblast differentiation and impeded adipocyte differentiation from mesenchymal progenitor cells. In vivo studies further demonstrated that the deletion of NELL2 in preosteoblasts resulted in a low bone turnover phenotype characterized by decreased cancellous bone mass in mice. Mechanistically, we identified Fibronectin 1 (Fn1) as a potential receptor for NELL2. Specifically, NELL2 interacted with the FNI-type domain located at the C-terminus of Fn1. Moreover, we found that NELL2 activated the focal adhesion kinase (FAK)/AKT signaling pathway through Fn1/integrin β1 (ITGB1), leading to the promotion of osteogenesis and the inhibition of adipogenesis. Notably, administration of NELL2-AAV was found to ameliorate bone loss in OVX mice. These findings underscore the significant role of NELL2 in osteoblast differentiation and bone homeostasis, suggesting its potential as a therapeutic target for managing osteoporosis.

overall_design: To investigate by which NELL2 regualtes osteoblast differentiation and bone homeostasis, we collected preosteoblasts from the calvaria of 3-day-old Col1-cre;Nell2fx/fx and Nell2fx/fx mice, and determine the effect of deletion of NELL2 on gene expression in calvarial preosteoblasts.


title: Behavioral abnormalities, cognitive impairments, synaptic deficits, and gene replacement therapy in a CRISPR engineered rat model of the Cri du Chat syndrome-associated 5p15.2 deletion

city: Beijing

first: Feng

address: 119 South Fourth Ring Road West, Fengtai District

institute: Beijing Tiantan Hospital, Capital Medical University

summary: The Cri du Chat Syndrome (CdCS), an untreatable genetic disorder, arises from a deletion on chromosome 5p. It manifests in distinct features, including a cat-like cry, facial abnormalities, microcephaly, and severe psychomotor/mental retardation. Lack of accurate animal models hinders research. We created a rat model with a similar deletion on chromosome 2q22 using CRISPR-Cas9, replicating CdCS's genetic aberration. This model exhibits deficits in social behavior, cognition, and anxiety. Our innovative gene replacement using AAV-Ctnnd2 via intravenous injection during early development mitigates cognitive impairments but not sociability or anxiety in CdCS rats. This study paves the way for gene therapy to tackle CdCS challenges.

overall_design: We collected samples from both hippocampus and prefrontal cortex of rats, including wild type (WT), CdCS genotype, and samples treated with adeno-associated virus (AAV) vectors. Specifically, we are interested in the impact of AAV-mediated gene delivery on gene expression, particularly with the AAV-Ctnnd2 vector. Each condition is represented by four biological replicates. Sample processing involved polyA RNA selection, focusing on mRNA sequencing. All samples were sequenced using paired-end reads on the Illumina Novaseq platform.

first: Jingjing

last: Shen

first: Yan

first: Yang

last: Liu


title: Effect of Fn1 knockdown or NELL2  overexpression on gene expression in stromal ST2 cells

overall_design: To elucidate the signaling pathway downstream of NELL2/Fn1, we conducted RNA-seq analysis using ST2 cells transfected with either NELL2 construct or Fn1 siRNA.


title: A correctable immune niche for basal-epithelial stem-cell reprogramming and post-viral lung diseases

city: Saint Louis

first: Michael

last: Holtzman

address: 425 S Euclid Avenue

institute: Washington University in Saint Louis

summary: Epithelial barriers are programmed for defense and repair but are also frequently the site of long-term remodeling disease. In general, this paradigm features activation of epithelial stem cells that coordinate organ development but persist into adult life to regenerate damaged tissues. Here we identify a Wfdc21-dependent monocyte-derived dendritic cell (moDC) population that functions as an early sentinel niche for basal-epithelial stem cells (basal-ESC) growth and feed-forward inflammation in mouse models of epithelial injury due to respiratory viral infections. This niche function depends on Gpnmb-CD44 signaling so that transient but properly timed antibody blockade of ligand or receptor provides long-lasting disease correction in these injuries. These same control points are found for mouse and human basal-ESC-derived organoids, and the corresponding biomarkers track with comparable lung diseases in humans. Together, the findings identify a mechanism to explain and modify basal-ESC reprogramming in what is otherwise a stereotyped, primordial response to epithelial injury.

overall_design: Total lung RNA were extracted from SeV-infected WT and Wfdc21KO mice at 12, 21, and 49 days post infection or control PBS challenge and  was purified and subjected to scRNAseq using the 10x Genomics platform

first: Kangyun

first: Yong

last: Zhang

first: Kelly

last: Sun

first: Dailing

last: Mao

first: Stephen

last: Austin

first: Erika

middle: C

last: Crouch

first: Steven

last: Brody

first: Derek

last: Byers

first: Christy

last: Hoffmann

last: Hughes


title: miRNA-seq of CD4+ T cells transfected by ASO or CRO

first: Hong

last: Zhou

address: 650 Xinsongjiang Road

department: Clinical Insititute of immunology

institute: Shanghai general hospital

summary: During the activation of CD4+T cells, the pri-miRNAs translocated from cytoplasma into nucleus.However, the mechanism remains unkown. We found that pri-miR-31 interact with nucleolin through G-guadruplex struction in pri-miR-31. We then transfected ASO to destribute the interaction of nucleolin and G4 struction. miRNA-seq was performed in our study.

overall_design: ASO and its control CRO was transfected into naïve CD4+ T cells. The transfected cells were activated by anti-cd3/28. After 48 hours, cells were collected and went for RNA extraction. miRNA-seq was then ferformed.

first: Zilong

last: Fang


title: RIP-seq reveals the interactome of nucleolin in activated CD4+ T cells

summary: During the actiation of CD4+T cells, the pri-miRNAs translocated from cytoplasma into nucleus.However, the mechanism remains unkown. We found that pri-miR-31 interact with nucleolin through G-guadruplex struction in pri-miR-31. We then transfected ASO to destribute the interaction of nucleolin and G4 struction. In order to identify the interacting RNA, including miRNA precuser and mRNA, we performed the RIP-seq Immunoprecipited by anti-nucleolin and IgG.

overall_design: Naïve CD4+ T cells derived from wild type C57 mice were activated by anti-CD3/28. Cells were lysated and Immunoprecipitated by antinucleolin and IgG. Paired reads were mapping to mm10 gemonic.

first: Zhixiao


title: Comparison of otic vesicle gene expression from E10.5 mouse and inner ear organoid cultures at 12 days-in-vitro with (BSFL) and without (BFL) TGFβ inhibition

city: Ann Arbor

first: Robert

last: Duncan

state: MI

address: 1150 W Medical Center Dr, 5315D Med Sci I

department: Otolaryngology - Head & Neck Surgery

institute: University of Michigan

summary: The early development of inner ear organoids—from germ layer to otocyst formation—is a highly controlled process with timed chemical cues that recapitulate major signals in vivo. We sought to elucidate additional morphogens that might guide this multi-stage process, improve efficiency, and influence cell fate decisions. Using a whole-transcriptomic approach with bulk RNASeq, we identified major differences in native otic vesicles (OVs) from E10.5 mice and stem cell-derived OVs from cultures at 12 days-in-vitro. Stem cell-derived samples included those treated with TGFβ inhibitors at early stages of differentiation--to suppress mesendodermal fates--and those without TGFβ inhibition, since other investigators identified this early inhibitory step as critical for organoid-genesis though dispensible for OV production. Differential gene expression between native and derived OVs identified factors related to anterior-posterior patterning as disregulated in the cell cultures, implicating aberrant retinoic acid (RA) signaling in the organoid culture paradigm.

overall_design: RNASeq analysis of E10.5 mouse otic vesicles and otic vesicles isolated from inner ear organoid cell cultures treated with (BSFL samples) and without (BFL samples) TGFβ inhibitors

first: Stacy

last: Schaefer

first: Liqian


title: IL-10 Targets IRF1/5 to Suppress IFN and Inflammatory Responses by Epigenetic Mechanisms [ATAC-Seq]

first: Bikash

last: Mishra

state: NY

address: 515 E 71st ST

institute: Hospital for Special Surgery

summary: Interleukin-10 (IL-10) is pivotal in suppressing inflammation and innate immune activation, in large part by suppressing induction of genes by potent inflammatory factors such as TLR ligands. Despite decades of research, molecular mechanisms underlying this inhibition have not been resolved. This study utilized an integrated epigenomic analysis of gene transcription, chromatin accessibility, histone modifications and transcription factor binding to investigate IL-10-mediated suppression of LPS and TNF responses in primary human monocytes. Instead of inhibiting core TLR4-activated pathways such as NF-kB, MAPK-AP-1 and TBK1-IRF3 signaling, IL-10 targeted IRF5 an IRF1-mediated amplification loop that is important for IFNB, ISG and inflammatory gene induction in monocytes. This resulted in near-complete suppression of ISGs, and significant inhibition of inflammatory NF-kB target genes, in whose activation IRFs play an amplifying role. Mechanisms of TLR4 and TNFR target gene inhibition included downregulation of chromatin accessibility, de novo enhancer formation, and IRF1-associated H3K27ac activating histone marks. These results describe an underappreciated suppression of IFN responses by IL-10 and provide epigenetic mechanisms by which IL-10 suppresses TLR/TNF-induced gene expression.

overall_design: To investigate regulation of LPS and TNF responses by IL-10 in primary human monocytes. We purified CD14+ monocytes from human buffy coats. Monocytes were cultured overnight at 37°C, 5% CO2 in RPMI-1640 medium supplemented with 10% heat-inactivated defined FBS, penicillin-streptomycin, L-glutamine and 20 ng/ml human M-CSF and treated with indicated stimulation.


title: ChlP-seq of MYC in HTA10-Myc/h2a and h2a

first: Xiang

last: Li

overall_design: To investigate the deposition of HTA10 in Arabidopsis, we analysed genome-wide HTA10 density by ChIP-seq.

first: Aiwu

last: Dong

first: Jiabing

last: Wu

first: Shuoming

last: Yang

first: Jiachen

last: Wang


title: IL-10 Targets IRF1/5 to Suppress IFN and Inflammatory Responses by Epigenetic Mechanisms [Cut & Run]


title: Transcriptomic analysis reveals the participation of NTRC in iron homeostasis throughout Arabidopsis development

city: Sevilla

first: Fernando

last: Rodríguez-Marín

state: Sevilla

address: Avda. Américo Vespucio, 49

country: Spain

institute: Instituto de Bioquímica Vegetal y Fotosíntesis

summary: NADPH-dependent thioredoxin reductase C (NTRC) plays a central role in redox regulation of chloroplast photosynthetic metabolism. Accordingly, Arabidopsis (Arabidopsis thaliana) NTRC null mutants show defective photosynthetic performance and growth inhibition. Remarkably, these mutants show almost wild type phenotype at the seedling stage, which raises the question of whether NTRC plays different functions throughout plant development. In this work, we have addressed this issue by performing transcriptome comparisons of Arabidopsis wild type and ntrc mutant lines at seedling and adult stages of development. In contrast with the high impact of NTRC on leaves from adult plants, the low transcriptomic differences in seedlings suggested a less-relevant function of NTRC at this stage of plant development. Notably, the ntrc mutant showed transcriptomic changes resembling the response to Fe excess throughout plant development, though this response was almost unique at the seedling stage. The lack of NTRC caused altered levels of Mn, Zn, Cu, S, P, K and Na, but no significant differences in the content of Fe, as compared with the wild type. Moreover, at the seedling stage, the lack of NTRC caused hypersensitivity to Fe deficit, but a protective effect in response to Fe excess, most likely due to lower ROS accumulation in the mutant seedlings. Our results reveal the different impact of NTRC throughout plant development and identify Fe homeostasis as a process highly affected by NTRC, most notably at the seedling stage.

overall_design: Two different transcriptomics experiments, adult and seedling stages, were carried out. For adult samples, eight-week-old short-day grown wild type and ntrc plants were randomly selected and young rosette leaves collected after 2 h of illumination at 125 µE m−2 s−1. Our experimental design consisted of three biological replicates for each genotype, each of them containing leaves from three individual plants. Wild type raw RNA-seq data from adult stage can be found in Gene Expression Omnibus identified with accession number GSE147793. For seedling samples, six-day-old continuous-light wild type and ntrc mutant grown in MS at 125 µE m−2 s−1 were collected. Our experimental design consisted of three biological replicates for each experimental condition.

first: Juan

last: Pérez-Ruiz

first: Francisco

last: Cejudo


title: ChIP-seq of H2A H2A.Z H2A.W H3 in Col-0, h2a, h2a.z, and h2a.w; ChIP-seq of H3K36me3 H3K9me2 in Col-0

overall_design: To investigate the interrelationship of histone H2A and its variants H2A.Z and H2A.W in Arabidopsis thaliana, we analyzed the ChIP-seq data to pick out the potential replacement sites. The H3K36me3 and H3K9me2 data were used to define chromosome arms and pericentromere regions.


title: IL-5 increases pro-fibrotic and pro-inflammatory signalling in severe asthmatic fibroblasts

city: Sharjah

first: Rifat

last: Hamoudi

state: Sharjah

address: M32 Sharjah Institute for Medical Research, College of Medicine, University of Sharjah, , Sharjah

department: Clinical Sciences

country: United Arab Emirates

institute: University of Sharjah

summary: Fibrosis is a hallmark feature of airway remodeling in asthma. However, the exact molecular mechanisms driving its development and progression remain inadequately understood. Interleukin-5 (IL-5) plays a potent role in the inflammatory response associated with eosinophils and asthma pathophysiology, but its direct impact on lung fibroblasts and contribution to fibrosis have yet to be fully explored. In our study, we investigated the pro-fibrotic effects of IL-5 on human lung fibroblasts derived from asthmatic and normal subjects. Following IL-5 stimulation, these fibroblasts were subjected to a series of experiments to assess IL-5’s impact on fibrosis. Our findings reveal that IL-5 triggers the release of several extracellular matrix (ECM) components,  and disrupts the balance of matrix metalloproteinases (MMPs) and tissue inhibitors of metalloproteinases (TIMPs) . This imbalance further disrupts the MMP/TIMP ratio. Additionally, IL-5 stimulation promotes the release of pro-inflammatory and pro-fibrotic cytokines,  Overall, these findings indicate a novel pro-fibrotic role of IL-5 through its direct action on lung fibroblasts, offering valuable insights into the therapeutic potential of targeting IL-5 to mitigate or possibly reverse airway remodeling in asthma.

overall_design:
In order to investigate the impact of IL-5 stimulation on lung derived fibroblasts, and what functional characteristics were gained by these cells post stimulation, RNAseq and bioinformatics analysis were conducted in human lung derived fibroblasts with or without IL-5 Stimulation
3 primary cell lines isolated from human lungs representing three different severe asthmatic patients, 3 primary cell lines isolated from human lungs representing three different healthy subjects, both were stimulated with  0.5ng/ml of IL-5 for 6h
Abberviations: N = Normal, D= Diseased, C= Unstimulated, T= Treated
Targeted RNA-Seq using Ion AmpliSeq whole transcriptome human gene expression kit

first: Rola

last: Abujabal

first: Reem

middle: S

last: Alhamidi

first: Alaa

last: Abed

first: Bassam

last: Mahboob

first: Khuloud

last: Bajbouj

first: Qutayba

last: Hamid


title: Epigenome-Wide Association Study of the Interaction between Alzheimer’s disease and Systemic Infection

city: Exeter

first: Katie

last: Lunnon

address: RILD Level 4, Barrack Road

department: Medical Research

institute: University of Exeter Medical School

type: Methylation profiling by genome tiling array

summary: Although most Alzheimer’s disease (AD) cases are sporadic, with no known aetiology, the onset and progression of the disease has been widely linked with inflammation both in the periphery and within the brain. Indeed, many AD sufferers ultimately die with a systemic infection, and infections during life can increase the risk of developing dementia and the rate of cognitive decline in AD patients. However, the mechanistic pathways linking inflammatory processes to AD onset and progression are not known. This study will use an epigenomic approach to elucidate the molecular mechanisms involved in the brain in AD following systemic inflammation. A better understanding of the neurobiological pathways altered in AD during systemic inflammation could ultimately identify new pharmacological targets, potentially improving the lives of millions of AD sufferers worldwide. This work identifies molecular mechanisms that are altered in AD brain during systemic inflammation, which can then be functionally characterised and targeted in in vitro modelling systems.

overall_design: We aimed to profile the genomic DNA methylome of prefrontal cortex brain tissue of Alzheimer’s disease and control patients with and without infection present at the time of death. DNA methylation was analysed in a cohort of 242 samples, including 131 AD patients (n=68 with infection) and 111 control participants (n= 47 with infection); using the Infinium Methylation EPIC array.

first: Lachlan

last: MacBean

first: Adam

last: Smith


title: Post-senescence reproductive rebound in Daphnia is associated with reversal of age-related transcriptional changes in lipid and protein metabolism

city: Johnson City

first: Lev

middle: Y

last: Yampolsky

state: Tennessee

address: 811 Lazywood Dr

department: Biological sciences

institute: East Tennessee State University

summary: A long-lived species of zooplankton microcrustaceans, Daphnia magna, sometimes exhibits late-life rebound of reproduction, briefly reversing reproductive senescence. Such events are often interpreted as terminal investment in anticipation of imminent mortality. We demonstrate that such post-senescence reproductive events (PSREs) neither cause not anticipate increased mortality. We analyze an RNAseq experiment comparing young, old reproductively senescent, and old PSRE Daphnia females. We first show that overall age-related transcriptional changes are dominated by the increase transcription of guanidine monophosphate synthases and guanylate cyclases, as well as two groups of presumed transposon-encoded proteins and by a drop in transcription of protein synthesis-related genes. We then focus on gene families and functional groups in which full or partial reversal of age-related transcriptional changes occur. This analysis reveals reversal, in the PSRE individuals, of age-related up-regulation of apolipoproteins D, lysosomal lipases, and peptidases and of age-related down-regulation of E3 ubiquitin kinases, V-type proton ATPases, and numerous proteins related to mitochondrial and muscle functions. While it is certain which of these changes enable reproductive rejuvenation, and which are by-products of processes that lead to it, we present some evidence that post-senescence reproductive events are associated with the reversal of age-related protein and lipid aggregates removal, apoptosis, and with restoration of mitochondrial integrity.

overall_design: Daphnia from a single clone sampled at ages of 20 days (young, reproducing females), reproducing females at age 130-170 days (old, reproducing) and post-reproductive females at the same age range (old, non-reproducing).

first: Ishaan

last: Dua


title: bulk RNA sequence of a41BB treated murine CD8+ T cells

city: CHICAGO

first: Bin

last: Zhang

state: IL

address: 300 E Superior St, Tarry 4-726

institute: Northwestern University

summary: We identify genes regulating metabolism in CD8+ T cells with a4-1BB treatment.

overall_design: Examination of gene profile in CD8+ T cells treated with a4-1BB in 4days culture in vitro

first: Jihae

last: Ahn


title: Spatial Coding Dysfunction & Network Instability in the Aging Medial Entorhinal Cortex

city: San Francisco

first: Karishma

middle: Joanne Bhatia

last: Pratt

state: CA

address: 513 Parnassus Ave, Med. Sci. Bldg, Room S1364

institute: UCSF

summary: Across species, spatial memory declines with age, possibly reflecting altered hippocampal and medial entorhinal cortex (MEC) function. However, the integrity of cellular and network-level spatial coding in aged MEC is unknown. Here, we leveraged in vivo electrophysiology to assess MEC function in young, middle-aged, and aged mice navigating virtual environments. In aged grid cells, we observed impaired stabilization of context-specific spatial firing, correlated with spatial memory deficits. Additionally, aged grid networks shifted firing patterns often but with poor alignment to context changes. Aged spatial firing was also unstable in an unchanging environment. In these same mice, we identified 458 genes differentially expressed with age in MEC, 61 of which had expression correlated with spatial firing stability. These genes were enriched among interneurons and related to synaptic transmission. Together, these findings identify coordinated transcriptomic, cellular, and network changes in MEC implicated in impaired spatial memory in aging.

overall_design: Neuronal nuclei were isolated from subdissected MECs to compare transcriptomes of young and aged mice with electrophysiological recordings.


title: Gene expression profile at single cell level of cells from the dura mater and brain of mice subjected middle cerebral artery occlusion (MCAO) or Sham treatment.

city: Fukuoka

first: Mitsuhiro

last: Kanamori

state: Fukuoka

address: Higashi-ku Maidashi 3-1-1

department: Allergy and Immunology

institute: Kyushu University

summary: The mouse dura mater shows strong immune responses after MCAO. We used single-cell RNA sequencing (scRNA-seq) to analyze the transcriptional changes in the dural cells. We also analyzed the brain from MCAO mice as a comparison.

overall_design: CD45-positive and -negative cells in the dura mater and CD45-positive CD11b-negative cells in the brain of MCAO or Sham-treated mice were sorted by Fluorescence-activated cell sorting (FACS) and analyzed using scRNA-seq.

first: Minako

last: Ito

first: Ako

last: Matsui


title: IL-10 Targets IRF1/5 to Suppress IFN and Inflammatory Responses by Epigenetic Mechanisms [RNA-Seq]

city: New York

first: Bikash

last: Mishra


title: Effect of Pseudomonas aeruginosa (WT and dFliC) infection on PMN- and M-MDSC

city: Paris

first: Maelys

last: BORN-BONY

address: 16 rue Henri Huchard

country: France

institute: INSERM

summary: Pseudomonas aeruginosa (P.a.) is a pathogenic opportunistic bacterium, classified as a priority by the WHO for the research of new treatments. As this bacterium is harmful trough the inflammation and tissue damage it causes, we investigated the role of Myeloid Derived Suppressor Cells (MDSC) in P.a. infections and their potential as a therapeutic tool. Using both ‘classically’ obtained MDSC (through mice bone-marrow differentiation), and a new procedure developped here (using the ER-Hoxb8 hematopoietic cell line), we observed that after administering intra-nasally a lethal dose of P.a (PAO1), intra-pulmonary transfer of MDSC, in both prophylactic and therapeutic protocols, markedly improves survival of P.a infected animals. Mechanistically, with a sub-lethal dose of P.a, we observed that MDSC transfer modulated lung tissue injury, down-regulated inflammatory responses and elicited lung repair. We further showed that WT-PAO1 and MDSC (and their subtypes PMN-MDSC and M-MCSF) could interact directly in vitro and in vivo, and that both PMN- and M-MDSC gene expression (assessed through RNA sequencing) was modulated after in vitro P.a. infection, and that WT-PAO1 (but not dFlic-PAO1) infection led to inhibition of T cell proliferation and promoted epithelial cell wound healing. Furthermore, we showed that the transcription factor Nr4A1 was up-regulated in both PMN- and M-MDSC- infected cells and may be an important mediator in the process.  Altogether, we highlight a potential beneficial role of MDSC in P.a. infection responses and suggest that the unique properties of MDSC make them attractive potential new therapeutic tools for patients with acute or chronic inflammatory diseases.

overall_design: Using MDSC differentiated from ER-Hoxb8 cell-line, we evaluated the effect of P.a. infection on their gene expression. Total MDSc were mock- or Pseudomonas aeruginosa strain PAO1 (WT or dFliC) infected for 6 hours at MOI 1. After infection, PMN- and M-MDSC were sorted by flow cytometry and analyzed separately.

first: Maëlys

first: Clémentine

last: CORNU

first: Bérengère

last: VILLERET

first: Romé

last: VOULHOUX

first: Jean-Michel

last: SALLENAVE

first: Valérie

last: GRATIO


title: mesendoderm differentiation with Hif-1a knockdown

city: Wuhu

first: Xiaopeng

last: Shen

address: 1 East Beijing Rd.

institute: Anhui Normal University

summary: To study the gene expression profile in the mesendoderm differerntiation of scramble control and Hif-1a knockdown, we performed RNA-seq on the total RNA samples collected from the differentiation of scramble and Hif-1a knockdown AB2.2 mESCs at differentiation day 4. Sramble and Hif-1a knockdown AB2.2 mESCs were  built by  infecting AB2.2 cells with lentiviruses. Each group contained three biological replicates. The expression matrix was obtained by Hisat2 followed by Stringtie.

overall_design: RNA-seq of scramble and shHif-1a AB2.2 cells at differentiation day 4

first: Meng

last: Li


title: Serum extracellular vesicles miR-1305 and miR-6785-5p serve as biomarkers for disease severity in psoriasis

city: Jinan

first: Q

last: Sun

state: Shandong

address: Medical College of Shandong University 44 Wenhua West Road, Lixia District,

institute: Shandong University; Qilu hospital

summary: Background: The role of serum extracellular vesicles (EVs) are less known in psoriasis. Objectives: To explore the transcriptomic profile of serum EVs and the potential biomarkers in psoriasis. Methods: EVs were isolated by differential ultracentrifugation and identified by transmission electron microscope. The diameters of EVs were detected using nanoparticle tracking analysis. Serum EVs-keratinocyte interaction was observed through confocal fluorescence microscopy. miRNA microarray and mRNA microarray were performed in serum EVs (n=4) and skin lesions (n=3), respectively. qRT-PCR and fluorescence in situ hybridization were used to detect the expression of miRNAs in serum EVs and skin lesions (n=15). Bioinformatics analysis was performed to predict the potential target genes and functions of miR-1305 and miR-6785-5p. Western blot, CCK-8 and Elisa were used to detect the EVs’ biomarkers, keratinocytes proliferation and cytokines secretion. Results: A total of 16 miRNAs and 1,725 mRNAs were significantly dysregulated in serum EVs and skin lesions, respectively. miR-1305 was downregulated and miR-6785-5p was upregulated both in serum EVs and skin lesions. Serum EVs could be uptaken by keratinocytes. MiR-1305 was downregulated and miR-6785-5p were upregulated in keratinocytes after cocultured with psoriasis serum EVs compared with controls. Psoriasis serum EVs promoted keratinocytes proliferation and the secretion of CCL20 and IL-8. Serum EVs miR-1305 and miR-6785-5p were associated with disease severity. Conclusions: Serum EVs might be involved in the activation of keratinocytes through loaded miRNAs in psoriasis. Serum EVs miR-1305 and miR-6785-5p can be served as biomarkers of psoriasis.

first: Jianjun

last: Yan

first: Yunyue

last: Zhen

first: Ruijie

last: Wang

first: Xueqing

first: Shan

last: Huang

first: Hua

last: Zhong

first: He

last: Wen

first: Qing


title: Succinate drives gut inflammation by promoting FoxP3 degradation through a molecular switch

city: Chicago

first: Hai

address: 303E Chicago Avenue

department: Department of Pathology

summary: Succinate levels are elevated in inflammatory bowel disease (IBD), but its role in disease pathogenicity remains unknown. This study shows that succinate promotes colitis in mice by reducing FoxP3 expression in regulatory T cells (Tregs) and increasing IL-17. Succinate selectively reduced the expression of 2-oxoglutarate dehydrogenase complex (OGDHc), the enzyme for succinyl-CoA synthesis, which in turn reduced FoxP3 succinylation and made FoxP3 lysine residues available for ubiquitination and Foxp3 protein degradation. Genetic deletion of Dlst, a member of OGDHc, in Tregs led to reduced FoxP3, impaired Treg function, and severe gut inflammation. Restoring FoxP3 fully rescued Dlst-deficient Treg immune suppressive functions. In IBD patients, FoxP3 and OGDHc levels were reduced in Tregs and negatively correlated with succinate levels and inflammation severity. This study identifies succinate as a pathogenic factor in IBD, uncovering a succinate-driven molecular switch that regulates FoxP3 stability and Treg function during inflammation.

overall_design: Splenic CD4+ T cells from iWT (WT) and Dlst-Treg iKO (KO) mice were cultured in Treg polarization condition for 2 days in the presence of 4-hydroxytamoxifen. Sorted iTregs (CD4+FoxP3-GFP+tdTomato-RFP+) were subjected to RNA sequencing.

first: Deyu

last: Fang


title: Clinical and molecular characterization of a novel LMX1A frameshift mutation near the C-terminus lead to familial non-syndromic sensorineural hearing loss

city: Shanghai

first: Shanhe

last: Yu

address: 197# Rui Jin Road II

institute: Shanghai Institute of Hematology，Rui Jin Hospital

summary: Next Generation Sequencing Facilitates Quantitative Analysis of HEI-OC1 cells transduced with vector control, LMX1A WT or c.915dup variant.

overall_design: mRNA profiles of HEI-OC1 cells transduced with vector control, LMX1A WT or c.915dup variant were generated by deep sequencing, in triplicate, using Illumina Navoseq 6000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks.

first: Min

last: Xiao


title: Foxo1 regulates intestinal tissue-resident memory CD8 T cell biology in an anatomic compartment- and context-specific manner

city: San Diego

first: John

last: Chang

address: UCSD

institute: UC San Diego

summary: Transcriptional regulation of diverse aspects of tissue-resident CD8 memory T cells (TRM) biology is nuanced and context-specific. Transcription factors (TF) that orchestrate TRM formation and maintenance are distinct between anatomic compartments, and predicting the roles of TF on TRM biology is challenging. Here, we applied the Taiji algorithm to map TF networks and identify Forkhead Box protein 01 (Foxo1) as differentially invested in intestinal TRM TF networks. Loss of Foxo1 in established TRM resulted in a survival advantage for small intestinal intraepithelial layer (siIEL) TRM compared with other intestinal compartments. SiIEL TRM were uniquely able to maintain expression of proliferative and anti-apoptotic cellular programs in the absence of Foxo1. This advantage was lost upon blockade of integrin αE (Itgae/CD103). These findings suggest that the TF networks maintaining siIEL TRM exhibit redundancy and highlight an underappreciated role of integrin signaling in TRM biology outside of tissue-retention.

overall_design: P14 WT CD45.1 and P14 Foxo1f/f Cre-ERT2+/- CD45.1.2 CD8 T cells were adoptively co-transferred into congenically distinct recipient mice. The recipient mice were infected with 2x105 plaque forming units of lymphocytic choriomeningitis virus 30 minutes after transfer. 21 days post-infection, mice were treated with 0.5mg/g tamoxifen intraperitoneally daily for 5 days, and then sacrificed 2 weeks later. CD8 T cells were isolated from spleen, small intestines, and colon, and incubated in an antibody cocktail containing antibody-derived tags against cell surface markers and fluorescence-conjugated antibodies. The congenically distinct CD8 T cells were separated by fluorescence-activated cell sorting. About 20,000 cells for spleen, siIEL, and siLPL samples were loaded onto Chromium Next GEM Chip M (10x Genomics) and 2,000 cells for cIEL and cLPL were loaded onto Chromium Next Gem Chip G (10x Genomics), and partitioned into Gel Beads. CITE-seq was then performed using previously described protocol (Stoeckius et al., 2017).

first: Paul

last: Hsu

first: Eunice

last: Choi

first: William

last: Wong

first: Yun

last: Lin

first: Sara

last: Vandenburgh

first: Yi

last: Liu

first: Priscilla

last: Yao

first: Cynthia

last: Indralingam

first: Ananda

middle: W

last: Goldrath

first: Wei

middle: T


title: Seryl-tRNA synthetase promotes translational readthrough via mRNA binding by involving the selenocysteine incorporation machinery

city: Toronto

first: Haissi

last: Cui

address: 80 St George St

department: Chemistry

country: Canada

institute: University of Toronto

summary: Translational readthrough of UGA stop codons by selenocysteine-specific tRNA (tRNASec) enables the synthesis of selenoproteins. Seryl-tRNA synthetase (SerRS) charges tRNASec with serine, which is modified into selenocysteine and delivered to the ribosome by a designated elongation factor (eEFSec in eukaryotes). Here we found that components of human selenocysteine incorporation machinery (SerRS, tRNASec, and eEFSec) also increased translational readthrough of non-selenocysteine genes, including VEGFA, to create C-terminally extended isoforms. SerRS recognizes target mRNAs through a stem-loop structure that resembles the variable loop of its cognate tRNAs. This function of SerRS depends on both its enzymatic activity and a vertebrate-specific domain. Through eCLIP-seq, we identified additional SerRS-interacting mRNAs as potential readthrough genes. Moreover, SerRS overexpression was sufficient to reverse premature termination caused by a pathogenic nonsense mutation. Our findings expand the repertoire of selenoprotein biosynthesis machinery and suggest an avenue for therapeutic targeting of nonsense mutations using endogenous factors.

overall_design: Ribosome profiling library construction   Ribosome profiling libraries were generated as previously described (37, 38) with some minor modifications. Briefly, two 10 cm dishes of cells were used for each biological replicate, and three biological replicates were prepared for each cell line (MDA-MB-231-empty vector, MDA-MB-231-SARS). Cell homogenization was performed in 1 ml lysis buffer (20mM Tris-Cl, pH 8.0, 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 100 µg/ml CHX, 1% (v/v) TritonX-100, 50 units/ml Turbo DNaseI). RNase I-treated lysates were overlaid on top of a sucrose cushion in 5 ml Beckman Ultraclear tubes and centrifuged in an SW55Ti rotor for 4 hours at 4ºC at 46,700 rpm. Pellets were resuspended and RNA was extracted using the miRNeasy kit (Qiagen) according to manufacturer’s instructions. 26-34 nucleotide RNA fragments were purified by electrophoresis on a 15% denaturing gel. Linker addition, cDNA generation (first-strand synthesis was performed at 50°C for 1 h), circularization, rRNA depletion, and amplification of cDNAs with indexing primers were performed. Library quality and concentration were assessed using high sensitivity D1000 screen tape on the Agilent tape station, Qubit 2.0 Fluorometer, and qPCR. All libraries were pooled and run on HiSeq4000 (SR75).  Ribosome profiling analysis  Ribosomal footprints were analyzed as described by Ingolia et al. (37) with these modifications: Trimgalore was used to trim off adapters and clip the first nucleotide off the 5’ end. Reads were then mapped to ribosomal RNA using bowtie2 (39) and unmapped reads were further mapped to the human transcriptome (v19) with STAR aligner (33). Expected read length distribution was tested with the R package RiboProfiling. To center ribosomes and obtain a list of genes with P-sites in their 3’ UTR, we used functionalities within Ribowaltz (40) and a custom python script by Scott Adamson, UConn, and Jax Laboratories. Observed/expected ratios were calculated as described elsewhere (38, 41, 42) using a custom script by Scott Adamson. Obs/exp indicates the number of observed codons in the A-site of the ribosome vs the calculated hypothetical expected number of observations. If ribosome pausing occurs, obs/exp > 1.

first: Markus

last: Terrey

first: Ze

first: Xianglei

last: Yang


title: Single-cell transcriptomics reveals cellular evolution underlying pleomorphic adenoma recurrence and malignant transformation

status: Public on Apr 10 2025

city: Chengdu

first: Chunjie

last: Li

state: Sichuan

address: No.14, Section 3rd, Renmin Nan Road

institute: West China Hospital of Stomatology, Sichuan University

summary: Pleomorphic adenoma (PA), the most common benign salivary gland tumor, presents unpredictable risks of recurrence and malignant transformation into carcinoma ex pleomorphic adenoma (CXPA), posing significant clinical challenges. To better delineate the tumor progression trajectory, we performed single-cell RNA sequencing on normal salivary glands, primary PA, recurrent PA (rPA), and CXPA, integrating cell trajectory reconstruction, differential gene expression analysis, and key gene network exploration to uncover molecular transitions and intercellular crosstalk underlying PA recurrence and malignant transformation. Our findings revealed GALNT13⁺ myoepithelial cells as CXPA-specific malignant progenitors, marking early malignant conversion, while MIF⁺ myoepithelial cells exhibited enhanced tissue-destructive capabilities. Fibroblasts played dual roles, enforcing fibrotic restraint in primary PA and promoting extracellular matrix degradation in CXPA. The tumor microenvironment demonstrated stage-specific adaptations, with CXPA favoring pro-inflammatory MIF–CD74/CD44 signaling, whereas rPA adopted immunosuppressive characteristics. Together, stromal reprogramming and immune-editing dynamics orchestrated microenvironmental adaptation, linking cellular heterogeneity to clinical aggressiveness. This study presents the first comprehensive molecular atlas of PA progression, highlighting the malignant specialization of myoepithelial subpopulations, fibroblast-mediated stromal remodeling, and immune-driven microenvironmental evolution, offering a valuable framework for precision stratification of malignant potential and future microenvironment-targeted therapeutic strategies.

overall_design: Fresh tumor tissues from human normal salivary gland, primary pleomorphic adenoma (PA), recurrent PA (rPA), and carcinoma ex pleomorphic adenoma (CXPA) were collected during surgery.  Single-cell suspensions were generated by enzymatic digestion and processed using the 10x Genomics Chromium Single Cell 3' platform.  scRNA-seq libraries were constructed and sequenced for all samples.  The data were analyzed to investigate cellular heterogeneity, infer tumor progression trajectories, and characterize changes in the tumor microenvironment during recurrence and malignant transformation.

first: Yike

first: Zhixuan

first: Guile

last: Zhao

first: Qi

last: Han

first: Zhangfan

last: Ding

first: Cheng

last: Wang


title: Transcriptional profiles are dramatically altered in circulating CD14+ monocytes in Rheumatoid Arthritis [RNA-seq]

city: Glasgow

first: Kieran

last: Woolcock

address: Sir Graeme Davies Building, 120 University Place

department: School of Infection & Immunity

institute: University of Glasgow

summary: Peripheral blood samples were collected from healthy controls and rheumatoid arthritis patients (active disease: DAS28 > 2.7), subsequently CD14+ monocytes were isolated using a positive selection kit, RNA was extracted and RNA-Seq was completed.

overall_design: RNA-Seq using the illumina NovaSeq6000 was performed on circulating CD14+ monocytes isolated from 15 healthy controls and 9 rheumatoid arthritis patients.

first: Nila

last: Servaas

first: Maarten

last: van der Kroef

first: John

last: Cole

first: Aridaman

last: Pandit

first: Carl

last: Goodyear


title: Growth response of bacteria on metal oxide nanoparticles by RNA-Seq analysis

city: Kolkata

first: A

last: G

state: West Bengal

address: B.T. Road

country: India

institute: INSTITUTE

summary: Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived B. coagulans transcriptome profiling (RNA-seq) of both control and treatment (treated with metal oxide nanoparticle)

overall_design: Methods: Bacteria from capsule was isolated, treated with metal oxide nanoparticle, RNA was extracted from control and treated bacteria, library was prepared and prepared libraries were sequenced on Illumina Hiseq X to generate 40M, 2x150bp reads/sample. Up to 75% of the sequenced bases were of Q30 value>90. Sequenced data were processed to generate FASTQ files and proceeded with data analysis.


title: Integrative Single-Cell RNA and ATAC Sequencing Reveals the Impact of Chronic Cigarette Smoking on Lung Epithelial Responses to Influenza and Hyperoxia

city: New Haven

first: Pei-Chun

last: Cha

state: CT

address: 333 Cedar Street

institute: Yale University

summary: Cigarette smoking is a significant risk factor for developing acute respiratory distress syndrome (ARDS), but the cellular and molecular mechanisms linking smoking to ARDS susceptibility remain unclear. Our goal was to improve our understanding of these mechanisms. To address this, we established a mouse model comparing long-term cigarette smoke exposure to non-smoking controls, examining responses to influenza infection and hyperoxia-induced lung injury. Six mice were divided into two groups: a non-smoking control and a smoking group subjected to cigarette smoke exposure for six months. After exposure, mice underwent infection with influenza virus or were subjected to hyperoxia. Single-cell RNA sequencing (scRNA-seq) and single-cell ATAC sequencing (scATAC-seq) were performed on lung tissues. Quality control analysis using Seurat (v5.1.0) and Signac (v1.13.1) retained 78,402 cells from scRNA-seq and 84,144 cells from scATAC-seq, with 32,305 matched cells identified across both datasets. Differential gene expression analysis revealed significant smoking-associated alterations in cellular responses to influenza infection and hyperoxia exposure. Pathway enrichment indicated heightened immune responses, inflammatory signaling, and cellular survival pathways in smoking-exposed animals. Integration of scRNA-seq and scATAC-seq identified key transcription factors (TFs), including those involved in immune regulation, chromatin remodeling, and cell survival, mediating these responses. Overall, this study underscores the role of chronic cigarette smoke exposure in exacerbating pathways critical to ARDS pathogenesis, providing potential targets for therapeutic intervention.

overall_design: Multiome-seq: Single cell data were from AKR/J mice lung tissue. scRNA and scATAC libraries were prepared using the 10x Genomics platform.

first: Zhenyang

last: Zou

first: Jessica

last: Nouws

first: Charles

last: Dela Cruz

first: Lokesh

last: Sharma

first: Xiting

last: Yan

first: Maor

last: Sauler


title: Physiological, anatomical, and transcriptomic analyses reveal the effects of acid rain stress on Akebia trifoliata and the mitigation potential of exogenous curcumin

city: Kunming City

first: Kai

state: Yunnan Province

address: No. 2, Puxin Road, Kunming National Economic and Technological Development Zone

department: College of Agriculture and Life Sciences

institute: Kunming University

summary: Acid rain is a global ecological issue severely threatening crop growth. Curcumin (CUR), a natural antioxidant, can enhance the tolerance of plants to abiotic stresses via physiological and molecular modes. As both medicine and food, Akebia trifoliata exhibits high economic value. The effects of acid rain stress on A. trifoliata and the mitigation potential of exogenous CUR remain unclear. To explore the impact of acid rain stress on A. trifoliata and the mitigation potential of exogenous CUR, we investigated the plant growth, physiological characteristics of leaves, anatomical structure, and gene expression of A. trifoliata under acid rain stress before and after treatment with exogenous CUR. The results indicated that under acid rain stress, the contents of chlorophyll a, chlorophyll b, total chlorophyll, and starch and thicknesses of upper and lower epidermis of leaves decreased by 58.16%, 77.88%, 64.77%, 63.85%, 58.93%, and 35.57%, respectively. Moreover, MDA, soluble sugar, soluble protein, and proline contents and production rate of oxygen free radicals increased by 82.55%, 43.20%, 44.55%, 64.40% and 345.77%, respectively. This suggested that acid rain stress affected the growth and development of A. trifoliata. A. trifoliata resisted acid rain stress by increasing SOD and CAT activities; thickness of leaf, palisade tissue, and spongy tissue; and ratio of palisade/spongy tissue. However, exogenous CUR could effectively facilitate plant growth, maintain integrity of anatomical structure of leaf, and relieve the damages to A. trifoliata caused by acid rain stress. Fifty μmol/L (CUR50) was the most optimal concentration. Transcriptomic analysis revealed that CUR0 vs Control, CUR50 vs Control, and CUR50 vs CUR0 had 2978, 3145, and 993 DEGs, respectively. KEGG enrichment analysis demonstrated that these DEGs are mainly associated with pathways such as ribosome, oxidative phosphorylation, plant hormone signal transduction, and phenylpropanoid biosynthesis. Collectively, this study, through physiological, anatomical, and transcriptomic analyses, elucidates the effects of acid rain stress on A. trifoliata and the mitigation potential of exogenous CUR, offering a theoretical foundation for the widespread cultivation of A. trifoliata and phytoremediation in acid rain-prone regions.

overall_design:
RNA - sequencing analysis of Akebia trifoliata leaves treated with curcumin under acid rain stress for 28 days.
There are three groups of total 9 samples with 3 biological replicates:
1. Control group: No curcumin (CUR) or simulated acid rain stress was applied
2. CUR0 group: simulated acid rain stress was applied without CUR supplementation
3. CUR50 group: 50 umol/L CUR was added under the same acid rain stress condition

first: Xingmei

last: Tao

first: Xiaoxu

last: Bi

first: Yongfu

last: Zhang


title: Rheumatoid Arthritis circulating CD14+ monocytes are epigenetically primed [ChIP-seq]

first: Kieran

last: Woolcock

summary: Peripheral blood samples were collected from healthy controls and rheumatoid arthritis patients (active disease: DAS28 > 2.7), subsequently CD14+ monocytes were isolated using a positive selection kit, ChIP-Seq was completed for H3K4me3 and H3K27me3.

overall_design: ChIP-Seq using the Illumina NextSeq 500 was performed on circulating CD14+ monocytes isolated from 15 healthy controls and 10 rheumatoid arthritis patients.

first: Nila