title: A homeobox transcription factor fine-tunes jasmonic acid biosynthesis to balance plant immunity and growth in Arabiodopsis [ChIP-seq]

city: hangzhou

first: xiaoxiao

last: Li

address: #866 Yuhangtang Rd.

institute: zhejiang university

summary: The activation of plant immunity is typically associates with biosynthesis of defensive metabolites, such as jasmonic acid (JA) and salicylic acid (SA), to establish an effective defence response. However, constitutive activation of immunity or excessive JA production can trigger additional pathways that negatively affect plant growth. The mechanism underlying these processes, regulated by hormone signalling pathways and their crosstalk, remains elusive. In this study, we identified a homeobox transcription factor HB34 that differentially regulates jasmonic acid biosynthesis genes and growth-promoting genes to regulate such trade-off between plant immunity and growth. Under normal condition, HB34 represses the improper activation of JA-responsive genes and loss of HB34 led to excessive JA accumulation and constitutively activated JA response, which are accompanied by inhibited plant growth. Notably, overexpression of individual growth-promoting gene was sufficient to compromise the growth-inhibition. Upon pathogen infection, the transcription of HB34 is downregulated, effectively derepressing JA biosynthesis and enhancing plant disease resistance. Together, these findings reveal HB34 as a molecular switch that balance plant defense and growth by modulating JA biosynthesis and IAA signaling pathway.

overall_design: To investigate whether HB34 could directly bind to thepromoter of the JA and IAA sihnaling pathway target genes as a transcription factor, genome-wide occupancy of YB2 were determined by ChIP-seq assays in the transgenic plants of hb34-GFP drive with native promoter.

first: Xiaoxiao

first: Zeng

last: Tao


title: A homeobox transcription factor fine-tunes jasmonic acid biosynthesis to balance plant immunity and growth in Arabiodopsis [RNA-seq]

status: Public on Jun 01 2026

country: China

type: Expression profiling by high throughput sequencing

overall_design: RNA-seq profiling of WT and hb34 mutant in 10-day-old seedling


title: Inherited Variant in MRC2 Causes Cardiac Fibroblast Dysfunction and Increases Atrial Fibrillation Susceptibility

city: Houston

first: Xander

middle: H T

last: Wehrens

state: TX

address: 1 Baylor Plz

country: USA

institute: Baylor College of Medicine

summary: Background. A recent study identified a rare variant in the MRC2 gene in individuals with familial reentrant supraventricular tachycardia, a Wolff-Parkinson-White (WPW) ECG pattern, and structurally normal hearts. WPW syndrome is associated with atrial fibrillation (AF), and MRC2 was recently proposed as a protective gene for AF. Objective. We aimed to determine whether the E990G-heterozygous (het) loss-of-function variant in MRC2 increases AF susceptibility and aberrant atrial cardiofibroblast (ACF) function in mice. Methods. Programmed electrical stimulation (PES) was performed to determine AF susceptibility in E990G-het mice and wild-type (WT) controls. ACFs were isolated from these mice and cultured, and their migration, and collagen deposition were quantified. Finally, transcriptomic profiling by RNA sequencing and secretomic/proteomic profiling by mass spectrometry were performed on ACFs and whole atrial tissue. Results. E990G-het mice exhibited increased susceptibility to pacing-induced AF and had decreased atrioventricular effective refractory periods compared to WT controls. ACFs isolated from E990G-het mice deposited greater amounts of acid-soluble collagen in 2D cultures as quantified by Sirius red staining compared with WT controls. Transcriptomic, secretomic, and proteomic profiling of cultured ACFs and whole-atrial tissue suggest that some fibrotic regulators are differentially expressed or secreted, including decreased ACF expression of matrix metalloproteinase 13 (MMP-13), which degrades collagen types I, II, and III; decreased ACF expression, ACF secretion, and atrial tissue levels of matrix metalloproteinase 12 (MMP-12), which degrades collagen types I, III, IV, elastin, and fibronectin; and increased tissue levels of cellular communication network factor 2/connective tissue growth factor (CCN2/CTGF), a profibrotic regulator. Conclusions. MRC2 E990G-het mice exhibit increased AF susceptibility, altered collagen deposition by ACFs, and differentially regulated fibrotic genes and proteins. Together, these findings suggest that excessive collagen deposition and reduced MMP-mediated collagen removal generate a substrate for the development of AF in the presence of a loss-of-function variant in MRC2.

overall_design: 8 WT and 7 MRC2 E990G-het mouse cardiac atria between 4 and 10 months old were harvested and immediately snap-frozen in liquid nitrogen.

first: Kevin

last: Ho

first: Hassan

last: Samee


title: DNMT1 RFTS mutation alters RNA splicing and drives neurodegeneration via its RNA-binding function [RNA-BisSeq]

city: Shanghai

first: Chenhan

last: Liao

address: 393 Middle Huaxia Road, Pudong, Shanghai

institute: ShanghaiTech University

summary: DNA Methyltransferase 1 (DNMT1) is a key enzyme in maintaining DNA methylation. Mutations in the RFTS domain of DNMT1 are associated with two neurodegenerative diseases: Hereditary sensory and autonomic neuropathy type 1E with dementia and hearing loss (HSAN1E) and Autosomal dominant cerebellar ataxia, deafness, and narcolepsy (ADCA-DN), the molecular pathogenic mechanisms of which have not yet been elucidated. Pre-mRNA alternative splicing is an important post-transcriptional process for increasing protein functional diversity in organisms, and the dysregulation of the alternative splicing process plays a significant role in the occurrence and development of neurodegenerative diseases.

overall_design: To study the function of DNMT1, we established NPCs carried DNMT1 point A570V mutation, and using RNAi to knockdown the protein level of DNMT1.

first: Guoping

last: Fan

first: Ganlu

last: Hu


title: DNMT1 RFTS mutation alters RNA splicing and drives neurodegeneration via its RNA-binding function [RRBS]

type: Methylation profiling by high throughput sequencing


title: DNMT1 RFTS mutation alters RNA splicing and drives neurodegeneration via its RNA-binding function [RNA-Seq]


title: RFTS mutation alters RNA splicing and drives neurodegeneration via its RNA-binding function


title: 5’ HOXD genes differentially regulate gene expression of Synovial Fibroblasts in hand joints

city: Zurich

first: Masoumeh

last: Mirrahimi

state: Zurich

address: Wagistrasse 14,

department: Rheumatology

country: Switzerland

institute: University Hospital Zurich

summary: We previously demonstrated that Homeobox (HOX) transcription factors are differentially expressed between joint locations and can accurately assign synovial fibroblasts (SFs) to their correct joint location. We show here that the expression of the 5’HOXD transcription factors HOXD10, HOXD11, and HOXD13 in SFs strikingly overlaps with predilection sites for the development of rheumatoid arthritis (RA). Changes in SFs gene expression after silencing 5’HOXDs aligned with joint-specific differences of RA SFs. In particular, we identify HOXD13 as regulator or primary cilia function in SFs modulating cell cycle, DNA damage and proteasome activity. Accordingly, we show joint specific differences in primary cilia morphology, DNA damage repair and proteasome activity. We thus propose that HOXD13 and primary cilia play a role in shaping joint-specific SFs functions that might underlie the pathognomic pattern of joint involvement in RA.

overall_design: Hand SFs were transfected with 50 nM antisense LNA targeting HOXD10 (Qiagen, Sequence: 5′-TGT CTG CGC TAG GTG G-3′), HOXD11 (Qiagen, Sequence: 5′-TGC TAG CGA AGT CAG A-3′), HOXD13 (Qiagen, Sequence: 5′-CAT CAG GAG ACA GTA T-3′), for 24hr and 48hr for RNA and protein extraction respectively. SF was transfected with 12.5 nM antisense LNA GapmeRs CBP (Qiagen, Sequence: 5′-GCG GCG ATC CTT TAG A-3′) or p300 (Qiagen, Sequence: 5′-TAG TCT GGT CCT TCG T-3′) for 24hr.  Transfections were carried out using Lipofectamine 2000 (Invitrogen) in accordance with the manufacturer’s instructions. Antisense LNA GapmeR Negative Control A (Cat. No 300610) served as the transfection control. Total RNA was isolated from SFs silenced for HOXD10, HOXD11, and HOXD13, as well as control SFs (n = 3 for each), 48hr post-transfection using the miRNeasy Mini kit (Qiagen), which includes on-column DNase I digestion. RNA quantity and quality were assessed using the Qubit RNA BR Assay Kit (Life Technologies) and the Agilent 2100 Bioanalyzer (Agilent Technologies, Inc.). RNA-seq libraries were prepared using the Illumina TruSeq Stranded Total RNA protocol and the TruSeq Stranded Total RNA Sample Preparation Kit. The quality and quantity of the libraries were evaluated with the Agilent 2100 Bioanalyzer using a DNA-specific chip and RT-qPCR with Illumina adapter-specific primers on the Roche LightCycler system (Roche Diagnostics). Diluted indexed long RNA-seq libraries (10 nM) were pooled in equal volumes, used for cluster generation with the TruSeq SR Cluster Kit v3- cBot-HS reagents, and sequenced using the TruSeq SBS Kit v3-HS reagents on the Illumina HiSeq 4000 platform. Genomics was performed at the Functional Genomics Center Zurich (FGCZ) of University of Zurich and ETH Zurich.

first: Caroline

last: Osplet

first: Kerstin

last: Klein


title: Characterization of a novel family of multitarget small molecules in glioblastoma

city: Donostia

first: Estefania

last: Carrasco-Garcia

state: Guipúzcoa

address: Dr. Begiritsain s/n

department: Oncology

country: Spain

institute: Biodonostia

summary: Glioblastoma is the most common and malignant primary brain tumor in adults with current treatment presenting limited effectiveness. Resistance to therapy is consequence of the high molecular and cellular heterogeneity. Multitarget small molecules (MSMs) are emerging as a novel therapeutic strategy for the treatment of complex diseases, including cancer. In the present work, we have generated a novel family of indole-based MSMs designed to inhibit monoamine oxidases (MAOs), cholinesterases (ChEs) and histone deacetylases (HDACs), while acting as histamine H3 receptor (H3R) antagonists and sigma 1 receptor (S1R) agonists. For this, selected pharmacophoric moieties of the parent compounds Contilisant and Belinostat HDAC inhibitor were juxtaposed. 9 MSMs were synthesized and most of them exerted cytotoxic effect on glioma cells. Among them, 3 molecules were selected (MTP142, MTP156 and MTP150), and additional experiments revealed that they inhibited glioma stem cell (GSCs) activity, did not present toxicity and are expected to cross the BBB. In vivo and Omic studies were performed with MTP150 molecule and results showed that it significantly reduced tumor growth in vivo, both alone and in combination with temozolomide (TMZ). Finally, transcriptomic and proteomic analyses on patient-derived GSCs revealed a deregulation in cell cycle and neurotransmission activity by the treatment with MTP150. In conclusion, our data reveal the efficacy of a novel family of MSMs in the pre-clinical setting of glioblastoma.

overall_design: The experiment was performed in patient-derived glioma stem cells (GNS166) treated with MTP150 at 5μM and control for four independent replicates.

first: Matheu

last: Ander


title: Evidence of a gut-adipose-liver axis: microbiota encroachment in metabolic dysfunction-associated steatotic liver disease

city: Orlando

first: Daria

last: Igudesman

address: 301 E Princeton St

institute: AdventHealth

summary: Metabolic dysfunction-associated steatotic liver disease (MASLD) affects ~40% of adults, but causal mechanisms remain elusive. Preclinical models implicate the gut microbiota in MASLD pathogenesis, yet translation to humans is hampered by instability and variability in microbial composition. We addressed these gaps by investigating whether stable, quantitative gut phenotypes including microbiota encroachment are pathological features of MASLD. Sigmoid colon biopsies were collected from participants with and without imaging-defined MASLD. Mucus immunostaining was paired with fluorescent in situ hybridization to image and quantify the distance separating bacteria from the colonic epithelium (i.e., encroachment). Secondary outcomes included intestinal permeability, colon histopathology, and estimates of central and adipose tissue insulin resistance (Adipo-IR). RNA-sequencing was combined with weighted gene network correlation analysis to explore relationships between colonic gene expression and clinical endpoints. Microbiota encroachment did not differentiate participants with MASLD from controls. Circulating lipopolysaccharide and flagellin-specific immunoglobulins (i.e., intestinal permeability), and colon histopathology were similar across cohorts. Adipo-IR and microbiota encroachment were related to a colonic gene network regulating insulin and lipid metabolism. Pathway analysis of this network revealed genes involved in hepatic steatosis and fibrosis, suggesting a gut-adipose-liver crosstalk.

overall_design: Cross-sectional observational study comparing gut phenotypes in participants with MASLD and disease-free controls.

first: Karen

last: Corbin

first: Benoit

last: Chassaing

first: Charlene

last: Dauriat


title: Cross-regulation of amino acid synthesis and anaerobic electron transfer by MetR-mediated methionine signaling

city: Hachioji

first: Atsushi

last: Kouzuma

state: Tokyo

address: 1432-1 Horinouchi

country: Japan

institute: Tokyo University of Pharmacy and Life Sciences

summary: Microorganisms living in nutrient- and energy-limited environments must finely coordinate anabolic and catabolic pathways. However, the molecular mechanisms underlying this balance remain poorly understood. Here, we report a mechanism cross-regulating amino acid biosynthesis and anaerobic respiration in bacterial cells. Using the model bacterium Shewanella oneidensis MR-1, we demonstrated that methionine activates extracellular electron transfer activity at submillimolar concentrations. This regulation is mediated by the transcription factor MetR, a canonical regulator of methionine biosynthesis. Under methionine-limited conditions, MR-1 upregulates methionine biosynthesis genes while repressing genes involved in extracellular electron transfer (metal reduction) and other anaerobic respiratory processes. Conversely, methionine availability relieves this repression, enhancing extracellular electron transfer. Furthermore, the MetR-mediated regulation of extracellular electron transfer was observed in Aeromonas hydrophila. These findings reveal a novel physiological role for MetR, suggesting its involvement in the coordinated energy distribution between anabolic and catabolic pathways.

overall_design: Transcriptomic profiles of the Shewanella oneidensis MR-1 metR-overexpression strain and the vector control strain were compared. Four biological replicates were prepared for each strain.

first: Hisae

last: Mogi

first: Kazuya

last: Watanabe


title: Rheb modulates mTORC1-independent metabolism is essential for lysosomal function in microglia

city: 深圳

first: Yingjie

last: Wang

state: Guangdong

address: No. 1088 Xueyuan Avenue, Nanshan District

institute: Southern university of science and technology

summary: Microglia are highly motile cells that respond to neuroinflammation and play a crucial role in maintaining CNS homeostasis through their degradation capacity. While metabolic flexibility is vital for peripheral immune cells to sustain cellular function, the adaptation of microglial metabolism to support degradation remains unexplored. In this study, we elucidate key metabolic regulatory mechanisms influencing the transcriptional activity in microglia. The loss of Rheb, an activator of mTOR, leads to reduced histone H3 acetylation, resulting in decreased transcription of lysosome-related genes and diminished degradation capacity. Conversely, inhibition of mTORC1 by Mios/GATOR2 or Torin1 enhances microglial lysosomal function, indicating that Rheb regulates lysosome biogenesis independently of mTORC1. Our transcriptional and metabolic profiling reveals that Rheb deficiency prompts microglia to increase glycolysis and glutaminolysis to compensate for a disrupted TCA cycle under environmental challenges. This impaired TCA cycle, correlated with epigenetic modifications, reduces microglia’s ability to clear myelin debris. In contrast, overexpression of Rheb in microglia enhances fAβ clearance in vivo. Our findings demonstrate that metabolic regulation of lysosomal function in microglia is critical for degradation, and enhancing this process offers therapeutic potential for treating age-related neuroinflammatory conditions.

overall_design: 8 weeks aged mice after Tamoxifen injection received four consecutive days of daily intraperitoneal injections of PBS or 1.0 mg/kg LPS. Cells were purified from the brains of female mice by MACS.

first: Xiaoxin

last: Xie


title: Transcriptomic analysis of ATG5 induced hepatocellular carcinoma in zebrafish

city: Singapore

first: Chao

last: Gao

address: 14 Science Drive 4

country: Singapore

institute: National University of Singapore

summary: ATG5 is a key autophagy effect in autophagosome formation; however, it also mediates autophagy-independent processes. ATG5 has been intricately linked to cancer where both tumor-promoting and tumor-suppressing functions of ATG5 have been described. We established a stable transgenic zebrafish to promote ATG5 functions in liver and found that overexpression of ATG5 in liver contributed to hepatocellular carcinoma.

overall_design: To investigate the potential oncogenic function of ATG5 in liver, we generated the transgenic zebrafish, Tg(fabp10a:mCherry-T2A-LexPR;LexOP:ATG5WT), using a mifepristone-inducible LexPR system. The transgenic zebrafish allows for the temporal control of human ATG5 expression in liver in the presence of mifepristone. RNA samples from normal liver (n = 3) and HCC (n = 3) were collected for RNA-seq.

first: Qiqi

last: Yang

first: Ira

last: Agrawal

first: Zhiyuan

last: Gong


title: Single nucleus RNA sequencing analysis reveals transcriptional heterogeneity of endometrioid endometrial cancer

city: Hefei

first: Yifan

last: Feng

state: Anhui

address: Jixi Road 218

institute: The Anhui Medical University

summary: Endometrial cancer (EC) is the sixth most prevalent malignancy affecting women worldwide, with an increasing incidence that poses a substantial public health challenge. This study investigates the tumor microenvironment (TME) of EC, particularly high grade endometrioid endometrial cancer (HEEC), utilizing single nucleus RNA sequencing (snRNA-seq). The analysis encompassed normal endometrium (NE), HEEC, middle grade endometrioid endometrial cancer (MEEC), and low grade endometrioid endometrial cancer (LEEC). Significant cellular heterogeneity was identified within the TME, including immune cells, fibroblasts, and epithelial cells. Notably, SULF1+ NREP+ fibroblasts were significantly enriched in HEEC and associated with aggressive tumor behavior. Additionally, the study highlighted the overexpression of metabolic pathways and immune checkpoint molecules in HEEC epithelial cells, including Human Leukocyte Antigen E (HLA-E) and Killer Cell Lectin Like Receptor C1 (KLRC1), which may contribute to immune evasion and enhanced tumor aggressiveness. Identifying the EYA transcriptional coactivator and phosphatase 1 (EYA1) gene as a prospective biomarker in HEEC due to its association with poor prognosis and the enhanced proliferative and migratory capabilities of EC cells. Furthermore, analyses of cell-cell interactions revealed critical signaling pathways, such as the Leucocyte Associated Immunoglobulin Like Receptor-1 (LAIR1)- Leukocyte Immunoglobulin-like Receptor B4 (LILRB4) axis in macrophages, which may play a role in immune suppression and EEC progression. A comprehensive single-cell level characterization of the TME in EEC offers critical insights into the molecular mechanisms driving EEC progression, while identifying potential therapeutic targets. These discoveries advance our understanding of EEC pathophysiology and hold promise for the development of targeted therapies, particularly in HEEC

overall_design: single cell sequencing of NE,LEEC,MEEC,HEEC

first: Min

last: Li

first: Yunxai

last: Cao


title: Extracellular Vesicle Online Knowledge Explorer (EVOKE) - A guiding tool for the selection of methods to prepare extracellular vesicles from human biofluids I

status: Public on Jun 10 2026

city: Ghent

first: sandor

last: Dedeyne

address: C. Heymanslaan 10

country: Belgium

institute: University Ghent

summary: Extracellular vesicles (EVs) exert multiple biological functions which has spurred their development as disease biomarkers and drug delivery vehicles. However, the wide range of EV preparation methods and the complexity of biofluids pose significant challenges for reproducible research and clinical translation. To address this difficulty, we developed the Extracellular Vesicle Online Knowledge Explorer (EVOKE)—a pioneering resource designed to assist researchers in evaluating and comparing EV preparation methods. To establish EVOKE, an international consortium was formed to systematically compare widely used EV preparation methods across diverse biofluids for key performance metrics using trackable reference materials and complementary characterization methods. EVOKE is the first freely accessible resource (www.evoke-tool.org) that guides researchers towards the informed selection of an optimal EV preparation method for a dedicated study goal, currently powered by over 2.4 million data points and amendable to future developments. It offers crucial insights into method-dependent efficiency, specificity, repeatability, and biomolecular variations and activity, ultimately steering informed method selection and reproducibility. In conclusion, EVOKE provides a strong foundation for coping with methodological challenges and advancing the clinical translation of EV research.

overall_design: EVs collected from cell culture supernatant conditioned by MDA-MB-231; EVs were prepared using 14 preparation protocols with 3 technical replicates


title: Rat somatic genome editing enables ER+ breast cancer modeling

first: Tobie

middle: D

last: Lee

state: Texas

address: One Baylor Plaza

summary: Genetically engineered mouse models have advanced cancer research but often fail to capture key features of certain human tumors. Rats, with distinct physiology and tumor biology, offer a powerful alternative, yet their use has been constrained by technical barriers to genome editing. Here, we develop efficient somatic genome editing approaches in rats, enabling both indel and substitution mutations, and apply them to model estrogen receptor (ER)-positive breast cancer, which represents ~70% of human cases but remains poorly represented in mice. The resulting rat tumors closely recapitulate human disease in histology, hormone responsiveness, and microenvironmental features. By contrast, identical genetic alterations in mice failed to yield ER+ tumors, underscoring fundamental species differences in tumorigenesis. This platform provides a versatile and scalable platform for rapid generation of clinically relevant rat tumor models, opening new avenues to investigate mechanisms of tumor biology, therapeutic response, and immune interactions in previously inaccessible cancer subtypes.

overall_design: Female rats constitutively expressing Cas9 were generated by crossing LE-ROSA26tm1(LSL-Cas9)Ottc and Wistar-Tg(CAG-Ncre)81Jmsk strains (RRRC #00833 and #301). Mammary tumors were induced by intraductal AAV delivery of oncogenic drivers (P53, Nf1, Pik3ca, or combinations), harvested, dissociated, and processed for scRNA-seq using the 10x Genomics Chromium 3' v3.1 platform. For in vivo treatments, compounds were dissolved in 80 µL DMSO and mixed with 1520 µL corn oil to a final concentration of 50 mg/mL; doses were administered weekly via subcutaneous injection at 2.5 µL/g body weight. The same DMSO/corn oil mixture was used as the vehicle control and administered at the same dosing volume and schedule.

first: Yunfeng

last: Ding

first: Wen

last: Bu

first: Yi

first: Xiang

last: Zhang


title: Endothelial PD-L1 brakes CD8+ T cell exhaustion, empowering anti-tumor immunity in non-small cell lung cancer

city: Leuven

first: Lisa

middle: M

last: Becker

address: Herestraat 49

institute: VIB KU Leuven Center for Cancer Biology

summary: Cancer immunotherapies targeting PD-(L)1 offer therapeutic potential but suffer resistance. The role of PD-L1 in tumor and myeloid cells has been extensively studied, while its function in tumor endothelial cells (ECs) is overlooked. Surprisingly, we identified an unknown role of EC-specific PD-L1 in delaying the exhaustion of tumor-infiltrating CD8+ T cells in a non-small cell lung cancer mouse model. Loss of endothelial PD-L1 reduces T cell activation and exac-erbates tumor growth. Initial inhibition of CD8+ T cells by endothelial PD-L1, prior to encoun-tering cancer cells, prevents T cells from prematurely reaching a terminal exhaustion state. Initial results suggest that high EC PD-L1 expression in NSCLC patient tumors might become a potential positive predictor of anti-PD-1 outcome. These unexpected findings highlight the significance of vessel-associated PD-L1 and suggest that EC PD-L1 blockade upon systemic treatment potentially negates the overall therapeutic effect, raising the question if this might contribute to therapy resistance.

overall_design: To better characterize the phenotypes of CD8 T cells in lung tumors from WT mice and mice lacking endothelial PDL1 (PDL1DEC mice), CD8 T cells were FACS-isolated and we performed bulk RNA sequencing. CD8 T cells were isolated either from (a) macropscopic lung nodules (core-enriched), or (b) paranchymal nodules (rim-enriched) in both WT and PDL1DEC mice

first: Peter

last: Carmeliet

first: Anh-Co

middle: K

last: Truong

first: Julia

last: Dmitrieva


title: DDX6 reshapes the cancer RNA editome to suppress RNA-induced innate immunity [RIP-Seq]

first: jinghe

last: xie

address: 21 Lower Kent Ridge Road

institute: nuh

summary: ADAR1 is thought to be an immune suppressor and maintains self-tolerance to endogenous nucleic acids through its A-to-I RNA editing catalytic activity. Its editing activity is tightly regulated by an array of different proteins and factors. In this study, we investigated the role of DDX6 in A-to-I RNA editing regulation and how this in turns regulate dsRNA-induced immunity.

overall_design: We fractionated cell lysates into cytosolic and nuclear fractions for RNA immunoprecipitation sequencing. DDX6-bound mRNA were immunoprecipitated for cDNA library construction. These libraries were sequenced using the DNBSEQ platform. We then performed alignment to the hg19 genome assembly and read counting at the gene- and transcript-level for differential gene enrichment analysis.

first: Larry

last: Ng

first: Vincent

last: Tano

first: Jinghe

last: Xie

first: Polly

last: Chen


title: Effect of inhibition of Dlx3 on gene expression alteration during alveolar bone healing

city: Beijing

first: Fang

address: No.22 Zhongguancun South Avenue

institute: Peking University

summary: The alveolar ridge loss and absorption strongly affects the following implantation and prosthodontic treatment. It is a clinical challenge and research hotspot to sustain the alveolar bone mass. Interestingly, the patients affected with Tricho-dento-osseous (TDO) syndrome present high density of skull and jaw bones, and can remain sufficient bone mass after tooth extraction in a long time. The mechanism of this phenomenon is of highly study value. To explore DLX3-the disease-causing gene of TDO syndrome, we constructed the mouse alveolar loss and healing model. After tooth extraction, gelatin sponge with GFP or with adenovirus vector that can suppress the expression of Dlx3 gene was put in normal murine alveolar socket, respectively. RNA sequencing of the alveolar bone of these two groups was performed to explore the downstream molecular alterations.

overall_design: The right upper incisor of 12-week-old mouse was extracted. Six days later, three samples of control group and five samples of sh-Dlx3 group were collected and sent for RNA-sequencing

first: Yang

last: Liu


title: Cell fate reprogramming of erythroid cells caused by reduction of H3K4me3 lead to a “retrograde manner” leukemia genesis [scRNA-seq_human]

city: zhengzhou

first: Hengchao

state: Henan

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

institute: zzu

summary: While it's established that methionine metabolism, can impact histone methylation to have a direct role in influencing cell fate determination, methionine metabolic regulation of hematopoietic stem cell commitment and erythroid differentiation is unknown. Here, we investigated how AHCY, an important enzyme in themethionine cycle and timely hydrolysis to sustain methylation reactions, regulates cell fate reprogrammingon in vitro and in vivo. Firstly, we observed that depletion or targeted pharmacological inhibition of AHCY in erythrocytes markedly inhibites cell proliferation, induces cell apoptosis and causes the appearance of other lineage cells. In addition, we applied single-cell sequencing to adherent and suspended cells and identified multiple cell populations, including stem/progenitor cells such as HSC, megakaryocyte/erythroid progenitor cells (MEP), common myeloid progenitor cells (CMP), and granulocyte monocyte progenitor cells (GMP), as well as immune cells such as macrophages and myeloid dendritic cells (mDC). We engrafted adherent and suspended cells into NCG-c-kit-Cas9-TM mice without irradiation. After 4 weeks and 12 weeks postengraftment, we observed human cell chimerism in marrow, peripheral blood and spleen. Importantly, we further found that AHCY-mediated histone methylation rather than DNA methylation leading to cell dedifferentiation including H3K4me3, H3K9me3, H3K27me3, H3K36me2 and H3K79me2 modifications. However, consistent phenotype can be observed only after specific inhibiting H3K4me3 on the terminal erythropoiesis. Integrating CUT&Tag sequencing and RNA-seq analysis revealed that expression of transcription factors(TFs), including those lineage-specific TFs (GATA2, CEBPA), are upregulated in dedifferentiation cells, and erythrocyte lineage-specific TFs (GATA1, KLF1) are significantly downregulated. Because AHCY gene expression was significantly lower in terminal erythroid cells of AML patients compared to healthy individuals, clinically, we next detected relatively low levels of H3K4me3 in erythroblasts from bone marrow of some leukemia patients. Colony formation detection was performed on these erythroblasts in vitro using modified semisolid clonal culture, and multiple CFU colony formation could be observed through morphological verification of colony types. These results reveal a previously unappreciated mechanism of methionine metabolism regulating erythropoiesis by affecting methylation modification. All these findings also reveal that histone methylation landscape reshapes the cell fate decision during human erythropoiesis. And we have demonstrated for the first time that the reduction of H3K4me3 leads to the occurrence of "retrograde" leukemia.

overall_design: Here, we set 0.5μM DZNep dosing which was an inhibitor of AHCY to inhibit AHCY activity. After treated with 0.5μM DZNep for four days, we performed a scRNA sequencing of DMSO and DZNep treated cells.

first: Lei

last: Sun

first: Mengjia

last: Li

first: Lixiang


title: Myonuclear reprogramming underlies muscle denervation and weakness following knee injury [ChIP-Seq]

city: Lexington

first: Alexander

middle: Romano

last: Keeble

state: KY

address: 900 S Limestone st

institute: Northwestern University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Muscle weakness following joint injury contributes to substantial functional deficits and disability. The molecular etiology of prolonged muscle atrophy and weakness following knee ligament injury remains undefined, limiting our understanding of the inceptive events underlying poor functional recovery. We studied the muscle transcriptome in men and women in response to ligament injury and surgical reconstruction, revealing substantial injury- and reconstructive surgery-dependent changes, with sustained increases in genes associated with neuromuscular junction remodeling. We identified histone deacetylase 4 (HDAC4) as one of the most upregulated targets in muscle following both injury and reconstruction, and multi-omics integration of HDAC4 ChIP-sequencing and RNA-sequencing revealed a coordinated repression of genes associated with metabolism and contractile function following injury. We further applied single nucleus RNA-sequencing and uncovered aberrant neuromuscular signaling and myonuclear reprogramming. Our multi-omics and single-nucleus transcriptome analyses demonstrate unique myocellular and neuromuscular adaptations that could explain persistent functional deficits following acute musculoskeletal injury.

overall_design: Skeletal muscle samples were combined from several participants from the Healthy, Injured and 7d post-Sx quadriceps samples to complete ChIP-seq performed by Active Motif. This approach was necessary to provide the requisite 150 mg of tissue per condition needed for ChIP-seq analysis of HDAC4 in skeletal muscle.

first: Nicholas

middle: T

last: Thomas

middle: R

first: Allison

last: Owen

first: Camille

last: Brightwel

first: Christine

last: Latham

first: Megan

middle: C

last: Graham

first: Kelsey

middle: A

last: Reeves

first: Jensen

last: Goh

first: Sara

last: Gonzalez-Velez

first: Douglas

middle: E

last: Long

last: Harrison

first: Phillip

last: Kern

first: Gregory

middle: S

last: Hawk

first: Caitlin

last: Conley

first: Jean

middle: L

last: Fry

first: Austin

middle: V

last: Stone

first: Katherine

last: Thompson

first: Darren

last: Johnson

first: Yuan

last: Wen

first: Brian

last: Noehren

first: Christopher


title: Cell fate reprogramming of erythroid cells caused by reduction of H3K4me3 lead to a “retrograde manner” leukemia genesis [CUT&Tag]

first: Hengchao

last: Zhang

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

overall_design: Here, we set 0.5μM DZNep dosing which was an inhibitor of AHCY to inhibit AHCY activity. After treated with 0.5μM DZNep for four days, we performed a H3K4me3 CUT&Tag sequencing of DMSO and DZNep treated cells.

first: Lei

last: Sun

first: Mengjia

last: Li

first: Lixiang

last: Chen


title: Cell fate reprogramming of erythroid cells caused by reduction of H3K4me3 lead to a “retrograde manner” leukemia genesis [RNA-seq]

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

overall_design: Here, we set 0.5μM DZNep dosing which was an inhibitor of AHCY to inhibit AHCY activity. After treated with 0.5μM DZNep for four days, we performed a RNA-seq of DMSO and DZNep treated cells.


title: Highly multiplexed single cell chromatin regulator and accessibility profiling elucidates chromatin dynamics in human B cell development and oncogenesis, and reveals an adverse prognostic gene expression signature in B lymphoblastic leukemias [patient]

city: Palo Alto

first: Reema

last: Baskar

address: 3373 Hillview Ave

institute: Stanford University

summary: Developing B cells undergo successive stages of chromatin reorganization which modulate DNA accessibility to control V(D)J recombination and gene transcription. These epigenetic shifts are mediated by histone modifications (e.g., H3K4me3, H3K27me3), histone-modifying enzymes (e.g., MLL1, LSD1), and chromatin remodelers (e.g., CTCF, DNMT1). We combined highly-multiplexed, multi-omic approaches to capture this choreographed dance – from single cell changes in chromatin modulators, to alterations in histone modifications, to genome-wide chromatin accessibility. This epigenetic map of normal human B cell differentiation enabled us to peer into the early origins of B cell leukemias and lymphomas – specifically, stage-specific chromatin accessibility at sites of recurrent chromosomal translocations and oncogenic transcription factors (TF). It further identified a chromatin state characterized by relative depletion of chromatin structure modulators and high leukemic TF accessibility, enriched in a small cohort of B lymphoblastic leukemias and associated with adverse prognosis.

overall_design: Chromatin accessibility profiling (ATAC-seq) of BALL patient samples

first: Patricia

last: Favaro

first: Warren

last: Reynolds


title: Lipocalin-2+ Mast Cells in Lymph Nodes Promote Cancer Stemness by a Mitochondrial-derived Peptide

city: Guangzhou

first: Qidong

last: Xia

address: No.107, Yangjiangxi Road, Guangzhou

department: Breast Tumor Center

institute: Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University

summary: Mast cells (MCs) play a pivotal role in multiple primary tumours, but their function remains largely an enigma in metastatic lymph nodes (LNs). Here, using single-cell RNA sequencing data, photoconversion technique, MC-deficient KitW-sh and lipocalin-2 deficient mice, we show that MCs in LNs promote stemness of tumour cells metastasizing to LNs and their further dissemination to distant organs. Mechanistically, lipocalin-2, secreted by LN MCs, facilitates mitochondrial RNA leakage by mitochondrial permeability transition pore (mPTP) opening, which promotes stem cell transcription factor-TFCP2L1 activity by mitochondrial peptide MOTS-c. Aptamer of MOTS-c or lipocalin-2 neutralization inhibit MC-mediated stemness of tumour cells and reduce lung metastasis burden in vivo. Collectively, we uncover the new function of LN MCs and provide an appealing therapeutic strategy for the progression of carcinoma.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for mast cells isolated from tumor metastatic lymph nodes or uninvolved lympn nodes of mice.

first: Xia

last: Qidong

first: Li

last: jiang


title: Lipocalin-2+ Mast Cells in Lymph Nodes Promote Cancer Stemness by a Mitochondrial-derived Peptide [EO771]

overall_design: Comparative gene expression profiling analysis of total RNA-seq data for EO771 cells with or without LCN2 recombinant protein treatment.


title: Thyroid Hormone Signalling is Essential for the Maturation and Survival of Cochlear Root Cells in Mice

first: zhifang

last: xie

address: 1665 Kongjiang Road

department: Ministry of Education-Shanghai Key Laboratory of Children's Environmental Health

institute: Xinhua Hospital, Shanghai Jiaotong University School of Medicine

summary: Thyroid hormone (TH) and/or its receptors (TRs) are essential for hearing, cochlear late-stage development, and maintaining endocochlear potential (EP). The mechanism underlying the EP reduction upon deficiency of TH or TRs remains unknown. The cochlear outer sulcus (root cell) is considered to be important for the maintenance of endolymph homeostasis and EP and undergoes dramatic morphological changes during the cochlear late-stage developmental window. It has been long neglected whether TH and/or TRs are required for root cell differentiation and function. Here we demonstrate a key role for TH or TRs in postnatal root cell development and survival in mice. Anti-thyroid drug-induced developmental hypothyroidism results in severe retardation in root cell differentiation. Targeted deletion of both TRα and TRβ but not individual TRβ in cochlear epithelium causes a similar impairment, compounded with an early-onset degeneration of root cells and a reduced EP, without obvious alterations in stria vascularis. Our results support that TRα and TRβ act redundantly in promoting root cell late-stage differentiation and maintaining its cellular homeostasis, and root cell dysfunction at least partially contributes to a reduced EP upon deficiency of TH or TRs.

overall_design: To reveal the molecular mechanisms underlying TH in the outer sulcus development, we microdissected the outer sulcus together with its underlying spiral ligaments from EU- or hypothyroid mice at P10, and conducted a whole-transcriptome analysis using RNA-seq

first: Zhifang

last: Xie

first: Weiping

middle: J


title: Highly multiplexed single cell chromatin regulator and accessibility profiling elucidates chromatin dynamics in human B cell development and oncogenesis, and reveals an adverse prognostic gene expression signature in B lymphoblastic leukemias

overall_design: Chromatin accessibility profiling of FACS gated developing B cell populations using InTAC-seq protocol


title: The response of epidermal nevi to simulated solar radiation using single-nucleus RNA sequencing of frozen tissue

city: Salt Lake City

first: Philip

last: Moos

state: UT

department: Pharmacology & Toxicology

institute: University of Utah

summary: This study addresses analysis of RNA in single nuclei (snRNAseq) from OCT embedded, frozen human skin/nevus tissue. In this study we created snRNAseq libraries from 6 donors each providing two nevi, one control, and one irradiated with 3-4 times the donor’s erythemal dose (MED) of simulated solar radiation. Both nevi were biopsied 24 hours after irradiation. With no enrichment for rare cell types, our analysis of snRNAseq data reveals the transcriptional diversity of interfollicular and nevomelanocytes, keratinocytes and fibroblast.  We also document changes in skin cells, endothelium and cutaneous immune cells elicited by solar simulated radiation.

overall_design: Single-nuclei RNA sequencing from OCT medium preserved skin punches from solar simulator irradiated and control nevi

first: Pamela

last: Cassidy

first: Sancy

last: Leachman


title: HNF4α is a target of the Wnt/β-catenin pathway and regulates colorectal carcinogenesis

city: Kunming, China

first: Jianwei

address: Kunming, China

institute: Yunnan University

summary: Hepatocyte nuclear factor 4alpha (HNF4α) is a transcription factor involved in liver function. Dysregulation of HNF4α leads to hepatocarcinogenesis. However, the role and mechanism of HNF4α in colorectal cancer is still unknown. Here we demonstrate that HNF4α is upregulated in colorectal cancers. and HNF4α upregulation promotes colorectal tumorigenesis. Notably, expression levels of HNF4α are positively correlated with the Wnt/β-catenin signaling pathway in colorectal cancer patients. Further, we showed that HNF4α is transcriptionally activated by Wnt/β-catenin/TCF3 and is at least partially responsible for the oncognesis activity of the Wnt signaling in colorectal cancer. Our findings indicate that HNF4α is a direct target of that Wnt/β-catenin pathway and could play an important role in colorectal carcinogenesis.

overall_design: Construct mRNA libraries using SW480 colorectal cancer cell line and SW480 colorectal cancer cell line overexpressing HNF4a, and perform RNA-seq using Illumina paired-end sequencing, with three biological replicates for each group.

last: Sang

first: Weiyu

last: Bai

first: Junling

last: Shen


title: GSK-J4 treatment in ovarian cancer cell lines (ATAC-Seq)

city: Cardiff

first: Marcos

last: Quintela

state: --- Select One ---

address: 52 Maindy Rd, Hadyn Ellis Building

department: European Cancer Stem Cell Research Institute

country: United Kingdom

institute: Cardiff University

summary: The deregulation of histone methylation profiles has been implicated in the pathogenesis of multiple diseases, including ovarian cancer, on of the most lethal gynaecological malignancies worldwide. The roles of de-methylases KDM6A/UTX and KDM6B/JDMJD3, generally associated with the maintenance of normal levels of H3K27 methylation, have not been investigated in detail in ovarian cancer, and their functions remain largely unknown. Here, we used the KDM6A/B targeting drug GSK-J4 to understand the implications of specific histone methylation in ovarian cancer. GSK-J4 triggered different responses including anti-proliferative activity, enhanced apoptotic cell death mechanisms and EMT differentiation, amongst others.

overall_design:
We treated OVCAR-3 ovarian cancer cells with GSK-J4 (UTX/JMJD3 inhibitor) and GSK-J5 control to understand the mechanism of action of GSK-J4 and its molecular targets.
The selection of treatment length (48h) and concentration (2.5µM) was based on IC50 results.
We undertook differential gene expression comparisons between control (GSK-J5) and GSK-J4.

first: Agne

last: Pociute

first: Natalia

last: Sikora

first: David

middle: W

last: James


title: GSK-J4 treatment in ovarian cancer cell lines

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

overall_design: Refer to individual Series


title: The role of lipocalin-2 in lung homeostasis, inflammation response, and recovery following organic dust exposure

city: San Jose

first: Eleana

middle: Stephanie

last: Guardado

address: 3166 Kimlee Dr

institute: Stanford

summary: Agricultural industry workers are frequently exposed to harmful dust particles and consequently have a higher risk of developing chronic lung inflammatory conditions such as chronic obstructive pulmonary disease (COPD). Lipocalin-2 (LCN-2) is an innate immune protein with paradoxical roles in both pro- and anti-inflammatory responses at mucosal sites; however, its role in the lung during homeostatic and inflammatory states, such as those induced by inhaled dusts, remain unknown. Here, we investigated the role of LCN-2 in a murine model of organic dust exposure-induced lung inflammation using wildtype C57Bl/6 (WT) and LCN-2 knockout (KO) mice exposed repetitively to extracts of dusts (DE) collected from swine confinement facilities. Repetitive DE exposure consisted of fifteen days of intranasal instillations with and without a three-day recovery period. Through these investigations, we identified an important function of LCN-2 in regulating tissue homeostasis and recovery following inflammatory injury in the lung. Additionally, compartmentalized effects on T cell and macrophage levels were observed in BALF vs. lung tissue in DE-exposed LCN-2 KO mice versus WT mice. Ablation of LCN-2 resulted in deficits in resolving histopathological markers of inflammation, and decreased levels of IL-10 after DE. Exogenous IL-10 administration partially rescued the histopathological markers of inflammation in LCN-2 KO mice after DE exposure. Taken together, these investigations highlight a novel role for LCN-2 in regulating lung homeostasis, inflammation response, and repair following organic dust-induced inflammation that may be mediated, at least in part, by IL-10.

overall_design: WT and LCN-2 KO mice were repetitively exposed to DE prepared from dusts collected from swine confinement facilities or their saline vehicle control. An aqueous solution of dust extract was prepared as described above and published previously and administered to mice as a 50 l intranasal instillation (IN) of 12.5% DE or saline under light isoflurane anesthesia. Male mice of 8-13 weeks old were given IN instillations in the mornings for 15 weekdays.  For this work, we evaluated two time points after repetitive DE exposure: 1) five hours after last IN (no recovery period), and 2) 72 hours after last IN (recovery period). For studies that included IL-10 administration, 1 ug of recombinant mouse IL-10 per 25 g mouse body weight was administered to LCN-2 KO animals on the day of the final DE IN and at 48 hr post final DE IN. Animals were euthanized with isoflurane and collection of bronchoalveolar lavage fluid (BALF) and lung tissue was performed as described below. For BALF collection, a cannula was first inserted into the trachea and secured by tying a knot with a suture around the trachea. A syringe was used to rinse/wash the whole lung with 1 ml of sterile 1X PBS, which was collected in a separate tube to prevent over-dilution in subsequent enzyme-linked immunoassays (ELISAs). The lungs were washed two additional times with 1 ml PBS, and combined in a second tube for downstream cellular analyses. After BALF collection, the left lung lobe was tied off, excised and frozen in RNAlater to be used for NanoString analyses. The right lung lobes were inflated with 0.5 ml of 10% formalin and hung with a constant pressure of 20 cm H2O for 24 hours while submerged in formalin for optimal lung morphology preservation (n = 3-8 mice per experimental group). Mouse NanoString Fibrosis V2 panels (Catalog #115000388; NanoString Technologies, Seattle, WA, USA) were used for quantification of 778 RNA transcripts using an nCounter Sprint Profiler. Three male mouse lungs were used from independent experiments for each experimental group. Upon harvest and proper storage of mouse lungs described previously, mouse lungs were thawed for RNA extraction. Lungs were rinsed with PBS followed by homogenization in 1 ml Trizol by using a 7 cm polypropylene pellet pestle in a microcentrifuge tube. A Purelink RNA Mini kit (Catalog #12183025; Invitrogen, Carlsbad, CA, USA) was used for the RNA extraction, which was performed per the manufacturer’s instructions. RNA integrity number (RIN) was acquired from the UC Riverside Institute for Integrative Genome Biology Core Facility by using an Agilent Bioanalyzer 2100 (Agilent, Santa Clara, CA, USA). All samples used had a RIN of 7-9. A codeset probe provided by the kit was hybridized for 18 hours with 50 ng RNA. Samples were brought up to volume with nuclease-free water and 32 ul were loaded onto an nCounter Sprint Cartridge (Catalog #100078; NanoString Technologies, Seattle, WA, USA). A total of 12 samples fit in one cartridge, thus a total of 12 samples were used for repetitive studies with no recovery or IL-10 administration, 12 samples for repetitive studies with recovery but no IL-10 administration, and 12 samples for chronic studies with recovery and IL-10 administration. All samples passed the NanoString system quality control (QC) test. Data were analyzed using nSolver 4.0 and by performing a NanoString Advanced analysis. The following housekeeping genes showing the strongest correlation with each other were used for normalization of gene expression: Acad9, Cnot10, Mtmr14, Nol7, Nubp1, Pgk1, Ppia, and Rplp0. The agglomerative analysis on nSolver was used to generate heatmaps. Per NanoString’s recommendation, 50 transcript counts was taken as the “count threshold”. The 20 most upregulated genes among all treatments were identified by the differential expression analysis. The STRING database (https://string-db.org) was used to explore protein-protein interactions among differentially regulated genes from NanoString that were statistically significant based on the unadjusted p-values [20].

first: Stephanie

first: Daniel

last: Ojeda-Juárez

first: Arzu

last: Ulu

first: Stefanie

last: Sveiven

first: Edward

last: Dominguez

first: SangYong

last: Kim

first: Shaiva

last: Patel

first: Marcus

last: Kaul

first: Tara

last: Nordgren


title: Single cell transcriptomics of impact of HIV on latent TB infection in a rhesus macaque model of Mtb/SIV co-infection

city: SAN ANTONIO

first: YI

last: ZOU

address: 8403 Floyd Curl Drive

institute: UTHSA-GCCRI

summary: HIV coinfection impairs Mtb-specific immunity resulting in reactivation of a latent TB infection (LTBI) in a subset of individuals. We performed Single cell RNA sequencing (scRNA-seq) on bronchalvolear lavage (BAL) samples collected at pre-determined time points from Mycobacterium tuberculosis (Mtb)/ Simian Immunodeficiency Virus (SIV) co-infected rhesus macaques. We identified a total of 14 clusters including monocytes, natural killer (NK) cells, T regs, central memory CD4+ T cells, B cells, club cells and neutrophils in the airways of Mtb/SIV co-infected rhesus macaques. Diminished expression of TH1 cell-specific transcription factors after SIV co-infection was not rescued despite effective cART. In contrast, SIV co-infection led to a reduction in the expression of immunoregulators in monocyte clusters; but increased expression of genes involved in interferon signaling, TH17 induction, T cell activation and tuberculosis associated immune reconstitution inflammatory syndrome (TB-IRIS). Increased inflammation and migratory gene expression was observed in dendritic cells upon SIV co-infection. Overall, the lungs of SIV co-infected macaques with LTBI-like controlled, asymptomatic Mtb infection are characterized by the presence of chronic immune activation at the transcriptomic level, which can persist despite cART. Our work identifies key cell subsets, including novel ones, impacted by HIV coinfection of a latent TB infection in a biologically relevant animal model.

overall_design: These cells were isolated from bronchoalveolar lavage of rhesus macaques co-infected with Mtb/SIV and treated with cART

first: Riti

last: Sharan

first: Yi

last: Zou

first: Korri

last: Weldon

first: Zhao

last: Lai

first: Todd

last: Bradley

first: Shabaana

last: Khader

first: Deepak

last: Kaushal


title: Combined single-cell profiling and functional analysis reveals the importance of pseudogenes in human early embryonic development

first: Liu

last: He

address: No. 5, Dongdan Sanjo, Dongcheng District

institute: Peking Union Medical College

summary: More and more studies have demonstrated that pseudogenes possess coding ability, and the functions of their transcripts in the development of diseases have been partially revealed. However, the role of pseudogenes in maintenance of normal physiological states and life activities has long been neglected. We identified pseudogenes that were dynamically expressed during human early embryogenesis, which showed different expression pattern from that of adult tissues. We explored the expression correlation between pseudogenes and the parent genes, part due to their shared gene regulatory elements or the potential regulation network between them. The essential role of three pseudogenes, PI4KAP1, TMED10P1 and FBXW4P1, in maintaining self-renewal of human embryonic stem cells was demonstrated. We further found that the three pseudogenes might perform their regulatory functions by binding to proteins or microRNAs. The pseudogene-related single-nucleotide polymorphisms were significantly associated with human congenital disease, further illustrating their importance during early embryonic development. Overall, this study is an excavation and exploration of functional pseudogenes during early human embryonic development, suggesting that pseudogenes are not only capable of being specifically activated in pathological states, but also play crucial functions in the maintenance of normal physiological states.

overall_design: To find out how pseudogenes influence gene expression in hESC, we also performed RNA-seq in WT/PI4KAP1-KD/ TMED10P1-KD/ FBXW4P1-KD hESC,each with two replicates.

first: Mengyao

last: Sun


title: Engrailed transcription factors regulate differentiation and survival of embryonic Purkinje cells and interneurons

city: New York

first: Alexandra

middle: L.

last: Joyner

state: New York

address: 430 E 67th St

department: Developmental Biology Program

institute: Sloan Kettering Institute

summary: In this study, we performed single cell sequencing of the inhibitory neuron lineage in mouse E15.5 control and  En1/2 CKO cerebella.

overall_design: Ptf1a-lineage neurons of the cerebellum labeled by tdTomato in control or Engrailed 1/2 knockout E15.5 embryos were isolated by FACS, and scRNA-seq using the 10X Genomics' Chromium Next GEM Single Cell 3' Reagent Kits (v3.1). Samples were then sequenced on a NovaSeq 6000.

first: Anjana

last: Krishnamurthy

first: Olivia

last: Nasef


title: Elucidating the molecular mechanisms underlying CRB1-related Leber congenital amaurosis (LCA)

city: London

first: Mariya

last: Moosajee

address: 11-43 Bath Street

department: Institute of Ophthalmology

institute: UCL

summary: Patients with genetic mutations in the CRB1 gene have varied clinical features and levels of disease severity ranging from Leber congenital amaurosis (LCA), early onset retinal dystrophy (EORD) to retinitis pigmentosa (RP). The relationship between genetic mutation and clinical presentation is not well understood. Our lab have characterised two disease models of CRB1 (Owen et al 2023); zebrafish and patient grown stem cell derived early retinas. Investigation reveals lack of the CRB1 protein prevents the retina from developing into a mature state with precise defined cell types, instead it is locked in an early stage of development with lots of cells dividing. To futher understand the underlying molecular mechanisms causing the CRB1 phenotype we have carried out transcriptome analysis of iPSC derived 3D retinal organoids at day 35.

overall_design: Gene expression analysis (RNA-seq) was carried out on CRB1 and wildtype control iPSC derived 3D retinal organoids at day 35, two clonal lines per condition, three replicates per clone.

first: Nicholas

last: Owen


title: Development and Validation of Targetable Prognostic Risk Score in Locally Advanced Nasopharyngeal Carcinoma [Affymetrix]

city: Hong Kong

first: Huaping

last: Li

address: 21 Sassoon Rd, Pok Fu Lam

country: Hong Kong

institute: The University of Hong Kong

summary: a novel gene signature for risk stratification of patients with locally advanced NPC and suggest potential therapies for high-risk patients.

overall_design: We identified 5 prognostic risk genes (SPP1, IL18BP, PALMD, WDR35, SOCS6) from the whole transcriptomic pattern of 99 advanced NPC FFPE samples by bootstrapping LASSO regression method. A prognostic risk prediction model was developed using Cox regression.

first: Chi-leung

last: Chiang

first: Jason Wing Hon

last: Wong


title: Interleukin-6 is critical in the development of gcn2-mutation associated pulmonary veno-occlusive disease in mice

city: Cambridge

first: Elaine

last: Soon

address: Keith Peters Building, Biomedical Campus, Hills Rd, Cambridge CB2 0XY

institute: Cambridge Institute for Medical Research (CIMR)

summary: Biallelic mutations in eukaryotic translation initiation factor 2 α kinase 4, EIF2AK4 (which encodes general control nonderepressible 2, GCN2) underpin heritable forms of pulmonary veno-occlusive disease (PVOD), a rare and fatal form of pulmonary hypertension. The mechanisms linking these remain uncharacterised. We demonstrate for the first time that homozygous loss of gcn2 is sufficient to cause mild pulmonary hypertension in mice. Single-cell transcriptomics of mouse lungs identified adventitial fibroblasts as having the greatest GCN2-dependent transcriptional differences, implicating them as key players in this model of PVOD. The most significantly upregulated pathways in gcn2-/- adventitial fibroblasts were inflammatory, and therefore we went on to demonstrate a pro-inflammatory phenotype in gcn2-/- mouse embryonic fibroblasts and gcn2-/- mice. When chronically exposed to lipopolysaccharide, the pulmonary hypertensive phenotype of gcn2-/- mice is exaggerated. Genetic ablation of interleukin-6 completely rescues both baseline and LPS-exaggerated pulmonary hypertensive phenotype.  In an orthogonal murine model of pulmonary hypertension induced by exposure to mitomycin-C, deletion of interleukin-6 again rescued the pulmonary vascular phenotype. Targeting Il6-dependent pathways may be useful in treating this deadly disease.

overall_design: Age- and sex-matched gcn2-/- and wild-type littermates from the same cage were sacrificed by cervical dislocation. The lungs were flushed with PBS-heparin (25U/ml), washed thrice in PBS, and finely minced. The lung homogenates were digested (using collagenase, dispase and DNase), filtered through a 100micron sieve, subjected to red blood cell lysis and then passed through a 50micron filter. Flow cytometry was used to isolate single live CD45-positive and CD45-negative cells and 16,000 cells were processed using the Chromium 3’ kit (10xGenomics, Leiden, the Netherlands). Sample processing and cDNA library preparation was performed by the Jeffrey Cheah Biomedical Centre and the Cancer Research UK genomics core facility. The cDNA was sequenced on a NovaSeq S2 or S4 chip (NovaSeq 6000, Illumina, UK).

first: Max

last: Schwiening

first: Qingyue

last: Gao

first: Mark

last: Southwood

first: Alexi

last: Crosby

first: Stephen

last: Moore

first: Jose

last: Valer

first: Benjamin

last: Dunmore

first: Paul

last: Upton

first: Niki

last: Veale

first: Roger

last: Thompson

last: Morrell

first: Stefan

last: Marciniak


title: Development and Validation of Targetable Prognostic Risk Score in Locally Advanced Nasopharyngeal Carcinoma

type:
Expression profiling by array
Other


title: Acute Myeloid Leukemia patient/ CD34+ healthy donor RNA-seq

first: Bettina

last: Nadorp

state: NY

address: 500 1st Ave

department: Medicine/Pathology

institute: NYU Langone Health

summary: AML is an aggressive and heterogenous hematologic malignancy. Here, we performed bulk RNA sequencing of 16 AML patients and primary hematopoietic cell populations, CD34+ HSC and CD14+monocytes to understand transcriptional and post-transcriptional mechanisms that drive leukemogenesis and block AML differentiation. Our findings provide a better understanding of gene regulatory pathways in AML in comparison to normal hematopoietic cells, which may provide new therapeutic strategy to selectively target AML cells.

overall_design: RNA-sequencing on bone marrow aspirates of AML patients and CD34+ cells

first: Yixiao

last: Gong

first: Eric

last: Wang

first: Iannis

last: Aifantis

first: Aris

last: Tsirigos


title: Gene expression profile at the single-cell level of skin and PBMC samples collected from patients with severe cutaneous adverse drug reactions (SCADR).

city: Lausanne

first: Evarist

last: Planet

state: Vaud

address: Route Cantonale

institute: EPFL

summary: Severe cutaneous adverse drug reactions (SCADR) encompass a wide spectrum of potentially dreadful disease entities resulting from a type IV delayed hypersensitivity reaction. Single-cell RNA sequencing (scRNA-seq) provides an opportunity to decipher potential cell-cell interactions and cell-type specific transcriptomic changes, amenable to therapeutic intervention, particularly in rare diseases with heterogenous clinical presentations and lacking experimental animal models, such as SCADR. We performed scRNA-seq on the skin of four patients diagnosed with SCADR syndromes including one toxic epidermal necrolysis (TEN), one Stevens-Johnson syndrome (SJS), one acute generalized exanthematous pustulosis (AGEP), and one extensive drug-related maculopapular rash (MPR), and three healthy controls.

overall_design: PBMCs were isolated from EDTA anticoagulated venous blood of SCADR patients and healthy volunteers after ficoll gradient sorting prior to FACS sorting of propidium negative (PI) cells using a Beckman Coulter MoFlo Astrios for dead cell removal. Sorted cells were immediately processed for scRNA-seq analysis. Skin biopsies were processed essentially as previously described by Kim D et al. (Nat Med. 2020;26(2):236-243. doi:10.1038/s41591-019-0733-7) with minor modifications. Alive cells were isolated with Beckman Coulter MoFlo Astrios after PI and Hoecht staining and immediately processed for scRNA-seq analysis.

first: Filipe

last: Martins


title: The critical role of spatio-temporal control in combinatorial chemo- and magnetic hyperthermia thermo-therapy: ‘the where’, ‘the how’ and ‘the when’

city: Braga

first: Juan

last: Gallo

address: avda Mestre Jose Veiga sn

department: Health

country: Portugal

institute: International Iberian Nanotechnology Laboratory

summary: Combinatorial treatments hold the key to the future of cancer treatment as they enhance therapeutic indexes by inducing synergistic effects and reducing resistance processes while often providing a safer option for patients with fewer off-target effects. However, combinatorial treatments bring extra problems to cancer management not only derived from the actual compatibility of the treatments, but also from their hands-on administration. Operational parameters such as administration order and dosing (dose, spacing) have to be optimized in order to positively impact patient prognosis. Here we present a systematic study on the optimization and the importance of these parameters within the framework of a combinatorial chemo-/thermo-therapy. Parameters like ‘where’, ‘how’ and ‘when’ are investigated in detail. Furthermore, we delve into the underlying biochemical mechanisms driving the observed effects through transcriptome analysis.

overall_design: Transcriptomic profile of B16F10 cells after different treatment conditions. Group 1: Control cells; Group 2: Cells treated with free DOX; Group 3: Cells treated with mLNVs + MH; Group 4: Cells treated with mLNVs-DOX + MH.

first: Lorena

last: García-Hevia

first: Andreia

middle: P

last: Magalhães

first: Nuria

last: Genicio

first: Íñigo

last: Casafont

first: Milene

last: Costa da Silva

first: Mónica

last: López Fanarraga

first: Manuel

last: Bañobre-López


title: A small RNA sequencing dataset from multiple tissues of Orestias ascotanensis collected at two seasonal time points

status: Public on Jun 22 2026

city: Santiago

first: Rorigo

last: Maldonado

address: Avenida Pedro de Valdivia 1509

country: Chile

institute: Universidad Finis Terrae

type: Non-coding RNA profiling by high throughput sequencing

summary: This study presents a small RNA sequencing (small RNA-seq) dataset from the Andean killifish Orestias ascotanensis, an extremophile teleost endemic to the Ascotán Salt Pan in the Chilean Altiplano. The dataset includes 42 libraries generated from gills, skin, and muscle tissues of 14 adult individuals sampled in summer and winter. Small RNA libraries were prepared using the Illumina TruSeq Small RNA Library Preparation Kit and sequenced on an Illumina NextSeq 500 platform

overall_design: This study includes small RNA sequencing (small RNA-seq) samples from the extremophile teleost fish Orestias ascotanensis. Samples were collected from 14 adult individuals captured at two seasonal time points (summer and winter). For each individual, three tissues—gills, skin, and muscle—were sampled and processed independently, resulting in a total of 42 biological samples. The experimental variables include tissue type and season. All samples represent biological replicates; no pooled samples were used. There are no technical replicates or control reference samples included in this submission.

first: Martin

last: Montecino

first: Rodrigo

last: Maldonado-Agurto


title: DDX6 reshapes the cancer RNA editome to suppress RNA-induced innate immunity

city: Singapore

first: jinghe

last: xie

address: 21 Lower Kent Ridge Road

institute: nuh


title: DDX6 reshapes the cancer RNA editome to suppress RNA-induced innate immunity [eCLIP]

summary: ADAR1 is thought to be an immune suppressor and maintains self-tolerance to endogenous nucleic acids through its A-to-I RNA editing catalytic activity. Its editing activity is tightly regulated by an array of different proteins and factors. In this study, we investigated the role of DDX6 in A-to-I RNA editing regulation and how this in turns regulate dsRNA-induced immunity.

overall_design: We immunoprecipitated helicase-bound (DDX6, DHX9, DDX21, DDX3X) RNA molecules and constructed cDNA libraries. These libraries were sequenced using Illumina Hiseq 4000 platform. We then identify the transcriptome-wide binding landscapes of each of these RNA helicases.

first: Leilei

last: Chen

first: Xi

last: Ren

first: Jinghe

last: Xie

first: Omer

last: An

first: SzeJing

last: Tang

first: Priyankaa

last: Pitcheshwar


title: DDX6 reshapes the cancer RNA editome to suppress RNA-induced innate immunity [Bulk RNA-seq]

overall_design: We constructed strand-specific cDNA libraries of total RNA samples harvested from helicase-depleted cells as well as their controls. These libraries were sequenced using Illumina Hiseq 4000 platform. We then identify differentially edited sites of helicase-depleted cells relative to control.

first: Yangyang

last: Song


title: Single cell transcriptome atlas revealed the feature of contemporary ZIKA virus induced microcephaly in mice

city: Jinan

first: Chi

last: Zhang

address: 44 Wenhua West Road

institute: Shandong University

summary: Zika virus (ZIKV), a mosquito-borne flavivirus, has imposed tremendous global threat to human health and was declared as a public health emergency of international concern by the World Health Organization in 2016. However, the pathogenic mechanism of ZIKV still lacks sufficient understanding. In recent years, the development of single-cell sequencing technology has provided a more precise approach for exploring disease mechanisms. Therefore, in this study, we depicted a high-resolution transcriptomic landscape and functional changes of brain immune and neural cells during disease progression of ZIKV, which will facilitate a better understanding of the underlying pathogenesis of ZIKV-induced microcephaly.

overall_design: Single cell RNA sequencing of mouse brain samples collected from groups of ICR mice (n=5) with ZIKV PRVABC-59 or FSS13025 infection or PBS injection at 10 dpi,.

first: Honglei


title: lncRNA profile of whole blood cells

city: Shanghai

first: Chunxia

last: Wang

state: Shanghai

address: No.355 Luding Road, Shanghai Children's Hospital, Shanghai Jiao Tong University School of Medicine

department: Department of Critical Care Medicine

institute: 上海交通大学附属儿童医院

summary: Arraystar human LncRNA microarray was performed on whole blood samples of 36 cases with bacterial sepsis and 20 children with non-bacterial sepsis to analyze differentially expressed LncRNAs

overall_design: Based on the first batch result of Arraystar human LncRNA microarray using 16 cases (12 cases with bacteria sepsis vs. 4 cases with non-bacteria sepsis), we firstly revealed the potential key relationship between lncRNAs landscape and pathogen infection (Preliminary data, data not shown). Then, the other batch of Arraystar human LncRNA microarray using 40 cases (24 cases with bacteria sepsis vs. 16 cases with non-bacteria cases) were added. Totally, these two batches included 36 cases with bacterial sepsis and 20 children with non-bacterial sepsis. To remove the batch effects, we merged 2 batches results, and all analyses were conducted with R version 4.0.5 and sva packages.


title: Transcriptional Profiling of P1 Neurons in Drosophila melanogaster

city: Middlebury College

first: Amanda

last: Crocker

state: Vermont

address: 276 Bicentennial Way

department: Neuroscience

institute: Middlebury College

summary: We report the application of low cell number sequencing of identifiable P1 neurons in male Drosophila melanogaster. We find these neurons display a diverse repertoire of receptors and signaling transcripts.  We also find that mating state results in differential expression and this aligns with previous reports of gene expression differences.

overall_design:
The Fru positive P1 cluster of neurons were used to look at general gene expression and changes induced by mating state.  4 sets of paired naive and mated male animals were used.  Animals were aged 3-6 days old.  Cells were harvested at the same chronological time for the animals across all experiments. All cells were harvested using a patch pipet from living animals of the genotype UAS>stop>GFP/+; fruFLP/NP2631-Gal4 on an electrophysiology rig within a half hour of the end of training. 12 Cells are found in this cluster.  Cells were amplified using the Clontech SMARTer Ultra Low Input RNA version 2 High Volume kit. Samples were run across 2 lanes.
Please note that each processed data .txt file has processed data for both *A and *B sample and is linked to the corresponding *A sample records.

first: Sama

last: Ahmed

first: Mala

last: Murthy


title: Genotype-phenotype relationships (VPA/CHIR99021 vs. control; p53 Null vs. WT) in bulk RNA-sequencing of small intestinal murine organoids [bulk RNA-seq]

city: Oxford, Oxfordshire

first: Xin

last: Lu

address: Roosevelt Drive

institute: Ludwig Institute for Cancer Research, University of Oxford

summary:
WT and Trp53 knock-out small intestinal organoids were cultured in standard ENR medium or treated with VPA and CHIR99021 for 5 days.
At the endpoint of the culture, RNA was extracted from the cells and analysed with paired-end RNA-sequencing.

overall_design: Biological duplicates were used in the experiment.

first: Xiao

last: Qin

first: Felix

middle: Y

last: Zhou

first: Thomas

last: Carroll


title: Bulk and single-cell RNA-seq

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

overall_design: Refer to individual Series


title: Defective cuticle-derived signals enhance extracellular ATP response and plant immunity

city: Columbia

first: Gary

last: Stacey

state: Missouri

address: 271E Christopher S. Bond Life Sciences Center

institute: University of Missouri at Columbia

summary: Extracellular ATP (eATP) acts as a damage-associated molecular pattern (DAMP) in both animals and plants. In plants, eATP is recognized by the purinergic receptors P2K1 and P2K2, which mediate responses to various environmental stresses. From a p2k1 suppressor screen, we identified two allelic mutants of the cutin biosynthesis gene, BODYGUARD (BDG). The BDG mutations specifically suppress p2k1 and p2k1p2k2 mutant defects in response to eATP. The suppression of p2k1 by bdg modifies plant defense against the necrotrophic fungal pathogen, Botrytis cinerea. In addition, the results show that the defective cuticle in bdg mutants generates cutin breakdown products, such as cutin monomers, which serve as signaling molecules to activate eATP response and plant immunity through an alternative eATP signaling pathway. Our data provide new insights into the signaling role of cutin and reveal the first link between the cuticle and eATP signaling.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Col-0, p2k1-3 mutant, bdg-8 mutant, and the p2k1-3 bdg-8 double mutant treated with mock or 150 μM ATP for 30 min.

first: Mengran

last: Yang

first: Jae hyo

first: Ha

middle: N

last: Duong

first: Li

last: Su

first: Sung-hwan

last: Cho

first: Daewon

last: Kim

first: Dong

last: Xu


title: Transposable Element-Driven Expansion of Enhancer RNA Repertoires Underlies Regulatory Innovation and Polyploid Adaptation in Cereal Crops [lncRNA-seq]

city: shanghai

first: yijing

last: zhang

address: 2005 Songhu Road

department: Biochemistry

institute: Fudan University

summary: Cereal genomes have undergone repeated polyploidization and transposable element (TE) proliferation, collectively generating complex regulatory landscapes. The evolutionary trajectories and functional implications of these landscapes, however, remain largely unexplored. By employing chromatin-bound RNA sequencing across seven cereal species, we systematically mapped 45,952 regulatory element transcripts (RETs), including 32,867 distal RETs corresponding to enhancer RNAs (eRNAs). Our analysis reveals that 56% of lineage-specific eRNAs originate from TE expansions, suggesting TEs as significant reservoirs of species-specific regulatory innovation in cereals. Notably, we uncovered a remarkable similarity in defense-related function, root-specific expression, and TE-derived origin of eRNAs across ancient and recent evolutionary layers of Triticeae, suggesting recurrent recruitment of TE-derived root-associated regulatory elements during Triticeae evolution. Furthermore, we found that young eRNA pairs in hexaploid wheat with high sequence similarity, many originating from RLG_famc8.3 and DTC_famc4.3, exhibit pronounced root specificity and coordinated expression, suggesting a targeted amplification and refinement of the successful ancestral regulatory strategy established after Triticeae divergence. To facilitate community access, we developed Cereal-eRNAdb (http://bioinfo.cemps.ac.cn/Cereal-eRNAdb/), a comprehensive database integrating 69,426 eRNAs with functional annotations across 296 samples. Our work indicates that TE-mediated innovation of root-specific eRNAs as a candidate mechanism that may contribute to Triticeae adaptation and provides a foundational resource for exploiting regulatory variation in cereal crop breeding.

overall_design: Seedlings (above-ground) of common wheat (Triticum aestivum cultivars ‘Chinesespring’‘AK58’ and ‘Fielder’), barley (Hordeum vulgare cultivar ‘Morex’), rye (Secale cereale cultivar ‘Weining’), maize (Zea mays cultivar ‘B73’) and rice (Oryza sativa cultivars ‘ZH11’ and ‘Jap’) were harvested after 9-day growth. The roots, leaf and embryos of three wheat species (Triticum aestivum cultivar ‘Chinese Spring’, Triticum urartu cultivar ‘G1812’ and Aegilops tauschii cultivar ‘AL8-78’) were collected as follows: roots in the Hoagland solution were harvested after 9-day growth; the fresh immature embryos were isolated 14 days post anthesis; leaf were were harvested after 9-day growth. All the above materials were flash frozen in liquid nitrogen followed by nuclei isolation. Nuclei were isolated from 1 mL tissue powder solubilized in 20 mL ice-cold Honda buffer (0.44 M sucrose, 1.25% Ficoll, 2.5% Dextron T40, 20 mM HEPES, pH7.4, 10 mM MgCl2, 0.75% Triton X-100, 0.5 mM EDTA, 1 mM DTT, 8 mM β-mercaptoethanol, 2 µg/mL pepstatin A, 2 µg/mL aprotinin, 2 mM PMSF). The mixture was incubated on ice for 5 min, then filtered through 110 µm nylon mesh and a 40 µm cell strainer. The crude nuclei were spun down at 3,500 g for 5 min at 4°C, followed by washes with 150 µL of resuspension buffer (50% Glycerol, 0.5 mM EDTA, 25 mM Tris-HCl, pH 7.5, 100 mM NaCl, 1 mM DTT, 8 mM β-mercaptoethanol, 2 µg/mL pepstatin A, 2 µg/mL aprotinin, 2 mM PMSF, 0.4 U/µL RNase inhibitor) and 300 µL of wash buffer (25 mM Tris-HCl, pH 7.5, 300 mM NaCl, 1 M urea, 0.5 mM EDTA, 1% Tween 20, 1 mM DTT, 8 mM β-mercaptoethanol, 2 µg/mL pepstatin A, 2 µg/mL aprotinin, 2 mM PMSF, 0.4 U/µL RNase inhibitor). Again, the obtained nuclei were washed with another 150 µL of resuspension buffer and 150 µL of wash buffer. CB RNA was extracted from washed nuclei using TRIzol reagent and subjected to genomic DNA removal by TURBOTM DNase (Life Technologies). After purification with RNA Clean & ConcentratorTM-5 kit (Zymo Research, R1013), ~1 µg CB RNA was subjected to rRNA depletion by a riboPOOL kit (siTOOLs Biotech, PanPlant-10 nmol) and polyA RNA removal by oligo (dT) beads (NEB, S1419). PolyA RNA was enriched from total RNA by oligo(dT) beads. Purified CB RNA and PolyA RNA were transformed into cDNA libraries using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB #E7765) and sequenced on an Illumina NovaSeq platform.

first: Yijing


title: Single cell transcriptomic profiling of caridac tissues from different degrees of septic shock mice

city: Chongqing

first: Chenyang

last: Duan

address: Changjiang Road

department: Department of Anaesthesiology

institute: Chongqing Medical  University

summary: Sepsis is a fatal organ dysfunction caused by the imbalance of host response caused by infection. It has the characteristics of high incidence rate, high mortality and high treatment cost. Heart is one of the most vulnerable target organs in sepsis. Sepsis can lead to myocardial depression, which is mainly manifested in the impairment of systolic function, cardiac enlargement, decreased ejection fraction and so on. Sepsis induced myocardial dysfunction (SIMD) is an important cause of septic shock and death. Therefore, using single-cell RNA sequencing to clarify the mechanisms of SIMD is of great significance to effectively prevent sepsis shock from developing into multiple organ dysfunctions (MODS) or even death.

overall_design: Cardiac tissues were obtained from C57 mice and analyzed using 10X genomics scRNAseq. The experimental groups include control group (n=2),Cecal ligation and perforation (CLP) 12h group (n=2), and CLP 24h group (n=2).


title: Assesing the Impact on Soybean Root Gene Expression of Inoculation with Hub microbes

city: East Lansing

first: Reid

last: Longley

state: MI

address: 612 Wilson Rd #106

department: Microbiology and Molecular Genetics

institute: Michigan State University

summary: Drought is an increasing threat to soybean (Glycine max) production worldwide. In addition to methods such as breeding and genetic modification, inoculation of plants or soils with single microbes and microbial consortia are being explored to mitigate the impacts of drought stress on crop plants. One criterion for selecting microbes within a consortium is to select hub taxa, which are those whose abundances appear to be highly correlated with abundances of other taxa in the microbiome. To assess the impact of microbial inoculations with hub taxa on soybean, I identified five hub taxa from soybean roots which were then used to inoculate soybeans grown in 75% sand and 25% no-till soil from the KBS LTER. No-till soil was used to match the environment from which hub taxa were identified and isolated, and because no-till soils are known to confer resilience to low-moisture stress. Inoculated and control plants were then exposed to low-moisture stress as seedlings. Selected hub taxa included two fungi (Humicola sp., and Gibellulopsis sp.) and three bacteria (Streptomyces sp., Massilia sp., and Caulobacter segnis). The impact of inoculation on plant hosts was assessed with phenotype measures (aboveground and belowground) and plant functional measures (transcriptomics and non-target metabolomics of roots). The impact on the microbiome was assessed using amplicon sequencing of DNA as well as cDNA created from RNA extracted from roots. Inoculation had a minor impact on the microbiome that was most apparent when a more active fraction of the microbiome was analyzed using cDNA. cDNA amplicon sequencing demonstrated that Bradyrhizobium was enriched earlier in inoculated samples compared to control samples and that Glomus was enriched earlier in control samples. Transcriptomics of soybean roots demonstrated that genes related to nodulation were upregulated in inoculated samples, and non-targeted metabolomics appeared to show a possible signal of increased nodulation related metabolites in inoculated samples. Molecular and metabolomics data agreed with phenotypic data which showed increases in nodulation as well as increased aboveground growth, likely related to increased nitrogen fixation activity. Experiments using field soils and enriching individual hub taxa revealed that this effect of increased resilience to drought and nodulation was reproducible with both Caulobacter segnis and Streptomyces treatments. Overall, these results support the hypothesis that hub taxa can be used as inocula to improve the performance and resilience of the host plants.

overall_design: RNA was extracted from soybean roots after seeds were inoculated with five hub taxa. RNA was extracted at five timepoints: pre-drought, three timepoints during drought, and post drought recover from soybean seedling. At each timepoint 3 inoculated plants and 3 controls were sampled and sequenced for a total of 30 samples. Each sample was sequenced across three lanes.

first: Longley

last: Reid

first: Trail

last: Frances

first: Chilvers

last: Martin

first: Bonito

last: Gregory


title: GSK-J4 treatment in ovarian cancer cell lines (RNA-Seq)

city: Cardiff

first: Marcos

last: Quintela

address: 52 Maindy Rd, Hadyn Ellis Building

institute: Cardiff University

summary: Ovarian cancer cell lines OVCAR-3, CAOV3 and SKOV were treated with GSK-J4 and GSK-J5 for 48 and 72 hours.

overall_design: Total RNA was obtained from OVCAR-3, CAOV3 and SKOV3 cells treated with GSK-J4 and GSK-J5 control (2.5uM)

first: David

last: James


title: Phf6 truncating mutation drives leukemogenesis via disrupted epigenetic regulation in mice

city: San Antonio

first: Ying

last: Guo

address: 8403 Floyd Curl Dr

institute: UT Health Science Center at San Antonio


title: Phf6 mutation induces leukemogenesis through altered chromatin state in mice (ChIP-Seq)

summary: To investigate the effect of PHF6 mutations in leukemogenesis, we generated Phf6R274X transgenetic(Tg) mice. Then we purified the cKit+ cells from bone marrow of Phf6R274XTg and WT mice, and performed ChIP-seq to study histone modification in hematopoietic stem and progenitor cells.

overall_design: H3K27ac, H3K4me1 and H3K4me3 ChIP-seq for bone marrow cKit+ cells from WT (n=2) and Phf6R274XTg (n=2)  mice.

first: Pingpin

last: Sui

first: Feng-Chun


title: Phf6 mutation induces leukemogenesis through altered chromatin state in mice (scRNA-Seq)

summary: To investigate the effect of PHF6 mutations in leukemogenesis, we generated Phf6R274X transgenetic(Tg) mice. Then we purified the Lineage-cKit+ cells from bone marrow of Phf6R274XTg and WT mice, and performed single cell RNA-seq to study hematopoietic stem cell differentiation trajectory.

overall_design: Single cell RNA-seq for bone marrow Lin-cKit+ cells from WT (n=2) and Phf6R274XTg (n=2)  mice.

last: Yang


title: Profiling anagen skin in control and Fgf5 mutant mice

city: Irvine

first: Maksim

last: Plikus

state: California

address: 845 Health Sciences Road

department: Developmental and Cell Biology

institute: University of California, Irvine

summary: We report transcriptomes of cells from adult mouse skin in anagen phase of the hair growth cycle, comparing control tamoxifen induced Nfatc1-CreER;mTmG mice with mutant tamoxifen induced Nfatc1-CreER;mTmG;Fgf5-/- mice. Dead cells were removed from whole skin tissue using dead cell removal kit (MACS). Remaining live cells were analyzed.

overall_design: Examination of single cell heterogeneity in anagen skin between Nfatc1-CreER;mTmG and Nfatc1-CreER;mTmG;Fgf5-/- mice.

first: Christian

middle: F

last: Guerrero-Juarez

first: Zhengquan

last: Yu

first: Ruiqi

last: Liu


title: ChIP-seq experiment of H3K4me3 and H3K27me3 in HH30 chicken neural tubes

city: Barcelona

first: Marian

last: Martínez-Balbás

state: Barcelona

address: Baldiri Reixac 4-8, EDIFICI HELIX

institute: IBMB-CSIC

summary: During development, the major class of chromatin regulators is the Polycomb group (PcG) proteins. In this context, they maintain the balance between self-renewal and differentiation. While the role of the Polycomb factor EZH2 has been well described in different developmental contexts, the in vivo activity of EZH1 has long been a puzzle. Here, we show that knocking down EZH1 in chick embryo neural tubes reduces neuronal differentiation without affecting progenitor proliferation or neuronal specification. Transcriptional profiling and functional assays demonstrate that EZH1 mainly acts as a transcriptional activator during neuronal differentiation. Importantly, genes involved in the actin cytoskeleton and cell dynamics that become activated during this process are   directly regulated by EZH1. Consistently, depletion of EZH1 in mature neurons leads to morphological alterations and neurite outgrowth defects. Overall, our findings underscore an essential role of EZH1 during early neurogenesis  in vivo and highlight the relevance of the dynamic EZH2 to EZH1 switch at the onset of neuronal differentiation.

overall_design: ChIP-seq of H3K4me3 and H3K27me3 were performed in HH30 chicken neural tubes. Input of HH30 is included.

first: Naiara

last: Akizu

first: María

last: García

first: Conchi

last: Estarás

first: Raquel

last: Fueyo

first: Stella

last: Pappa

first: Simona

last: Iacobucci

first: Raul

last: Ortiz

first: Carme

last: Gallego

first: Vittorio

last: Sartorelli

first: X

last: De la Cruz

first: Martínez-Balbás

last: Marian


title: Phf6 mutation induces leukemogenesis through altered chromatin state in mice (RNA-Seq)

first: Ying

last: Guo

summary: To investigate the effect of PHF6 mutations in leukemogenesis, we generated Phf6R274X transgenetic(Tg) and Phf6 KO mice. Then we purified the Lineage-cKit+Sca-1+ cells from bone marrow of Phf6R274XTg, Phf6 KO and WT mice, and performed bulk RNA-seq to profile the transcriptom.

overall_design: RNA-seq for bone marrow Lin-cKit+Sca-1+ cells from WT (n=4), Phf6 KO (n=3) and Phf6R274XTg (n=4)  mice.

first: Pingpin

last: Sui

first: Feng-Chun

last: Yang


title: The 8p11-p12 amplicon oncogene ASH2L regulates expression of genes involved in tumorigenic processes via promoter H3K4me3 in luminal breast cancer.

city: Charleston

first: Gary

last: Hardiman

state: SC

address: 135 Cannon Street

department: Medicine

institute: Medical University of South Carolina

summary: Amplification of the 8p11-p12 genomic region occurs in 30% of luminal B breast cancers and results in coordinate overexpression of several oncogenes, including ASH2L, which upregulates gene expression via promoter tri-methylation of lysine 4 on histone 3 (H3K4me3). Since 8p11-p12 amplification is associated with endocrine resistance, the major cause of breast cancer mortality, understanding the underlying biology is essential to improving treatment options for patients. To explore the role of amplified and overexpressed ASH2L on epigenetic regulation of gene expression, we performed H3K4me3 ChIP-seq and RNA-seq in breast cancer cells with ASH2L amplification and overexpression following ASH2L knockdown and assessed the biological effects of the suite of genes identified in this manner. We discovered that ASH2L-regulated genes are implicated in cell cycle processes and response to the CDK4/6 inhibitor palbociclib and confirmed these effects in additional breast cancer cell lines. We also discovered that ASH2L regulates expression of another 8p11-p12 amplicon oncogene NSD3, also an epigenome modifier, which has previously been shown to result in overexpression and estrogen-independent activation of ERα. Together, these data establish ASH2L as a breast cancer oncogene and an important component of the 8p11-p12 amplicon that acts as an oncogenic unit in breast cancer.

overall_design: Nine total samples: three biological replicates of LacZ control, ASH2L knockdown with shRNA construct 275, and ASH2L knockdown with shRNA construct 276

first: Jamie

last: Mills

first: E

last: Hazard

first: Antonio

last: Giordano

first: Yueying

first: Robert

last: Wilson

first: Dongjun

last: Chung

first: Stephen

last: Ethier


title: NF-кB determines the carcinogenic potential of necroptosis in liver

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

summary: Background: Genetic inhibition of NF-кB in hepatocytes favors Caspase-8/3-dependent apoptosis driving hepatocellular carcinoma (HCC) development in mice, but NF-кB is hyper-active in most human HCCs. RIPK1-RIPK3-MLKL-dependent necroptosis represents an alternative form of programmed cell death (PCD). We show here that IкB-Kinase-(IKK)-dependent activation of NF-кB in hepatocytes induces a hyper-reactive form of cell-death responses towards necroptosis and thereby promotes hepatocarcinogenesis. This sequence is driven by NF-кB-dependent transcription of inflammatory and mitogenic cytokines like IL-6, MCP-1 and CCL20, which are released directly from necroptotic hepatocytes, serving as damage-associated-molecular-patterns (DAMPs) / alarmins to promote inflammation, hepatocyte- and oval-cell-proliferation, genetic alterations and hepatocarcinogenesis. In line, we identified an NF-кB-necroptosis-signature in human HCCs associated with an unfavorable patients' prognosis. In contrast, absence of NF-кB activation switches necroptosis towards a hypo-reactive, anti-carcinogenic form of cell-death. These results reveal that parenchymal NF-кB activation serves as an intracellular relay determining the reactivity and carcinogenic potential of PCD pathways.

overall_design: Microarray analysis was performed from whole liver samples from 7-day-old mice. A total of 16 samples, from 4 different genotypes, were used for microarray analysis.

first: Mihael

last: Vucur

first: Jérémie

last: Gautheron

first: Arlind

last: Adili

first: Anne

last: Schneider

first: Florian

last: Reisinger

first: Olivier

last: Govaere

first: Christoph

last: Roderburg

first: Kristian

last: Unger

first: Mark

last: Boekschoten

first: Sanchari

last: Roy

first: Carlos

last: Villacorte-Martin

first: Vincenzo

last: Mazzaferro

first: Josep

middle: M

last: Llovet

first: Felix

last: Heymann

first: Achim

last: Weber

first: Ulf

last: Neumann

last: Luedde

first: Mareike

last: Hoß

first: Bettina

last: Hermanns-Sachweh

first: Tania

last: Roskams

first: Thomas

last: Longerich

first: Ralf

last: Weiskirchen

first: Frank

last: Tacke

first: Christian

last: Trautwein

first: Fabian

last: Geisler

first: Augusto

last: Villanueva

first: Mathias

last: Heikenwalder

first: Tom


title: Lineage Plasticity Driven by GATA6 Loss Fuels Colorectal Cancer Metastasis [RNA-seq_met]

city: New York

first: Norihiro

last: Goto

address: 413 East 69th Street

department: Department of Medicine

institute: Weill Cornell Medicine

summary: Colorectal cancer (CRC) liver metastases are the leading cause of CRC-related mortality, yet the specific genetic and epigenetic drivers that promote this process remain poorly understood. Here, we established a pro-metastatic CRC organoid library through serial orthotopic transplantation of organoids derived from mouse liver metastases. Integrative RNA-seq and ATAC-seq analyses of these organoids uncovered distinct transcriptomic and chromatin accessibility profiles correlating with metastatic potential. These pro-metastatic epigenetic changes were characterized by reactivation of fetal-like programs and downregulation of LGR5+ intestinal stem cell signatures. Notably, they converged on the silencing of the transcription factor GATA6, which occurs in liver metastases in both mice and humans. Genetic ablation of GATA6 in mouse models significantly enhanced liver metastasis while having minimal impact on primary tumor growth. Mechanistically, the loss of GATA6 induced the pro-metastatic epigenetic state and promoted the generation of LGR5- cancer cells. Together, these findings demonstrate that GATA6 loss drives liver metastatic progression by reprogramming cancer cells into a pro-metastatic epigenetic state through the hijacking of developmental programs.

overall_design: We established organoids from liver metastases and transplanted them into the colons of immunocompetent mice again. As controls, we also established organoids from the primary tumours and retransplanted them as well. We repeated these transplants for three rounds, thereby establishing multiple lines of organoids from both primary tumours and liver metastases in each round.

first: Saori

first: Omer

last: Yilmaz


title: ZNHIT1-dependent H2A.Z deposition at meiotic prophase I underlies pachytene gene expression and meiotic progression during male meiosis [H2A.Z ChIP-seq]

status: Public on May 31 2026

first: Jiang

last: Yamei

address: Songhu Road

summary: Accurate meiotic progression is important for gamete formation and the generation of genetic diversity. However, little is known about the identity of chromatin regulators that underlie mammalian meiosis in vivo. Here, we identify the multifaceted functions of the chromatin remodeler ZNHIT1 in governing meiosis. The expression of *Znhit1* gradually increases during the meiotic prophase, and *Znhit1* knockout in spermatocytes results in arrested pachytene development, impaired DNA double-strand break repair, and defective homologous recombination. Single-cell RNA sequencing and transcriptome analysis reveal that *Znhit1* loss dysregulates meiotic transcriptional programs at the pachytene stage. Chromatin immunoprecipitation data show that ZNHIT1 is needed for the incorporation of the histone variant H2A.Z into pachytene chromatin. Moreover, we found that H2A.Z cooperates with the transcription factor A-MYB to co-bind DNA elements and control gene activity. Our findings provide insights into the regulatory mechanisms governing meiotic progression and highlight ZNHIT1 as a critical regulator of meiotic progression.

overall_design: To investigate how ZNHIT1 modulates the genomic occupancy of H2A.Z, we conducted H2A.Z ChIP-seq analysis in germ cells.

first: Shenfei

last: Sun

first: Yamei

last: Jiang

first: Ning

first: Qiaoli

last: Zhang

first: Hongjie

last: Pan

first: Fujing

last: Huang

first: Xinna

first: Yuxuan

last: Guo

first: Xiaoyu

last: You

first: Kai

last: Gong

first: Wei

last: Wei

first: Hanmin

last: Liu

first: Zhenju

last: Song

first: Yuanlin

first: Xiaofang

last: Tang

first: Miao

last: Yu

first: Runsheng

last: Li

first: Xinhua

last: Lin


title: ZNHIT1-dependent H2A.Z deposition at meiotic prophase I underlies pachytene gene expression and meiotic progression during male meiosis [scRNA-seq]

first: Jiang

overall_design: To explore the biological effects induced by ZNHIT1 depletion in germ cells, we conducted single-cell RNA sequencing for relevant analysis.

first: Shenfei

first: Yamei