title: Performance evaluation and methods comparison of transcriptomic-based novel approach methods (tNAMs) for the characterization of wastewater treatment effluent

city: Durham

first: Steven

middle: Thomas

last: Purucker

state: NC

address: 109 TW Alexander Dr

institute: US EPA

summary: The complexity of wastewater treatment effluents (WWTE) complicates efforts to fully characterize the risk they pose to aquatic ecosystems. Transcriptomic-based novel approach methods (tNAMs) may provide the necessary resolution, sensitivity, and breadth to provide a more comprehensive characterization of these mixtures; however, a rigorous evaluation of tNAM performance is lacking. To address this, the current study aimed to systematically evaluate the consistency of the gene expression responses over time and under varying experimental approaches. Two-day post hatch (dph) fathead minnow (FHM) were exposed to clean laboratory water (moderately hard reconstituted water; MHRW) or one of four grab samples taken at an upstream site or within a WWTE in the morning and afternoon for two successive days. Concurrently, 2-dph FHM were also deployed at each site. RNA-seq analysis was conducted on all exposed fish. Differential expression analysis was conducted on fish from exposures to individual grab samples as well as a count data pooled across grab samples, providing both a discrete and time integrated analysis. For all effluent exposed fish, differentially expressed genes (DEGs) were identified relative to the fish exposed to the MHRW control or to the upstream site. The size of the DEG sets was used as an indicator of WWTE potency and the degree of overlap among respective DEG sets as a metric of consistency. With either comparator (MHRW or upstream), clear time dependent differences were observed across individual grab samples from exposures to the effluent but not the upstream site, with morning samples having much larger DEG set sizes than afternoon. With the MHRW comparator, considerable DEG overlap was observed among grab samples, with near complete overlap in morning samples. However, DEG set sizes were greatly reduced with the upstream comparator, with effectively no DEGs identified in afternoon sampling events and morning samples having minimal overlap. Deployed fish and the pooled grab sample composite exposures had similar results when the upstream site served as the comparator. In contrast, DEG sets were highly consistent among composite approaches with the MHRW comparator. DEG sets overlapped significantly between the upstream and effluent sites when compared to the MHRW, suggesting some consistency in their composition. This was confirmed using non-targeted analysis (NTA) for the first morning sample and a targeted analytical method for all grab samples. Overall, results indicate that gene expression is highly consistent over time and across exposure regimens; however, this is only the case with the use of the MHRW control. Direct contrasts between fish exposed to the WWTE and the upstream site displayed minimal consistency, which do not appear to reflect effluent composition. These results suggest that gene expression, if paired with NTA data, may provide a powerful tool to evaluate the risk posed by WWTE and to link gene expression with specific chemicals.

overall_design: RNA-seq profiling of larval fathead minnow exposed in the laboratory to moderately hard reconstituted water or individual grab samples collected from multiple site upstream and downstream of a site of a wastewater treatment and a drinking water treatment plants. Samples include successive sampling conducted in the morning and afternoon over two successive days, as well as FHM deployed at the same sites concurrent with grab sampling.

first: David

last: Bencic

first: Adam

last: Biales

first: Morgan

last: Hu

middle: T


title: Targeting the TNFα/TNFR1 axis to alleviate inflammation in experimental acute pancreatitis

status: Public on Aug 01 2026

city: Nanchang

first: Pan

last: Zheng

address: 17 of Yongwaizhengjie Street

country: China

institute: The Affiliated Hospital of Nanchang University

type: Expression profiling by high throughput sequencing

summary: Acute pancreatitis (AP) is an inflammatory disorder of the pancreas that can progress to systemic inflammatory response syndrome and multiple organ failure with high mortality. TNFα (tumor necrosis factor-alpha), a key proinflammatory cytokine elevated in early AP, triggers both pancreatic inflammation and acinar cell apoptosis through TNFR1 (tumor necrosis factor-alpha receptor 1) binding. Our study first revealed significant upregulation of TNFα and TNFR1 across three distinct AP animal models. Genetic ablation of Tnfr1 resulted in markedly attenuated AP severity in Tnfr1-/- mice, characterized by reduced inflammatory cell infiltration and decreased tissue inflammation. In bulk RNA analysis identified downregulation of interferon-related genes (Ifi209, Marcksl1, Ifit3, Oas3) in inflammatory cells of Tnfr1-/- mice. Pharmacological inhibition of the TNFα/TNFR1 axis using pomalidomide pretreatment similarly attenuated AP inflammation and significantly suppressed these interferon-associated genes. Notably, therapeutic administration of pomalidomide post-AP induction reproduced these protective effects, confirming the translational potential of targeting this signaling pathway.

overall_design: RNA sequencing analysis of Tnfr1-/- mice and wild-type mice in the context of caerulein-induced AP can provide valuable insights into the role of TNFα/TNFR1 axis   in acute pancreatitis pathogenesis.

first: Yin

last: Zhu

first: Nianshuang

last: Li


title: RNA-seq and ATAC-seq analysis of 5-azacytidine-treated HepG2 cells reveals epigenetic reactivation of BFL-1 and SQOR in hepatocellular carcinoma

city: 강남구

first: Wonjin

last: Woo

state: 서울 — Seoul

address: 서울시 강남구 도곡로237 강남세브란스 의생명연구센터 1층 김락균 교수님 실험실

country: South Korea

institute: Yonsei University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Hepatocellular carcinoma (HCC) remains a major therapeutic challenge with poor prognosis due to treatment resistance. Epigenetic silencing of tumor suppressor genes through promoter hypermethylation contributes to oncogenesis and resistance to cell death stimuli. We employed low-concentration 5-azacytidine (5-AZA) treatment to identify epigenetically silenced genes that modulate cell death susceptibility in HepG2 hepatocellular carcinoma cells without inducing baseline cytotoxicity. HepG2 cells were treated with 0, 2, and 10 μM 5-azacytidine for 4 days, followed by integrative RNA-seq and ATAC-seq analysis to characterize transcriptomic changes and chromatin accessibility patterns. This approach revealed coordinated promoter opening and transcriptional reactivation of methylation-silenced genes, particularly BFL-1 (BCL2A1) and SQOR, whose reactivation enhanced cell death susceptibility to TNF-α/CHX and sorafenib treatments. Our findings provide mechanistic insights into epigenetic vulnerabilities in HCC and demonstrate the utility of multi-omics approaches for identifying therapeutically tractable targets for precision epigenetic editing strategies.

overall_design: HepG2 hepatocellular carcinoma cells were treated with 5-azacytidine at three concentrations (0 μM control, 2 μM, and 10 μM) for 4 days. Following treatment, cells were harvested for both RNA-seq and ATAC-seq analysis to examine transcriptomic changes and chromatin accessibility patterns. Each condition includes biological replicates for both sequencing approaches.

first: Lark Kyun

last: Kim


title: Menin orchestrates corticogenesis via epigenetic activation of EphA4 in late-born neurons [snRNA-Seq]

city: Xiamen

first: shuzhong

last: wang

state: Fujian

address: Xiangan South Road

department: School of Medicine

institute: Xiamen University

summary: The development of the mammalian cerebral cortex is tightly regulated by epigenetic mechanisms. However, the role of epigenetic modifications in gene regulation and their impact on neocortical function remain poorly understood. Here, we demonstrate that Menin, encoded by the multiple endocrine neoplasia type 1 (Men1) gene, is essential for neurogenesis. Deficiency in Men1 disrupts the formation of the laminated neocortex, particularly in the upper-layer neurons. In Men1-deficient late-born neurons, migration to their final positions is impaired, accompanied by defective neuronal polarization. Mechanistic studies reveal that Menin regulates global chromatin accessibility at transcriptional start sites of genes critical for neuronal development. The loss function of Menin primarily reduces H3K4me3 deposition at promoter regions. Notably, complementation with EphA4 in late-born neurons mitigates polarization defects in the context of Men1 deficiency. These findings support the importance of Menin in corticogenesis, providing insight into the formation of the cerebral cortex.

overall_design: Nucleus were isolated and analyzed using snRNA-seq

first: Shuzhong

last: Wang

first: Kai

last: Zhuang

first: Liurong

last: Chen

first: Li

last: Zhong

first: Yibo

last: Qu

first: Jie

last: Zhang


title: Menin orchestrates corticogenesis via epigenetic activation of EphA4 in late-born neurons

overall_design: Cut&Tag Seq of Menin, H3K4Me3, H3K27me3, H3K9ac, RNA polII


title: Effect of lactate accumulation on translation and transcription in MDA-MB-231 breast cancer cells

city: Hangzhou

first: Yichen

last: Xu

address: Yuhangtang Road 866

institute: Zhejiang University

summary: Dynamic coordination of energy metabolism and protein synthesis is pivotal to cell fitness, especially in cancer cells that frequently encounter microenvironmental challenges. Yet it remains unclear whether this rapid communication depends on complex regulatory signaling pathways or can be governed by a single molecule. Here, we show that intracellular accumulation of lactate, a central product of glycolysis, is sufficient to acutely repress mRNA translation. Mechanistically, lactate is charged to the 3′ end of tRNA, a site canonically reserved for amino acids, generating translation-defective lactyl-tRNAs. This mechanism may have evolved to restrict protein synthesis during metabolic imbalance, such as when glycolytic activity exceeds lactate clearance, and is particularly relevant in highly glycolytic cancer cells, which frequently experience prolonged hypoxia and elevated lactate levels. Notably, triple-negative breast cancer (TNBC) cells evade this repression by maintaining low intracellular lactate, even under hypoxic stress. Blocking lactate export via monocarboxylate transporter (MCT) inhibition re-establishes translational repression, diminishes cancer cell fitness under metabolic stress, and impairs tumor progression. These findings uncover a unique metabolite-tRNA charging event that directly rewires translational output and reveal a metabolic vulnerability with therapeutic potential.

overall_design: RNA-seq and ribo-seq profiling of MDA-MB-231 cells with DMSO or AZD0095 treatment for 4-hour

first: Xinyu


overall_design: ATAC-seq of Men1-WT(Control) and Men1-cKO(NCKO) in late-born neurons. The neurons were labeled by Flash-Tag and collected at E18.5.


title: Interrogating the Synergistic Potential of Gemcitabine and Focused Ultrasound–Induced Thermal Ablation in Breast Cancer: Insights from the BR54 Trial via Spatial Transcriptomics

city: Charlottesville

first: Anwaruddin

last: Mohammad

state: VA

address: Pinn Hall

department: Bioinformatics Core

country: USA

institute: University of Virginia

summary:
Breast tumors frequently exhibit resistance to immunotherapy due to their immunosuppressive tumor microenvironment (TME). Preclinical evidence indicates that combining thermal high-intensity focused ultrasound (T-FUS) with the chemotherapeutic gemcitabine (GEM) can significantly alter this TME, promoting recruitment and activation of antitumor immune cells and facilitating durable, T cell–mediated tumor control. We hypothesize that GEM preconditioning enhances T-FUS-induced inflammatory responses by reducing anti-inflammatory cell abundance in the transition zone, thereby amplifying the infiltration and activation of effector immune cells.
Leveraging the ongoing BR54 clinical trial (NCT04796220), we analyzed resected breast cancer specimens, collected approximately 14 days post-T FUS treatment, with or without prior GEM pretreatment. Using NanoString’s CosMx Spatial Molecular Imager and 1000-plex RNA panel, we performed spatially-resolved gene transcription profiling within histologically defined regions, including FUS-induced thermal lesions and adjacent tumor areas. Our analysis focused on quantifying myeloid cell, T cell, and NK cell signatures, evaluating effector molecule gene expression, and assessing immunosuppressive-to-effector cell ratios.
Comparative analyses between FUS-treated patient samples (with or without GEM pretreatment) and archival untreated controls, as well as pre- to post-treatment biopsy comparisons, were conducted to evaluate therapy-induced remodeling of the TME. This project aims to elucidate the potential synergistic effects of GEM combined with T-FUS in breast cancer and establish the CosMx platform as a robust tool for integrated spatial multiomics analysis in clinical oncology research.

overall_design:
Samples were derived from one archival specimen and two patients that were a part of a randomized, Phase 1, 3-arm, open-label study to evaluate the safety and immunologic effects of GEM, FUS, and their combination in early stage breast cancer. The patients included in this data contribution were a part of ARM B and Arm C: Arm A: Gemcitabine (900 mg/m2), Arm B:  FUS ablation, Arm C: Gemcitabine (900 mg/m2) + FUS ablation. In total, 5 samples are included in this data contribution. Punch biopsies were collected one week prior to T-FUS treatment. Targeted tumors were then resected approximately two weeks later.   The focused ultrasound ablation targeted 50% of the tumor. The total number of sonications, power and dosing were dependent upon the size, shape, depth, subcutaneous fat distributions and vascularity of the targeted tumors.
**Please note that there are 2 samples on the VBC94-VBC106; 'Breast-FUS(1)(Above) AND Breast-FUS+GEM(1)(Below)' chip, which correspond to sample1 and sample2 sample records. The raw data files (for both samples) are linked to the sample1 sample records.

first: Awndre

last: Gamache

first: Ana

last: Oliveira

first: Timothy

middle: N

last: Bullock


title: Temporal and Clonal Resolution of Cellular Evolution Under Stress

city: Seattle

first: Kevin

middle: Z.

last: Lin

state: Washington

address: 3980 15th Avenue NE

department: Biostatistics

institute: University of Washington

summary: Dissecting cellular evolution under transient versus persistent stress is essential for understanding both healthy and pathological processes. Yet cellular stress responses involve nonlinear dynamics and survival bottlenecks, making them challenging to study. We develop a framework that combines single-cell multiomic lineage tracing with statistical modeling to quantify how individual cells contribute to the future population, by explicitly modeling exponential expansion and intra-clonal heterogeneity. Applied to a cancer model under short- and long-term treatment, we identify clones primed to endure treatment versus ones that survive by producing diverse progeny, enabling characterization of molecular features enriched in each clonal survival strategy. This framework can quantify treatment-driven selection and adaptation, revealing that their relative contributions to population dynamics vary between treatments. Furthermore, short- and long-term treatment results in expansion of distinct clones characterized by different gene programs and transcription factor activity. Notably, certain pathways such as AP-1 signaling can limit initial cancer cell growth but promote later resistance, and such opposing associations are consistently observed in independent experiments and clinical data. Together, this study introduces a generalizable approach for investigating cellular evolution in a time- and clone-resolved manner, and highlights time-dependent molecular programs that underlie stress responses.

overall_design: Unique DNA barcodes were introduced into cancer cells via lentiviral transduction. After a brief period of expansion, we split the population into three arms and exposed each to a distinct treatment: cobalt chloride (CoCl2), which simulates hypoxic signaling; a combination of dabrafenib and trametinib, targeted therapies for BRAF-mutant melanoma; or cisplatin, a DNA-damaging chemotherapeutic. We collected cells at three time points to capture the trajectory of treatment response: day 0 (untreated baseline), day 10 (short-term survivors on treatment), and week 5 (long-term persisting cells). At each time point, we performed multiomic profiling with the 10X Multiome platform to jointly measure transcriptomic state, chromatin accessibility, and clonal identity through targeted amplification and sequencing of the integrated barcodes.

first: Dylan

last: Shaff

first: Sydney

middle: M

last: Shaffer


title: RAD21 reshapes H3K4me3 modification to drive lung adenocarcinoma progression by activating ERK1/2 signal [ChIP-seq]

city: Beijing

first: Chu

last: Xiao

state: Beijing

address: Nanli panjiayuan, Chaoyang District, Beijing

department: Thoracic Surgery

institute: Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College

summary: RAD21, the core unit of the cohesin complex, is involved in the transcriptional regulation of cells. The high-frequency copy number amplification of RAD21 is general in multiple cancer types and positively correlated with high mRNA levels, such as lung adenocarcinoma (LUAD). However, its role in LUAD is unclear. We found that RAD21 is a poor prognostic factor for LUAD patients. Functionally, depletion of RAD21 using shRNAs impairs LUAD cell proliferation and metastatic ability. Transcriptome sequencing reveals that RAD21 loss inactivates epithelial-mesenchymal transition (EMT) and MAPK signaling pathways in LUAD cell lines, which can be rescued by exogenous RAD21. Pharmacologic ERK1/2 inhibition with specific inhibitor ulixertinib exhibits superior repression on the RAD21-driven high metastatic ability. Clinical exploration using specimens from LUAD patients further validates the correlation between RAD21 and the ERK1/2-EMT process. Taken together, our work reveals the regulatory relationship between RAD21-mediated epigenetic regulation and metastasis signaling cascade in LUAD. The favorable therapeutic efficacy of ulixertinib in mouse models with lung metastasis provides a therapeutic rationale for ERK1/2 inhibition in RAD21-high LUAD.

overall_design: ChIP-seq profiling of RAD21 and H3K4me3 was performed on: (1) RAD21-knockdown A549 cells (A549_shRAD21) generated via lentiviral vectors of RAD21-targeting shRNA; (2) Control A549 cells transfected with empty vectors (A549_shNC).

first: Tao

last: Fan

first: Chunxiang

last: Li

last: He


title: Analysis of gene expression in irradiated intratumoral mouse T cells

city: Chicago

first: CRI

last: Bioinformatics

state: IL

address: 5801 S. Ellis Ave.

institute: University of Chicago

summary: We aimed to identify promoters activated by ionizing radiation (IR) specifically in T cells by analyzing gene expression in intratumoral mouse T cells after in vivo IR treatment . Whole-body irradiation (WBI) was used instead of local IR to avoid contamination by non-irradiated T cells newly infiltrating from the periphery. MC38 tumor-bearing B6 mice received 1 or 5 Gy WBI, and differential gene expression was analyzed in FACS-sorted T cells from tumors at 1 h, 6 h, or 24 h post-irradiation, vs. T cells sorted from non-irradiated tumors.

overall_design: RNA expression by Illumina Microarray in mouse T cells sorted from MC38 tumors at 1,6,24 h after the tumor-bearing mice received 1 Gy or 5 Gy of whole body irradiation, or no radiation.

first: Elham

last: Masoumi

first: Paulina

last: Walczak

first: Takemasa

last: Tsuji

first: Edurne

last: Luque

first: Agnes Julia

last: Bilecz

first: Junko

last: Matsuzaki

first: Christian

last: Fernandez

first: Kunle

last: Odunsi

first: Ralph

last: Weichselbaum

first: Ainhoa

last: Arina


title: RAD21 reshapes H3K4me3 modification to drive lung adenocarcinoma progression by activating ERK1/2 signal

overall_design: RNA-seq profiling was performed on: (1) RAD21-knockdown LUAD cells (A549_shRAD21, H358_shRAD21) generated via lentiviral vectors of RAD21-targeting shRNA; (2) RAD21-overexpressing A549 cells (A549_RAD21OE); (3) Control cells transfected with empty vectors (A549_shNC, H358_shNC, A549_EV). Triplicate RNA-seq libraries were constructed for each cell line.

first: Jie


title: Integration of cell-type resolved spatial proteomics and transcriptomics reveals novel mechanisms in early ovarian cancer

summary: High-grade serous carcinoma (HGSC) is the most common ovarian cancer subtype, typically diagnosed at late stages with poor prognosis. Understanding early molecular events driving HGSC progression is crucial for early-stage cancer detection and development of effective treatment stategies. We performed and integrated spatial cell-type resolved proteomics and paired transcriptomics across 25 women with precursor lesions of the fallopian tube and/or HGSC. Epithelial cell signatures revealed early activation of SUMOylation machinery, increased ATR and Wnt signaling, and enhanced MHC-I antigen presentation along the disease trajectory. The stroma exhibited extracellular matrix (ECM) remodeling and interferon-mediated inflammation. Serous tubal intraepithelial carcinomas (STICs) in cancer patients contained a pro-coagulative signature and reduced APOA1/2 compared to STICs in individuals without cancer. Functional studies confirmed the role of epithelial-derived TRIP13 and SUMOylation, and cancer-associated fibroblast-derived SULF1 and BGN in HGSC progression. These findings provide unique molecular insights into HGSC pathogenesis and identify potential new therapeutic targets for intervention.

overall_design:
ROIs of epithelial and stromal compartments of fallopian tubes and omentum were analyzed with the Nanostring GeoMx platform. The cohort included tissue from individuals with dysplastic lesions of the fallopian tubes (p53 signatures, Serous Tubal Intraepithelial Lesions or STILs and Serous Tubal Intraepithelial Carcinoma or STICs) with or without concurrent HGSC and omental metastasis.

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Submitter states that missing raw files are due to file loss.
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first: Andreas

last: Metousis

first: Hilary

middle: A

last: Kenny

first: Aasa

last: Shimizu

first: Lisa

last: Schweizer

first: Shani

last: Ben-moshe

first: Agnes

first: Rahul

last: Krishnan

first: Jingwen

last: Zhang

first: Isabel

last: Alcazar

first: Lucy

last: Kelliher

first: Mallika

last: Ravi

first: Tejas

last: Samantarey

first: Sabrina

last: Richter

first: Yan

first: Jiying

last: Wang

first: Sophia

last: Steigerwald

first: Fabian

middle: J

last: Theis

first: Florian

last: Rosenberger

first: Thierry

last: Nordmann

first: Seiko

middle: D

last: Yamada

first: Ricardo

last: Lastra

first: Matthias

last: Mann

first: Ernst

last: Lengyel


title: ZBP1 Senses Splicing Aberration by Z-RNA for Cell Death

first: Boxin

address: 良渚实验室1369号

institute: 良渚实验室

summary: RNA splicing, a highly regulated process performed by the spliceosome, is crucial for eukaryotic gene expression and cellular function. Numerous cellular stresses including oncogenic insults dysregulate RNA splicing, often provoking inflammatory responses and cell death. However, the molecular signals produced by spliceosome aberration and how cell sensed and responded to them remain elusive. Here we show that spliceosome inhibition induces the widespread formation of unique, left-handed nucleic acids, Z-form dsRNA that were predominantly derived from transcripts of exonic and intronic regions of mis-spliced RNA in the nucleus. Then those Z-RNA was translocated into cytoplasm in a RanGTP-dependent manner. Sensing of the accumulation of Z-RNA by the host sensor ZBP1 triggered cell death, mainly for RIPK3-MLKL dependent necroptosis. Collectively, these findings delineate a previously uncharacterized mechanism in which Z-NA sensing by ZBP1 responds to global aberrations of RNA splicing to trigger inflammatory cell death.

overall_design: Cross-link immunoprecipitation (CLIP) of MEF cells were referred to Wang et al22. Briefly, Zbp1 KO MEF cells reconstituted with 3*Flag-ZBP1-WT or 3*Flag-ZBP1-ZαDM were treated with or without PladB for 8 h. After treatment, the cells were overlaid with 1.5 mL PBS and crosslinked with 150 mJ/cm2 (254 nm) (CX-2000, analytic Jena). Cells were lysed in 1 ml RIPA buffer (50 mM Tris-HCl pH 8.0, 150 mM NaCl, 1% NP-40, 0.1% SDS, 0.5% deoxycholate, 2 mM EDTA) for 30 min, and then 12.5 μL RNasin Plus (Promega) was added, followed by centrifuging at 12,000 rpm for 15 min. The clean cell lysates were incubated with anti-Flag agarose beads (HUABIO, HAK21024) overnight at 4℃. Next day, the beads were washed twice with high-salt wash buffer (50 mM Tris-HCl pH 8.0, 500 mM NaCl, 1% NP-40, 0.1% SDS, 0.5% deoxycholate) and once with RIPA buffer. After wash, beads were resuspended in 100 μl of reverse buffer (100 mM Tris-HCl pH8.0, 10 mM EDTA, 1% SDS, 100 mM DTT) with 10 μl 5M NaCl and 50 μg proteinase K. Beads were then incubated in a heating block at 42 °C for 1 h to digest peptide, followed by 65 °C for 1.5 h to reverse the crosslink. The immunoprecipitated RNA was extracted with the TRIzol method, and purified RNA was used for RNA sequencing. Libraries were quantified using a Quant-iT PicoGreen ds DNA assay (Thermo Fisher Scientific) or by low-pass sequencing with a MiSeq nano kit (Illumina). Paired-end 150 cycle sequencing was performed on a NovaSeq 6000 (Illumina).

first: Yuenan

last: Zhou


title: A cross-species single-cell landscape of the vertebrate olfactory epithelium

city: Wuhan

first: Yang

last: Liu

address: No. 7 Donghu South Road, Wuchang District, Wuhan, Hubei Province

institute: Institute of Hydrobiology, Chinese Academy of Sciences

summary: We performed single-cell transcriptome sequencing of the olfactory epithelium of C57BL/6J strain mouse. We also studied the cell types and adaptive evolution of the olfactory epithelium among zebrafish, mouse and human

overall_design: ScRNA-seq profiling of wildtype C57BL/6J mouse olfactory epithelium tissue

first: Wenjun

last: Chen

first: Zufa

last: Ding

first: Dan

last: Yu

first: Lingling

last: Zheng

first: Yuhan

last: Niu

first: Haifeng

last: Jiang

first: Shunping

last: He

first: Liandong

last: Yang


title: Transcriptome analysis of three Bacillus cereus strains comparing non-conditioned growth medium (nk) with conditioned (k; pre-incubated with CaCo-2 cells), accomplished by RNA sequencing

city: Hannover

first: Nadja

last: Jessberger

address: Bischofsholer Damm 15

department: Institute for Food Quality and Food Safety

country: Germany

institute: University of Veterinary Medicine Hannover, Foundation

summary: Enteropathogenic Bacillus cereus can cause toxico-infections manifesting in diarrhea and abdominal pain. It is still not completely understood why individual isolates differ in enterotoxin production and pathogenicity, and which signals trigger toxicity in the host environment. The overall transcriptional response of three formerly well-characterized strains to a simulated intestinal environment was assessed in the present study. Two high toxic strains F837/76 = MHI 1505 and NVH 0075-95 = MHI 3053, and one low toxic strain RIVM BC90 = MHI 3178 were investigated.

overall_design: Growth conditions: RPMI 1640 medium, no FCS, 2 % casein hydrolysate and a total glucose content of 1 %. The media were used directly (non-conditioned; nk) or after 22 h pre-incubation with CaCo-2 cells (conditioned; k) and subsequent filtering through a 0.2 µm filter. 50 ml of these media were inoculated with the bacterial pre-culture to a start OD600 of 0.05. Incubation took place statically in 80 cm2 culture flasks in a humidified incubator at 37 °C and 7 % CO2. After 3h, samples for RNA preparation were taken.


title: Small activating RNA AW1-51 (CEBPA-51) elicits targeted DNA demethylation to promote gene activation [RNA-seq]

city: Boston

first: Annalisa

last: Di Ruscio

state: Massachusetts

address: 3 Blackfan Circle

institute: Harvard Medical School Initiative for RNA Medicine

summary: Small activating RNAs (saRNAs), are short double-stranded RNAs designed to upregulate transcription of target genes. By this virtue, they can be used to restore expression of genes frequently silenced in cancer. AW1-51 (also referred to as CEBPA-51), the first saRNA therapeutic to enter clinical evaluation, has demonstrated biological activity and safety in Phase II trials for hepatocellular carcinoma, both as monotherapy and in combination with sorafenib, and in Phase 1a/1b in combination with pembrolizumab for patients with advanced solid tumors. It targets the master regulator CCAAT enhancer-binding protein alpha (CEBPA), abnormally silenced by DNA methylation in a wide range of hematological and not hematological malignancies. However, the molecular events enabling this mechanism are only partially elucidated. In this study, we uncovered the molecular basis for AW1-51-induced transcriptional reactivation of CEBPA demonstrating that by directly promoting DNA demethylation of CEBPA promoter restores CEBPA expression, protein synthesis, and consequently cell differentiation. These findings unveil AW1-51 as a prototype for RNA-based precision medicine enabling conditional expression of CEBPA in diseases characterized by aberrant gene silencing and extending its potential therapeutic impact beyond cancer.

overall_design: RNA-seq of  K562 and A549 cell lines after AW1-51 saRNA or a non targetting saRNA (NC) 72h after treatment

first: Lucrezia

last: Rinaldi

first: Juan Rodrigo

last: Patiño-Mercau

first: Giulia

last: Gaggi


title: Long read RNA sequencing reveals a new long non-coding RNA that regulates somatic cell reprogramming and pluripotency

city: Quebec City

first: Samer

last: Hussein

state: Quebec

address: 9 rue Mcmahon

department: Departement of medecine

country: Canada

institute: CHU de Québec - Université Laval

summary: The recent development of long-read RNA sequencing (lrRNAseq) technologies has paved the way to the exploration of RNA isoform diversity and its relevance to better understand the gene regulatory network that sustains cell fate and plasticity. However, drawing conclusions regarding the functionality of these newly identified isoforms is still very scarce. Here, we devised a very efficient system to reprogram cells towards an induced pluripotent cell state and leveraged the strengths of lrRNAseq in order to study the isoform diversity of reprogramming. This strategy enabled us to identify differential isoforms throughout the reprogramming process, with a pressure on novel non-coding isoforms to be regulated. More specifically, we highlight a new long non-coding RNA (lncRNA) whose isoform switch during reprogramming enhances the conversion of cells’ identity towards pluripotency. Conversely, we show that knocking-down this lncRNA in mouse embryonic stem cells hinders the maintenance of a pluripotent state and primes the cells for differentiation. Together, our study provides a comprehensive resource to study full-length isoform regulation and mechanisms at stake during reprogramming, but more importantly it demonstrates the power of lrRNAseq to identify functionally relevant gene isoforms in the context of pluripotency.

overall_design: We performed Oxford nanopore technologies long-read RNA sequencing of mouse reprogramming timelines from Neural progenitor cells (NPCs) to induced pluripotent stem cells (iPSCs). Two separate reprogramming methods were used (OKMS and OKS reprogramming). Time points for both methods include days (D) 0 (NPCs-OKS/OKMS), 2, 4, 6, 10, 14 and 20. Control wild-type (WT) NPC and Embryonic Stem Cells (ESC) lines as well as WT NPCs after 2 days in FBS-LIF medium supplemented with doxycycline are also included. ESC lines used to generate all cell lines present in this submission are either R1 (RRID: CVCL_2167) or Oct4-GFP (R1 ESCs harboring a GFP reporter gene under the control of the Oct4 gene promoter from Viswanathan et al., Biotechnology and Bioengineering 2003). Sequencing was performed with two approaches : a Direct cDNA sequencing approach using kit SQK-DCS109 followed by sequencing on R9.4.1 MinION flowcells, and a PCR cDNA sequencing approach using kit SQK-NBD114.24 followed by sequencing on R10.4.1 flowcells.

first: Victoire

last: Fort

first: Gabriel

last: Khelifi

first: Valérie

last: Watters

first: Victoria

last: Micha

first: Mitra

last: Cowan

first: Nobuko

last: Honma

first: Yojiro

last: Yamanaka


title: Efficacy of Neoadjuvant Chemotherapy Combined with Anti-PD-1 Monoclonal   Antibody in Locally Advanced Resectable Oral Squamous Cell Carcinoma: A Single-Arm Phase II Clinical Trial

first: Yi

last: Xu

address: Qiutao Street 166

summary: Background: Neoadjuvant chemotherapy (NAC) combined with anti-PD-1 antibody is a potential treatment option for resectable oral squamous cell carcinoma (OSCC). It is important to be able to predict the effectiveness of NAC combined with anti-PD-1 antibody in clinical practice. Methods: In total, 30 patients with locally advanced, resectable OSCC (T3–T4, N0–N2, M0) who received two cycles of neoadjuvant chemoimmunotherapy (NACI) consisting of albumin-bound paclitaxel (250 mg/m2) and cisplatin (75 mg/m2) with the anti-PD-1 monoclonal antibody sintilimab (200 mg) were enrolled in this single-arm phase II trial. Twenty-three patients underwent surgical resection and seven received nonsurgical therapy. The primary and secondary end points were pathological response and clinical response, respectively. We utilized artificial intelligence (AI)-powered nuclear segmentation and classification to preliminarily assess the level of inflammatory cell infiltration in patients before NACI. Transcriptome RNA sequencing (RNA-seq) analysis was used to identify differentially expressed genes and immune cell subtypes between patients with and without major pathological response (MPR). Results: The MPR rate was 39.1% among 23 patients who underwent surgical resection. The objective response rate (ORR) was 43.3%. The primary location of OSCC was associated with the pathological response. There were no significant differences in the overall level of inflammatory cell infiltration between patients with and without MPR. Immune infiltration analysis of RNA-seq data revealed significant differences in the proportions of M1- and M2-type macrophages between the MPR and non-MPR groups. Conclusions: This study reveals the potential efficacy of NAC combined with anti-PD-1 antibody in treating OSCC patients, with acceptable side effects. This strategy can effectively inhibit clinical progression of locally advanced OSCC. The pathological response may be related to the degree of M1 macrophage infiltration.

overall_design: The primary end point was the pathological response rate determined according to H&E-stained slides obtained during surgery by an experienced pathologist. First, the histologically recognizable tumor bed area was identified, defined as the region within the excised specimen occupied by viable tumor cells, along with areas showing necrosis, keratin fragments, scar formation, fibrosis, and multinucleated giant cell reactions. Then the proportion of viable tumor cells within the tumor bed area was subsequently quantified as a percentage. Patients were classified according to the response categories proposed by Tetzlaff12. We defined patients with MPR and pCR as the MPR group, while those with pPR and NPR were defined as the non-MPR group.

first: Xiaotong

first: Huiyong

last: Zhu


title: Microgravity suppresses oral squamous cell carcinoma growth through Piezo1-mediated regulation of calcium ion homeostasis and the autophagy pathway

summary: Background: Oral squamous cell carcinoma (OSCC) is the most common form of oral cancer, with metastasis significantly contributing to its poor prognosis. Emerging research suggests that microgravity may exert anti-tumor effects by inducing cell death, although the precise mechanisms remain unclear. Methods: Rotary Cell Culture System (RCCS) was used to simulate microgravity, allowing observation of its effects on the proliferation and migration abilities of tumor cells. Key genes and pathways influenced by simulated microgravity were identified using RNA sequencing (RNA-seq). In the tongue load-bearing tumor mouse model, we utilized a hindlimb unloading (HU) method to simulate microgravity and investigate its impact on tumor growth, as well as to validate the involvement of identified key genes and pathways. Results: Simulated microgravity induced significant morphological changes in OSCC cells, leading to the formation of multicellular spheroids and altering their biological behavior. RNA sequencing identified PIEZO1 as a key mechanosensitive gene upregulated under microgravity, along with the activation of autophagy-related pathways. In vivo experiments using a tongue load-bearing mouse model demonstrated that simulated microgravity suppressed tumor growth, which was associated with enhanced autophagy and disrupted calcium homeostasis. Piezo1 inhibition partially reversed these effects, confirming its critical role in microgravity-induced OSCC suppression. Conclusion: Simulated microgravity suppresses OSCC growth through Piezo1-mediated calcium dysregulation and enhanced mitophagy. Inhibiting Piezo1 reverses these effects, suggesting its potential as a therapeutic target. This study highlights microgravity-based approaches as promising strategies for OSCC treatment.

overall_design: Within this study, we aim to investigate the significant target genes and pathways influenced by a microgravity environment, as constructed by the Rotary Cell Culture System (RCCS), on the biological behavior of the human oral squamous cell carcinoma cell line, HSC-3. Our objective is to elucidate how microgravity alters the cancer cell phenotype, including proliferation, differentiation, migration, and invasion, thereby identifying potential molecular mechanisms that could be targeted for therapeutic interventions.


title: Copy Number Gains of VPS72 Drive De Novo Lipogenesis and Hepatocarcinogenesis via ATF3/mTORC1/SREBP1 Axis [RNA-seq]

city: Hong Kong

first: Qinglin

last: Zhang

address: Room 7N07, Kadoorie Biological Sciences Building, The University of Hong Kong, Sai Ying Pun

institute: The University of Hong Kong

summary: Hepatocellular carcinoma (HCC) is the predominant form of primary liver  cancer and a major contributor to cancer-related mortality globally. Central to  its pathogenesis is the dysregulation of lipid metabolism in hepatocytes,  leading to abnormal lipid accumulation. Our bioinformatics analysis has  identified the histone acetyltransferase complex subunit VPS72 as being  associated with HCC, yet the precise molecular mechanisms through which  VPS72 contributes to hepatocarcinogenesis remain poorly understood. Our  analysis of extensive HCC patient cohorts identifies a significant proportion  with VPS72 copy number gains, which are strongly linked to adverse  prognostic outcomes. By integrating RNA-Seq, ChIP-Seq, ATAC-seq, and  experimental validation, we show that VPS72 overexpression activates  mTORC1signaling, subsequently promoting lipid synthesis and driving HCC  progression. We further uncover that VPS72 modulates the epigenetic  landscape by enhancing DNA methylation at the ATF3 promoter, resulting in  ATF3 repression and subsequent activation of mTORC1. This study elucidates  a novel regulatory axis that links dysregulated lipid metabolism with HCC  progression, highlighting potential epigenetic and metabolic targets for  therapeutic intervention.

overall_design: RNA-Seq profiling of VPS72 overexpression Huh7 cell line versus Flag-tagged cell line (negative control) consctructed by lentivirus infection for 24h

first: Yunxing

last: Huang

first: Yin

last: Tong


title: Chemical tracking of DNMT1-specific activity during mESC ground state transition using WGBS

city: Vilnius

first: Kotryna

last: Kvederaviciute

address: Sauletekio av. 7

department: Life Sciences Center

country: Lithuania

institute: Vilnius University

type: Methylation profiling by high throughput sequencing

summary: The enzymatic methylation of cytosine to 5-methylcytosine in DNA is a crucial epigenetic process implicated in mammalian development and disease. DNA methylation results from the collective performance of three AdoMet-dependent DNA methyltransferases (DNMTs), whose catalytic interplay and temporal dynamics remain poorly elucidated. In this study, we generated a Dnmt1 knock-in mESC line with a N1580A mutation at a single allele, while retaining a functioning wild-type protein. The heterozygous DNMT1 N1580A knock-in line, together with the DNMT1 wild-type, homozygous N1580A knock-in, and knockout mouse embryonic stem cells were subsequently assessed for genome-wide CpG methylation levels using whole-genome bisulfite sequencing. Next, monoallelic DNMT1 N1580A KI cells underwent electroporation using the synthetic cofactor analogue Ado-6-azide and genomic targets unique to DNMT1 were subsequently assessed with Dnmt-TOP-seq. Finally, a comprehensive examination of DNMT1-specific events during mESC ground state transition was conducted. Taken together, the present study paves the way for in vivo monitoring of DNMT1 activity in living tissues in a variety of biological contexts.

overall_design: Genome-wide evaluation of DNA methylation levels in mouse embryonic stem cells. Global DNA methylation was analyzed in E14TG2a cells bearing the wild-type, heterozygous or homozygous Dnmt1 N1580A knock-in substitution, or Dnmt1 knock-out using whole genome bisulfite sequencing

first: Vaidotas

last: Stankevicius

first: Saulius

last: Klimasauskas


title: Chemical tracking of DNMT1-specific activity during mESC ground state transition using Dnmt-seq

overall_design: Genome-wide tracking of DNA methyltransferase Dnmt1 action in mouse embryonic stem cells. Mouse Dnmt1-directed DNA modifications were analyzed in E14TG2a cells bearing the heterozygous Dnmt1 N1580A knock-in substitution and during mESC ground state transition from naïve to “primed” cells following the delivery of Ado-6-azide by electroporation. Wild-type Dnmt1 cells were used as a control. Heterozygous mutant analysis experiments were carried out in triplicates, cell state transition analysis was carried out in duplicates.


title: High-fat diet triggers chemerin-dependent immune reprogramming that exacerbates acute kidney injury [scRNA-seq]

city: Shanghai

first: Bo

last: Deng

address: 639 Zhizaoju Road

department: Division of Nephrology

institute: Shanghai Ninth People's Hospital, School of Medicine, Shanghai Jiaotong University

summary: Obesity presents a known risk factor for acute kidney injury (AKI), but the precise mechanism underlying this phenomenon remains incompletely elucidated. In this study, we demonstrated that short-term high-fat diet (HFD) feeding aggravated kidney injury in AKI mice. Through multi-omics analysis, we identified chemerin (encoded by Rarres2) as a distinctive renal injury-related adipokine enriched in AKI tubular epithelial cells (TECs), particularly following exposure to HFD. Elevated chemerin levels were confirmed in the serum and kidney biopsy samples of AKI patients with obesity, exhibiting a negative correlation with renal function. Rarres2-/- mice were protected from HFD-induced vulnerability toward AKI as well as different types of AKI after standard diet, emphasizing its direct effect on AKI independent of metabolic factors. Mechanism investigation showed the receptor of chemerin-chemerin chemokine-like receptor 1 (CMKLR1) was expressed on renal mononuclear phagocytic cells (MPCs). By single-cell RNA sequencing (scRNA-seq) analysis, unique Cmklr1hi clusters were identified in renal MPCs following AKI, exhibiting enhanced chemotaxis and pro-inflammatory capacity. Functionally, chemerin acted as a chemoattractant to enhance the chemotaxis of Cmklr1hi MPCs. Finally, supplementation of MPCs-derived cytokines reversed kidney injury in Rarres2-/- mice confirming the role of chemerin-CMKLR1 axis in promoting inflammation and kidney damage. Collectively, we identified chemerin as a specific inflammatory and metabolic target that functions through potent pro-inflammatory Cmklr1hi macrophages. Our study suggests that targeting the chemerin-CMKLR1 axis could be a promising therapeutic strategy for AKI patients, especially those with metabolic syndrome.

overall_design: We performed scRNA-seq of single cell suspension from cisplatin-treated kidneys.

first: Zhenkai

last: Wu

first: Shuai

last: Ma

first: Feng

last: Ding


title: PHLDA2 promotes breast cancer metastasis by increasing extracellular matrix deposition and vascular permeability

city: Irvine

first: Hannah

last: Savage

address: 839 Health Sciences Road

institute: University of California Irvine

summary: There is a critical need to define drivers of metastasis in order to identify novel drug targets and improve patient prognosis. These are particularly necessary for receptor negative Triple Negative Breast Cancer (TNBC) for which there are no targeted therapy options. Our previous work identified a potential breast cancer metastasis promoting gene known as Pleckstrin-Homology like Protein 2, PHLDA2. In this study, we define the novel role of PHLDA2 as a pro-metastatic gene in TNBC and investigate its mechanism. Bulk sequencing of TNBC cells overexpressing PHLDA2 reveal upregulation of genes related to cell migration, extracellular matrix deposition, and vascular permeability. We validate these bulk sequencing results using in vitro and in situ assays.

overall_design: 120,000 HCI010 GFP or HCI010 PHLDA2-GFP PDX cells were injected into mammary fat pads to allow tumors to form. Three mice were injected per group. After 1.5 months, tumors were excised from mice and digested into single cell suspension. Fluorescence-activated cell sorting (FACS) was performed to isolate GFP+ tumor cells. Cells were spun down and processed for bulk RNA sequencing.

first: Paige

middle: V

last: Halas

first: Tatyana

last: Lev

first: Angela

middle: L

last: Samy

first: Stephanie

last: Hachey

first: Connie

last: Chan

first: Radhika

last: Domadia

first: Iana

last: Lin

first: Sharmila

last: Mallya

first: Jessica

last: Gonzalez

first: Christopher

last: Hughes

first: Dennis

first: Devon

last: Lawson


title: Chemical tracking of DNMT1-specific activity during mESC ground state transition using RRBS

first: Kotryna

last: Kvederaviciute

overall_design: Genome-wide evaluation of DNA methylation levels in mouse embryonic stem cells. Global DNA methylation was analyzed in E14TG2a cells bearing the heterozygous or homozygous Dnmt1 N1580A knock-in substitution or in E14TG2a cells bearing the heterozygous Dnmt1 N1580A knock-in substitution during mESC ground state transition from naïve to “primed” cells using RRBS.

first: Vaidotas

last: Stankevicius

first: Saulius

last: Klimasauskas


title: Role of Cancer-Associated Fibroblasts in Prognostic Stratification of Advanced-Stage Gastric Cancer through Interacting with Endothelial and Malignant Epithelial Cells [Cell Lines RNA-seq]

city: Chengdu

first: Heng

last: Xu

state: Sichuan

address: 17#, section 3, South Renmin Road

institute: Sichuan University

summary: Patients with advanced gastric cancers (AGCs) would experience poor prognosis, lacking investigation on comprehensive ecosystem profile and specific prognostic factors. Here, we conducted patient stratification based on unsupervised clustering of transcriptomic profile of 108 normal/tumor AGC pairs and integrated single-cell RNA transcriptome profile of 116 gastric cancer/normal samples, revealing the heterogeneity of AGC, which can be stratified into distinct AGC-related signature (AGCRS)-based patient groups with different prognosis. AGCRS scores are over-presented in cancer-associated fibroblasts (CAF) and increase in metastasis-enriched subtypes (e.g., myofibroblastic CAF). More prolific cell-cell communications were observed between CAF and metastasis-enriched epithelial/endothelial through collagen-related interactions. Experimentally, CAF conditional-medium can enhance the tube formation of endothelial cells and HOXC-AS2-related migration ability of gastric cancer cells. Particularly, HOX-AS2 can facilitate the nucleus translocation of YBX1 through direct binding in cytoplasm and induce the epithelial-mesenchymal transition. Our findings highlight the potential prognostic role of AGC heterogeneity induced by CAF-related communications.

overall_design: RNA-seq of two human gastric cancer cell lines (BGC-823, HGC-27).


title: Spliceosome inhibition generates Z-form RNAs to active ZBP1-mediated cell death

first: Boxin

last: Zhang

summary: RNA splicing, a highly regulated process performed by the spliceosome, is crucial for eukaryotic gene expression and cellular function. Numerous cellular stresses including oncogenic insults dysregulate RNA splicing, often provoking inflammatory responses and cell death. However, the generalized mechanisms by which cell sensed and respond to splicing dysregulation remain elusive. Here we show that spliceosome inhibition induces the widespread formation of unique, left-handed nucleic acids, Z-form nucleic acids (Z-NAs) from the nucleus. These Z-NAs were double-stranded RNA (dsRNA) that were predominantly derived from transcripts of mis-spliced intronic RNA. Spliceosome inhibition induced the egress of these Z-RNA from the nucleus to the cytoplasm in an active manner. Sensing of the accumulation of Z-RNA in the cytosol by the host sensor ZBP1 triggered cell death, mainly for RIPK3-MLKL dependent necroptosis. Collectively, these findings delineate a previously uncharacterized mechanism in which Z-NA sensing by ZBP1 responds to global aberrations of RNA splicing to trigger inflammatory cell death.

overall_design: ZBP1 was pull down by corresponding antibodies.The immunoprecipitated RNA was purified for RNA sequencing.

first: Yuenan

last: Zhou


title: Circulating miRNAs as Biomarkers for Arsenic-Induced Hepatotoxicity and Systemic Health Impacts in a Rural Pakistani Population

city: Maastricht

first: Julian

last: Krauskopf

address: Universiteitssingel 50

country: Netherlands

institute: Maastricht University

type: Non-coding RNA profiling by high throughput sequencing

summary: Arsenic (As) exposure through contaminated drinking water poses significant health risks, particularly in rural populations with limited access to clean water. This study investigated the impact of chronic As exposure on circulating microRNA (miRNA) profiles as potential biomarkers for organ injury, including hepatotoxicity. Plasma samples from 57 individuals in a rural population of Punjab, Pakistan, were collected and stratified into low, medium, and high As exposure groups based on urinary As levels. Small RNA sequencing identified 15 miRNAs associated with As exposure. Among them, three liver-enriched miRNAs—miR-122-3p, miR-194-5p, and miR-192-5p—were significantly negatively correlated with urinary As levels, suggesting their role in As-induced liver toxicity. Additionally, brain-enriched miRNAs, including miR-92b-3p, were positively associated with As exposure, while miR-376b-3p was negatively associated, indicating potential neurological effects. Pathway enrichment analysis revealed significant associations between these miRNAs and key biological pathways, including oxidative stress, lipid metabolism, and inflammatory responses. Our findings underscore the potential of circulating miRNAs in non-invasive biomonitoring of environmental toxin exposure and provide mechanistic insights into As-induced health effects, including carcinogenic risks and neurological impacts.

overall_design: To investigate the effects of arsenic exposure on miRNA expression, plasma samples from 55 individuals were collected and stratified into low (0-50 µg/g creatinine), medium (51-100 µg/g creatinine), and high (>101 µg/g creatinine) As exposure groups based on urinary arsenic levels. Small RNA sequencing was performed using Illumina NovaSeq 6000 to identify differentially expressed miRNAs associated with arsenic exposure. The study employed elastic net regression and linear mixed-effect models (LMM) to assess the association between miRNA expression and log2-transformed urinary As levels, accounting for batch effects and significant covariates selected based on univariate analysis.

first: Jacco

last: Briede


title: Mechanism of action of sodium propionate on the growth inhibition of Malassezia restricta.

city: Singapore

first: Viduthalai

last: Rasheedkhan Regina

address: 60 Nanyang Drive

country: Singapore

institute: Singapore Centre for Environmental Life Sciences Engineering

summary: Malassezia restricta is a human skin associated fungus that is associated with scalp conditions such as dandruff and seborrheic dermatitis. The relative abundance of M. rectricta to Cutibacterium acnes is significantly higher under in diseased scalp condtions, when compared to healthy scalp. We have identified propionate, a short chain fatty acid produced by C. acnes, that can inhibit the growth of M. restricta. In this study, we treated M. resticta with sodium propionate and studied the transcriptome at different time points (0.5, 1, 3, 6, 12, and 24 hours) to understand the mechanism of action of the short chain fatty acid. We found that propionate induces iron-starvation response in M. restricta, leading to cell death.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Malassezia restrcta with and without sodium propionate teratment.

first: YikYan

last: Chong

first: Xianghui

last: Liu

first: Tarun

last: Chopra

first: Rohan

last: Williams

first: Scott

last: Rice


title: Role of Cancer-Associated Fibroblasts in Prognostic Stratification of Advanced-Stage Gastric Cancer through Interacting with Endothelial and Malignant Epithelial Cells [AGC RNA-seq]

overall_design:
We performed a whole transcriptome sequencing study on paired tumor and normal tissues from AGC patients, delineating two RNA signature groups based on their distinct RNA expression pattern.
Total RNA was extracted from 108 paired tumor and normal tissue samples using the Qiagen AllPrep DNA/RNA Mini Kit (Cat. No. 80204, Qiagen, Germany) following the manufacturer’s protocol.

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Submitter states that missing raw data are being made available in the Genome Sequence Archive (GSA) for human.
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title: Large scale manufacture of human gallbladder epithelial cells to generate hepatocytes via chemical defined approach for clinical utility

first: Chen

last: fei

address: Xiangyin road

institute: The Second Military Medical University

summary: Generation of liver stem cells hold a great promise for treating liver disease or drug screening. We established a chemical defined and xeno-free approach to manufactured large-scale human gallbladder epithelial cells (hGBECS) in GMP condition for clinical utility. The cell products were characterization of growth ability, phenotype, frozen-thaw viability, genetic stability, bio-safety assessments for in vitro tests, and tumorigenicity assessments, acute toxicity experiments for in vivo tests. We then established a protocol to generate functional hepatocytes from hGBECS (hGBECS-dHEPs). The derived hepatocytes exhibited typical liver function: glycogen storage, lipid synthesis, uptake ability, Albumin secretion, urea production and drug metabolism. Also, these cells were applied for tests of liver toxic drugs and anticancer drugs. We further assessed these derived hepatocytes for Cu2+ transportation and alcohol metabolism. Transplantation of these cells in vivo could rescue mice from liver failure. We provide these large-scale, rapid, safe source of functional hepatocytes from hGBECS to serve as a bio-bank for clinical application of treating liver disease.

overall_design: Human gallbladder tissue were obtained from donor hospital. Cells were isolated and cultured in a established, chemical defined medium and named as hGBECs. After medium modification, hGBECs were differentiated into hepatocytes. Hepatic function tests were performed to prove these cells with typical liver function.

first: Fei

last: Chen

first: Minjun

last: Wang

first: Junling

last: Gao

first: Zijun


title: MAD2L1 supports MYC-driven liver carcinogenesis in mice and predicts poor prognosis in human hepatocarcinoma

city: Guangzhou

first: Xinjun

last: Lu

state: Guangdong

address: #33 Yingfeng Rd

institute: SYSU

summary: Mitotic arrest deficient 2 like 1 (MAD2L1) is a component of the mitotic spindle assembly checkpoint implicated in cancer cell proliferation and tumorigenesis. The functional role of MAD2L1 in hepatocellular carcinoma (HCC) has not been adequately investigated, especially in vivo. In the current manuscript, we sought to address the function of MAD2L1 in hepatocarcinogenesis. We found that MAD2L1 expression is upregulated in human HCCs, where its expression is associated with higher aggressive tumor grade, elevated proliferative activity, and poor prognosis. In human HCC cell lines, silencing of MAD2L1 led to decreased cell growth. RNAseq results demonstrated that silencing of MAD2L1 induces the expression of genes associated with cell cycle, DNA replication, and various cancer-related pathways, supporting the critical role of MAD2L1 during HCC growth and differentiation. In a c-MYC-induced mouse HCC model, we revealed an increased expression of Mad2l1. Furthermore, CRIPSR-based gene silencing of Mad2l1 prevented c-MYC-driven mouse liver development. Altogether, our study indicates that MAD2L1 plays a critical role in hepatocarcinogenesis, and MAD2L1 suppression might be a promising therapeutic approach for treating human HCC.

overall_design: To investigate the function MAD2L1 in hepatocellular carcinoma (HCC), we sought to address the function of MAD2L1 in hepatocarcinogenesis in HCC. The expression of MAD2L1 was knocked down by siRNA.

first: Ya

first: Jiahao

last: Xue

first: Matthias

last: Evert

first: Diego

last: Calvisi

first: Xin

first: Xue


title: Transcriptome analysis of a Sinorhizobium meliloti exoX deletion strain.

city: Stanford

first: Melanie

last: Barnett

state: CA

address: 371 Jane Stanford Way

department: Biology

institute: Stanford University

summary: We characterized the transcriptome of a Sinorhizobium meliloti exoX deletion mutant (MB1129)

platform_organism:
Sinorhizobium meliloti
Medicago truncatula

overall_design: Gene expression profiling of Sinorhizobium meliloti strains was performed using custom Affymetrix GeneChips. Strain MB1129 (exoX deletion marked with a hygromycin resistance cassette), was compared to strain MB1157, which carries hygromycin resistance in the SMc01380-SMc01267 intergenic region (a neutral genomic location).

first: Sharon

middle: R

last: Long


title: A novel variant of the CYCS gene causes thrombocytopenia through deregulated Tumor Necrosis Factor signaling

city: Athens

first: Eleni

last: Katsantoni

state: Attiki

address: Soranou tou Efesiou 4

department: Basic Research Department

country: Greece

institute: Biomedica Research Foundation Academy of Athens

summary: The human CYCS gene encodes for Cytochrome C (Cytc), a small mitochondrial protein with important cellular functions including energy production and apoptosis. Mutations in the CYCS gene have been linked to the development of mild autosomal dominant thrombocytopenia, which is included in the group of inherited thrombocytopenias. Here we report the identification of a novel heterozygous variant of the CYCS gene (c.292T>C (p.Tyr98His)) found in a Greek family with thrombocytopenia. Its functional role in several cellular processes has been examined to delineate the mechanisms underlying the thrombocytopenic phenotype of the patients. The novel variant has been associated with increased megakaryocyte apoptosis, and has led to decreased ATP levels through the reduced superoxidase activity of Cytc in megakaryocytic cells. RNA-Seq has provided information about the effect of the CYCS variant on Tumor Necrosis Factor (TNF) signaling, revealing a dual mechanism through the negative enrichment of TNF via nuclear factor kappa B (NFKB) signaling in combination with the positive enrichment of the TNF via p38 . Downregulation of the TNF via NFKB pathway has led to increased apoptosis observed in megakaryocytic cells, probably through a decrease in anti-apoptotic signaling mechanisms. Furthermore, the positive enrichment of the TNF via p38 signallng has also contributed to the induced apoptosis of megakaryocytic cells caused by the variant and the blockade of megakaryocyte differentiation determined in patient samples. Collectively, this study has revealed a connection between the novel CYCS variant and the thrombocytopenic phenotype through deregulated TNF mediated  pathways in megakaryocytic cells, providing novel therapeutic targets for CYCS-related thrombocytopenias

overall_design:
To model the effect of the novel CYCS (NM_018947.6):c.292T>C (p.Tyr98His) variant in megakaryocytic the (NM_018947.6):c.292T>C (p.Tyr98His) variant has been inserted in Dami cells through Homology-directed repair using the CRISPR-Cas9 System.
Differential gene expression analysis was performed using data obtained from RNA-seq of 3 mutant Dami clones and 4 wild type Dami clones.

first: Eirini

middle: S

last: Fasouli


title: Immunomodulatory mechanisms of Bojungikki-tang through systematic transcriptomic analysis_MatureDC

city: Daejeon

first: Musun

last: Park

address: 1672 Yuseong-daero, Yuseong-gu

institute: Korean Institute of Oriental Medicine

summary: This study aimed to identify the modes of action (MOA) of water extract of Bojungikki-tang (BJIKT) and major four ingredients in immune cell lines. The four main ingredients were designated as Panax ginseng C. A. Meyer, Astragalus mongholicus Bunge, Atractylodes japonica Koidzumi, and Glycyrrhiza uralensis Fisher, which are the main active herbs of BJIKT. The immune-related cell lines used for transcriptome production are Jurkat (CD4+ T cells), RPMI8226 (B cells), NK-92MI (NK cells), M1MO (macrophages, differentiated from THP-1), and Mature DC (dendritic cells, differentiated from THP-1), respectively. This dataset contains transcriptome expression information for the Mature DC cell line.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for water extract of BJIKT and major four ingredient (500 ug/mL, 125 ug/mL, respectively), and mixture of four ingredients (Total 500 ug/mL, mixed 125 ug/mL each)

first: Sang-Min

first: Jin-Mu

last: Yi


title: Immunomodulatory mechanisms of Bojungikki-tang through systematic transcriptomic analysis_M1MO

summary: This study aimed to identify the modes of action (MOA) of water extract of Bojungikki-tang (BJIKT) and major four ingredients in immune cell lines. The four main ingredients were designated as Panax ginseng C. A. Meyer, Astragalus mongholicus Bunge, Atractylodes japonica Koidzumi, and Glycyrrhiza uralensis Fisher, which are the main active herbs of BJIKT. The immune-related cell lines used for transcriptome production are Jurkat (CD4+ T cells), RPMI8226 (B cells), NK-92MI (NK cells), M1MO (macrophages, differentiated from THP-1), and Mature DC (dendritic cells, differentiated from THP-1), respectively. This dataset contains transcriptome expression information for the M1MO cell line.


title: Immunomodulatory mechanisms of Bojungikki-tang through systematic transcriptomic analysis_NK-92MI

summary: This study aimed to identify the modes of action (MOA) of water extract of Bojungikki-tang (BJIKT) and major four ingredients in immune cell lines. The four main ingredients were designated as Panax ginseng C. A. Meyer, Astragalus mongholicus Bunge, Atractylodes japonica Koidzumi, and Glycyrrhiza uralensis Fisher, which are the main active herbs of BJIKT. The immune-related cell lines used for transcriptome production are Jurkat (CD4+ T cells), RPMI8226 (B cells), NK-92MI (NK cells), M1MO (macrophages, differentiated from THP-1), and Mature DC (dendritic cells, differentiated from THP-1), respectively. This dataset contains transcriptome expression information for the NK-92MI cell line.


title: Immunomodulatory mechanisms of Bojungikki-tang through systematic transcriptomic analysis_Jurkat

summary: This study aimed to identify the modes of action (MOA) of water extract of Bojungikki-tang (BJIKT) and major four ingredients in immune cell lines. The four main ingredients were designated as Panax ginseng C. A. Meyer, Astragalus mongholicus Bunge, Atractylodes japonica Koidzumi, and Glycyrrhiza uralensis Fisher, which are the main active herbs of BJIKT. The immune-related cell lines used for transcriptome production are Jurkat (CD4+ T cells), RPMI8226 (B cells), NK-92MI (NK cells), M1MO (macrophages, differentiated from THP-1), and Mature DC (dendritic cells, differentiated from THP-1), respectively. This dataset contains transcriptome expression information for the Jurkat cell line.


title: Immunomodulatory mechanisms of Bojungikki-tang through systematic transcriptomic analysis_RPMI8226

summary: This study aimed to identify the modes of action (MOA) of water extract of Bojungikki-tang (BJIKT) and major four ingredients in immune cell lines. The four main ingredients were designated as Panax ginseng C. A. Meyer, Astragalus mongholicus Bunge, Atractylodes japonica Koidzumi, and Glycyrrhiza uralensis Fisher, which are the main active herbs of BJIKT. The immune-related cell lines used for transcriptome production are Jurkat (CD4+ T cells), RPMI8226 (B cells), NK-92MI (NK cells), M1MO (macrophages, differentiated from THP-1), and Mature DC (dendritic cells, differentiated from THP-1), respectively. This dataset contains transcriptome expression information for the RPMI8226 cell line.


title: An IL-21-expressing effector CD8+ T cell subset provides superior control of infection and cancer

city: Beijing

first: Zixuan

last: Zhao

address: Shuangqing road 30

institute: Tsinghua University

summary: CD8+ T cells are critical in immune responses against pathogens and malignancies. After activation, antigen-specific CD8+ T cells differentiate into cytotoxic effector cells, which are regarded to be phenotypically similar and unlike CD4+ T cells, do not contain different functional subsets. Interleukin 21 (IL-21), well known to be primarily produced by CD4+ T cells, exerts multifaceted effects on the regulation and function of CD8+ T cells. In this study, utilizing IL-21 reporter and fate-mapping mice, we have uncovered a new population of IL-21-expressing CD8+ T cells in the context of infection and cancer. These T cells, coined as Tc21 cells, exhibited remarkable proliferative and cytotoxic capacities, with elevated expression levels of IFNγ and GZMB, than IL-21- T cells. Tc21 cells efficiently developed into memory cells during acute infections and maintained a less dysfunctional state in chronic infection. Importantly, Tc21 cells played a pivotal role in mounting effective protection to virus and cancer. Collectively, these findings highlight an effector subset of IL-21-expressing CD8+ T cells pivotal in host protection, and may suggest new approaches of cancer immunotherapy.

overall_design: IL-21-VFP and IL-21cre-RosaYFP mice were infected by LCMV-Armstrong strain (2×10^5 p.f.u./mouse) or LCMV-Cl13 strain (2×10^5 p.f.u./mouse). Day 5 post both infections, CD8+CD44+VFP+ and CD8+CD44+VFP- cells, or CD8+CD44+YFP+ and CD8+CD44+YFP- cells were isolated from spleens of IL-21-VFP and IL-21cre-RosaYFP mice for RNA extraction. Day 30 post both infections, CD8+CD44+YFP+ and CD8+CD44+YFP- cells were isolated from spleens of IL-21cre-RosaYFP mice for RNA extraction

first: Xiaohong


title: CD73 enhances hepatic Treg functions by enzymatic and non-enzymatic pathways in NAFLD development [CUT&Tag]

city: beijing

first: xinjie

last: zhong

address: No. 95 Yong 'an Road

institute: Beijing Friendship Hospital

summary: CD73 is known as a functional molecule highly expressed by Treg and increasing after FFA (free fatty acids) stimulated. We found that FFA upregulated the transcription factor Gata2 expression in Treg. CUT&Tag assay was performed to investigate the Gata2 binding promoter sites in Treg.

overall_design: Regulatory T cells (Treg) were stimulated with 200µM FFA (free fatty acids) with anti-CD3/CD28 antibody treatment in vitro for 48h. Gata2 antibody, CUT & Tag Assay Kit were used to extract the binding site of Gata2. Then the libraries were sequenced by Illumina Nova Seq 1.5 in Berry Genomics.

first: Hua

last: Jin

first: Xinjie

last: Zhong

first: Guangyong

last: Sun

first: Dong

last: Zhang


title: Low salinity does not impact immune related gene expression or fatty acid biosynthesis in juvenile Florida pompano (Trachinotus carolinus) exposed to Vibrio spp.

city: Fort Pierce

first: David

last: Bradshaw

state: FL

department: Aquaculture & Stock Enhancement

institute: Florida Atlantic University at Harbor Branch Oceanographic Institute

summary: Maintaining marine salinities in inland aquaculture systems can be cost-prohibitive. As such, there has been an emphasis on the identification of marine species that can be reared at low salinities. The Florida pompano (Trachinotus carolinus) is a popular sportfish that can survive in salinities as low as 5 ppt and has been identified as a potential target species for commercial production. Vibrio spp., bacterial pathogens ubiquitous in aquaculture systems, are capable of quickly decimating aquaculture populations. However, there is limited data available on the effects of salinity influences on Vibrio susceptibility in juvenile Florida pompano. This study investigated the influence of lowered salinity on the immune response of juvenile Florida pompano exposed to Vibrio across a 14-day period through assessment of transcriptomic changes, fatty acid biosynthesis, and identification of internal and external signs of vibriosis.  During the experimental period, there were no differences in osmoregulatory or immune related gene expression, no obvious signs of vibriosis, and no changes in fatty acid biosynthesis in fish exposed to 8, 12, 20, or 28 ppt seawater. These results suggest juvenile Florida pompano are resilient to salinity changes and exhibit baseline molecular machinery capable of responding to pathogenic challenges across a range of salinities, making them strong candidates for rearing in inland aquaculture.

overall_design: Our study was designed to determine how various salinities affects juvenile Florida Pompano fish health with transcriptomics (RNA-seq), Vibrio plating, and fatty acid analysis. a holding tank at 28 ppt (marine control). Prior to initiation of the experiment, a total of 300 juvenile pompano (~5g) were transferred from their larviculture facility (Proaquatix, Vero Beach, FL) to a recirculating aquaculture system (RAS) tanks at 28 ppt at FAU-HBOI facilities. Salinity treatments included marine control (28 ppt), estuarine (20 ppt), isosmotic (12 ppt), and hypoosmotic (8 ppt) treatments. Each treatment was run in triplicate (n= 3, total 12 tanks) in a 300 L RAS tanks. In each tank, 25 fish were stocked to replicate production stocking densities. In order to avoid undue stress on the fish, salinities in the estuarine, isosmotic, and hypoosmotic tanks were lowered from marine (28 ppt) to their target salinities over the course of 4 days at the rate of -2 ppt, -4 ppt, and -5 ppt per day in estuarine, isosmotic, and hypoosmotic tanks, respectively. During this time, the 28 ppt marine control tanks underwent partial water changes to mimic water exchanges occurring in the estuarine, isosmotic, and hypoosmotic tanks. Target salinities were achieved and maintained through a combination of treated marine water and dechlorinated freshwater. Fish were fed commercially available fish pellets (provided by Proaquatix) at a rate of approximately 2% body weight per day. Sampling was conducted at the initiation of the experimental period, prior to any salinity transfer (Day 0) and at 14-days post salinity transfer. Samples were collected for the following endpoints: Vibrio verification (water samples), transcriptome analysis (gills, livers, and anterior intestines), fatty acid analysis (liver), and overall fish morphology/ biometrics (images). On each sampling day, two fish per tank were sampled: one for tissues for transcriptomics and one for liver fatty acid analysis.  In order to ensure sufficient RNA yields for transcriptomic analysis, the liver, anterior intestine, and gill lamellae (removed from three gill arches on the left side of the fish) were dissected and pooled in 1 mL cryovials, then flash frozen at -80oC. Additional liver samples collected for fatty acid analysis were dissected and flash frozen at -80oC in individual cryovials. All samples were stored at -80oC until RNA extraction or fatty acid extraction.

first: Elizabeth

middle: B

last: Allmon

last: Bradshaw II

first: Carlie

last: Perricone

first: Sahar

last: Mejri

first: Marty

last: Riche

first: Paul

last: Wills

first: Maria

last: Sepúlveda


title: Long-term photodynamic exposure as an oxidative stress disease model in D. melanogaster

city: Bryan

first: Irtisha

last: Singh

state: Texas

address: 8447 Riverside Pkwy

department: Cell Biology and Genetics

institute: Texas A&M University Health Science Center

summary: Accurate and effective study of human diseases is often improved by the utilization of animal models to increase subject count and avoid human risk. Additionally, animal disease models offer advantages of speed, quantity, and reproducibility. Diseases influenced by increased oxidative stress range from cardiovascular disease to the complex processes of aging. To hasten the study of these oxidative diseases, long-term photodynamic exposure (PDE) is proposed as an oxidative stress disease model in Drosophila melanogaster (fruit flies). PDE is utilized to induce excess reactive oxygen species (ROS) generation in vivo through the consumption of the photosensitizer methylene blue (MB) mixed with standard Drosophila media. ROS causes biological damage through oxidative stress (OS) and is hypothesized to accelerate systemic decline, reducing lifespan and locomotion efficacy. Results show a reduction of mean lifespan by 73% in the 100 μM MB PDE group, and 90% in the 1 mM MB group. Startle-induced negative geotaxis (SING) was used to evaluate locomotion efficacy. Average SING scores decline drastically and showed consistent impairment 86% sooner in the 100 μM MB PDE group. Brain vacuole volumes were evaluated by confocal fluorescence microscopy, noting a doubled volume in the PDE group. Finally, mRNA sequencing revealed significant differential expression of genes related to stress and immune responses. These results are biologically significant and qualify long-term PDE in Drosophila as an experimentally amenable animal model of stress. This serves a role in hastening development of prevention and treatment in age-related diseases.

overall_design: To investigate the effects of long-term photodynamic exposure (PDE) on oxidative stress response in Drosophila melanogaster, the gene expression profiles of male PDE (n=6) and female PDE (n=7) treatment flies was compared to normal male (n=7) and normal female (n=5) controls.

first: Jace

last: Willis

first: Alec

last: Monhollen

first: Caitlin

middle: E

last: Sangdhal

first: Cheslee

middle: H

last: Karasek

first: Vsevolod

last: Cheburkanov

first: Abhinaya

last: Muruganandham

first: Vladislav

last: Panin

last: Yakovlev

first: Vanderlei

last: Bagnato


title: In vitro propagated viromes and selective phage cocktail for NEC prevention in preterm pigs

city: Copenhagen

first: Malene

middle: Roed

last: Spiegelhauer

address: Dyrlaegevej 68

country: Denmark

institute: University of Copenhagen

summary: Necrotizing enterocolitis (NEC) is a severe intestinal disorder connected to a gut microbiota dysbiosis. Approximately 7-8% of very low birth weight (VLBW) infants are diagnosed with NEC with mortality rates reaching 20-50%. Fecal virome transfer (FVT) is an approach where the bacteria-free fecal fraction from a healthy donor is administered to a patient with a GM dysbiosis. FVT contains e.g. bacteriophages, eukaryotic viruses, and metabolites. Oral administered FVT from healthy milk-fed term pigs shows promising potential in preventing NEC in the preterm piglet model. However, efficacy and safety are inconsistent between experiments. In the current study, we aim to explore methods of creating reproducible FVT-like treatments and test if these act preventive against NEC and possess minimal side effects in the preterm piglet model. Using cesarean-delivered, formula-fed preterm pigs, we compare the NEC preventive effect of native donor fecal virome (nFV) with: 1) a defined bacteriophage cocktail targeting NEC-associated bacteria; and 2) a chemostat fecal virome propagation with lactose as the major carbohydrate source (cFV), and 3) chemostat fecal virome propagation with lactose and milk oligosaccharides (cFV-OS). All methods will be compared to control treatment with SM buffer (SM).

overall_design: 67 preterm pigs were delivered by cesarean section from 3 sows at 90 % gestation. They were block randomized by birth weight and gender to one of the four treatment groups: 1) a defined bacteriophage cocktail; and 2) a chemostat fecal virome propagated with lactose as the major carbohydrate source (cFV), 3) a chemostat fecal virome propagated with lactose and milk oligosaccharides (cFV-OS), and 4) vehicle control (SM). All treatments were administered by oral gavage twice daily on days 1 and 2 of life. The pigs were fed milk formula to induce NEC-like intestinal lesions and euthanized on day 5. After euthanasia, mesenteric lymph nodes were collected from each pig and snap-frozen in liquid nitrogen. Missing sample from pig 103.

first: Simone

last: Offersen

first: Duc

last: Nguyen

first: Anders

last: Brunse


title: TET Proteins Control Early-Stage Stem Cell Differentiation via H3K27me3, Not DNA Demethylation

city: Jerusalem

first: Shlomtzion

last: Lahav

address: Edmond J. Safra Campus, Givat Ram

country: Israel

institute: The Hebrew University of Jerusalem

summary: TET proteins reportedly have dual functions as mediators of DNA demethylation and H3K27me3 deposition in embryonic stem cells (ESCs) and during differentiation. To further explore the role of TET proteins in early ESC differentiation, we conducted mapping experiments on wild-type and cells lacking all three TET proteins (TET-TKO) at three stages: in ESCs, immediately after exit from pluripotency, and at the early differentiation stage. We observed minimal differences in transcriptional and DNA methylation levels between wild-type and TET-TKO cells during ESCs and after exit from pluripotency. However, H3K27ac sequential chromatin immunoprecipitation followed by sequencing (ChIP-seq) and bisulfite-seq and single-cell RNA-seq maps demonstrated that during differentiation TET-TKO cells lost their ability to activate the differentiation to extraembryonic endoderm (XEN). This inability was not due solely to higher levels of DNA methylation, as enhancers that were unaffected by TET also showed higher levels of DNA methylation. Loss of XEN differentiation was associated with reduced levels of H3K27me3 during the pluripotency stage. We were able to rescue the effect of TET deficiency by co-culturing TET-TKO ESCs with wild-type ESCs. The co-culturing approach restored XEN differentiation, even though TET proteins were absent during differentiation. We propose that DNA demethylation catalyzed by TET proteins is of minimal importance during the initial stages of differentiation. Instead, the key regulatory function of TETs lies in establishing the ESC ground state through H3K27me3 chromatin deposition.

overall_design: 1. ChIP (H3K27ac) bisulfite WT and TET-TKO differentiated cells. 2. Single cell and bulk RNAseq data of WT and TET-TKO 3. H34Kme3 and H3K27me3 ChIPseq data from WT and TET-TKO ESCs

first: Lahav

last: Shlomtzion

first: Herchcovici

last: Sapir

first: Ratgauzer

last: Sofia

first: Sun

last: Xue

first: Alajem

last: Adi

first: Ram

last: Oren


title: S-phase-induced RNAs licensing DNA replication control ORC1 engagement at early DNA origin sites [RIP-seq]

city: Boston

first: Annalisa

last: Di Ruscio

address: 3 Blackfan Circle

institute: Harvard Medical School Initiative for RNA Medicine

summary: Coordinated initiation of DNA replication is essential to ensure efficient and timely DNA synthesis. Yet the mechanism governing the “initiation” process in eukaryotic cells remains elusive. Here, we present data demonstrating a novel feature of RNAs transcribed in the proximity of actively replicating gene loci. We show that S-phAse-RNAs aNChoring ORC1 (ANCORs) to the histone variant H2A.Z are licensors of the DNA replication process. The concomitant ANCOR-H2A.Z interaction is essential for the cell to initiate duplication of their genetic heritage. Widespread and locus-specific perturbations of these transcripts correlate with anomalous replication patterns and loss of the replicative marker at the origin site.

overall_design: RIP-seq

last: Ummarino

first: Daniel

middle: G

last: Tenen

first: Alex

middle: K

last: Ebralidze


title: S-phase-induced RNAs licensing DNA replication control ORC1 engagement at early DNA origin sites

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

overall_design: Refer to individual Series


title: S-phase-induced RNAs licensing DNA replication control ORC1 engagement at early DNA origin sites [RNA-seq]

overall_design: Transcriptional profiling of S-Phase induced RNAs upon synchronization in the G1/S phase by performing nascent RNA sequencing (nasRNA-seq) at an earlier (S1) and later (S2) time point after the release on the S-phase over a course of five hours


title: S-phase-induced RNAs licensing DNA replication control ORC1 engagement at early DNA origin sites [ChIP-seq]

overall_design: ChIP-seq


title: β-hydroxybutyrate Induces upregulation of Glutamate Uptake and Transporter Expression in Astrocytes

city: Xi'an

first: Sen

last: Shang

address: West Xianning Road

institute: Xi'an Jiaotong University

summary: The ketone body β-hydroxybutyrate (BHB) has been reported to exert neuroprotective function and to be the promising treatment for  neurodegenerative diseases such as Parkinson's disease and Alzheimer's disease. Astrocytes are the most abundant glial cells in central nervous system which have been proved to play a pivotal role in the development and progression of neurodegenerative diseases. BHB is known to alter neuronal metabolism and function, but its effects on astrocytes are poorly understood. Here we carried out the transcriptome sequencing analysis to examine differential expression genes induced by BHB in astrocytes and identified that slc1a3 which encoding the glutamate transporter EAAT1 was significantly upregulated in BHB treatment.  Our findings suggested a novel mechanism for the neuroprotective effects of BHB and reinforced the beneficial effect of BHB on central nervous system (CNS).

overall_design: To investigate the effect of BHB on astrocyte, we performed gene expression profiling analysis using  data obtained from RNA-seq of 3 BHB treated and 3 control primary astrocytes

first: Fei

last: Gao

first: Qi

last: Zhang


title: Integrated Analysis of lncRNA-miRNA-mRNA Interaction Network in Myocardial Ischemia-Reperfusion Injury During Cardiopulmonary Bypass Surgery in Mouse

city: Guiyang

first: kaiyuan

last: chen

state: Guizhou Province

address: Beijing Road,Yunyan District

department: Cardiovascular

institute: the Affiliated Hospital of Guizhou Medical University


title: Integrated Analysis of lncRNA-miRNA-mRNA Interaction Network in Myocardial Ischemia-Reperfusion Injury During Cardiopulmonary Bypass Surgery in Mouse [RNA-seq]

summary: The Long non-coding RNA (LncRNA) miRNA competing endogenous RNA (ceRNA) regulatory network play a pivotal role in the intricate orchestration of cardiovascular diseases, governing their onset and progression.In order to delve deeper into the ceRNA mechanism underlying myocardial ischemia-reperfusion injury (MIRI), we conducted a randomized division of six 8-week-old male C57BL/6J mice into two groups: the Sham group and the ischemia/reperfusion (I/R) group. Subsequently, we employed the Langendorff isolated heart perfusion system to carry out the experiment. Following the completion of the experiment, cardiac samples were meticulously collected and evenly partitioned into two segments: one for lncRNA library sequencing and the other for small RNA library sequencing. By leveraging the sequencing data, we meticulously scrutinized the disparities in lncRNA, miRNA, and mRNA expression profiles between the two sample sets, thereby unearthing the lncRNA-miRNA-mRNA ceRNA regulatory network that assumes a pivotal regulatory role in MIRI.

overall_design: Whole transcriptome RNA sequencing was performed to evaluate the differential expression profiles of lncRNAs, miRNAs, and mRNAs between the MIRI model group (I/R group) and the Sham group. Bioinformatics techniques were utilized to analyze ceRNA networks. Furthermore, pivotal lncRNA-miRNA-mRNA networks were identified and validated using reverse transcription-quantitative polymerase chain reaction (RT-qPCR).

first: Kaiyuan

last: Chen

first: Guiyou

last: Liang


title: HDA9 Epigenetically Regulate Mitochondria, Chloroplast Redox Systems Under ABA Signaling

city: Seoul

first: Zein Eddin

last: Bader

state: Seoul

address: 서울특별시 광진구 광나루로22나길 3

department: Biomedical Science and Engineering

institute: Konkuk University

summary: The regulation of stomatal aperture in plants is impacted by changes in hormones and the environment and is controlled by a complex signaling cascade within guard cells. Mitochondria and chloroplast play a crucial role in regulating reactive oxygen species (ROS) production in plants, which also triggers stomatal movement. However, the regulation of ROS production in mitochondria and chloroplasts still need to be addressed. Abscisic acid (ABA) stimulates ROS production in guard cells, leading to stomatal closure during drought stress. Transcriptomic analysis in Arabidopsis reveals increased expression of ROS-inducing proteins NADPH oxidases and decreased expression of ROS scavengers, including mitochondrial complex I and III. The mechanism regulating ROS inducers and scavengers during ABA and drought stress remains unclear. Our study proposes epigenetic regulation of the mitochondria and chloroplast proteins by Histone deacetylase 9 (HDA9). Loss of function mutant hda9-1 displays ABA insensitivity, representing HDA9's negative regulation in ABA stress. Transcriptomic analysis of hda9-1 also shows increased expression of cytochrome C oxidase-like protein thioredoxin M-4 and ferrdoxin-1, and decreased expression of NADPH oxidases, in contrast to wild-type plants. ChIP-seq analysis using anti HDA9-FLAG antibodies reveals enrichment of cytochrome C oxidase-like protein, thioredoxin M-4, and ferrdoxin-1 loci. Our data suggest that HDA9 binds to these loci on the chromatin and represses their transcription in response to ABA stress.

overall_design: transcriptomic analysis of hda9-1 mutant plant compared to Col-0 wildtype plant.

first: Zein


title: Integrated Analysis of lncRNA-miRNA-mRNA Interaction Network in Myocardial Ischemia-Reperfusion Injury During Cardiopulmonary Bypass Surgery in Mouse [miRNA-seq]


title: Unravelling functions of a novel miRNA-aquaporin module linked to rice domestication

city: Bengaluru

first: Shivaprasad

last: Padubidri V.

state: Karnataka

address: GKVK Campus, Bellary Road

country: India

institute: National Centre for Biological Sciences, TIFR

summary: To understand the effect of over-expression and knock-out of two rice aquaporins, transcriptome analysis was performed from leaves of verified stable transgenic lines

overall_design: Transgenic lines over-expressing two rice aquaporins of PIP family: OsPIP2-7 and OsPIP2-1 [ZmUbiquitin::3xFLAG-OsPIP2-7 and ZmUbiquitin::3xMyc-OsPIP2-1] and T-DNA-free Knock-out lines for the same two genes made using CRISPR-Cas9

first: V

last: Padubidri

first: T

last: Sujith

first: Anushree

last: Narjala


title: ‘An NF2 wildtype malignant meningioma cell line for basic and translational science’

status: Public on Jul 31 2026

city: Seattle

first: Brendan

middle: F

last: Kohrn

state: WA

address: 1705 NE Pacific St.

department: Department of Laboratory Medicine and Pathology

institute: University of Washington

type: Methylation profiling by genome tiling array

summary: We generated new IOMM-Lee genomic and mtDNA variant data and determined proliferation rate and colony-forming efficiency. Genomic DNA methylation profiling data were collected though not further analyzed as part of the primary manuscript.

overall_design: Methods: Methylation profiling was performed using the same WES DNA sample, and an Infinium MethylationEPIC v2.0 kit that targets ~930K unique methylation sites in biologically significant regions of the human genome (Illumina)

first: Perry

last: Chien

first: Megan

last: Nguyen

first: Timothy

last: Martins

first: Samuel

last: Emerson

first: Scott

last: Kennedy

first: Raymond J Monnat

last: Jr.


title: Multiple Argonaute complexes orchestrate epigenetic silencing in the Arabidopsis germline [RIP-Seq]

city: Klosterneuburg

first: Xiaoqi

last: Feng

address: Am Campus 1

department: Cell Biology

country: Austria

institute: Institute of Science and Technology Austria

summary: We report AGO4/5/6/9-bound sRNAs map to pol iv-dependent sRNA clusters in the Arabidopsis thaliana male sexual lineage that regulates gene expression in meiocytes. We found that AGO4/6/9 but not AGO5 participate in RdDM in meiocytes, and AGO5 plays a subtle role in repressing TEs silenced by AGO4/6/9 and Pol IV in meiocytes.

overall_design: Whole genome bisulfite sequencing, RIP-seq and RNA-seq of wild type and AGO mutant samples in Arabidopsis male sex cells.

first: Jincheng

last: Long

first: Chao

last: Yang

first: Shujuan

last: Xu

first: Joke

last: Jaeger-Braet

first: Wenjing

last: She

first: Seijiro

last: Ono

first: James

last: Walker

first: Ygor

last: Souza-Vieira

first: Arp

last: Schnittger


title: Multiple Argonaute complexes orchestrate epigenetic silencing in the Arabidopsis germline [RNA-Seq]

middle: d


title: Cohesin loading at regulatory elements shapes 3D genome folding during erythropoiesis [Micro-C U937]

city: Cambridge

first: Varshini

last: Ramanathan

address: Building 56 Room 787B, 32 Vassar Street

department: Biological Engineering

institute: Massachusetts Institute of Technology

summary: During erythropoiesis, differentiating cells silence much of the genome while maintaining high expression of select genes. It remains unclear whether this transcriptional specialization is linked to specific changes in 3D genome organization. We generated deep Micro-C maps across human erythropoiesis to understand the relationship between cis-regulatory elements and cohesin-mediated loop extrusion during erythroid differentiation. Shifts in erythroid 3D genome structure during differentiation and under perturbations of transcription factors and cohesin subunits/cofactors indicates that a subset of CREs concentrate loop extrusion near key genes during erythroid differentiation.

overall_design: Micro-C was performed on U937 clones with and without knockout of the cohesin complex subunit STAG2.


title: Cohesin loading at regulatory elements shapes 3D genome folding during erythropoiesis [Micro-C]

overall_design: Micro-C was performed on CD34+ hematopoeitic stem and progenitor cells derived from the peripheral blood of two healthy donors that were differentiated to day 5 (Phase 1), day 9 (Phase 2), and day 13 (Phase 3).


title: Embryonic TGF-β signaling instructs long term HSPC clonality and inflammatory landscape

city: Bronx

first: Teresa

last: Bowman

state: NY

address: 1300 Morris Park Ave

institute: Albert Einstein College of Medicine

summary: Embryonic hematopoiesis is essential for establishing lifelong blood and immune system function. During development, hematopoietic stem cells (HSPCs) acquire intrinsic programs that persist into adulthood and can influence disease susceptibility, yet the molecular signals governing these early-life decisions remain poorly understood. Here, we investigated the role of Transforming Growth Factor-β (TGF-β) signaling in regulating HSPC lineage bias and long-term hematopoietic outcomes. Using the zebrafish model, we found that transient inhibition of TGF-β signaling during a critical developmental window altered HSPC frequency and migration after their emergence from the hemogenic endothelium into the caudal hematopoietic tissue, analogous to the mammalian fetal liver. Single-cell transcriptomic analysis of embryonic HSPCs revealed repression of migration- and cytoskeleton-associated genes alongside increased expression of myeloid/macrophage-related genes following ALK5 inhibition. Functionally, early ALK5 blockade reduced macrophage numbers and promoted an M2-like immunosuppressive transcriptional profile. These developmental perturbations produced sustained effects on hematopoietic and immune function into adulthood, including elevated inflammatory responses in the marrow and impaired regenerative capacity after myeloid injury. Together, our findings identify embryonic TGF-β signaling as a key developmental regulator of HSPC fate and immune programming, with potential implications for immune dysfunction and susceptibility to inflammatory disease later in life.

overall_design: Zebrafish embryos were treated with DMSO-control or with the ALK5 inhibitor SB431542 at 30-50 hpf. gata2b+ cells and mCherry+ cells were sorted out using FACS from, respectively, 3dpf and 6dpf whole zebrafish larvae,

first: Marta

last: Mastrogiovanni

first: Anastasia

last: Nizhnik

first: Joaquín

last: Cantón-Sandoval

first: Sofia

last: de Oliveira


title: Sequential pathogen exposure normalizes the brain neuroimmune microenvironment and reveals a tissue-resident memory CD8 T cell-microglia axis shaping adult neurogenesis

city: Iowa City

first: Cori

middle: E.

last: Fain

state: Iowa

address: 25 S. Grand Ave, Carver College of Medicine

department: Pathology

institute: University of Iowa

summary: T cells are increasingly recognized as long-term residents of the adult brain, where they accumulate with age and exhibit regional diversity. However, the functional consequences of brain T cell residency on CNS microenvironments are not well-understood, particularly in non-aged populations. Conventionally used, young adult Specific Pathogen Free (SPF) mice, exhibit low numbers of T cells in the brain compared to young adult humans, limiting translational relevance. In this work we utilize our Specific Pathogen Experienced (SPExp) mouse model, in which prior peripheral microbial exposures lead to significant enrichment of tissue-resident memory (Trm) T cells in the brain, generating a neuroimmune state more closely resembling adult humans. Using this model we recently demonstrated that the presence of resident T cells in the brain influences seizure outcomes in young mice. Here we combined spectral flow cytometry, single-cell RNA sequencing, tissue clearing, behavioral analyses, intravital imaging and blockade strategies to define how CD8 Trm impact brain microenvironment. At immune memory timepoints following peripheral pathogen exposures, SPExp mice exhibited CD8 Trm localization near neurogenic niches in the brain. Sholl analysis of microglia in the vicinity of these neurogenic niche CD8s displayed a more activated phenotype. Intravital imaging demonstrated that CD8 Trm are motile and form sustained contacts with microglia in vivo, corresponding to the changes in activation state. RNAseq identified robust CD8 T cell-dependent transcriptional changes in microglia. Differential expression revealed distinct primed and senescence-associated microglial phenotypes enriched for interferon-signaling, metabolic stress adaptation, and immune surveillance genes and down regulated neuronal support and signaling genes; with reversal of this upon CD8 T cell depletion. Additionally, KEGG/GO analyses suggest induced microglial states downregulate support for neuronal development. Flow and imaging data found neural stem cells (NSCs) were increased in the niches, but proliferation was abrogated. Proliferation of NSCs was restored after CD8 depletion. Together, these findings identify CD8 Trm as key regulators of microglial state and neurogenesic capacity in the brain, establishing a new paradigm for adaptive immune regulation of brain function at homeostasis.

overall_design: We harvested whole brains of 12 weeks old female mice in three groups. Our uninfected control group (n=3), our SPExp group (n=3) in which mice were infected with five distinct non-CNS infections (Puerto Rico-8/34 influenza A virus (PR8-IAV), murine cytomegalovirus (MCMV) strain K181, vaccinia virus (VacV), attenuated Listeria monocytogenes, and lymphocytic choriomeningitis virus (LCMV) strain Armstrong), and SPExp mice administered 2 doses of anti-CD8 depletion antibody (n=2). All of these pathogens are easily clearable by the mice and 30 days after the last infection we harvested whole brains and isolated the nuclei for single-nuclei RNA sequencing.

first: John

middle: T

last: Harty


title: Cohesin loading at regulatory elements shapes 3D genome folding during erythropoiesis

overall_design: Micro-C was performed on CD34+ hematopoeitic stem and progenitor cells derived from the peripheral blood of healthy donors that were differentiated to day 13 (Phase 3).