title: Nanog expression at naïve to prime transition biases lineage specification [CHIP-seq]

summary: FGF2 and FGF4 treatment of mouse embryonic stem cells (mESC) was shown to induce different levels of Nanog expression in mES cells and gastruloids and consequently, give rise to differences in lineage specification during early gastrulation. The aim of this study was to identify genes regulated by Nanog that underlie these biases in lineage specification

overall_design:
ChIP-seq of Nanog was performed on early stage gastruloids. Time 0h, cells primed with FGF2 for the first 48h and after wnt activation (by addition of chiron, CHIR).
The information for the antibody used in the ChIP-seq study are as follows:
Vendor: Cell Signaling Technology
Cat Number: 8822
Lot number: 4


title: Analysis of Gene Expression Heterogeneity Reveals Therapeutic Targets and Novel Regulators of Metastasis

status: Public on Dec 31 2025

city: Chicago

first: Marsha

middle: Rich

last: Rosner

state: IL

address: 929 E 57th St

country: USA

institute: University of Chicago

type: Expression profiling by high throughput sequencing

summary: Tumor cell heterogeneity has been implicated in metastatic progression of solid tumors such as triple-negative breast cancer (TNBC), leading to resistance and recurrence. We hypothesize that genes with low cell-to-cell transcriptional variability may be effective therapeutic targets, and that analysis of variability may facilitate identification of new metastatic regulators. Here we demonstrate, using single cell RNA sequencing, that the metastasis suppressor Raf Kinase Inhibitory Protein (RKIP) reduced overall transcriptional variability in TNBC xenograft tumors. Focusing on genes with reduced variability in response to RKIP, we identified targetable gene sets such as oxidative phosphorylation and showed that metformin could inhibit RKIP-expressing but not control tumor growth. We also found many regulators of cancer progression including a novel epigenetic metastasis suppressor, KMT5C.  These studies demonstrate that a metastatic regulator can alter transcriptional variability in tumors and reveal the importance of genes involved in heterogeneity as potential therapeutic targets and regulators of metastatic progression in cancer.

overall_design: RKIP vs CTRL mouse study: 1 × 10^6 BM1-VC or BM1-RKIP cells were injected orthotopically into the mammary fat pad of athymic nude mice (Harlan Envigo). The mice were sacrificed three weeks after tumor cell implantation. Primary tumors were collected for single-cell isolation and single-cell RNA-seq. Three replicate experiments were performed totalling three RKIP tumors and three CTRL tumors. For BM1 KMT5C primary tumor growth experiments: 1 × 10^6 BM1-VC or BM1-KMT5C cells were injected orthotopically into the mammary fat pad of athymic nude mice (Charles River). The mice were euthanized four weeks post tumor cell implantation. Primary tumors from five KMT5C mice and five CTRL mice were collected for RNA sequencing.

first: Dongbo

last: Yang


title: A novel H2B variant with TERRA-promoter enrichment, H2BW2, forms decompacted nucleosomes in human spermatogenesis

city: Hong Kong

first: Toyotaka

last: Ishibashi

address: Rm6260, Academic Building, HKUST, Clear Water Bay, Kowloon

department: Division of Life Science

country: Hong Kong

institute: The Hong Kong University of Science and Technology

type: Genome binding/occupancy profiling by high throughput sequencing

summary: During spermatogenesis, histones are gradually replaced by testis-specific histone variants, transition proteins, and eventually protamine in elongating spermatids. H2BW2 is a mammalian testis-specific histone H2B variant. The amino acid sequence of H2BW2 is relatively close to another primate testis-specific histone variant H2BFWT, however, there is very little known about the functions of H2BW2. Here, we found that H2BW2 destabilizes nucleosomes by reducing the interactions between histone H2A-H2BW2 dimers and DNA. These interactions may be reduced by changing to less positive surface charge in the alpha 1 helix of H2BW2, and amino acids to neutral or negative charge residues in loop 1 and the acidic patch. Single-molecule optical tweezers assay shows that the H2BW2 nucleosome destabilizes the interactions between H2A-H2B and DNA by affecting both unwrapping and rewrapping rates, and decreases the energy barrier of their interactions by ~35%. Importantly, H2BW2 was highly enriched in the telomere repeat-containing RNA (TERRA) promoters in human testis. The presence of H2BW2 in the TERRA promoter upregulated TERRA expressions and associated with longer telomeres. Our results suggest that H2BW2 participates in the maintenance of telomere length by enhancing the expression of TERRA in early spermatogenesis.

overall_design: Explore the distribution of H2BW2 in the genome within the human testis from two donors and stable expression HeLa cells.

first: Thi

middle: T

last: Nguyen

last: Ding

first: Mingxi

last: Deng


title: Mechanical force coordinates with estrogen to orchestrate alveolar bone homeostasis via PIEZO1

city: Shanghai

first: Lingyong

last: Jiang

state: Shanghai

address: No.639, zhi zao ju road

country: China

institute: Shanghai jiao tong University

summary: Healthy alveolar bone is the cornerstone for oral function and oral treatment. In the aging population, increasingly postmenopausal women requiring dental services experiences alveolar bone loss due to estrogen deficiency. Both local factors (occlusal force lose) and systemic factors (estrogen deficiency) affects their alveolar bone health, but the association remains to be clarified. Here, we identified that occlusal force is critical in maintaining alveolar bone mass and PIEZO1 coordinates mechanical force and estrogen, thus orchestrating alveolar bone homeostasis. Mechanistically, both occlusal force loss and PIEZO1 deletion may impair the osteogenesis of alveolar bone and sequentially regulate catabolic metabolism through Fas ligand (FasL)-induced osteoclastic apoptosis. PIEZO1 may promote the activity of signal transducer and activator of transcription 3 (STAT3) and estrogen receptor 1 (ESR1), which cooperatively increase Fasl transcription. This study thus revealed a cooperation between occlusal force and estrogen in maintaining alveolar bone homeostasis through a PIEZO1-STAT3/ESR1-FasL pathway. Our work supports restoration of occlusal force with dental therapies early and suggests that preventing alveolar bone loss is the major priority. PIEZO1 may serve not only as a treatment target for occlusal force loss-induced alveolar bone loss but also as a potential target for metabolic bone loss, especially in older patients.

overall_design:
In this study, we used a CRISPR/Cas9-based system to knock out Piezo1 in C3H10 T1/2 cells (Piezo1 knock out_C3H10, denoted CPK) to understand the molecular mechanism underlying mechanical force transfer.Assay for transposase- accessible chromatin using sequencing (ATAC-seq) was used to determine chromatin accessibility in Ctrl_C3H10 (GFP) and CPK cells.

In this study, to identify mechanosensor of occlusal force, we compared gene expression profiles of the osteogenic cell line C3H10 T1/2 under static and cyclic mechanical strain (CMS) by RNA-seq. CMS with a 0.5 Hz sinusoidal curve set at 10% elongation was applied for 8 h every day for 3 days.

first: Yiling


title: CRISPRa screen identifies a role for c-KIT signaling in tamoxifen resistance, potentially through upregulation of ABC transporters

city: ITHACA

first: BROOKE

last: MARKS

state: NEW YORK

address: HUNGERFORD ROAD

institute: CORNELL UNIVERSITY

summary: Resistance to endocrine therapy is a common problem in patients with estrogen receptor  alpha (ERa) positive breast cancer. In this study, we took a non-biased genome-wide approach to identify novel mechanisms of endocrine resistance using a clustered regularly interspaced short palindromic repeats (CRISPR) activating (CRISPRa) screen. Results from the screen identified 109 candidate resistance-associated genes, with several of these genes, such as EGFR and SRC, having been previously associated with endocrine resistance. One candidate gene that has not been previously associated with endocrine resistance is the tyrosine kinase receptor, c- KIT. We further tested for associations between c-KIT and endocrine resistance and found that c-KIT overexpressing cells proliferate more rapidly in the presence of tamoxifen compared to control cell lines. To gain deeper insight into the potential role of c-KIT signaling in tamoxifen resistance, we next performed precision nuclear run-on and sequencing (PRO-seq) analysis of c- KIT overexpressing cells to identify downstream factors that may mediate the c-KIT response. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of the overexpressed genes found that the only class of factors that was significantly induced by c-KIT was the ATP-binding cassette (ABC) transporters; specifically, ABCA1, ABCA4, and ABCG1. Interestingly, overexpression of two of these ABC transporters, ABCA1 and ABCG1, significantly correlated with worse prognosis in ERa+ breast cancer patients following endocrine therapy. We then tested for potential therapeutic effects of c-KIT inhibition on endocrine resistance and found that the c-KIT inhibitor Gleevec appears to synergize with tamoxifen to suppress MCF-7-S cell growth. Together, our findings support the hypothesis that c-KIT signaling promotes endocrine resistance via the induction of ABC transporter activity. Additionally, our studies suggest that     inhibition of c-KIT signaling may represent a novel strategy for preventing or overcoming endocrine resistance in ERa+ patients.

overall_design: sgRNA abundance and PRO-seq experiments from MCF-7 tamoxifen sensitive subclones cells. Inducible doxycycline system (-/+ dox treated cells) followed by tamoxifen treatment (-/+ tam) to investigate targets important in resistance.

first: Brooke

middle: A

last: Marks

first: Scott

last: Coonrod

first: Lauren

last: Choate

first: Charles

middle: G

last: Danko


title: Chronic intermittent hypoxia in DEN-induced rat model of HCC

city: La Tronche

first: Sophie

last: Rousseaux

address: Bd de la Chantourne

department: IAB

country: France

institute: INSERM-UGA

summary: Using RNA-seq analysis, we investigated whether obstructive sleep apnea (OSA)-related chronic intermittent hypoxia (IH) can influence HCC progression and aggressiveness.

overall_design: 7-week-old Fischer 344 male rats were treated weekly with intra-peritoneal injections of 50 mg/kg DEN for 14 weeks in order to develop HCC. Nodule/tumor number and size were evaluated by ultrasound, and the animals were then divided into two equivalent groups (n=9/group). During the following period of 6 weeks, the rats were exposed to intermittent hypoxia (IH group) or to normoxia (N group) during eight hours of the daytime sleeping period of rats.

first: Florent

last: Chuffart

first: Zuzana

middle: M

last: Jilkova

first: Lydie

last: Carreres


title: Transcriptomic analysis of Treg cells with RORa knockout

city: Lille

first: Artemii

last: Nikitin

address: 1,  Rue du Professeur Calmette

institute: Inserm

summary: We created mice with specific KO of Rora in Foxp3-expressing Treg cells. Treg cells were sorted from WT and KO mice from spleen of CD-fed mice, eWAT from HFD-fed mice, mediastinal lymph nodes and lungs from mice upon the HDM-induced asthma model.

overall_design: Primary mouse Treg cells isolated from spleen of CD-fed mice, eWAT from HFD-fed mice, mediastinal lymph nodes and lungs from mice upon the HDM-induced asthma model.

first: Denis

last: Mogilenko

first: David

last: Dombrowicz


title: HDAC3 is required for self-renewal and metabolism of Ams [CUT&TAG]

city: Beijing

first: Zhimin

last: He

address: No. 1 Qinghuayuan Street

department: School of Medicine

institute: Tsinghua University

summary: HDAC3 is required for the maintenance of AM population and proper metabolism through transcription regulation together with ATF2

overall_design: Cut& Tag assay analyzed the binding sites of HDAC3 and ATF2 on AM genome.

first: Li

last: Wu

first: Maocai

last: Luo

first: Tao

first: Yijun

last: Zhang


title: RNA profiling changes of HDAC3 knockout AMs

summary: HDAC3 is required for the maintenance of AM population and proper metabolism

overall_design: Examination of transcriptome changes of control and HDAC3 knockout Aleolar macrophages from 6 week old mice.

first: Macai


title: Heterologous synthesis of poly-γ-glutamic acid enhanced drought resistance in maize (Zea mays L.)

city: Jinan

first: MA

last: Haizhen

state: Shandong

address: Daxue Road

institute: Qilu University of Technology

summary: Drought stress is the main factor restricting maize yield. Poly-γ-glutamic acid (γ-PGA) could significantly improve the drought resistance and yield of many crops. However, its high production costs and unclear long-term impact on soil ecology limit its large-scale application. In this study, genes (PgsA, B, C) that participate in γ-PGA synthesis were cloned from Bacillus amyloliquefaciens and transformed into maize for the first time. Under drought stress, transgenic maize significantly increased the ear length, ear weight and grain weight by 50% compared to the control, whereas the above yield characteristics increased by 2.33, 13.06, 19.34 and 18.36%, respectively under normal growth conditions. γ-PGA was mainly expressed in the mesophyll cells of maize leaf rosette structure and improved drought resistance and yield by protecting and increasing the expression of genes for the photosynthetic and carbon fixation. This study is an important exploration for maize drought stress molecular breeding and building resource-saving agriculture.

overall_design: In the soil drought stress experiment, the control and transgenic maize seeds were sown in pots (height: 15 cm, diameter: 10 cm) containing two seedlings each. Seedlings were exposed to drought stress at the three-leaf stage by stopping watering and sheltering them from rain. After five days of drought treatment (the soil water content decreased to 9.8%), and the leaves were sampled for RNA sequencing.

first: Ma

last: Can

last: Panpan

first: Xiao

last: Ning

first: Xu

last: Jieting

first: Yan

last: Jianbin

first: Liu

last: Xingwang

first: Zhang

last: Shengkui

first: Xia

last: Tao


title: HDAC3 is required for self-renewal and metabolism of AMs

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

overall_design: Refer to individual Series


title: Transcriptomic study of  potential effects of Treg cell-expressed ROR-alpha on gene expression profile of adipose tissue.

first: Artemii

summary: Treg cells are important regulators of homeostasis and metabolic inflammation in visceral adipose tissue. Treg cells from visceral adipose tissue express high levels of Rora gene. A mouse model of Treg-specific ROR-alpha knockout was developed to study potential role of ROR-alpha in visceral adipose tissue Treg cells.

overall_design: eWAT was isolated from HFD or chow diet-fed mice


title: RNAseq of low-pigmented and high-pigmented cells from mouse B16 melanoma cell lines (experiment 2)

city: Melbourne

first: Pacman

last: Szeto

state: VIC

address: 89 Commercial Road

department: Medicine

country: Australia

institute: Monash University

summary: Functional variation due to underlying genetic and phenotypic heterogeneity poses a major challenge to long-term melanoma management. Melanin pigment production is the hallmark of normal melanocytic differentiation but varies significantly between and within melanoma tumours. Detailed assessment of the functional consequences of pigment heterogeneity in viable melanoma samples has been experimentally challenging.   Here, we developed a novel method to prospectively separate melanoma cell populations based on the presence of intracellular melanin using fluorescence-activated cell sorting (FACS). We find that nearly all pigmented patient melanomas and melanoma cell lines comprise mixtures of cells ranging from very high to low or undetectable pigment content. Using viable sorted cells, we interrogated the functional characteristics of low pigmented cells (LPC) and high pigmented cells (HPC) in the B16 mouse melanoma cell line.

overall_design: The B16 mouse melanoma cell lines were cultured and separated into low pigmented cells (LPC) and high pigmented cells (HPC) based on their melanin pigment content by fluorescence-activated cell sorting (FACS), exploiting the light scattering properties of intracellular melanin. RNA sequencing was performed on sorted cells with 3x replicates for each group.

first: Gamze

middle: K

last: Abali

first: Peinan

last: Zhao

first: Nicholas

middle: C

last: Wong

first: Mark

last: Shackleton


title: Expanded transcriptomic analysis of human hepatic stellate cells links novel coding and noncoding products to human liver fibrosis

city: Boston

first: Alan

middle: C.

last: Mullen

state: MA

address: 55 Fruit St.

department: Department of Medicine

institute: Massachusetts General Hospital

summary: We have performed analysis of the transcriptome of human HSCs to define the long noncoding (lnc) RNAs expressed in this cell type, including many not previously annotated. Through analysis of full-length RNA transcripts, we identified additional lncRNAs that were not assembled by short reads. We also discovered new isoforms of protein coding genes that encode amino acid sequences that are not present in annotated isoforms. Analysis of non-polyadenylated RNAs did not identify additional genes encoding long noncoding RNA transcripts, but did reveal the presence of hundreds of circular (circ) RNAs, including those with potential for translation. Incorporating these transcripts and genes into analysis of a published dataset of human liver fibrosis revealed the induction of lncRNAs, novel protein isoforms, and circRNAs associated with development of disease. These results identify RNAs and amino acid sequences expressed in HSCs and associated with human liver disease that may serve as therapeutic targets to inhibit fibrosis or biomarkers to benchmark progression of disease.

overall_design: Transcriptomic analysis of primary human hepatic stellate cells using polyA-enriched RNA, ribosomal RNA-depleted RNA and full-length RNA sequencing.

first: Amin

last: Mahpour


title: RNAseq of low-pigmented and high-pigmented cells from LM-MEL-28 human melanoma cell line.

summary: Functional variation due to underlying genetic and phenotypic heterogeneity poses a major challenge to long-term melanoma management. Melanin pigment production is the hallmark of normal melanocytic differentiation but varies significantly between and within melanoma tumours. Detailed assessment of the functional consequences of pigment heterogeneity in viable melanoma samples has been experimentally challenging.   Here, we developed a novel method to prospectively separate melanoma cell populations based on the presence of intracellular melanin using fluorescence-activated cell sorting (FACS). We find that nearly all pigmented patient melanomas and melanoma cell lines comprise mixtures of cells ranging from very high to low or undetectable pigment content. Using viable sorted cells, we interrogated the functional characteristics of low pigmented cells (LPC) and high pigmented cells (HPC) in the LM-MEL-28 patient-derived melanoma cell line.

overall_design: The LM-MEL-28 patient-derived melanoma cell lines were cultured and separated into low pigmented cells (LPC) and high pigmented cells (HPC) based on their melanin pigment content by fluorescence-activated cell sorting (FACS), exploiting the light scattering properties of intracellular melanin. RNA sequencing was performed on sorted cells with 3x replicates for each group.


title: Transcriptomic landscape of human primary stromal cells upon therapy-induced senescence (genotoxic chemotherapy and ionizing radiation)

first: Yu

last: Sun

address: 320 Yueyang Rd, Life Sciences Building A #1508

department: Shanghai Institute of Nutrition and Health

institute: Chinese Academy of Sciences

summary: Cellular senescence is a permanent state of cell cycle arrest that promotes tissue remodeling during embryonic development and after trauma or injury, but can also contribute to the decline of organ regenerative potential and tissue normal function, to local and systemic inflammation, and to tumorigenesis in aged organisms. For years, the identification, characterization, and pharmacological elimination of senescent cells have gained attention in the research field of aging and age-related diseases. However, the non-specificity of current senescence markers and the existence of different senescence programs strongly limit these tasks. Here, we profiled the genome-wide expression of primary normal human prostate stromal cells (PSC27) upon therapy-induced senescence (TIS), with the aim to determine molecular regulators of senescence phenotypes and define the inherent correlation of gene expression pattern with the extensive senescence-associated 3D genome reorganization. This TIS-specific configuration of chromosome architecture brings active genes located in genomic regions adjacent to senescence-associated heterochromatin domains (SAHDs) in close spatial proximity and favors their expression. These data may provide a baseline to further explore show how multi-omics and 3D mapping can identify critical features of cellular senescence and discover key determinants of senescence and SAHF formation in the genome-wide landscape.

overall_design: RNA-seq examination of genome-wide transcriptional changes of primary normal human prostate stromal cells (PSC27) in proliferating versus senescence phase generated by the chemotherapeutic agent bleomycin or gamma-ray ionizing radiation. .

first: Changxu

last: Wang


title: Transcriptomic profiling of senescent human stromal cells upon medicinal intervention with dihydromyricetin

summary: Aging and age-related pathologies can be delayed by specifically targeting the senescence-associated secretory phenotype (SASP), a hallmark feature of senescent cells. Achieving the goal using natural or synthetic agents would have a tremendous impact on the quality of lifespan and burden of age-related chronic diseases. We report the potential of dihydromyricetin (DMY), a bioactive phytochemical constituent that can be found in natural plants such as Rattan tea extract (RTE), in targeting senescent cells via suppression of the SASP. This study demonstrates the efficacy of DMY as medicinal agent in controlling the influence of senescent human stromal cells and provides a strong rationale for its future use in aging intervention and geriatric medicine.

overall_design: Examination of in vitro efficacy of DMY in treating human senescent stromal cells (PSC27 line). This assay was performed beyond previous studies reporting its effects in including but not limited to cardioprotection, anti-diabetes, hepatoprotection, neuroprotection, anti-tumor, and dermatoprotection. Although DMY was also applied for treatment of bacterial infection, osteoporosis, asthma, kidney injury, nephrotoxicity and so on, the biological mechanisms of DMY are generally linked with to anti-oxidation and anti-inflammation. Our understanding of the pharmacological function of DMY and its preclinical value remains limited and deserves substantial assessment in aging-related diseases.

first: Qixia

last: Xu


title: Defective prelamin A processing promotes RIPK1-driven necroptosis and inflammation in premature aging

city: shanghai

first: yuanxin

last: yang

address: 100 Haike Road, Zhangjiang Hi-tech Park, Pudong, Shanghai

institute: the Interdisciplinary Research Center of Biology and Chemistry

summary: Alterations in the architecture and dynamics of the nuclear lamina have a causal role in normal and premature aging. Accumulation of progerin, a toxic isoform of lamin A, or prelamin A, the precursor protein of lamin A, is the major underlying cause of premature aging syndromes. However, the molecular mechanism that mediates premature aging remains poorly defined. Here we report that the accumulation of farnesylated forms of prelamin A at the nuclear lamina triggers RIPK1 kinase-dependent signaling that leads to inflammation and RIPK3-mediated necroptosis in multiple tissues of a mouse model of accelerated aging (Zmpste24-/- mice). We show that prelamin A recruits RIPK1 in the nucleus to facilitate its activation in response to TNFα stimulation. Inhibition of prelamin A farnesylation prevents its accumulation at the nuclear envelope, and consequently reduces RIPK1 activation and necroptosis. The causality of RIPK1-driven necroptosis and inflammation in premature aging was demonstrated by genetic inactivation of RIPK1 or knockout of RIPK3, which prevented the premature degeneration of multiple tissues and organs in Zmpste24-/- mice and significantly extended their longevity. Our findings provide in vivo proof of principle for the feasibility of inhibition of RIPK1 kinase to slow down the progression of physiological and pathological aging.

overall_design: mRNA profiles of livers, intestines and skins from 12-week-old Zmpste24+/+, Zmpste24-/-, Zmpste24-/-; RIPK1D138N/D138N mice were generated by deep sequencing, in triplicate or duplicate, using Illumina

first: Daichao

first: Yuanxin

last: Yang

first: Lingjie

last: Yan


title: Genome-wide mapping of the chromatin enrichment of CEBPB in NCM460 cell

first: Jian

state: Hong Kong Special Administrative Region

address: 83 Tat Chee Avenue, Kowloon

department: Department of Biomedical Sciences

institute: City University of Hong Kong

summary: In this study, the region harboring the SNP rs2643219 was found to be a putative enhancer.ChIP-qPCR shown that the CEBPB can bind the region. So, ChIP-seq was carried out in colon epithelium-derived NCM460 cells to validate the binding of CEBPB to the genomic region and discover candidate loci interacting with the putative enhancer.

overall_design: CEBPB ChIP-seq on human NCM460 cells. Two independently replicative experiments were performed (rep1 and rep2), and input was used as control.

first: Yong-Qiang

last: Ning

first: Wen-Ju


title: Polybrominated diphenyl ethers (PBDEs) exposure during pregnancy alters microRNA expression profile in rat placenta

city: Zunyi

first: Yi-jun

last: Liu

state: Guizhou

address: No.6 Xuefu West Road, Xinpu New District

institute: Zunyi medical university

type: Non-coding RNA profiling by high throughput sequencing

summary: Polybrominated diphenyl ethers (PBDEs) are well-known endocrine disrupting chemicals (EDCs), and have been found to affect reproduction and development. The placenta, as the interface between maternal and fetal circulation, is constantly exposed to maternal EDCs. The present study investigated PBDEs-induced changes in miRNAs in rat placenta, and the potential mechanism of developmental toxicity. Female rats were exposed to 500 mg/kg/day decabromodiphenyl ether (BDE-209) from gestational day 0 (GD 0) to GD 20. miRNAs were isolated from the placenta on GD 20. Expression of miRNAs were analyzed using next-generation sequencing, and validated by reverse transcription-quantitative polymerase chain reaction (RT-qPCR). A total of 55 miRNAs were found changed significantly in the exposure group, among which 46 were down-regulated and 9 were up-regulated. Rno-miR-17-5p, rno-miR-503-5p, rno-miR-374-5p, rno-miR-369-3p, rno-miR-29a-3p were confirmed to be down-regulated, rno-miR-148a-3p was validated up-regulated in the exposure group. The bioinformatic analysis showed that the predicted miRNAs target genes were involved in vascular endothelial growth factor (VEGF) signaling pathway, suggesting the role of PBDEs-induced developmental toxicity via the interference with the angiogenesis process in placenta. Our findings demonstrated evidence of altered microRNA expression with PBDEs exposure, thus providing novel insights into mechanisms of PBDEs developmental toxicity.

overall_design: A total of 21 healthy female and 7 male Sprague–Dawley (SD) rats, 7 weeks of age and weighing 180-200g each were obtained from the Southwest Medical University Animal Center, Luzhou, China. All rats were kept in cages under a temperature of 23 ± 2°C, relative humidity of 40–60%, and 12:12 reversed day-night cycle with access to food and water ad libitum. BDE-209 (99% pure, CAS no. 1163–19–5) was obtained from Chengdu Huaxia Chemical Corporation (Chengdu, China), and administered by gavage after being dissolved in corn oil (vehicle). After two weeks acclimation, female rats were mated with male rats at a ratio of 3:1 overnight and vaginal smears of female rats was checked the next morning. The day when the sperm is observed under the microscope was assigned as gestational day 0 (GD 0). The resulting 16 pregnant rats were randomly assigned to Exposure and Control group (8 rats per group) based on weight match. Rats in each group were exposed daily to 500 mg/kg/day BDE-209, and corn oil, respectively, by gavage once per day for 20 days from GD 0 to GD 20. At GD 20, rats were anesthetized with inhaled isofluorane 4h after the last dose. Placentas were obtained, flash frozen with liquid nitrogen and stored at - 80 °C.

first: Yijun

first: Yan

last: Xie


title: Transcriptome of U251-APP cells with CTCF-binding sites knockout

city: Kunming

first: Yong-Gang

last: Yao

state: Yunnan

address: 32 Jiaochang Donglu

department: Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province

institute: Kunming Institute of Zoology

summary: Two CTCF-binding sites (CTCF-A and CTCF-B) might mediate frequent chromatin interactions in the 11p11.2 locus and contribute to the co-regulation of genes within the 11p11.2 locus. In order to verify whether knockout of these CTCF-binding sites could influence expression of genes in the 11p11.2 locus, and explore the subsequent consequences of the knockout, we knocked out two CTCF-binding sites (CTCF-A and CTCF-B) in U251 cell with a stable expression of mutant APP 128 (M671L) (U251-APP cells). RNA-seq (by IlluminaHiseq 4000) and following analyses were then performed to detect genes whose expression were influenced by CTCF-binding sites knockout.

overall_design: Differential expression genes were obtained by comparing gene expression levels in CTCF-binding site knockout cells (CTCF-A or CTCF-B) vs. wild-type controls (WT). Four replicates were used for each group.

first: Min

first: Deng-Feng

last: Zhang


title: Transcriptomic profiling of senescent human blood vessel cells upon medicinal intervention with ginkgo boliba extract or rattan tea extract

summary: Aging and age-related pathologies can be delayed by specifically targeting the senescence-associated secretory phenotype (SASP), a hallmark feature of senescent cells. Achieving the goal using natural or synthetic agents would have a tremendous impact on the quality of lifespan and burden of age-related chronic diseases. We report the potential of ginkgo boliba extract (GBE), a commonly used dietary supplement and traditional herbal medicine for hundreds of years in China as an antioxidant and free radical scavenger, or rattan tea extract (RTE), a medicinal agent used for many years for the treatment of inflammation, fatty liver, tumor, diabetes and hyperlipidemia, in targeting senescent cells via suppression of the SASP. This study demonstrates the efficacy of GBE and RTE as medicinal products in controlling the influence of senescent human blood vessel cells and provides a strong rationale for their future use in aging control and geriatric medicine.

overall_design: Examination of in vitro efficacy of GBE and RTE in treating human senescent blood vessel cells (HUVEC). This assay was performed beyond previous studies reporting their effects in including but not limited to cardioprotection, anti-diabetes, hepatoprotection, neuroprotection, anti-tumor and dermatoprotection.


title: Sperm circular RNAs: Types, expression patterns and epigenetic potential

city: Barcelona

first: Meritxell

last: Jodar

state: Barcelona

address: C/ Casanova, 143 Planta 1 Ala nord

department: Biomedical Sciences

country: Spain

institute: Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS) - Hospital Clínic de Barcelona - Universitat de Barcelona

summary: Circular RNAs (circRNAs) are a widely distributed new type of non-coding RNAs with important potential regulatory roles. They are synthesized by backsplicing and lack the 3’-free end, which confer a higher stability and longer half-lives than linear RNAs. We aimed to characterize and experimentally validate human sperm circRNAs. Our results showed a complex and stable population of sperm exonic and intronic circRNAs. The RNase R resistance treatment test revealed three distinct specific expression patterns for sperm circRNAs. In contrast to circRNAs described in somatic cells, most of sperm circRNAs are mostly in their circular form without the presence of their linear cognates. Surprisingly, we also identified some circRNAs sensible to the RNase R treatment due to a non-stochastically decircularization. Sperm circRNAs arise mainly from genes enriched in epigenetic functions. Additionally, several previously reported sperm RNA elements required to achieve a live birth and/or altered in obese patients were found in the present study as being circRNAs. Likewise, some early embryonic circRNAs appear to be specifically provided by sperm and potentially translated to functional peptides. Altogether, these results suggest that sperm circRNAs could be crucial for fertility and early embryogenesis and could probably modulate some phenotype traits of the offspring.

overall_design: Description of the circular RNA profile of 3 human normozoospermic sperm samples using the KNIFE algorithm.

first: Ada

last: Soler-Ventura

first: Ainize

last: Odriozola

first: Judit

last: Castillo

first: David

last: Delgado-Dueñas

first: Juan

last: Corral

first: Josep

middle: L

last: Ballescà

first: Rafael

last: Oliva


title: RNA-seq for rapid response to glyphosate in Ambrosia trifida

city: Fort Collins

first: Todd

last: Gaines

state: CO

address: 1177 Campus Delivery

department: Agricultural Biology

institute: Colorado State University

summary: Giant ragweed (Ambrosia trifida) is an economically disruptive weed in US corn and soybean production. Populations of this species have evolved a unique glyphosate resistance mechanism involving rapid cell death in mature leaves, also known as rapid necrosis. This abiotic stress resistance mechanism may be due to utilization of stress response pathways typically associated with biotic stresses such as pathogens. To study the genetic basis of this rapid response, an RNA-Seq time course study was conducted on young and mature leaves of glyphosate-resistant and -susceptible individuals, before and after glyphosate treatment. A major difference in gene regulation following glyphosate application was observed between young and mature leaves in the glyphosate-resistant individuals. Many differentially expressed genes were related to broad plant pathways with cross-functionality including plant stress and cell death pathways, phytohormone synthesis, response to oxidative stress, cellular metabolism, and pathogen defense pathways. Metabolic network analysis revealed that most of the genes involved in jasmonate biosynthesis were up regulated in response to glyphosate treatment in resistant mature leaves whereas this pathway was not induced in susceptible plants. The glyphosate-resistant plants appear to perceive glyphosate differently than susceptible plants, pointing to the potential role of a yet to be characterized receptor that senses glyphosate or its action and triggers the rapid necrosis response in mature leaves. Additional steps are needed for functional validation to test the hypothesis of causal relationship between function of these candidate genes of interest and the glyphosate resistance rapid response phenotype.

overall_design: Samples were collected from old leaves and young leaves of three GS and three GR RR plants (Figure 1) immediately prior to glyphosate treatment and at the following time points after glyphosate treatment: 15, 60, and 180 min after treatment (MAT). In total 48 samples were collected for the RNA-seq experiment consisting of two biotypes, three biological replicates, two tissue types, and four treatment time points. The RNA-seq experiment conducted using Illumina HiSeq of these 48 cDNA libraries generated 2.1 billion reads ranging from 33 to 57 million reads per sample.

first: Christopher

middle: R

last: Van Horn

first: Karl

last: Ravet

first: Dean

middle: J

last: Pettinga

first: Crystal

middle: D

last: Sparks

first: Eric

last: Patterson

first: Sascha

last: Gille

first: Roland

last: Beffa

first: Franck

middle: E

last: Dayan

first: Philip

last: Westra


title: The crown-root inducible system (CRIS) coupled to RNAseq allows identifying the early molecular events of crown-root initiation in barley (Hordeum vulgare L.)

city: Olomouc

first: Ales

last: Pecinka

address: Šlechtitelů 31

country: Czech Republic

institute: Institute of Experimental Botany of the AS CR

summary: The molecular regulation of root initiation in monocots is still poorly understood. We report the development of the auxin-based crown-root inducible system (CRIS) in barley (Hordeum vulgare L.). Using this system coupled to RNAseq, we investigated the molecular events occurring during the early steps of crown-root (CR) initiation. The sequencing on the Illumina NovaSeq6000 platform yielded over 123 Gb data, representing more than 408 million reads. Using the last released barley annotation (Morex v2 Gene Models, 2019), we found that 427 genes were downregulated by auxin whereas 764 genes were upregulated. This study provides the first analysis of early event of crown-root initiation in cereals. It will serve as comparison with known genes in rice, maize and other cereals, and could be used in metagenomics studies.

overall_design: Transcriptomic analysis of crown-root initiation in barley using an auxin-based inducible system, called crown-root inducible system (CRIS). Twelves samples representing 4 conditions in 3 independent biological replicates were analyzed. Sequencing was performed on NovaSeq6000 platform using a S1 flow-cell and pair-ended reads (2x150bp).

first: Dieu

last: Nguyen

first: Martin

last: Kovačik

first: Kateřina

last: Holušová

first: Pascal

last: Gantet

first: Aleš

last: Pečinka

first: Véronique

last: Bergougnoux


title: Transcriptome alteration in Nrf2 mutant developing oligodendrocytes treated with interferon gamma and thapsigargin in comparison with wild-type developing oligodendrocytes treated with interferon gamma and thapsigargin

first: Brian

last: Popko

address: 303 E. Chicago Avenue

department: Neurology

institute: Northwestern University

summary: Developing oligodendrocytes from Nrf2 mutant and wild-type mice were treated with 1) interferon gamma for 1, 8, 24 and 48 hours or 2) thapsigargin for 1, 8 hours. Treated samples were normalized to untreated control samples from the same batch and compared to Nrf2 mutant samples from the same batch.

overall_design: 50 samples, 2 treatments (IFN-gamma and thapsigargin), 1 control (untreated), 2 genotypes (wild-type and Nrf2 homozygous null), 4 timepoints for untreated controls and IFN-gamma, 2 timepoints for thapsigargin. 2 replicates for wild-type samples in each timepoint, 4 replicates for Nrf2 mutant samples in each timepoint.

first: Harini

last: Shah

first: Moones

last: Heidari


title: Tenofovir and dolutegravir reduce human T-cell leukemia virus 1 transmission and de novo viral spread in vivo

first: James

middle: Patrick

last: Cooney

state: Victoria

address: 1G, Royal Parade, Parkville

institute: The Walter and Eliza Hall Institute

summary: Human T-leukemia virus 1 (HTLV-1) is an oncogenic retrovirus with no available curative therapy. In-vitro data suggests HTLV-1 may be susceptible to certain HIV-1 antiretroviral compounds but their value, if any, in the context of a clinically-relevant transmission model is unknown. We addressed this knowledge gap by investigating the efficacy of the anti-retroviral compounds, tenofovir and dolutegravir, in preventing HTLV-1 transmission and infection in a humanised mouse model of HTLV-1 subtype c (HTLV-1c) infection, the first of its kind. Characterisation of this model revealed that HTLV-1c and HTLV-1 subtype a (HTLV-1a) showed subtle differences in natural history of disease but not as striking  as the differences observed clinically, indicating additional host and environmental contributors to human disease. Single cell RNA sequencing of CD4+ T cell VDJ transcripts revealed poly- and oligoclonal expansion of HTLV-1c-infected CD4+ T cells. We show that tenofovir significantly reduces HTLV-1 transmission in vivo at clinically relevant doses when administered as pre-exposure prophylaxis. Further, tenofovir and dolutegravir combination significantly attenuates viral spread and disease progression during early infection. Our data support the use of tenofovir and dolutegravir against HTLV-1 transmission and early infection. Routine use of these drugs as effective prophylactic agents against HIV-1 infection will facilitate their rapid translation to HTLV-1 clinical trials.

overall_design:
Splenocytes from 3x mock-infected and 3x HTLV-1c-infected humanised NOD-scid IL2Rgammanull mice were labelled with unique human Total-seqC oligonucleotide-conjugated ‘hashtag’ antibodies (BioLegend) and anti-human fluorescent antibodies against CD45 (Pecy5), CD4 (APC-H7) and CD45RO (Pe-CF594) before isolating human CD4+ memory T cells by FACS. Five samples were labelled with a unique hashtag. The sixth sample was labelled with an equal ratio combination of all five hashtags that could be identified during demultiplexing having a mixture of all five. 2,000 memory CD4+ T cells form each mouse were pooled (12,000 cells total) before single cell gel beads in emulsion (GEM) generation and barcoding in a 10X Genomics chromium controller (Chromium single cell 5' library and gel bead kit, PN-1000014). 5’-gene expression, cell surface protein (hashtag), and VDJ (Chromium single cell VDJ enrichment kit for T cells, PN-2000008/9) libraries were prepared as per manufacturer’s instructions (10X Genomics). Libraries were sequenced by Illumina paired-end next generation sequencing on a NextSeq 500 machine. Data analysis was performed using R v4.0.0 (R Foundation for Statistical Computing, Vienna, Austria) and Bioconductor v3.11.
Infected_1: Hashtag 1: TotalSeq-C0251
Infected_2: Hashtag 2: TotalSeq-C0252
Infected_3: Hashtag 3: TotalSeq-C0253
Uninfected_1: Hashtag 4: TotalSeq-C0254
Uninfected_2: Hashtag 5: TotalSeq-C0255
Uninfected_3: Hashtag 1,2,3,4,5: equal ratios

middle: P

first: Marc

last: Pellegrini

first: Peter

middle: F

last: Hickey


title: Transcriptomic profiling of human senescent cells upon medicinal intervention with cocoa extract

first: Yu

last: Sun

summary: Multiple lines of evidence suggest that aging and age-related pathologies can be delayed by specifically targeting the senescence-associated secretory phenotype (SASP), a hallmark feature of senescent cells. Achieving the goal using natural or synthetic agents would have a tremendous impact on the quality of lifespan and burden of age-related chronic diseases, including cancer. We report the potential of cocoa extract (CCE), a natural product derived from defatted cocoa powder and enriched in polyphenols, in targeting senescent cells via suppression of the SASP. This study demonstrates the efficacy of cocoa extract in controlling the influence of senescent cells and provides a strong rationale for their future use in aging control and geriatric medicine.

overall_design: Examination of in vitro efficacy of CCE in treating human senescent cells. This assay was performed beyond previous studies reporting their effects in treatment of disorders including but not limited to cardiovascular diseases, obesity and diabetes.

first: Zhengbing

last: Ding


title: A549-derived exosomes transform fibroblasts into cancer-associated fibroblasts (microRNA)

city: Tianjin

first: Jian

last: Zhang

address: Huanhu West Road, Hexi District

institute: Tianjin Medical University Cancer Institute and Hospital

summary: The communication between tumor-derived exosomes and stroma plays a critical role in facilitating cancer progression. We detected the mRNA expression levels after MRC5 was transfected with shRNAs targeting FOXN3 or incubated with A549 cells-derived exosomes. We reported that in lung cancer microenvironment, tumor cells exhibit a great capacity to convert normal fibroblasts (NFs) to cancer-associated fibroblasts (CAFs). We showed that tumor cells secrete a subset of exosomal microRNAs directly targeting FOXN3, which leads to the activation of fibroblasts. Activated CAFs further promote cancer growth by entering tumor tissues. These results demonstrate that intercellular crosstalk between tumor cells and fibroblasts is mediated by tumor-derived exosomes, providing potential targets for treatment of lung cancer.

overall_design: Examination of mRNA expression of MRC5 treated with A549 cells-derived exosomes or transfected with shRNAs targeting FOXN3

first: Shuangli

last: Mi


title: Transcriptome alteration in wild-type developing oligodendrocytes treated with interferon gamma and thapsigargin in comparison with untreated wild-type developing oligodendrocytes

city: Chicago

summary: Developing oligodendrocytes from wild-type 6-7 day old mice were treated with 1) interferon gamma for 1, 8, 24 and 48 hours or 2) thapsigargin for 1, 8 hours. Treated samples were normalized to untreated control samples from the same batch.

overall_design: 40 samples, 2 treatments (IFN-gamma and thapsigargin), 1 control (untreated), 4 timepoints for control and IFN-gamma; 2 timepoints for thapsigargin. 4 replicates each time point


title: Transcriptomic profiling of human senescent cells upon medicinal intervention with ginkgo boliba extract or rattan tea extract

summary: Aging and age-related pathologies can be delayed by specifically targeting the senescence-associated secretory phenotype (SASP), a hallmark feature of senescent cells. Achieving the goal using natural or synthetic agents would have a tremendous impact on the quality of lifespan and burden of age-related chronic diseases. We report the potential of ginkgo boliba extract (GBE), a commonly used dietary supplement and traditional herbal medicine for hundreds of years in China as an antioxidant and freeradical scavenger, or rattan tea extract (RTE), a medicinal agent used for many years for the treatment of inflammation, fatty liver, tumor, diabetes and hyperlipidemia, in targeting senescent cells via suppression of the SASP. This study demonstrates the efficacy of GBE and RTE as medicinal products in controlling the influence of senescent cells and provides a strong rationale for their future use in aging control and geriatric medicine.

overall_design: Examination of in vitro efficacy of GBE and RTE in treating human senescent cells. This assay was performed beyond previous studies reporting their effects in including but not limited to cardioprotection, anti-diabetes, hepatoprotection, neuroprotection, anti-tumor, and dermatoprotection.

first: Qixia

last: Xu


title: Mutual repression of the RNA-binding protein PCBP2 and long non-coding RNAs in induced pluripotent stem cells

first: Carol

last: Wilusz

state: Colorado

address: 1682 Campus Delivery

department: Microbiology, Immunology and Patholgy

summary: Data from our lab and others have previously implicated that C-rich elements (CREs) are enriched in mRNAs that are destabilized in pluripotent stem cells compared to fibroblasts. PCBP2 is an RNA-binding protein that interacts with CREs and can influence mRNA degradation. We sought to decipher the influence of PCBP2 on gene expression in human induced pluripotent stem cells (iPSC).

overall_design: To investigate the impact of PCBP2 on relative transcript abundances in human iPSCs, we performed RNA-seq on RNA isolated from cells subjected to control or PCBP2 siRNA-mediated depletion for either two or six days and compared their transcriptional profiles. For each treatment, two replicates of control and three of PCBP2 knockdown were evaluated.

first: Adam

last: Heck

first: Joseph

last: Russo

first: Donald

last: Evans

first: John

last: Brown

first: Jeffrey

first: Erin

middle: O

last: Nishimura


title: A549-derived exosomes transform fibroblasts into cancer-associated fibroblasts

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

overall_design: Refer to individual Series


title: Iphenethiol effect on seedlings

city: Bunkyo-ku, Tokyo

first: Shinji

last: Okada

address: 1-1-1 Yayoi

country: Japan

institute: The University of Tokyo

summary: Analysis of effects of iphenethiol treatment on 7-day old Arabidopsis Columbia-0 (Col-0) seedlings. Iphenethiol, induces the triple response, a characteristic ethylene-induced phenotype, by mimicking ethylene function through ethylene signaling pathways.

overall_design: 15 arrays are included. 7-day old Arabidopsis seedlings were treated with 1-Aminocyclopropane-1-carboxylic acid (ACC) for 3 or 24 hours, or iphenethiol for 24 hours, Mock treatments for 3 or 24 hours were performed as control experiments. Total RNA extracted from 3 biological replicates in each group was used.

first: Nobutaka

last: Kitahara

first: Masashi

last: Suzuki

first: Tadao

last: Asami


title: Transcriptomic analysis and identification of paracrine factors responsible for protective effects of keratinocytes on UVB-mediated melanocyte responses

city: Bangkoknoi

first: Uraiwan

last: Panich

state: Bangkok

address: 2 Siriraj Hospital, Wang Lang, Siriraj

department: Department of Pharmacology

country: Thailand

institute: Faculty of Medicine Siriraj Hospital

summary: Ultraviolet radiation (UVR) is detrimental to human skin through triggering various types of cellular damage accountable for photodamage and increased risk of developing skin cancers including cutaneous non-melanoma and melanoma. UVB irradiation can cause the loss of cellular integrity, direct damage to DNA and mediate cellular responses including apoptosis and oxidative stress in skin cells including melanocytes (MC). We previously reported that nuclear factor E2-related factor 2 (Nrf2), a transcription factor regulating antioxidant defenses, in keratinocytes (KC) played a protective role in UVB-induced DNA damage and apoptosis in MC. In this study, we will employ transcriptomic approaches to determine the candidate paracrine factors secreted by KC responsible for their protective effects on UVB-mediated MC responses including oxidative stress, apoptosis and melanogenesis. Then, the protective effects of the candidate paracrine factors on UVB-induced MC responses will be determined using small-interfering RNA-mediated silencing of the candidate paracrine factor (siPF) in MC-KC co-culture system and mouse model of photoaging.

overall_design:
RNA sequencing profiles of identification of paracrine factors responsible for the paracrine protective effects of KC
Basal (non-irradiated) and UVB irradiated mRNA profiles of primary human epidermal keratinocytes (KC), human keratinocyte (HaCaT) cells, primary human dermal fibroblast (HDF)  were generated by RNA-sequencing, using Illumina Hiseq 2000.

first: Saowanee

last: Jeayeng

first: Malinee

last: Saelim

first: Pongsakorn

last: Buraphat

first: Somponnat

last: Sampattavanich


title: Immune gene signatures in oropharyngeal cancers are associated with inverse prognosis by HPV-status

city: Ulm

first: Simon

last: Laban

address: Frauensteige 14a, Haus 18

department: Department of Otorhinolaryngology and Head & Neck Surgery

country: Germany

institute: Ulm University Medical Center

summary: In this study, we used RNA sequencing to identify and validate immune gene signatures for OPSCC to classify tumors as hot and cold. Finally, we assessed the prognostic impact of hot and cold immune gene signatures by HPV-status. The ‘hot’ immune signature was associated with a good prognosis in HPV-positive patients and contrarily, a poor prognosis in HPV- negative patients.

overall_design: mRNA profiles of 51 primary OPSCC tumors

first: Jasmin

last: Ezić

first: Jaya

last: Thomas


title: High-resolution single-nematode transcriptomic datasets of plant-parasitic nematodes from juveniles to adults

status: Public on Dec 30 2025

city: wuhan

first: xuemeng

last: han

address: shizishan street

institute: HZAU

summary: Plant-parasitic nematodes (PPNs) pose major agricultural threats, yet their transcriptional regulatory mechanisms remain poorly understood. Deciphering these mechanisms is critical for advancing knowledge of nematode development and host interactions, and for guiding the rational design of integrated control strategies. However, the lack of reliable synchronization of nematode development within plant hosts, together with the stringent requirements of high-throughput sequencing library preparation, hinders comprehensive transcriptomic profiling across distinct developmental stages. To overcome this limitation, high-resolution, single-nematode RNA-seq data was generated for eight developmental stages of Meloidogyne incognita (from second-stage juveniles to adults) using a low-input Smart-seq2 approach. The resulting dataset comprises 75 high-quality transcriptome libraries with at least five biological replicates per stage, enabling robust and reproducible analyses.

overall_design: The high-resolution, single-nematode RNA-seq data was generated for eight developmental stages of Meloidogyne incognita (from second-stage juveniles to adults) using a low-input Smart-seq2 approach. The resulting dataset comprises 75 high-quality transcriptome libraries with at least five biological replicates per stage, enabling robust and reproducible analyses.


title: A549-derived exosomes transform fibroblasts into cancer-associated fibroblasts (mRNA)

first: Jian

last: Zhang

first: Shuangli

last: Mi


title: A glycan-based adjuvant expands the breadth and duration of protection of mRNA-based vaccines.

first: Duane

middle: R.

last: Wesemann

address: 77 Avenue Louis Pasteur

department: Medicine, Division of Allergy and Clinical Immunology

institute: Brigham and Women's Hospital

summary: Inflammation initiated in response to a microbial encounter, or deliberately induced upon vaccination, is central for the activation of adaptive lymphocytes. The stimulation of pattern recognition receptors (PRRs) orchestrates the inflammatory programs that regulate adaptive immunity. Here, we took advantage of an mRNA-based vaccine generated against the ancestral spike protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to test whether tuning inflammation via PRR stimulation enhances the efficacy of mRNA vaccines. We combined mRNA-based vaccine with mannadjuvant, a formulation of fungal mannan and aluminum hydroxide that targets Dectin-2, a C-type lectin PRR. In mice and non-human primates, mannadjuvant increased the magnitude and durability of the response elicited by the mRNA-based vaccine, and it also led to the induction of neutralizing antibodies directed against variants of concern with a high escape capacity, overcoming antigenic imprinting. Mechanistically, we demonstrated that prolonged type I interferon production and potentiated interleukin-1 signaling are necessary and sufficient to exert the activities of mannadjuvant in mice and in human myeloid cells.  Overall, our data demonstrate that an anti-fungal PRR can be harnessed to create more potent and durable mRNA-based vaccines.

overall_design: We performed single-cell RNA sequencing (scRNA-seq) coupled with single-cell B cell receptor sequencing (scBCR-seq) in mice that received Comirnaty alone or Comirnaty formulated with mannadjuvant. As an additional group for direct comparison of B cell responses, mice were immunized with a monovalent Comirnaty vaccine developed against the spike protein of XBB.1.5 (hereafter referred to as XBB.1.5-Comirnaty). Briefly, C57BL/6 mice were immunized intramuscularly (i.m.) in the thigh muscle with Comirnaty alone or Comirnaty plus mannadjuvant. At day 56 after priming, the draining lymph nodes were collected and processed into single-cell suspensions by enzymatic digestion. A total of 1–2 × 10⁶ cells were stained with 0.5 µg of cell hashing antibodies (BioLegend Total-Seq™ C antibodies, Hashtags 1–12) following Fc receptor blocking with TruStain FcX™ PLUS (anti-mouse CD16/32; BioLegend, Cat. #156604), according to the manufacturer’s protocol. After incubation with hashing antibodies, cells were washed, stained with surface antibodies, and processed for fluorescence-activated cell sorting (FACS). Spike-positive germinal center (GC) B cells expressing B cell receptors (BCRs) specific for either WA1 or XBB.1.5 spike protein were sorted and subjected to scRNA-seq and scBCR-seq. Single-cell suspensions of FACS-sorted GC B cells from four biological samples were processed using the Chromium GEM-X Single Cell 5′ Reagent Kit v3 (Cat. #1000699, 10x Genomics) and the Single Cell 5′ Gel Bead Kit v3 (Cat. #1000700, 10x Genomics). Cells (27,000–35,000 per channel) were loaded onto a Chromium X Series instrument (10x Genomics) to generate single-cell gel beads-in-emulsion (GEMs), following the manufacturer’s instructions. The recovery rate was approximately 45–55%. Captured cells were lysed within individual GEMs, and released RNA was barcoded during reverse transcription. 5′ gene expression (GEX) libraries, single-cell V(D)J libraries (Cat. #1000255, 10x Genomics), and cell surface protein libraries were prepared according to the manufacturer’s protocols. Library quality was assessed using an Agilent 2200 TapeStation, and final libraries were quantified by qPCR using the KAPA Library Quantification Kit for Illumina platforms. Libraries were diluted to 2 nM and pooled into two separate batches. A total of 650 pM of pooled libraries was mixed with 5% PhiX control library prior to sequencing. Sequencing was performed in two independent runs on an Illumina NextSeq 2000 platform using the P4 XLEAP-SBS Reagent Kit (200 cycles), with paired-end reads configured as follows: 28 cycles for read 1, 10 cycles for the i7 index, 10 cycles for the i5 index, and 90 cycles for read 2. Sequencing achieved a median depth of approximately 32,000 reads per cell for gene expression, 55,000 reads per cell for BCR libraries, and 5,000 reads per cell for hashtag (ADT) libraries.

first: Kautilya

last: Jena

first: Pengxiang

last: Qu

first: Lauren

last: Baracco

first: Shahab

last: Saghaei

first: Keerti

last: Keerti

first: Zahra

last: Allahyari

first: Daniel

last: Boehmer

first: Moriah

last: Mitchell

first: Carly

last: Dillen

first: Hai-Yun

last: Li

first: Enqi

last: Liu

first: Valentina

last: Poli

first: Océane

last: Dufies

first: David

last: Hoytema van Konijnenburg

first: Roberto

last: Spreafico

first: Caihong

last: Bi

first: Rebecca

last: Hall

first: Michael

last: Kruppa

first: Zuchao

last: Ma

first: Amy

last: Gravitte

first: Douglas

middle: W

last: Lowman

first: Harry

last: Ensley

first: Pierre

last: Marty

first: Laurent

last: Boyer

first: Rémy

last: Collomp

last: Wiliams

first: Victor

first: Pui

last: Lee

first: Peter

last: Nigrovic

first: Jeffrey

last: Karp

first: Stephen

last: Elledge

first: Yi

last: Wu

first: Matthew

last: Frieman

first: Ivan

last: Zanoni


title: Gene expression data of distal colon mucosa from young and old human

first: 唐

last: 伟评

address: 2 Anzhen Rd, Chaoyang District,

institute: Beijing Institute of Heart Lung and Blood Vessel Diseases

summary: The disruption of the mucosal barrier of the digestive tract is a common pathological change in the elderly, which often causes inflammatory bowel disease among old people. Given that RNA molecules are dysregulated in numerous diseases, we performed high‑throughput analysis to compare RNA expression profiles in normal distal colon mucosa between young and aged individuals. Samples were obtained from 3 young adults (27, 28, and 36 years of age) and 3 aged adults (72, 79, and 81 years of age).

overall_design: A total 6 normal clinical colon mucosa tissue samples from different colorectal cancer patients were collected immediately after surgical resection prior to any other therapeutic intervention. All patients fulfilled the inclusion criteria as follows: (1) Age: young adults 27-36 years old and elderly adults 72-81 years old; (2) All patients were chemotherapy and radiation therapy naïve; (3) The removed normal tissue samples located at descending colon (distal colon). After collection, the samples were stored at -80 °C.

first: Tingyi

last: Sun

first: Deshan

last: Zhou


title: Gene expression changes in Ube2i-deleted mouse uterus on postnatal day 21 (PND21).

city: Guangzhou

first: Ji-Long

last: Liu

address: 483 Wushan Rd

institute: South China Agricultural University

summary: We specifically deleted Ube2i in the female reproductive tract using the Pgr-Cre driver. To portray the molecular mechanism for Ube2i function in uterus, uterine tissues were collected from Ube2i f/f and Ube2i d/d mice on PND21 and subjected to RNA-seq analysis.

overall_design: Uterine tissues were collected from Ube2i f/f and Ube2i d/d mice on PND21 and subjected to RNA-seq analysis.


title: Chromatin accessibility and transcriptome in human neuronal model exposed to Parkinson's environmental toxins [RNA-Seq]

city: Changsha

first: Jingchao

last: Hong

address: Xiangya Street

institute: Central South University

summary: Parkinson's disease is a complex neurodegenerative disorder where environmental factors play a predominant role in sporadic cases. While environmental toxins are implicated in PD pathogenesis via epigenetic pathways, the specific alterations in chromatin accessibility induced by these toxins remain poorly characterized. To address this gap, we established in vitro models using the human neuroblastoma cell line SH SY5Y, a well established neuronal model, exposed to the PD associated environmental toxins rotenone and MPP+. We performed RNA sequencing to profile the transcriptome and Assay for Transposase-Accessible Chromatin sequencing to map genome-wide chromatin accessibility landscapes under toxin exposed conditions. This integrated dataset provides a comprehensive resource detailing both gene expression and chromatin accessibility dynamics in response to PD relevant environmental neurotoxins and will facilitate investigations into transcriptional regulation, biomarker discovery, and the epigenetic basis of environmentally linked sporadic PD.

overall_design: SH-SY5Y cells (ATCC) were cultured in DMEM/F12 (1:1) medium (Gibco, MA, USA) supplemented with 10% fetal bovine serum (Gibco, MA, USA). Cells were plated in 6-well plates at a density of 5 × 105 cells/mL and incubated overnight at 37°C with 5% CO2. Experimental groups were treated with 5 mM MPP⁺ (Selleck, Houston, USA) and 10 μM rotenone (Sigma, Saint Louis, USA).  Negative control (NC) wells received equivalent volumes of dimethyl sulfoxide (DMSO) vehicle (Sigma, Saint Louis, USA). After 24-hour exposure, cells were harvested for RNA sequencing and ATAC-seq analyses. Three biological replicates per group (NC, MPP⁺, Rotenone) were processed for RNA-seq, while two replicates per group were analyzed by ATAC-seq

first: Juanjuan

last: Huang


title: The cytokine receptor Fn14 is a molecular brake on neuronal activity that mediates circadian function in vivo

city: Cold Spring Harbor

first: Lucas

last: Cheadle

address: 1 Bungtown Road

institute: Cold Spring Harbor Lab

summary: To survive, organisms must adapt to a staggering diversity of environmental signals, ranging from sensory information to pathogenic infection, across the lifespan. At the same time, organisms intrinsically generate biological oscillations, such as circadian rhythms, without input from the environment. While the nervous system is well-suited to integrate extrinsic and intrinsic cues, how the brain balances these influences to shape biological function system-wide is not well understood at the molecular level. Here, we demonstrate that the cytokine receptor Fn14, previously identified as a mediator of sensory experience-dependent synaptic refinement during brain development, regulates neuronal activity and function in adult mice in a time-of-day-dependent manner. We show that a subset of excitatory pyramidal (PYR) neurons in the CA1 subregion of the hippocampus increase Fn14 expression when neuronal activity is heightened. Once expressed, Fn14 constrains the activity of these same PYR neurons, suggesting that Fn14 operates as a molecular brake on neuronal activity. Strikingly, differences in PYR neuron activity between mice lacking or expressing Fn14 were most robust at daily transitions between light and dark, and genetic ablation of Fn14 caused aberrations in circadian rhythms, sleep-wake states, and sensory-cued and spatial memory. At the cellular level, microglia contacted fewer, but larger, excitatory synapses in CA1 in the absence of Fn14, suggesting that these brain-resident immune cells may dampen neuronal activity by modifying synaptic inputs onto PYR neurons. Finally, mice lacking Fn14 exhibited heightened susceptibility to chemically induced seizures, implicating Fn14 in disorders characterized by hyperexcitation, such as epilepsy. Altogether, these findings reveal that cytokine receptors that mediates inflammation in the periphery, such as Fn14, can also play major roles in healthy neurological function in the adult brain downstream of both extrinsic and intrinsic cues.

overall_design: Hippocampal tissue from adult C57BL/6 mice was dissected, and nuclei were isolated by mechanical dissociation and lysis. Single nuclei were processed using the 10x Genomics Chromium platform with the Chromium Single Cell 3' Library and Gel Bead Kit v4 (polyA priming) according to the manufacturers instructions to generate snRNA-seq libraries. Libraries were sequenced on an Illumina HiSeq 2000 instrument with paired-end reads.

first: Austin

last: Ferro

first: Dominic

last: Vita

first: Trevor

last: Fallon

first: Anosha

last: Arshad

first: Leah

last: Boyd

first: Tess

last: Stanley

first: Qianyu

last: Lin

first: Adrian

last: Berisha

first: Uma

last: Vrudhula

last: Gomez

first: Irene

last: Sanchez-Martin

first: Jeremy

last: Borniger


title: High-throughput RNA-sequencing of preadipocyte subsets in obese mice

city: Shanghai

first: Chunxing

last: Zheng

address: 320 Yueyang Rd.

institute: Shanghai Institute of Nutrition and Health

summary: We identified a population of obesity-promoted adipogenic preadipocytes that co-expressed Fabp4 and ICAM-1. Fabp4-Cre;mTmG mice were treated with high-fat diet for 16 weeks. The inguinal adipose tissues were collected and digested to obtain vascular and stromal fractions (SVF). The mature adipocytes, CD31-CD45-Sca-1+PDGFR-α+ICAM-1+EGFP+, CD31-CD45-Sca-1+PDGFR-α+ICAM-1+EGFP-, CD31-CD45-Sca-1+PDGFR-α+ICAM-1- cell population were isolated for RNA-seq.

overall_design: Total RNA of four cell populations form two independent experiments were pooled together for RNA sequencing.

first: Qian

last: Yang

first: Yufang

last: Shi

first: Ying

last: Wang


title: Single-cell transcriptomics reveals tissue architecture in breast carcinosarcoma

city: nanjing

first: Qingsong

last: Yan

address: xianlin

institute: Nanjing University of Chinese medicine

summary: Breast carcinosarcoma is a rare and highly aggressive subtype of metaplastic breast cancer.Single-cell RNA sequencing revealed a heterogeneous cellular ecosystem within breast carcinosarcoma.

overall_design: landscape of breast carcinosarcoma

first: Meiling


title: Gene expression profile of PBMCs in lung transplants with BOS and those without BOS

first: Wei

last: Zhang

state: Illinois

address: 840 S. Wood Street

department: Pediatrics & Institute of Human Genetics

institute: University of Illinois

summary: Gene expression profiling was performed in PBMCs collected from 26 lung transplant recipients at 3 and 10 months after transplantation and prior to development of BOS. Results: there was a substantial proportion of genes (~1800) changed over time in BOS patients but not in non-BOS patients.

overall_design: 60 pieces of samples


title: Immune Checkpoint B7x Promotes Immune Evasion and Resistance to PD-1/PD-L1 Blockade in Bladder Cancer

city: Bronx

first: Deyou

state: NY

address: 1301 Morris Park Avenue

department: Department of Genetics

institute: Albert Einstein College of Medicine

summary: Cancer cells adopt multiple strategies to avoid detection and destruction by the immune system, including exploiting immune checkpoint pathways. B7x (B7-H4, B7S1, or VTCN1), a member of the B7/CD28 family, is frequently expressed in advanced bladder cancer (BC), yet its role in BC progression and resistance to therapy remains poorly understood. Resistance to PD-1/PD-L1 immune checkpoint blockade immunotherapy significantly limits durable responses, with only 20%–25% of patients with muscle-invasive BC achieving long-term benefits. Here, we demonstrated that B7x mRNA and protein expression were associated with poor survival outcomes in muscle-invasive BC patients and mouse models of BC. Stable expression of B7x in immune-competent BC mouse models resulted in enhanced tumor growth and splenomegaly, driven by the exclusion and suppression of tumor-infiltrating anti-tumor immune cells and the enrichment of pro-tumor and immunosuppressive cells. Consistently, in the IMvigor210 clinical trial, high B7x mRNA expression was correlated with poorer survival in muscle-invasive BC patients treated with PD-L1 blockade. Notably, combination therapy targeting B7x alongside PD-1/PD-L1 or CTLA-4 blockade reduced tumor burden and overcame resistance to monotherapy. These findings establish B7x as a substantial driver of immune evasion in BC and highlight its potential as a therapeutic target to improve immune checkpoint blockade efficacy in muscle-invasive BC.

overall_design: Given the significant tumor growth-enhancing effect of B7x observed in BBN963 and, to a lesser extent, UPPL1541 tumors, but not in MB49, we conducted bulk RNA-seq on BBN963, UPPL1541, and MB49 cell lines (n = 5) to identify immunomodulatory factors contributing to their sensitivity to B7x.

first: Marc

last: Pulanco

first: Xiang Yu

first: Alexander

last: Sankin

first: Xingxing

last: Zang


title: A circadian rheostat drives proton electrochemical gradients to optimize cell-type specific growth in Arabidopsis

city: Cerdanyola del Vallès

first: LU

last: XIONG

address: Carrer de la Vall Moronta

institute: CRAG

summary: Plant growth relies on the activity of key transcription factors. Here, we uncover a mechanism for organ-specific growth driven by opposing electrochemical signals that propagate in a cell-type-specific manner. Using a genetically encoded pH sensor and a pH-sensitive dye, we show that apoplastic pH in epidermal cells oscillates antiphasically relative to phloem pH. The clock component CCA1 lowers apoplastic pH in hypocotyl epidermal cells while increasing it in companion cells. This opposing regulation promotes hypocotyl growth but inhibits root elongation. Mechanistically, CCA1 activates auxin signaling in shoots while repressing SUCROSE TRANSPORTER 2 and the electrogenic (H+)-pump ATPase AHA3 by directly binding their promoters. The repression decreases sucrose loading into the phloem and slows transport velocity. Expressing CCA1 in the phloem is sufficient to inhibit root elongation, whereas AHA3 over-expression in CCA1 over-expressing seedlings rescues root growth. Thus, a circadian rheostat orchestrates electrochemical signals to optimize source capacity with sink demand.

overall_design: RNA-Seq profiling of Arabidopsis Wild-Type (Col-0) shoots and roots and their counterpart CCA1 overexpressing plants from 8-day-old seedlings under constant 15 µE of white fluorescent light at 22°C

first: Paloma

last: Mas

first: Lu

last: Xiong


title: Chromatin accessibility and transcriptome in human neuronal model exposed to Parkinson's environmental toxins [ATAC-Seq]

first: Jingchao

last: Hong

first: Juanjuan

last: Huang


title: Gene expression changes in UBE2I-knockdown primary human endometrial stromal cells (hESCs) compared to control cells

first: Ji-Long

last: Liu

summary: To portray the molecular mechanism for UBE2I function in hESCs, cell treated with siUBE2I and siNC were subjected to RNA-seq analysis.

overall_design: The hESCs treated with siUBE2I and siNC were subjected to RNA-seq analysis


title: DOT1L-mediated CDK9 methylation is essential for DNA double-strand break repair [RNA-seq]

city: Seoul

first: Yugyeong

last: KIM

address: 84, Heukseok-ro

department: Life science

country: South Korea

institute: Chung-Ang University

summary: P-TEFb is a key regulator of transcription elongation and is composed of cyclin-dependent kinase 9 (CDK9) and cyclin T1. DOT1L is a histone H3K79 methyltransferase. Here, we show that treatment with the DOT1L inhibitor EPZ-5676 induces transcriptome changes in HCT116 cells. We further demonstrate that DOT1L methylates CDK9 at lysine 56 and that CDK9 methylation-deficient mutant  K56A reshapes genome-wide CDK9 occupancy. Notably, changes in CDK9 occupancy are particularly pronounced at double-strand break (DSB)-related genes and are associated with the regulation of their transcription. This idataset includes RNA-seq and ChIP-seq data generated from HCT116 cells.

overall_design: RNA-seq was pereformed in CDK9-knockdown HCT116 cells reconstituted with either CDK9 WT or K56A mutant. Other RNA-seq was performed in EPZ-5676 treated HCT116 cells.

last: Kim

first: Chul-Hong

first: Sang Beom

last: Seo


title: Eukaryotic translation initiation factor 3B regulates pancreatic cancer cell proliferation by interacting with RAB14

city: suzhou

first: yán

last: hu

address: No. 58 Changsheng South Road, Taicang 215400, Jiangsu, China

department: Central Laboratory

institute: The First People's Hospital of Taicang

summary: To study the regulatory role of EIF3B in the proliferation of pancreatic cancer (PC) cells.

overall_design: We assessed EIF3B and RAB14 expression in PC tissues using The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) datasets. RNA sequencing was performed to identify the candidate targets of EIF3B. The interaction between EIF3B and RAB14, along with its functional implications, was validated through RNA immunoprecipitation, actinomycin D treatment, and luciferase reporter assays. The regulatory influence of EIF3B and RAB14 on cell cycle signaling pathways was examined utilizing gene set enrichment analysis (GSEA) and Western blotting.

first: Yan

last: Hu


title: RNA Sequencing of 16D Prostate Cancer Cell Lines with genetic knockout and rescue of OGDHL

city: Los Angeles

first: Andrew

middle: Scott

last: Goldstein

state: CA

address: 610 Charles E Young Dr East

department: Urology

institute: University of California, Los Angeles

summary: The goal of this study was to perform transcriptomics of prostate cancer cells with genetic knockout and rescue of OGDHL treated with the Androgen Receptor Pathway Inhibitor Enzalutamide (Enza) or Vehicle (DMSO)

overall_design: Prostate cancer cells were infected with lentivirus containing CAS9 and a gRNA targeting OGDHL (sgOGDHL). Cells were then maintained in Androgen Receptor Pathway Inhibitor (Enza) for 6 weeks to adapt. Knockout cells were then infected with lentivirus carrying control enhanced green fluorescent protein (eGFP), knockout-resistant full-length (FL) OGDHL, or knockout-resistant deleted mitochondrial targeting sequence (dMTS) mutant of OGDHL.

first: Matthew

last: Bernard


title: Circadian and Light Perturbed Circadian Gene Expression in Prochlorococcus marinus MED4

city: Richland

first: Lindsey

middle: N

last: Anderson

state: WA

address: 3300 Stevens Dr

department: Biological Sciences Division

institute: Pacific Northwest National Laboratory

summary: A circadian gene expression study in model marine cyanobacteria Prochlorococcus marinus MED4 was performed in order to evaluate circadian gene expression and identify genes which were regulated dependent on circadian photoperiod or light intensity.

overall_design: Prochlorococcus marinus MED4 was cultured in adapted Pro99 media prepared using Salish Seawater (Sequim, Washington) and 2X standard concentrations of Pro99 N/P sources, while maintaining 1× concentration of Pro99 trace metals. Cultures were acclimated to a circadian photoperiod of 12:12 h light:dark at an incident white-light intensity of 45 µmol photons m⁻² s⁻¹ and a temperature of 22 °C for XX days / generations prior to sampling. Accimaltion was performed in a single XL batch flask before splitting samples into individual 50mL tubes. Circadian perturbed samples were exposed to extended periods of light during circadian night (ZT = 14, 16h) or dark during circadian day (ZT = 2, 4h). Destructive sampling was performed for three biological replicates every two-hours across a full circadian cycle. At each time point, biological replicates were harvested via rapid filtration and flash-frozen in liquid nitrogen.

first: Pavlo

last: Bohutskyi

first: Zachary

last: Johnson

first: Xialou

last: Li

first: Natalie

last: Sadler

first: Margaret

middle: S

last: Cheung

first: Weijun

last: Qian


title: Phagocytosis of necroptotic cells optimizes type 1 conventional dendritic cells for induction of a cytotoxic T-cell response

city: Leiden

first: Jannie

last: Borst

address: Albinusdreef 2

department: Immunology

country: Netherlands

institute: Leiden University Medical Center

summary: Whether a T-cell response to dead cells arises depends on whether they harbor recognizable  antigens, but also how dead cell debris impacts conventional dendritic cells (cDCs). In all tissues, cell debris is continuously phagocytosed by cDCs that can migrate to lymph nodes (LNs) and initiate T-cell responses, depending on their maturation state. The cDC1 lineage excels at antigen cross-presentation, which is required for induction of the cytotoxic CD8+ T-lymphocyte (CTL) response. At steady state, cDC1s undergo homeostatic maturation, which leads to T-cell non-responsiveness. This cDC1 state has recently been defined by ex vivo transcriptomics as resulting from phagocytosis of apoptotic cell debris. Necroptotic (tumor) cell death has been described as more immunogenic than apoptotic cell death, but its impact on cDC maturation has not been defined. In this study, we use an in vitro model to compare side-by-side the impact of well-defined apoptotic versus necroptotic tumor cell debris on the CTL response induced by cDCs, as well as on phenotype and function of both cDC1s and cDC2s. We confirm that cDC2s are less efficient than cDC1s in dead cell phagocytosis and find that they minimally respond to it in terms of gene expression. Apoptotic cell debris is more efficiently phagocytosed by cDC1s than necroptotic cell debris and induces a cDC1 cell state in vitro that has an evident transcriptomic relationship to the homeostatic maturation state defined ex vivo, thus validating our approach. We identify necroptosis as more potent than apoptosis in inducing a CTL response and attribute this to the ability of necroptotic cell debris to induce a specific, transcriptomically defined maturation state in cDC1s, characterized by cytokine and phosphoinositide signaling, cytoskeletal and metabolic activity and functional differentiation. We suggest that this cDC1 signature may be used to diagnose immunogenicity of necroptosis ex vivo.

overall_design: Bulk RNA sequencing of murine primary splenic cDC1 and cDC2 co-cultured for 6 h with medium from wildtype TC-1 cells, or medium from apoptotic TC-1-iBimS cells, or medium from necroptotic TC-1-iRIPK3 cells.

first: Mo

last: Staal

first: Zhixian

last: Wang

first: Douwe

last: Bosma

first: Julia

last: Busselaar

first: Ellen

last: Schrama

first: Evert

last: de Vries

first: Yanling

last: Xiao


title: A bioactive hydrogel harnessing the regenerative potential of notochordal cells serves as instructive cell carrier for nucleus pulposus repair [scRNA-seq human]

city: Utrecht

first: Frank

last: Riemers

address: Uppsalalaan 8

institute: Utrecht University

summary: Natural biomatrices are popular owing to their ability to mimic tissue-specific biological properties. These properties are crucial for the intervertebral disc, a particularly demanding tissue whose degeneration is a major cause of chronic lower back pain. Degeneration starting within the core of the disc, the nucleus pulposus (NP), is marked by the loss of notochordal cells (NCs) and associated healthy extracellular matrix. The regulative potential of the NC-secretome was exploited  through a PEG-based hydrogel formulated with decellularized porcine notochordal cell matrix (dNCM). Even under conditions which mimic the degenerate niche, the hydrogel supported maintenance of the phenotype of native porcine NCs, well-known for the difficulty in preserving their vacuolated morphology. dNCM-PEG hydrogel carrying human mesendodermal progenitors (hMEPCs; iPSC-derived and capable of differentiating into NCs), was injected into NP explants with enzymatically induced matrix degradation and subjected to dynamical loading. hMEPCs engrafted successfully and a healthy disc cell phenotype was observed. Injection of dNCM+hMEPCs into degenerated discs in a pilot experimental dog study indicated that ~7 % of the 0.5 million hMEPCs engrafted. Single cell RNAseq analysis showed over 30 % of the engrafted and recovered hMEPCs co-expressed Collagen Type II and Aggrecan consistent with a functional phenotype. No tumorigenic or systemic immunogenic side effects were observed. At the tissue level, TBXT expression, as well as matrix quality, were enhanced in the treated degenerate disc tissues. Together, this study highlights the translational potential of combining cell-based therapies with a bioactive material containing part of the NC secretome, warranting further development and validation.

overall_design: A pilot study using a validated preclinical dog model was performed to explore the potency of intradical injection of hMEPCs supported by dNCM. Initially, moderate degeneration was induced by partial nuclectomy (NX) in alternate IVD levels (L1-L1, L3-L4, L5-L6, L7-S1). One month after induction, these levels were intradiscally injected with dNCM+hMEPCs. Three months after the treatment the L7-S1 disc level was processed for single cell RNA sequencing together with a disc (T12-13) in which NX was performed of a dog of the same litter that was not treated with dNCM+hMEPCs which was used as degenerated control.

first: Lisanne

middle: T

last: Laagland

first: Elias

last: Salzer

first: Georgina

last: Targa Fabra

first: Xiaole

last: Tong

first: Deepani

last: Poramba-Liyanage

first: Julie

last: Warin

first: Kieran

last: Joyce

first: Joseph

last: Snuggs

middle: M

first: Lizette

last: Utomo

first: Seyed

middle: A

last: Kamali

first: Tara

last: Schmitz

first: Noemy

last: Vergara Vera

first: Christine

last: Le Maitre

first: Benjamin

last: Gantenbein

first: Bjorn

last: Mei

first: Anne

last: Camus

first: Keita

last: Ito

first: Abhay

last: Pandit

first: Marianna

last: Tryfonidou


title: Commensal-driven serotonin production modulates in vivo delivery of synthetic and viral vectors

city: Hefei, Anhui

first: Guorong

last: Zhang

address: No. 96 Jinzhai Road

institute: University of Science and Technology of China

summary: In vivo delivery systems (IDS) are designed to protect and transport therapeutics, but their efficacy is limited by low delivery efficiency. Here, we reveal that intestinal microbiota critically modulates IDS delivery efficiency by promoting hepatic clearance, whereas disrupting host-microbe interactions markedly enhances drug and gene delivery. Mechanistically, intestinal epithelial sensing of microbial stimuli triggers serotonin production that activates Kupffer cells. Transient inhibition of serotonin signaling, via receptor blockade or dietary intervention, attenuates hepatic clearance and improves systemic delivery. This strategy enhances the efficacy of IDS-based chemotherapy and oncolytic virotherapy and enables body-wide improvements in somatic genome editing and mRNA-based protein replacement. Together, these findings uncover a gut-liver immune axis that broadly constrains IDS performance, offering general approaches to improving in vivo therapeutic delivery.

overall_design: KCs from Vil1Cre-Myd88fl/fl mice treated with or without serotonin were used for bulk RNA sequencing.


title: Integrated Clinical and microRNA Signatures for Predicting Altitude-Related Hypertension

city: TianJin

first: Yan

last: Li

address: NO.23 PingJiang street

department: Family Planning

institute: The second hospital of Tianjin medical university

summary: Essential hypertension (EH) remains a leading contributor to cardiovascular and cerebrovascular disease worldwide. However, the molecular mechanisms driving EH under chronic hypoxia, particularly among long-term residents of high-altitude regions, remain unclear. MicroRNAs (miRNAs), as critical post-transcriptional regulators, offer a promising link between hypoxia, inflammation, and vascular remodeling.

overall_design: We established a high-altitude cohort including normotensive entrants (N), altitude-related hypertension (ARH), and long-term essential high-altitude hypertension (EHH). Clinical indicators, biochemical markers, and cytokines were analyzed using the compareGroups R package. Differential miRNA expression determined by |log₂FC| > 1.5 and adjusted P < 0.05. Functional enrichment analyses were conducted via clusterProfiler, and PPI networks were constructed using STRING and Cytoscape. Diagnostic performance was assessed using ROC analysis.


title: N6-methyladenosine RNA methylome analyses  in podocytes of Nup93R388W-knock in (KI) mice (strain: 129S1/SvlmJ)

city: San Antonio

first: Kexin

last: Xu

state: Texas

address: 7703 Floyd Curl, MC 8257

department: Molecular Medicine

institute: UT Health Science Center at San Antonio

summary: To identify N6-methyladenosine RNA methylome, we performed MeRIP-seq using murine podocytes isolated from Nup93R388W-knock in (KI) mice

overall_design: N6-methyladenosine RNA methylome profiling by high throughput sequencing (MeRIP-seq) in podocytes isolated from Nup93 wild-type (Nup93 +/+) and Nup93 homozygous R388W mutant (Nup93 RW/RW) mice

first: Zhang

last: Zhao

first: Lee

last: Jihoon

first: Xu

last: Kexin


title: An arrhythmogenic cardiomyopathy pig model by PKP2 heterozygous knockout

city: BeiJing

first: Yue

address: North Lishi Road

institute: Fuwai Hospital, Chinese Academy of Medical Sciences

summary: Patients with arrhythmogenic cardiomyopathy (ACM) have a high incidence of ventricular arrhythmias and a significant risk of sudden death. However, the difficulty in obtaining myocardial tissue samples from ACM patients at the early stage of the disease, coupled with the lack of animal models that can simulate the characteristics of human ACM, has severely hindered in-depth research into its pathogenesis.

overall_design: Total RNA was extracted from right ventricular tissue of PKP+/- and WT pig using RNeasy Mini Kit.). A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. The library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated. The index of the reference genome was built using Hisat2 v2.0.5. and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.


title: 4-OI treatment inhibit LPS-induced neutrophil inflammatory responses

city: Chong qing

address: 30 Main Street, Gao Tanyan

institute: Army Medical University

summary: Our in vitro cell research has revealed that LPS stimulation can induce the upregulation of the immune response gene 1 (Irg1) in neutrophils. Itaconic acid is a metabolic derivative generated by Irg1,4-octyl itaconate, which is exogenous itaconate, can exert protective effects in acute colitis.  we utilized RNA sequencing-based omics analysis to explore the impact of 4OI treatment on the activation of inflammatory responses in neutrophils and the underlying mechanisms.Transcriptomic analysis revealed that 4-OI suppresses inflammatory signaling pathways including NF-κB and Toll-like receptor pathways.The experiment was divided into 3 groups, including the control group, the LPS stimulation experimental group, and the 4-OI treatment group.

overall_design: RNA-seq profiling of bone marrow-derived Wide type neutrophils were activated by LPS, and 4-OI was added to inhibit the inflammatory response.

first: Tao

last: Wang

first: Guojian


title: Early Radial Extracorporeal Shockwave Stimulation on Proximal Tibial Circular Osteotomy Site Enhanced Heterotopic Skin Wound Healing via Small Extracellular Vesicles

city: Changchun

first: Tiecheng

last: Yu

state: Jilin

address: Xinmin Street No.1

department: Department of Orthopaedics

institute: the First Hospital of Jilin University

summary: Wound healing represents a complex biological process necessitating innovative therapeutic approaches, particularly for chronic wounds such as diabetic foot ulcers (DFUs). Inspired by the regenerative effects of tibial bone transport for DFUs, we explored whether radial extracorporeal shockwave therapy (rESWT) at the tibial circlularr osteotomy site (TOE) could enhance wound healing in rats. We found that TOE accelerated dorsal foot wound healing via small extracellular vesicles (sEV). This sEVs showed strong regenerative effects and modulated macrophage polarizations in vitro and in vivo. Single-cell sequencing revealed mesenchymal stem cells as the likely sEV source, with rESWT triggering sEV release through ATP/P2X7R/p38MAPK pathway. Proteomic analysis identified five differentially expressed proteins in sEVs, with Thbs1-enhanced sEVs enhancing wound healing by promoting IL4-induced M2 macrophage polarization. This innovative approach represents a promising alternative strategy for wound management, with potential for future DFU treatment.

overall_design: Single-cell RNA sequencing (scRNA-seq) was performed on all nine samples from circular osteotomy tissues at the proximal tibia to elucidate the cellular origins of the pro-healing sEVs derived from TOE. We established a 3-mm circular osteotomy model at the proximal tibia (TO model) and a concurrent 4-mm full-thickness cutaneous wound on the ipsilateral dorsum of the foot in Sprague-Dawley rats (n=9, 6-8 weeks old). Shock wave therapy was administered to the osteotomy site on postoperative days 2 and 4. Tissue samples from the proximal tibial osteotomy site were collected at 4 and 24 hours after each shock wave session (TOE group), with non-treated osteotomy site samples (TO group) serving as controls. An additional baseline sample (TO_2d_0h) was obtained prior to shock wave intervention on postoperative day 2. Single-cell RNA sequencing (scRNA-seq) was subsequently performed on all nine samples.

first: Xiaoping

last: Xie

first: Songqi

last: Bi

first: Bang

last: Su

first: Rongqi

last: Zhou

first: Xudong


title: A bioactive hydrogel harnessing the regenerative potential of notochordal cells serves as instructive cell carrier for nucleus pulposus repair  [scRNA-seq dog]

first: Frank

last: Riemers

overall_design: AA pilot study using a validated preclinical dog model was performed to explore the potency of intradical injection of hMEPCs supported by dNCM. Initially, moderate degeneration was induced by partial nuclectomy (NX) in alternate IVD levels (L1-L1, L3-L4, L5-L6, L7-S1). One month after induction, these levels were intradiscally injected with dNCM+hMEPCs. Three months after the treatment the L7-S1 disc level was processed for single cell RNA sequencing together with a disc (T12-13) in which NX was performed of a dog of the same litter that was not treated with dNCM+hMEPCs which was used as degenerated control.

first: Lisanne

last: Laagland

first: Elias

last: Salzer

first: Georgina

last: Targa Fabra

first: Xiaole

last: Tong

first: Deepani

last: Poramba-Liyanage

first: Julie

last: Warin

first: Kieran

last: Joyce

first: Joseph

last: Snuggs

first: Lizette

last: Utomo

first: Seyed

last: Kamali

first: Tara

middle: C

last: Schmitz

first: Noemy

last: Vergara Vera

first: Christine

middle: L

last: Le Maitre

first: Benjamin

last: Gantenbein

first: Bjorn

last: Mei

first: Anne

first: Keita

first: Abhay


title: RNAseq analysis of Sorghum under nitrate limitation and recovery at different time points.

city: Cold Spring Harbor

first: Sunita

last: Kumari

state: New York

address: One Bungtown Road

institute: Cold Spring Harbor Lab

summary: Nitrogen availability strongly influences sorghum growth, physiology, and yield, making enhanced nitrogen use efficiency (NUE) critical for agricultural sustainability. To characterize transcriptional responses to nitrate availability in sorghum, we profiled genome-wide gene expression changes under nitrate-sufficient, nitrate-limiting, and nitrate-recovery conditions. This dataset provides temporal resolution of nitrate-responsive regulation in roots and leaves, enabling comparative insights into nitrogen signaling and assimilation.

overall_design: Sorghum (Sorghum bicolor, genotype BTx623, v3.1.1 reference genome) seeds were germinated on rag dolls and transferred to hydroponic tanks containing full-strength Hoagland nutrient solution at 10 days after germination (10 DAG). After 12 days under nitrate-sufficient conditions, plants at the 5th leaf stage (21 DAG) were transferred to a nitrate-limiting nutrient solution in which Ca(NO₃)₂ and Mg(NO₃)₂ were replaced with CaCl₂ and MgSO₄. Root and leaf tissues were harvested at the following time points under nitrate limitation: 0 min (baseline), 30 min, 3 hours, and 24 hours (1 day). After 24 hours of nitrate deprivation, nitrate was added back to the nutrient solution. Recovery samples were collected at: 24 h + 30 min and 24 h + 48 h (2 days). Three biological replicates were collected per tissue and treatment, with each replicate consisting of pooled tissue from five plants. RNA-seq libraries were prepared using the NEBNext RNA-seq Library Prep Kit and sequenced on the Illumina NextSeq 2000. Reads were processed with Trimmomatic, aligned to the Sorghum bicolor BTx623 v3.1.1 genome using STAR, and quantified with StringTie. Differential expression analysis was performed using DESeq2.

first: Janeen

last: Braynen

first: Lifang

last: Zhang

first: Michael

last: Reguski

first: Andrew

last: Olson


title: Thrombospondin 1 Aggravates the Progression of Heart Failure with Preserved Ejection Fraction by Inhibiting Mitophagy

city: Taiyuan

first: Xingpeng

last: Bu

address: No. 85, Jiefang South Road

institute: Shanxi Medical University

summary: Heart failure with preserved ejection fraction (HFpEF) accounts for over half of all heart failure cases, yet its underlying mechanisms remain poorly understood. Recent evidence suggests that mitochondrial dysfunction and impaired mitophagy play pivotal roles in HFpEF pathogenesis. Thrombospondin 1 (Thbs1), a matricellular protein, is implicated in cardiovascular remodeling, but its role in HFpEF has not been elucidated. Here, we demonstrate that Thbs1 expression is significantly elevated in the myocardium of HFpEF mice and that Thbs1 exacerbates cardiac dysfunction by suppressing mitophagy. Using a well-established "two-hit" mouse model (high-fat diet and L-NAME), we show that AAV9-mediated knockdown of Thbs1 alleviates diastolic dysfunction, cardiac fibrosis, and myocardial inflammation. RNA sequencing and proteomics analyses revealed enrichment of the PI3K/Akt/mTOR pathway in HFpEF hearts, which was attenuated by Thbs1 silencing. Mechanistically, Thbs1 knockdown restored autophagic flux, promoted mitochondrial clearance, and improved mitochondrial homeostasis in cardiomyocytes. These findings establish Thbs1 as a key regulator of impaired mitophagy in HFpEF and suggest that targeting Thbs1 may provide a therapeutic avenue for treating this complex syndrome.

overall_design: Male C57BL/6 mice were fed a high-fat diet (HFD; 60% kcal from fat, D12492, Research Diets) and received L-NAME (0.5 g/L, Sigma-Aldrich) in drinking water (pH 7.4) for 12 consecutive weeks. Control mice were fed standard chow and given regular drinking water. After 12 weeks, cardiac function, body weight, and blood pressure were assessed.


title: RNAseq analysis of Maize  under nitrate limitation and recovery at different time points.

summary: Nitrogen (N) is a key macronutrient required for plant growth, development, and yield. Improving nitrogen use efficiency (NUE) in maize is important for sustainable crop production and reducing fertilizer-associated environmental impacts. To investigate transcriptional responses to nitrate availability, we examined genome-wide gene expression dynamics in maize under nitrate-limiting, and nitrate-recovery conditions. This dataset captures rapid transcriptional shifts in both roots and leaves during nitrate deprivation and subsequent nitrate resupply.

overall_design: Maize (Zea mays, inbred line B73, v5 reference genome) seeds were germinated on rag dolls and transferred to hydroponic tanks containing full-strength Hoagland nutrient solution at 7 days after germination (DAG). After 12 days of growth under nitrate-sufficient conditions, plants at the 5th leaf stage (15 DAG) were switched to a nitrate-limiting solution in which Ca(NO₃)₂ and Mg(NO₃)₂ were replaced with CaCl₂ and MgSO₄. Root and leaf tissues were collected at the following time points under nitrate limitation: 0 min (baseline), 30 min, 3 hours, and 24 hours (1 day).After 24 hours of nitrate deprivation, nitrate was reintroduced to the nutrient solution to assess recovery responses. Recovery samples were collected at 24 h + 30 min and 24 h + 48 h (2 days).