title: Non-viral CISH locus-specific integrated FAPα CAR-T cells achieve potent anti-tumor efficacy in glioblastoma

first: guozhu

last: xie

address: Shatainan Road No.1023-1063

institute: Southern Medical University

summary: CAR-T cells have been used to treat patients with glioblastoma (GBM) in clinical trial settings, by targeting GBM-associated antigens. However, the efficacy of these CAR-T cells remain limited mainly due to heterogeneous expression of tumor antigen and their anergy in tumor microenvironment (TME). Cytokine-inducible SH2-containing protein (CIS, encoded by the gene CISH) is a potent intracellular checkpoint inducing T cell anergy. Here, we identified fibroblast activation protein alpha (FAPα) as a highly attractive target for CAR-T cell therapy against GBM based on its dual expression pattern (on tumor cells and perivascular cells) in GBM. A panel of nanobodies specific for FAPα were then isolated using a yeast surface display library. FAPα-targeting CAR-T cells were developed using the isolated nanobody and verified for their specific cytotoxicity to GBM cells. Furthermore, a non-viral circular single-stranded DNA (cssDNA)-based CRISPR/Cas9 targeted genome editing (cssDNA/CRISPR/Cas9) technology was used to integrate CAR cassettes at CISH locus to generate CISH-knockout (CISH-KO) CAR-T cells. The resulted CISH-KO CAR-T cells exhibited robust proliferation and potent anti-GBM activity in vitro and in vivo compared with conventional lentivirus-transduced CAR-T cells. Our proof-of-concept study demonstrates that CISH-KO FAPα-targeting CAR-T cells engineered by non-viral locus-specific integration represent a promising therapeutic approach for GBM.

overall_design: RNA-seq profiling of widetype T cells, LV transduced CAR-T cells and CISH ko CAR-t cells.

first: Xie

last: guozhu

first: Dong

last: xin


title: cMaf supports Zeb2 expression for primitive hematopoiesis (Multiome)

status: Public on Dec 26 2025

city: Saint Louis

first: Jing

last: Chen

state: MO

address: 600 S Euclid Ave

country: USA

institute: Washington University in St. Louis

type: Genome binding/occupancy profiling by high throughput sequencing

type: Expression profiling by high throughput sequencing

summary: Tissue-resident macrophages (TRMs) are essential for tissue homeostasis and play a key role in disease and pathology. They originate from distinct waves of hematopoietic progenitors, including primitive, transient-definitive, and definitive hematopoiesis. We found that loss of the Zeb2 ‒165kb enhancer impairs  monocyte development and alters TRM transcriptional landscapes, with only HSC-derived monocytes requiring Zeb2 for their development. In Zeb2∆‒165kb mice, primitive TRMs persist in tissues due to the lack of replacement by later hematopoietic waves, and Maf is required for maintaining Zeb2 expression in primitive macrophages.

overall_design: Fetal Liver CD45.2+CD64+ cells were isolated from E12.5 wildtype and KO embryos. Single nuclei were extracted and submitted for snRNA- and scATAC-seq sequencing using 10X genomics multiomic platform.

first: Theresa

middle: L

last: Murphy

first: Kenneth

middle: M


title: Chromatin Assembly Factor 1 is Required for Normal Gene Repression and Facultative Heterochromatin Formation in Neurospora crassa [ChIP-seq]

city: Athens

first: Zachary

middle: A

last: Lewis

state: GA

address: 120 E. Green St.

department: Microbiology

institute: University of Georiga

summary: Formation of facultative heterochromatin by Polycomb Repressive Complex 2 (PRC2) is a well conserved epigenetic mechanism that functions to control transcriptional dynamics across eukaryotes. PRC2 catalyzes histone H3 lysine 27 tri-methylation (H3K27me3), a histone post-translational modification that helps maintain stable gene repression. Gene repression by PRC2 is important for organismal development and defects in PRC2 function are associated with human ailments, such as Weaver syndrome and various cancers. In this study, we reveal the replication-dependent histone chaperone, Chromatin Assembly Factor 1 (CAF-1), is required for normal facultative heterochromatin formation in model fungus N. crassa. CAF-1 deficiency results in widespread misregulation of gene expression, particularly within facultative heterochromatin domains, which is accompanied by a rearrangement of H3K27me3 patterns. Regional losses of H3K27me3 are associated with reduced levels of ASH-1 catalyzed H3K36 methylation, and gains of histone modifications associated with active transcription. Furthermore, analysis of a double mutant deficient for both CAF-1 and PRC2 activity revealed that these complexes play distinct roles in maintaining gene repression and facultative heterochromatin. Collectively, these results shed light on CAF-1's role in maintaining a repressive chromatin environment.

overall_design: ChIP-seq performed on mycelial tissue after overnight growth in WT and mutant strains

first: Eduardo

middle: V

last: Torres

first: Collin

middle: D

last: Link

first: Rochelle

last: Yap

first: Aileen

middle: R

last: Ferraro

first: Abigail

last: Deaven

first: Jackie

middle: F

last: Pelham


title: Genome-scale DNA methylome and transcriptome profiling of midgut of Bombyx mori infected with BmCPV

status: Public on Dec 25 2025

city: suzhou

first: Xiaolong

last: Hu

state: jiangju

address: renai road

country: China

institute: soochow university

type: Methylation profiling by high throughput sequencing

summary: DNA methylation, as well as histone modifications, is an important regulatory mechanism for altered gene expressions. Our previous study has shown that Bombyx mori cytoplasmic polyhedrosis virus (BmCPV) infection could change the level of trimethylation of lysine 9 of histone 3 (H3K9me3) and acetylation of lysine 9 of histone 3 (H3K9ac), thus regulating the mRNAs expressions in the midgut of silkworm, B. mori. However, the correlation between genome-scale DNA methylome and transcriptome remains underexplored. In this study, whole genome bisulfite sequencing (WGBS) was performed on the midgut of BmCPV-infected silkworms at 48 h and 96 h post infection, and corresponding midguts of uninfected silkworms. And intersection genes were screened by correlation analysis between differentially methylated regions (DMR)-associated genes and differentially expressed genes (DEGs). Above analysis will contribute to further understanding how BmCPV regulate gene expression through epigenetic modification at the genome-wide level.

overall_design: WGBS profiling of BmCPV-infected silkworm midguts and untreated silkworm midguts

first: Qunnan

last: Qiu

first: Chengliang

last: Gong

first: Zhe

last: Liu

first: Yuqing

last: Huang

first: Huilin

last: Pang

first: Liuyang

last: Li

first: Min

last: Zhu


title: Transcriptomics of K562/S and K562/R, KU812/S and KU812/R of imatinib resistant cell using RNA-sequencing.

city: Kharghar

first: Rukmini

last: Govekar

state: Maharashtra

address: Sector 22, Utsav Chowk-CISF Rd, Owe camp

department: Cancer Research Institute

country: India

institute: Advanced centre for Treatment, Research and Education in Cancer

summary: CML-CP Patients showing resistance to Imatinib, due to Bcr-Abl mechanisms of resistance  are treated with 2nd and 3rd generation TKIs but some non-responders shown Bcr-Abl independant mechanism of resistance. We hypothesize that this could be due to activation of novel pathway, or activation of downstream molecules of Bcr-Abl pathway. In this study we have performed Transcriptomics and epigenomics analysis of K562 and KU812 CML-BC cell sensitive and resistant to imatinib, ITGB3  showed high transcript levels, and was also  hypomethylated in K562/R cells as compared to sensitive counterparts and showed higher protein levels  in both K562 and KU812 resistant cell lines. Previous studies in the lab also showed  ITGB1 as a differentiator in proteomic analysis and further on-going studies indicate its role in resistance. ITGB1 was however not modulated at transcriptional level.  The protein levels of ITGB3 were significantly increased in resistant cells (K562; KU812: while those of ITGB1 were significantly decreased in resistant cells (K562; KU812. With the known switching of integrins, whether higher expression of ITGB3 had a role in modulating the levels of transcriptionally non-regulated ITGB1 was investigated in K562/S cells with ITGB1 knocked down (KD)  protein levels of ITGB3 were upregulated as compared to VC. Similarly,  knock down of ITGB3 in K562/R resulted in increased level of  ITGB1 protein. These striking results confirmed switching of integrins and explained reduced levels of ITGB1 despite no alteration at genomic or transcriptomic level in resistant cells.

overall_design: RNA-Sequencing of K562 and KU812 CML-BC cells sensitive and resistant t0 imatinib.

first: Shashi

last: Kumari

first: Rahul

last: Mojidra

first: Mythreyi

last: Narasimhan


title: A dual role for GLI3 signaling in neural crest development

city: Cincinnati

first: Simon

middle: J. Y.

last: Han

state: OH

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

summary: Neural crest cells (NCCs) are a multipotent cell population that undergo specification, epithelial-to-mesenchymal transition, migration, and differentiation into a plethora of cell types. A wealth of studies across various embryonic model systems have established dogma as to the molecular mechanisms and signaling cascades that contribute to NCC development. While Wnt, FGF, and BMP signaling pathways have well-established and essential roles in several aspects of NCC development, the Hedgehog (HH) signaling pathway has received limited attention for any specific role in this process. Herein, we propose two distinct, temporal roles for the transcription factor GLI3 in NCC development. Gli3, and other members of the HH pathway, were robustly co-expressed with established NCC induction and specification markers in chick, mouse, and human embryonic stem cell derived NCCs. Early knock-down of GLI3 reduced expression of key markers of NCC specification and conditional knock-out of Gli3 post-specification specifically impaired the ability of cranial NCCs to differentiate into ectomesenchymal derivatives. Together, these results demonstrate dual, novel roles for GLI3 in early NCC specification and later in cranial NCC differentiation.

overall_design: scRNA-seq of E13.5 Gli2f/f;Gli3f/f; Wnt1-Cre mandibular prominences

first: Kelsey

middle: H

last: Elliott

middle: J

first: Samantha

last: Brugmann


title: Analysis of local mucosal immune dysregulation to guide pilot directed therapy for long-COVID olfactory loss [TCR-seq]

city: Durham

first: Sarah

last: Kim

state: NC

address: 481 MSRB1

institute: Duke University

summary: To further define local mechanisms impacting peripheral olfactory structures, we obtained olfactory biopsies from subjects with post-COVID olfactory loss (hyposmia) or controls for viral, single cell and T cell receptor assays. Here we identified clonally expanded T cell subsets with a pro-inflammatory profile.

overall_design: Biopsies of human olfactory epithelium collected from three long-COVID hyposmics and three normosmic control patients and processed for 5' GEX and TCR sequencing

first: Vincent

last: D'Anniballe

first: John

middle: B

last: Finlay

first: Tiffany

last: Ko

first: Michael

last: Wang

first: Bradley

last: Goldstein


title: Analysis of local mucosal immune dysregulation to guide pilot directed therapy for long-COVID olfactory loss [5' GEX]


title: Chemotherapy triggers immune evasion by fostering LEPR+ Kupffer cell differentiation in liver metastases

city: Shanghai

first: Xuege

address: 320 Yueyang Road

institute: Shanghai Institute of Nutrition and Health

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series

first: Qiang

last: Pan


title: Themis directs T cell exhaustion by promoting PD-1 signaling and regulating expression of transcription factors TCF-1 and TOX

city: Xiamen City

first: GUO

last: FU

address: No. 4221, Xiang'an South Road, Xiang'an District, Xiamen, Fujian Province

institute: Xiamen University

summary: T cell exhaustion is a protective mechanism during chronic viral infections, but it can impair anti-tumor immunity. Themis, a T cell-specific protein, is critical for CD8+ T cell homeostasis, cytokine responsiveness, and anti-Listeria responses. In Themis-deficient mice infected with LCMV C13, a chronic virus, we observed severe lung injury and premature death. Single-cell analysis revealed that Themis-deficient effector CD8+ T cells, while producing higher levels of TNF and IFN-γ, were impaired in population expansion due to poor cell sustainability. Biochemical studies showed that Themis binds PD-1, promoting PD-1 phosphorylation and SHP-2 recruitment. Beyond its role in restraining effector T cell function, Themis is essential for the development of Tpex cells by promoting TCF-1 expression and driving transcriptional and epigenetic changes. Moreover, Themis supports TOX and PD-1 expression, ensuring the maintenance of terminally exhausted T cells (Tex). This study reveals the multifaceted roles of Themis in the progression of T cell exhaustion.

overall_design: Primary murine tissues were collected from co-transfer p14 mice, with tissues isolated at different time points following infection with LCMV-clone 13. A total of 4 single-cell samples were prepared, consisting of CD4+ T cells from spleen or lung tissues, with both wild-type (WT) and knockout (KO) groups, at 5 days post-infection (dpi). The isolated single-cell suspensions were processed using the DNBSEQ platform, which was run on the DNBelab C4 portable single-cell system (BGI). This system facilitates high-throughput cell capture and gene expression profiling.

first: jian

last: tang

first: yuzhou

last: bao


title: Intervertebral disc spheroids as an in vitro multicellular platform for recapitulating the microenvironment of intervertebral disc degeneration

city: Seoul

first: Tae-won

address: Gamasan-ro 20-gil, 8

department: Medical science

country: South Korea

institute: Korea university

summary: Intervertebral disc (IVD) degeneration (IVDD) is a major contributor to chronic low back pain (LBP), representing a significant burden on the spinal healthcare system and a leading cause of long-term disability worldwide. Reliable in vitro models are lacking and thus monocultures of cell lines and 2D-based culture models are still used to study the patho-mechanisms of IVDD. We established functional multicellular IVD spheroid cultures using primary human annulus fibrosus (AF), nucleus pulposus and microglial cells. The IVD spheroid culture was observed to facilitate the IVD-specific phenotype and function. The spheroid culture markedly increased the expression of inflammatory mediators and chemokines in the presence of pro-inflammatory cytokines IL-1b, a master regulator of IVDD. Furthermore, we implemented our microfluidic chemotaxis platform to investigate microglial neuroinflammation in response to our reconstituted IVD spheroid models. Transcriptome sequencing revealed that microglia stimulated by potential contributing factors derived from IVDD spheroids exhibited a significant upregulation of chemotactic factors and cytokines including CCL2, 3, 4, 5, CXCL8, IL6, and IL1b (p < 0.05). Moreover, we observed considerable activation and infiltration of microglia induced by soluble factors derived from IVDD spheroids, which is expected to occur during IVDD. The chemotactic effects on microglia were reduced upon neutralization of CCL-2, IL-8 or inhibition of NF-kB signaling. These robust in vitro IVD spheroids can be used to model IVDD and provide a valuable platform for the assessment and development of IVDD therapeutics.

overall_design:
Samples: SV40 human microglia cells were treated with DF12, SPCM, SPCM_IL for 48 hours.
DF12: DMEM/F12 medium
SPCM: A spheroid was cultured in DMEM/F12 for 48 hours, and the supernatant was collected. The spheroid consisted of 1.8 × 10^4 nucleus pulposus cells and 3.2 × 10^4 annulus fibrosus cells.
SPCM_IL: A spheroid was cultured in DMEM/F12 with 1 ng/ml of IL-1β for 48 hours, and the supernatant was collected. The spheroid consisted of 1.8 × 10^4 nucleus pulposus cells and 3.2 × 10^4 annulus fibrosus cells.

first: Tae-Won

first: An-Gi

first: Min-Ho

last: Hwang

first: Hyuk

last: Choi


title: The gene expression profile of JAR cells co-cultured with NK cells.

city: Nagoya

first: Kosuke

last: Yoshida

state: Aichi

address: 65 Tsuruma-cho

country: Japan

institute: Nagoya University

summary: Immune cells play a critical role in cancer progression. In choriocarcinoma, the importance of natural killer (NK) cells has been highlighted, but their impact remains unclear. This study analyzed gene expression changes in choriocarcinoma cells when co-cultured with NK cells in vitro.

overall_design: JAR cells were co-cultured with NK cells in the presence of 100 IU/mL IL-2 at a ratio of 5:1. As a control, JAR cells were cultured with 100 IU/mL IL-2 without NK cells. After 24 hours of incubation, JAR cells were isolated using flow cytometry, and total RNA was extracted with the miRNeasy Mini Kit. Subsequently, mRNA-sequencing was performed.

first: Mayu

last: Shibata

first: Akira

last: Yokoi

first: Kaoru

last: Niimi


title: Dissecting the intra- and intertumoral heterogeneity of adrenocortical carcinoma by single-cell multi-omics analyses [I]

city: Chengdu, Cihna

first: Xaingyu

state: Sichuan

address: No.17 Renming road section3

department: State Key Laboratory of Biotherapy, West China Hospital, Sihcuan University.

institute: Sichuan University

summary: Adrenocortical carcinoma (ACC) is a rare but aggressive malignancy originating in the adrenal cortex, characterized by significant intra- and intertumoral heterogeneity. In this study, we employed a combination of whole-genome sequencing, single-cell RNA sequencing, T cell receptor sequencing, spatial transcriptome sequencing, and multiple fluorescent staining to construct a comprehensive multi-omics landscape of ACC. Our findings demonstrated that, although all tumor cells exhibited a "confused cell identity" feature, distinct subpopulations were present in each ACC patient. Among these, the LDLR+ and MKI67+ subpopulations expressed elevated levels of C1A signature genes and established robust communication with endothelial cells through NECTIN-PVR and NOTCH2-JAG pairs, both significantly associated with poor prognosis. Interestingly, the PCDH15+ subpopulations displayed moderate levels of both C1A signature genes and extracellular matrix related genes. On the other hand, the HLA-B+ and subpopulation exhibited the highest levels of antigen-processing related genes, a characteristic not previously reported. The amalgamation of these distinct subpopulations facilitated the stratification of ACC patients into subtypes with varying prognoses. Patients (Group II) dominated by LDLR+ and MKI67+ subpopulations exhibited the worst prognosis, while those (Group III) with a higher proportion of PCDH15+ subpopulation demonstrated the most favorable outcomes. Significantly, patients (Group I) with a higher prevalence of the HLA-B+ subpopulation also showed notably increased LAG3+ memory CD8 T cells, indicating their potential suitability for immunotherapy. Despite responding averagely to conventional treatment, this subgroup was predicted to be responsive to immunotherapy. Notably, one patient from Group I exhibited a positive response to camrelizumab treatment after relapse with mitotane, leading to a successful outcome, while two patients from Group II did not respond favorably. Our study offers insights into the single-cell level heterogeneity of ACC and provides valuable implications for precision treatments for this disease.

overall_design: With approval from the Ethics Committee of West China Hospital, Sichuan University, we collected 3 adjacent normal adrenal tissues from 3 aldosterone producing adenoma patients who are diagnosed with adrenal venous sampling and CT, and ACC tumor samples from 8 pathologically diagnosed ACC patients during surgical resections. Their ages varied from 18 to 64, with a median of 50. Clinical characteristics including sex, age, plasma levels of aldosterone, ACTH, cortisol, metanephrine, normetanephrine, testosterone, estradiol, progesterone, hormone activity, 24h urine levels of cortisol, duration from diagnosis to surgery, specimen type, tumor size, ENST stage and TNM stage are listed in Supplementary Table 1. Three patients were included in our clinical trial (Registration number: ChiCTR1900028111) and received ICI plus apatinib treatment.

first: Xiangyu

first: Shengzhuo

last: Liu

first: Yu

first: Chong

last: Chen


title: AUF1 modulates senescence via regulating transcription and alternative splicing of immune response genes in auditory hair cells

city: Nanchang

first: Xubo

email: cchxb560@126.com, ndefy17049@ncu.edu.cn

state: Jiangxi Province

address: Minde Road 1st

institute: The Second Affiliated Hospital of Nanchang University

summary:
Background: AU-rich element RNA-binding factor 1 (AUF1) is a multifunctional RNA binding proteins (RBPs) in post-transcriptional gene regulation. However, it remains unclear whether or not AUF1 has a function in the regulation of inflammation and senescence as a splicing factor in auditory hair cells.
Results: SiAUF1 was found to promote the level of apoptosis in HEI-OC1 cells. The RNA-seq results indicated the extensive regulation of the expression of hundreds of genes by AUF1 knocked down cells. The genes down-regulated by siAUF1 were significantly involved in immune responses and cellular apoptosis. AUF1 regulated the alternative splicing of genes, such as FASTK, MAP4, and hnRNPDL, that are involved in mitochondrial functioning and cellular apoptosis. Furthermore, the published transcriptomic data of aging mice demonstrated that the expression of AUF1 and immune response were highly exhibited in aging animals. Moreover, RBMS3 was also found to be an potential important gene target of AUF1 to modulate apoptosis.
Conclusion: To our knowledge, this is the first investigation of its kind that has described the transcriptome-wide analysis of AUF1-regulated expression and alternative splicing profiles and has demonstrated the possible mechanisms of AUF1 regulating immune response, apoptosis, and alternative splicing, which could aid future researches on cellular biology and contribute to the deciphering of the aging process and presbycusis.

overall_design: RNA-seq was used to analyze the global transcript level and alternative splicing in AUF1 siRNA-treated HEI-OC1 cells (siAUF1) and control cells. Integration analysis was carried out using published transcriptome and AUF1-RNA interactome datasets.

first: Lihua

last: Li

first: Kai

last: Xu

first: Xue

last: Bai

first: Wenjing

last: Wu

first: Zhilin

last: Zhang


title: Inhibition of Medium-Chain Fatty Acid Receptor GPR84 Enhances Metabolism, Cytotoxicity and Anti-Tumor Function of CD8 T cells

city: New Orleans

first: Jovanny

last: Zabaleta

state: LA

address: 1700 Tulane Ave

department: Interdisciplinary Oncology

institute: LSUHSC

summary: GPR84 is a medium-chain free fatty acid receptor predominately expressed on myeloid cells. Previous studies identified GPR84 as an enhancer of pro-inflammatory myeloid cell response and a regulator of metabolic homeostasis. However, the role of GPR84 on T cell function and metabolism remains wholly unexplored. This study tested the effect of GPR84 modulation on CD8+ T cell function and metabolism in vitro, and examined its effect on anti-tumor function in adoptive cellular therapy models. Inhibition of GPR84 with the antagonist GLPG1205 promoted CD8+ T cell differentiation, proliferation, cytokine production, and cytotoxicity. This effect was confirmed using CRISPR-Cas9 GPR84 deleted CD8+ T cells. In contrast, treatment with the GPR84 agonist DL175 inhibited proliferation, cytokine production and cytotoxicity. These functional changes were paralleled by changes in metabolic activity. GPR84 antagonist GLPG1205 increased glucose uptake, glycolysis, oxidative phosphorylation (OXPHOS) and ATP production, which enhanced the energetic fitness of CD8+ T cells. Furthermore, stimulation of antigen-specific CD8+ T cells with GPR84 antagonist in vitro, or deletion of GPR84 in antigen specific T cells before adoptive cellular therapy resulted in a significantly enhanced anti-tumor effect in vivo. This study is the first demonstration that GPR84 modulation in T cells can enable more effectively killing of tumor cells and reduce tumor growth, and opens a novel approach to significantly enhance the efficacy of adoptive cellular therapies including CAR-T, TIL or CAR-NK cells.

overall_design: Cells (T cells and bone marrow-derived MDSC) were treated with GPR84 agonist or antagonist for 48h and the RNA was extracted to determine the effect on gene expression on each cell type

first: Phaethon

last: Philbrook

first: Matthew

last: Dean

first: Liqin

last: Zheng

first: Julio

last: Vázquez-Martínez

first: Darwin

last: Chang

first: Jessica

middle: K

last: Mandula

first: Timothy

middle: I

last: Shaw

first: Dorota

last: Wyczechowska

first: Jone

last: Garai

first: Ramesh

middle: T

last: Puttalingaiah

first: Maria

last: Sanchez-Pino

first: Satyajit

last: Das

first: Shiun

first: José

last: Conejo-Garcia

first: Paulo

middle: C

last: Rodriguez

first: Augusto

last: Ochoa


title: Transcriptional profiling of HLCZ01 cells with or without HBV infection.

city: Jinan

first: Yang

last: Sun

state: Shandong

address: No.44 Wenhua West Road

department: Immunology

institute: Shandong University

summary: To explore the biological processes affected by HBV infection, high throughput sequencing was performed in HLCZ01 cells with or without HBV infection.

overall_design: To explore the effects of transcriptome by HBV infection, HLCZ01 cells with or without HBV infection were harvested for high throughput sequencing.


title: METTL3 in Diabetic Cardiomyopathy

city: Boston

first: Haobo

last: Li

state: MA

address: MEDR410 / Lunder Bldg Dock, 255 Charles St

department: Department of Anesthesia, Critical Care, and Pain Medicine

institute: Massachusetts General Hospital and Harvard Medical School

summary:
To investigate the role of METTL3 in diabetic cardiomyopathy, 6-week-old mice were fed either a chow diet or high-fat diet (HFD) for 18 weeks followed by low doses of STZ injections, some of the mice were then injected with AAV expressing control or METTL3 in cardiomyocytes for 8 weeks.
We then performed gene expression profiling analysis using data obtained from RNA-seq.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from heart tissues from mice treated with control or METTL3 overexpression.

first: Chunyan

last: Wang


title: Regulation of Cortical Neural Stem Cells by Microglial Hat1

status: Public on Dec 24 2025

city: beijing

first: huiyang

last: Jia

state: Beijing

address: China

institute: Institute of Zoology, Chinese Academy of Sciences

summary: The mice were on a C57BL/6J background. Microglia-specific Hat1 knockout mice were generated by crossing Cx3cr1-cre mice with Hat1-flox mice. Mouse cerebral cortices were harvested at embryonic day 14 (E14). Cells were stained with CD45 and CD11b, sorted for double-positive populations, and subjected to sequencing.

overall_design: we used cre-loxp system  to condition knock out Hat1 in mouse microglia. At E14, microglia were isolated and subjected to sequencing processing.We processed the raw 150-bp paired-end Illumina reads using CASAVA to generate FASTQ files, then removed adapter-contaminated reads, reads containing undetermined bases (N), and low-quality reads in which bases with Qphred ≤ 20 accounted for more than 50% of the read length; Q30 scores and GC content were calculated and all downstream analyses were based on these high-quality clean reads. Clean reads were aligned to the reference genome using HISAT2 (v2.0.5) with the corresponding gene model annotation, and gene expression levels were quantified as FPKM, taking both gene length and sequencing depth into account. Differential expression between sample groups was assessed with DESeq2 (or DESeq when biological replicates were not available) using a negative binomial model and Benjamini–Hochberg correction, designating genes with adjusted P ≤ 0.05 as differentially expressed. Differentially expressed genes were then subjected to GO and KEGG pathway enrichment analysis using the clusterProfiler package, and terms/pathways with P<0.05 were considered significantly enriched.


title: cMaf supports Zeb2 expression for primitive hematopoiesis (TRM RNA-seq)

first: Jing

last: Chen

summary: Tissue-resident macrophages (TRMs) are essential for tissue homeostasis and play a key role in disease and pathology. They originate from distinct waves of hematopoietic progenitors, including primitive, transient-definitive, and definitive hematopoiesis. We found that loss of the Zeb2 ‒165kb enhancer impairs monocyte development and alters TRM transcriptional landscapes, with only HSC-derived monocytes requiring Zeb2 for their development. In Zeb2∆‒165kb mice, primitive TRMs persist in tissues due to the lack of replacement by later hematopoietic waves, and Maf is required for maintaining Zeb2 expression in primitive macrophages.

overall_design: TRMs were isolated from the lung, liver, brain and spleen of wildtype and Z165KO mice and performed bulk RNA-seq.

first: Theresa

last: Murphy

first: Kenneth


title: Single-Cell RNA Sequencing Reveals the Heterogeneity of the Human Retinal Pigment Epithelium

city: Rensselaer

first: Farhad

last: Farjood

state: NY

address: 1 Discovery Drive

institute: Neural Stem Cell Institute

summary:
Purpose: In this work, we performed single-cell RNA sequencing on adult human RPE cells to characterize heterogeneity in human RPE and identify the RPE stem cells.
Methods: RPE cells were isolated from four adult human donor eyes. Single-cell RNA sequencing for cells from one donor eye was performed using 10X Genomics pipeline to survey the RPE subpopulations. For RPE cells from the other three donor eyes, the ICELL8 pipeline was used to obtain a broader and more in-depth survey of gene expression. RNA sequencing results were analyzed using the Seurat package for R.
Results: Uniform Manifold Approximation and Projection (UMAP) analyses for the 10x data showed 8 different RPE subpopulations. Within the different RPE subpopulations we found a cluster with cones-specific transcripts (ARR3, PDE6H and OPN1MW), clusters with rod RNA (RHO and PDE6A), and a cluster with transcripts involved in vascular endothelial growth factor signaling (TF and SPP1). ICELL8 results revealed a small subpopulation of RPE cells positive for RPE65 that also expressed early retinal developmental genes (VIM, GNL3), and MKI67, a marker of actively cycling cells, making the cells of this cluster strong candidates for being the RPE stem cells. Our immunostaining for potential markers of clusters uncovered in our single-cell RNA-Seq results, further verify the identity of RPE populations.
Conclusions: Our single-cell RNA sequencing results show that RPE is a heterogeneous tissue. Of the varied subpopulations, we have identified a small population with the potential to proliferate and expressing stem cell markers, suggesting that they may be the RPE stem cells.

overall_design: Single cell RPE mRNA profiles of freshly dissociated human RPE cells.

first: Nicholas

last: Labbe

first: Carol

last: Charniga

first: Thomas

last: Kiehl

first: Sally

last: Temple

first: Jeffrey

last: Stern

first: Nathan

last: Boles


title: Improvement of Muscle Fiber Structure and Meat Quality in Tan Sheep by Adding Succinate to the Diet

city: Yinchuan

first: Wenyi

last: Ren

address: 489 Helanshan West Road, Xixia District, Yinchuan City, Ningxia

department: College of Animal Science and Technology

institute: Ningxia University

summary: succinate (SUC), as a feed additive, can regulate muscle fiber structure and fat deposition, and has a positive effect on meat quality. In this study, 30 male Tan sheep lambs were selected to investigate the effects of SUC in diet on Tan sheep production performance, lamb quality, muscle fiber structure, liver and longissimus' muscle entities (LT) transcriptomes. Different levels of SUC were fed (0%, 1.0%, 2.0%, respectively) and the experiment lasted for 60 days. Compared with CON group, 2% SUC group significantly increased average daily gain from 1 to 15 days and 46 to 60 days during the experiment period, and significantly increased dry matter intake from 1 to 15 days, 16 to 30 days and 46 to 60 days during the experiment period (P<0.05). Both 1% SUC group and 2% SUC group could decrease feed to gain ratio and increase carcass weight (P<0.05). The slaughter rate of 2% SUC group was significantly increased (P=0.012). In both 1% SUC and 2% SUC groups, shear force and cooking loss were decreased, intramuscular fat was increased, and a* of LT muscle was increased (P=0.036). In addition, the muscle fiber structure of Tan sheep LT muscle in 1% SUC group and 2% SUC group was changed, the diameter of muscle fiber was decreased, the cross-sectional area of type Ⅰ and type Ⅱa muscle fiber was decreased, and the density of type Ⅰ muscle fiber was increased (P<0.05). Transcriptomic results showed that the addition of SUC can change the expression of muscle development and muscle fiber type transformation genes. Differential genes are mainly involved in various pathways related to lipid metabolism, energy metabolism and muscle development, improve muscle glucose uptake capacity, and improve meat quality in circadian rhythm. In conclusion, SUC can regulate the nutritional metabolism of Tan Sheep, change the muscle fiber structure of Tan Sheep, and improve the production performance and meat quality. Our results show that adding 1% SUC to the Tan sheep diet is productively more beneficial.

overall_design: Thirty 5-month-old male Tan sheep (31.38 ± 0.88 kg) with similar health status and body weight were randomly divided into three groups, with five stalls per group (4 m × 4 m) and two sheep per stall. The groups were as follows: C group (basal diet), T1 group (basal diet + 1% succinate), and T2 group (basal diet + 2% succinate). The diets for each group were formulated based on the "Nutritional Requirements of Sheep" (Ministry of Agriculture of China, 2021) and the actual production needs of Tan sheep. The pretrial period lasted 10 days, and the formal trial period lasted 60 days. During the experiment, all sheep had free access to water and were fed twice daily at 06:30 and 17:30.

first: Ning

last: Zhang

first: Xiaofeng

last: Xu

first: Lili


title: The Novel Nrf2 Agonist Neobavaisoflavone Attenuates Periodontitis by Inhibiting Osteoclastogenesis through Iron Homeostasis Regulation and Senescence Suppression

city: Wuhan

first: Yaoting

last: Ji

state: Hubei

address: No.237 Luoyu Road

institute: Wuhan University

overall_design: In this experiment, we induce RAW264.7 cells to differentiate into osteoclasts. The experimental group is treated with 8 μM neobavaisoflavone, while the control group receives an equal volume of the solvent DMSO. Our aim is to investigate the potential mechanism by which neobavaisoflavone exerts an inhibitory effect on osteoclast differentiation.

first: Yilin

last: Liao


title: Reciprocal interactions between EMT and BMP signalling drive collective cell invasion.

city: Cambridge

first: Benjamin

last: Steventon

address: Downing Street

department: Department of Genetics

country: United Kingdom

institute: University of Cambridge

summary: During collective cell invasion, epithelial-to-mesenchymal transition (EMT) and morphogen signalling-mediated cell fate specification are traditionally viewed as a linear cascade: morphogens drive cell fates that activate EMT programs. Here, we uncover reciprocal coupling between EMT initiation and BMP signalling mediated by SNAI2 and SMAD1. Using substrate-induced EMT in ex vivo explants, we demonstrate that EMT initiation upregulates SMAD1 expression, priming cells for BMP signalling competence across germ layers. Single-cell RNA sequencing reveals SNAI2 and SMAD1 co-expression in EMT initiation regions, and SNAI2 overexpression is sufficient to induce ectopic SMAD1 expression in vivo. While BMP signalling is dispensable for EMT initiation, it regulates cell fate proportions, dispersal dynamics, precursor region depletion rates, and migration directionality. This coupling provides a mechanism for synchronising cell fate specification with invasion progression during axis elongation, positioning EMT as a process that actively modulates morphogen competence to coordinate tissue-level cell behaviours during collective cell invasion.

overall_design: Single cell RNA sequencing of gastrula-stage chick embryos, collected as part of a larger node ablation experiment. Only unablated control embryos were used for this analysis. Control embryos were harvested at HH3/3+ stage, with additional incubation for 0.5h, 2.5h, or 5.0h.

first: Yuri

last: Takahashi

first: Alexandra

last: Neaverson

first: Lara

last: Busby


title: WSTF deficiency reprograms regulatory networks by linking locus‑specific chromatin remodeling to altered isoform expression and misdirected signaling [mRNA-seq]

city: Tallahassee

first: Shahin

last: Behrouz Sharif

state: Florida

address: 319 Stadium Dr.

department: Biological Sciences

institute: Florida State University

summary: Loss of the chromatin remodeler WSTF (BAZ1B), a gene deleted in Williams syndrome, causes reproducible, genome-scale reprogramming of chromatin states and transcript processing that links altered chromatin composition to misprocessed transcripts and aberrant signaling. Using engineered HCT116-WSTFKO cells and patient-derived Williams syndrome cell lines, we combine transcriptome profiling, microscopy, chromatin CUT&RUN, and histone post-translational modification (HPTM)-defined chromatin state modeling to show that WSTF localizes to promoters and gene bodies of actively transcribed loci together with ASH2L and CBP. Loss of WSTF causes depletion of ASH2L/CBP, selective loss of H3K4me2 and multiple acetylation marks, and gain of Polycomb components.  This loss results in systematic conversion from a multi-mark active promoter/enhancer chromatin landscape to a hypoacetylated, H3K4me2-depleted, PRC-enriched landscape. These chromatin changes coincide with widespread isoform switching and splicing alterations in genes encoding chromatin regulators and signaling pathways. This WSTF deficiency produces Wnt/β-catenin hyperactivation. A locus-specific example at TCF7L2 demonstrates how gene body loss of active marks drives isoform switching that alters DNA binding domains and decouples stabilized nuclear β-catenin from canonical target engagement. Our results link signaling dysregulation to developmental pathway misregulation consistent with Williams syndrome phenotypes.

overall_design:
mRNAseq profiling  of wild-type HCT116 cells and two biological replicates of its WSTF knock-out derivative.
mRNAseq profiling  of Corriel-derived B-cell lines including GM14295, GM14296, and GM14297, corresponding to William's syndrome family.

first: Jonathan

last: Dennis


title: Transcriptomic responses of synovial and peripheral blood mononuclear cells in horses with naturally occurring osteoarthritis

city: Fort Collins

first: Steven

last: Dow

state: CO

address: 300 W Drake Rd

department: Clinical Sciences

institute: Colorado State University

summary: Osteoarthritis (OA) is the most common disease affecting equine joints, and represents an important source of pain, reduced athleticism, and economic loss. Earlier detection of OA processes in terms of structural and biochemical alterations to the synovial environment could allow development of biomarker tests to detect disease and implementation of treatment regimens prior to potentially irreversible joint destruction.

overall_design: Synovial fluid cells and PBMC were isolated from healthy horses or those with degenerative joint disease. Horses were determined to be healthy or to have OA via lameness evaluation, radiographs, and response to diagnostic analgesia of the affected joint in OA. Horses were excluded who had received medications or joint injections within the last two months. RNA sequencing of cells was performed using an Illumina based platform. Cytokine analyses of synovial fluid and plasma were performed via multiplex immunoassay (23 cytokines) and correlated to transcriptomic findings

first: Lynn

last: Pezzanite

first: Lyndah

last: Chow

first: Gabriella

last: Piquini

first: Ashana

last: Patel

first: Meagan

last: Rockow

first: Luke

last: Bass

first: Dean

last: Hendrickson


title: Multi-Omics Integration Identifies a Prognostic Signature Guiding Precision Survival in Advanced HCC

city: Beijing

first: Fengna

last: Yan

address: No. 8 Jingshun East Street, Chaoyang District

department: Beijing Ditan Hospital

institute: Capital Medical University

summary: Hepatocellular carcinoma (HCC) remains a leading cause of cancer-related mortality globally, with over 70% of patients diagnosed at intermediate or advanced stages where curative treatments are no longer feasible. Current prognostic tools are inadequate to capture the heterogeneity of outcomes in this population, underscoring the critical need for integrated predictive models that incorporate multimodal data.

overall_design: Plasma samples were collected from 242 patients with advanced HCC (BCLC B–D) who received first-line systemic therapy at two medical centers, from January 2020 and December 2023. Plasma proteomic profiling was performed using the DB4000 Deep Blood DIA Proteome platform with data-independent acquisition and Astral mass spectrometry. Proteomic differences between survivors and non-survivors were assessed via principal component and differential abundance analyses. Candidate biomarkers were validated by ELISA, and their cellular origins and prognostic relevance were explored using single-cell RNA sequencing of HCC tissues.


title: Molecular basis of NFIB-Mediated Regulation of Oncogenic Transcription

city: Taipa

first: He

last: Song

state: Macau

address: Avenida da Universidade Research Building N22

department: Institute of Chinese Medical Sciences

country: Macau

institute: University of Macau

summary: The Nuclear Factor I (NFI) family of transcription factors orchestrates key regulatory programs in development, differentiation, and metabolism, with dysregulation implicated in various pathological conditions, including cancer. Among them, NFIB displays significant context-dependent roles, functioning either as an oncogene or a tumor suppressor depending on cancer type. Despite its emerging clinical relevance, the molecular basis of NFIB-mediated DNA recognition and transcriptional regulation in cancer remains poorly understood. Using HeLa cells as a model, we demonstrate that NFIB promotes oncogenic phenotypes, as CRISPR-Cas9-mediated knockout significantly impairs cell proliferation, migration, and invasion. Transcriptomic analysis reveals that NFIB regulates a cohort of cancer-associated genes, including FGFR3 and PDGFRB. To elucidate the underlying mechanism, we performed biochemical characterization and found that both full-length NFIB and its DNA-binding domain (DBD) exist as monomers in solution and bind DNA with 1:1 stoichiometry, challenging long-standing models proposing DBD-mediated dimerization. High-resolution crystal structures of NFIBDBD bound to ChIP-seq-derived DNA motifs reveal a monomeric binding mode driven by base-specific recognition of the TGGCA sequence. Mutational disruption of key DNA-contacting residues abolishes both DNA binding and transcriptional activation in luciferase reporter assays. Together, these findings define the molecular mechanism underlying NFIB-dependent gene regulation and establish a structural framework for its oncogenic activity, providing insights with potential therapeutic implications for targeting NFIB-driven cancers.

overall_design: RNA-seq profiling of wild-type HeLa cells and NFIB knockout cells, with four biological replicates included for each condition.

first: Ci

last: Zhu

first: Ding

last: Xiao

first: Yueyu

last: Wang


title: Ex Vivo Hypothermic Perfusion Enables 48-Hour Heart Preservation and Bench-Top Functional Recovery via Normothermic Reperfusion in a Porcine Model

city: Philadelphia

first: Ting

last: Peng

state: PA

address: CTRB 6200

department: Pathology and Laboratory Medicine

institute: Children's hospital of Philadelphia

summary: Background: Ex vivo oxygenated perfusion systems is a promising approach to extend cardiac allograft preservation beyond the typical 4–6h limit allowed by static-cold-storage (SCS).  Hypothermic oxygenated perfusion (HOPE) has been proven to safely preserve donor hearts, yet its underlying molecular mechanisms have not been extensively evaluated.   Objectives: The aim of the study is to characterize cardiomyocyte viability, transcriptomic and metabolomic responses, and functional recovery of porcine hearts preserved with HOPE for up to 48h, including evaluating their ability to regain sinus rhythm following bench-top normothermic reperfusion (NMP).  Methods: Seventeen Yorkshire pigs underwent donor cardiectomy. In the first arm, ten hearts were preserved for up to 48h using either SCS (n=5) or HOPE (n=5). Endomyocardial biopsies were collected at 0, 12, 24, and 48h for histology, RNA sequencing, flow cytometry, and metabolomics. In the second arm, six HOPE-preserved hearts (3h, 24h, 48h) and two SCS-preserved heart (3h and 24h) underwent 2h NMP to simulate transplantation and assess reanimation.  Results: HOPE preserved cardiomyocyte viability and structural integrity for 48h, in contrast to SCS in both arms of the study. RNA sequencing and untargeted metabolomics revealed conserved energy-substrate profiles in HOPE and progressive ischemic metabolite accumulation in SCS. All HOPE hearts regained stable sinus rhythm.  Conclusions: HOPE enables 48h ex vivo heart preservation while maintaining cardiomyocyte integrity, normal gross and microscopic architecture, and rapid functional recovery on bench-top reperfusion in a preclinical model. These findings establish a foundation for redefining clinical preservation times and widening geographic donor access.

overall_design: RNA-seq profiling of swine myocardial tissue biopsied (1) at T0h, T12h, T24h and T48h of either SCS or HOPE preservation, and (2) after  T3h, T24h and T48h of HOPE or T24h of SCS, followed by 2h of Normothermic Machine Perfusion.


title: Dissecting the intra- and intertumoral heterogeneity of adrenocortical carcinoma by single-cell multi-omics analyses [II]

first: Xaingyu

last: Pan

first: Xiangyu

first: Shengzhuo

last: Liu

first: Yu

first: Chong

last: Chen


title: A Novel Murine Model of Sjögren's Syndrome Using Lacrimal Autoantigen

first: Siyuan

last: Li

address: No. 1 Dongjiaominxiang, Dongcheng District

institute: Beijing Tongren Hospital

summary: Purpose: Sjögren's syndrome (SS) is a group of chronic autoimmune diseases primarily targeting exocrine glands, including the lacrimal glands (LG). Involvement of the lacrimal glands leads to severe dry eye, also known as Sjögren’s syndrome-associated dry eye (SSDE). Current, available animal models of SS are achieved by using autoantigens from salivary gland. This study aims to establish a SSDE mouse model using lacrimal glands as autoantigen. Methods: To establish the LGSS model, autoimmune responses were induced in mice using homogenized lacrimal gland proteins. LGSS mice were evaluated at various timepoints after immunization to determine SS development. SS phenotype such as tear and saliva secretion, lymphocyte infiltration in the lacrimal and salivary glands and serum autoantibody levels was assessed. Immune cell profiles in the spleen and cervical lymph nodes were evaluated via flow cytometry. In addition, corneal epithelial intactness, goblet cell density, lacrimal gland injury were evaluated to assess lacrimal gland involvement and secondary ocular surface damage. RNA sequencing and gene enrichment analysis of diseased lacrimal glands were performed. Results: LGSS mice demonstrated a reduced tear and saliva secretion, increased lymphocyte infiltration, and elevated autoantibody levels that are similar to common SS mice. Additionally, the established LGSS mice demonstrated increased populations of Th1 and Th17 cell, along with  lacrimal gland and ocular surface damage. RNA sequencing revealed that LGSS mice shared a common genetic profile with NOD mice, the spontaneous SS model, such as Parp9, Cdkn2c, and Ifi35. Additionally, LGSS mice exhibited several uniquely expressed genes, including metabolism-related genes (Cbs, Dlst, Sardh) and genes associated with cellular processes (Actc1, Tnnc1). Conclusion: The LGSS mice have been shown that successfully replicates several key features of SS and demonstrates significant lacrimal gland and ocular surface damages, making it a valuable animal model to study SSDE.

overall_design: The global gene expression of lacrimal gland in LGSS mice, NOD mice and the control mice was analyzed and compared (n=3).

first: Yaqiong

first: Peng

last: Zhang

first: Fengyang

last: Lei

first: Lei

last: Tian

first: Ying

last: Jie


title: NAT10 drives head and neck squamous cell carcinoma proliferation via ac4C modification of DDIT4 mRNA

city: Nanjing

first: Junguo

address: No.321 Zhongshan Road

institute: Nanjing Drum Tower Hospital

summary: To investigate the function NAT10 in the regulation of proliferation, we established SAS cell lines in which target gene has been knocked down by siRNA.

overall_design: RNA-seq profiling of wildtype SAS cells and its knockdown derivative (siNAT10)

first: Panpan

first: Qian

first: Yue

last: Jiang

first: Hui

first: Zheng

last: Liang

first: Xiaoyun

last: Qian

first: Xia

last: Gao


title: Evaluation of Metaplastic Triple-Negative Breast Cancer Extracellular Matrix Structure and Protein Composition

first: Elizabeth

middle: Carol

last: Martin

address: 1430 Tulane Avenue

department: Medicine

institute: Tulane University

summary: Alterations in the tumor extracellular environment and matrix stiffness promotes tumor progression. Furthermore, correlational studies have identified enrichment of extracellular matrix (ECM) proteins (glycoproteins, collagens) in breast tumors. Despite these findings, there has yet to be an interdisciplinary analysis of both ECM composition and structural architecture in rare breast tumors, such as metaplastic breast cancer. Here, we explored changes in ECM protein expression and architecture in a triple-negative breast cancer (TNBC) metaplastic tumor through SEM, proteomics, and RNA sequencing. SEM revealed tumor pore size was larger compared to control adipose tissue. Oscillating rheometry demonstrated increased ECM stiffness in the tumor compared to control adipose breast adipose. Proteomic analysis of the metaplastic TNBC tumor showed significant enrichment for ECM proteins, notably glycoproteins compared to control adipose. Interestingly, these samples showed no observed changes in expression for major fibrillar collagens COL1A1 and COL1A2, and a reduced expression of COL3A1. To determine the impact of less characterized ECMs in metaplastic TNBC, we overexpressed MFAP2 in primary metaplastic breast cancer cells and performed RNA sequencing. MFAP2 overexpression was associated with upregulation of epithelial-to-mesenchymal transition related genes . Overall, our results establish an extracellular signature and onco-architecture for the metaplastic triple-negative tumor type.

overall_design: Metaplastic TNBC (TU-BcX-4IC)  cell line constructed to overexpress the matrix protein MFAP2 or control vector. Overexpression (OE) was chieved through the transfected with 5 μg of pCMV6-Entry Mammalian Expression Vector DNA (Origene, MA, USA) and MAGP1 5ug (MFAP2) (NM_017459) Human Tagged ORF Clone (Origene, MA, USA). Following stable selection of MFAP2 overexpressing cell lines, RNA sequencing was performed. For RNA sequencing, metaplastic TU-BcX-4IC and TNBC cell line with pCMV6 Vector or MFAP2 OE cells were cultured in a T75 flask (Thermo Scientific, Waltham, Massachusetts, USA) grown to 80% confluency and collected for RNA extraction.

first: Jorge

last: Belgodere

first: Matthew

middle: E

last: Burow

first: Katherine

last: Hebert


title: Quantifying the effects of lack of Stim2 on neuronal origin cells at single cell resolution

city: Warsaw

first: Shamba

middle: S.

last: Mondal

address: Księcia Trojdena 4

country: Poland

institute: International Institute of Molecular and Cell Biology

summary: Stromal interaction molecule (STIM) proteins reside on the endoplasmic reticulum (ER) membrane and regulate Ca2+ homeostasis and signaling. The stim2a and stim2b double-knockout zebrafish have problems with vision, altered retinal pigment epithelium and thinner ganglion cell layer, and display decreased survival under low oxygen conditions. Also, genes related to light perception are downregulated in the (stim2a;stim2b)-/- zebrafish. In this study, we investigated the effect of lack of Stim2 on neuronal origin cells with single cell RNA sequencing. Utilizing a manifold learning-based method, we identified the subset of cells that were affected the most by the double-knockout. We found that genes involved in development of retina and trigeminal placode were downregulated in that subset of cells in the (stim2a;stim2b)-/- zebrafish. According to marker gene expression, (stim2a;stim2b)-/- zebrafish had decreased number of retinal ganglion cells expressing midkine b (mdkb), amacrine cells (ptmaa, ptmab), cells of the inner nuclear layer (calb2a), and trigeminal placode or sensory neurons (elavl4, slc17a6b) than (stim2a;stim2b)+/+ zebrafish. Furthermore, global downregulation of genes, especially ribosomal protein coding genes, linked with abnormality of retinal pigmented epithelium and brain development in general, and genes involved in oxidative phosphorylation and autophagy was observed in the subset of cells most affected by the double-knockout. Altogether, the results revealed potential mechanisms through which Stim2 may regulate vision/sensory circuitry, cellular response to hypoxia, and prevent neurodegeneration.

overall_design: Neuronal origin cells from 5 dpf (stim2a;stim2b)+/+ and (stim2a;stim2b)-/- zebrafish were isolated based on fluorescence activated cell sorting according to the presence or absence of GCaMP5G fluorescence signal, and analyzed with scRNA-seq.

middle: S

first: Rishikesh

last: Gupta

first: Jacek

last: Kuznicki


title: Spatial genome organization is associated with nematode programmed DNA elimination

city: Knoxville

first: Jianbin

last: Wang

state: TN

address: 1311 Cumberland Avenue, Ken and Blaire Mossman Building Rm 309

institute: The University of Tennessee

summary: Programmed DNA elimination (PDE) is a notable exception to genome integrity, characterized by significant DNA loss during development. In many nematodes, PDE is initiated by DNA double-strand breaks (DSBs), which lead to chromosome fragmentation and subsequent DNA loss. However, the mechanism of nematode programmed DNA breakage remains largely unclear. Interestingly, in the human and pig parasitic nematode Ascaris, no conserved motif or sequence structures are present at chromosomal breakage regions (CBRs), suggesting the recognition of CBRs may be sequence-independent. Using Hi-C, we revealed that Ascaris CBRs engage in three-dimensional (3D) interactions before PDE, indicating that physical contacts between break regions may contribute to the PDE process. The 3D interactions are established in both Ascaris male and female germlines, demonstrating inherent genome organization associated with the CBRs and to-be-eliminated sequences. In contrast, in the unichromosomal horse parasite Parascaris univalens, transient pairwise interactions between neighboring CBRs that will form the ends of future somatic chromosomes were observed only during PDE. Intriguingly, we found that Ascaris PDE, which converts 24 germline chromosomes into 36 somatic ones, induces specific compartmentalization changes. Remarkably, Parascaris PDE generates the same set of 36 somatic chromosomes, and the 3D compartment changes following PDE are consistent between the two species. Overall, our findings suggest that CBRs spatially demarcate the retained and eliminated DNA and may contribute to their spatial organization during Ascaris PDE. We also demonstrated that the 3D genome reorganization of the somatic chromosomes in these nematodes following PDE is evolutionary and developmentally conserved.

overall_design: Hi-C was performed using samples from different embryonic and larvals stages of Ascaris suum and intestines and germlines of both adult male and female worms.

first: James

last: Simmons


title: Chronic acidosis drives reversible metabolic plasticity and survival adaptation in multiple myeloma

city: Zhunan Town

first: Wun-Shaing

middle: Wayne

last: Chang

state: Miaoli County

address: No. 35, Keyan Road

department: National Institute of Cancer Research

country: Taiwan

institute: National Health Research Institutes

summary: Multiple myeloma (MM) is a plasma cell malignancy that evolves within the complex bone marrow microenvironment, where sustained extracellular acidosis remains an underexplored but biologically significant stressor. To investigate the long-term impact of acidotic stress, we developed MM cell models chronically cultured under mildly acidic conditions, mimicking the gradual acidification seen during disease progression. This approach revealed a biphasic cellular response: initial exposure impaired proliferation, triggered apoptosis, and disrupted metabolic activity, whereas prolonged acidification induced a dynamic, reversible state marked by metabolic recovery, mitochondrial remodeling, and restored growth. Transcriptomic profiling uncovered distinct gene expression programs associated with this chronic adaptation, including 11 genes strongly correlated with disease stage and overall survival in MM patients. These findings suggest that extracellular acidosis is not simply a metabolic byproduct but a persistent selective pressure that shapes MM progression through metabolic plasticity and clonal evolution.

overall_design: MM cells were cultured at pHe 6.8 that reflects the acidity commonly found in the diseased bone marrow niche, for defined durations categorized as short-term acidification (S.A., 2–4 weeks), and long-term acidification (L.A., 8–10 months) groups. A parallel control group (Ctrl) was maintained at physiological pHe 7.4, consistent with freshly obtained parental cells. A total of three groups in duplicates were established.

middle: W


title: ChIP-seq experiment of transcription factor NFAT in Diaphorina citri

city: Fuzhou

first: You

last: Li

state: Fujian

address: No.15 Shangxiadian Road

institute: Fujian Agriculture and Forestry University

summary: ChIP-seq experiment of transcription factor NFAT in Asian citrus psyllid Diaphorina citri. This experiment will figure out what gene was transcripted by NFAT in Diaphorina citri

overall_design: The CHIP-Seq experiment included three biological replicates for each condition ( NFAT antibody and control IgG) .

first: Yu

last: Du

first: Mengle

last: Sun

first: Taiyun

last: Wei


title: WSTF deficiency reprograms regulatory networks by linking locus‑specific chromatin remodeling to altered isoform expression and misdirected signaling [CUT&Run]

first: Shahin

last: Behrouz Sharif

overall_design:
CUT&RUN of WSTF, SNF2H, ASH2L, CBP, EZH2, CBX4, LaminB, H2AK119ub, H3K4me1, H3K4me2, H3K4me3, H3K9ac, H3K9me3, H3K9ac, H3K14ac, H3K27me3, H3K27ac, H3K36me2, H4K5ac, H4K8ac, H4K12ac, and H4K20me1 in two technical replicates of HCT116 cells
CUT&RUN of SNF2H, ASH2L, CBP, EZH2, CBX4, LaminB, H2AK119ub, H3K4me1, H3K4me2, H3K4me3, H3K9ac, H3K9me3, H3K9ac, H3K14ac, H3K27me3, H3K27ac, H3K36me2, H4K5ac, H4K8ac, H4K12ac, and H4K20me1 in two biological replicates of HCT116-WSTFKO cells

first: Jonathan

last: Dennis


title: Expression data from HEK-293 cells treated with different CDK8/19 inhibitors

city: Heidelberg

first: Angga

last: Prawira

address: Im Neuenheimer Feld 344

department: Molecular Virology

country: Germany

institute: University Hospital Heidelberg

summary: Hepatitis delta virus (HDV) enters hepatocytes via the receptor NTCP and requires CDK8/19 Mediator kinases to establish its infection by RNA Polymerase II. Here, we are interested in assessing the class effect of various CDK8/19 inhibitors and investigating the possible off-target effects caused by them.

overall_design: HEK-293 cells overexpressing the NTCP receptor were treated with 500 nM MSC2530818, 2 µM SEL120, or 50 nM CCT251545 between d1-5 post-seeding. Cells were harvested for RNA extraction and subjected to the human Clariom S assay, ThermoFisher.

first: Yi

last: Ni


title: Research on the mechanisms underlying Arctium lappa L. polysaccharide-induced proliferation of epidermal stem cells

city: Suzhou

first: Rui

middle: xing

last: Hou

state: Jiangsu

address: No.5, Tayun Road, Wuzhong District

department: Key Laboratory of Hand Surgery

institute: Suzhou Ruihua Orthopedic Hospital

summary: To elucidate the mechanism by which Arctium lappa L. polysaccharide (ALP) promotes epidermal stem cell (EpSC) proliferation, we performed RNA sequencing on EpSCs from mice that were treated with either 30 μg/mL ALP or a vehicle control for 48 hours. This approach provided a comprehensive view of the ALP-regulated transcriptome profile.

overall_design: RNA-seq profiling of episcs derived from mice treated with 30 μg/ml ALP or a vehicle control (0.06% DMSO) for 48 hours.

first: Ruixing

first: Ting


title: Gene expression profiles in S2-007, S2-020 and S2-028 pancreatic ductal adenocarcinoma cell lines

city: Yonago

first: Hirotoshi

last: Mochida

state: Tottori

address: 86 Nishi-cho

department: Pathology

institute: Faculty of Medicine, Tottori University

summary: To investigate the subcellular localization of maspin in pancreatic ductal adenocarcinoma (PDAC) and its functional relevance, gene expression profiles were analyzed in S2-007 (expressing nuclear and cytoplasic maspin), S2-028 (expressing cytoplasmic-only maspin), and S2-020 (expressing weakly maspin) cells. The data provides insight into the differential function of maspin in PDAC depending on its subcellular localization.

overall_design: Total RNA from these cells were recovered using Rneasy MINI Kit. To purify the strand-specific mRNA library, the mRNA was reverse transcribed into cDNA using random primers, and then the synthesized double-strand cDNA was fragmented, and the cDNA was subsequently ligated adapters. Transcriptome sequencing in strand-specific mRNA-seq library was performed using illumine NovaSeq 6000 Sequencing System.

first: Tomohiko

last: Sakabe

first: Yoshihisa

last: Umekita


title: effect of depletion of Znf143 on gene expression of C2C12 myoblasts with or without induction for myogenic differentiation

city: GuangZhou

first: Xingan

last: Zhao

state: GuangDong

address: 1023-1063 shatai South Road

department: School of Basic Medical Sciences

institute: Southern Medical University

summary: In adults, muscle stem cells (muscle satellite cells, MuSCs) can be recruited to supply myoblasts for routine muscle fibre homeostasis or muscle regeneration. Epigenetic regulation is essential for the proliferation and differentiation of muscle stem cells and myoblasts. We here report that Znf143 is critical for proliferation and differentiation of myoblasts. Znf143 depletion in C2C12 myoblasts dramatically repressed their myogenic differentiation, impairing multiple biological processes including striated muscle contraction, muscle cell differentiation, and myofibril assembly. This is consistent with the limited regeneration of skeletal muscle after freeze injury in mice with MuSC-specific Znf143 ablation.

overall_design: C2C12 myoblasts were transfected with siRNA of non-targeting control or Znf143, then left untreated or induced for myogenic differentiation for 5 days. The resultant cells were then harvested for RNA-seq analysis.

first: Jiaxin

last: Wen

first: Qiongzhi

first: Hanwen

last: Liu

first: Zhipeng

last: Zou

first: Xiaochun

last: Bai


title: Synergistic Effects of High-Fiber Diet and N-Carbamylglutamate on Sow Reproductive Performance via Uterine Microbiota-PI3K/Akt Modulation

first: Yaxu

last: Liang

state: 江苏省

address: 江苏省南京市玄武区南京农业大学

institute: Nanjing agricultural university

summary: Landrace x Yorkshire sows were selected to investigate the synergistic effects of high fiber diet and 0.05% NCG on reproductive performance through transcriptomic analysis of endometrium samples.

overall_design: The sows were randomly assigned to four dietary treatment groups (n = 100 per group) as follows: low-fiber group (LF; 3.73% crude fiber); low-fiber + NCG group (L+N; 3.73% crude fiber + 0.05% NCG); high-fiber group (HF; 7.46% crude fiber); high-fiber + NCG group (H+N; 7.46% crude fiber + 0.05% NCG). The experimental was initiated on the day of breeding and continued throughout the entire gestation period of 114 days.

first: Hongyang

last: Wang

first: Yongsong

last: Tan


title: Luspatercept with Immunosuppression Reducess Inflammation in Patients with Severe Aplastic Anemia by Inhibiting Monocyte Pyroptosis [RNA-Seq]

city: Tianjin

first: Rong

last: Fu

address: xinxing street

institute: Tianjin Medical University General Hospital

summary: Aplastic anemia (AA) is a bone marrow failure disorder caused by diverse etiologies. AA pathogenesis involves aberrant immune activation and an imbalanced inflammatory bone marrow microenvironment. Previous studies have shown that inhibition of transforming growth factor-β (TGF-β) signaling in patients with AA can improve multilineage hematopoietic recovery and immune balance. This study is the first to demonstrate the synergistic mechanisms of TGF-β inhibitor luspatercept in combination with Cyclosporine and Eltrombopag for the treatment of severe aplastic anemia (SAA) by acting on monocytes. The aim was to explore the effects of the drug Luspatercept on monocyte cell lines by performing RNA-seq after treating the THP-1 cell line. Mechanistic investigations further showed luspatercept suppressed pyroptosis in monocytes, reshaping the immune microenvironment, and attenuating pro-inflammatory cytokine secretion and cytotoxic molecule expression in CD8+T cells. This groundbreaking study uncovers that Luspatercept can reduce inflammation and pyroptosis through multi-target immune modulation, which provides a novel therapeutic strategy for AA.

overall_design: We used the human mononuclear cell line THP-1 and induced pyroptosis with ATP and LPS. Based on whether Luspatercept was used in combination with cyclosporine and eltrombopag, three samples were divided into four groups: normal control (NC), pyroptosis model (PM, without drug intervention), pyroptosis model with cyclosporin A + eltrombopag (CE), and pyroptosis model with cyclosporin A + eltrombopag + luspatercept (CEL). RNA transcriptome sequencing was performed.

first: Zining

first: Jiaming

last: Hu

first: Yiyu

last: Guo

first: Xinrui

last: Zhang

first: Yu

last: Gao

last: Song


title: Dermatomyositis is characterized by JAK1-mediated monocyte-driven vasculopathy and inflammation

city: Ann Arbor

first: J. Michelle

last: Kahlenberg

state: MI

address: NCRC 20-1841, 2800 Plymouth Rd

department: Department of Internal Medicine – Division of Rheumatology and Department of Dermatology

institute: University of Michigan

summary: Dermatomyositis (DM) is a rare yet devastating autoimmune disease characterized by inflammatory and vasculopathic changes in skin and muscle. DM and systemic lupus erythematosus (lupus) skin lesions have overlapping clinical and histopathological features, yet disparate responses to available therapeutics. DM skin disease is often relapsing and recalcitrant. To investigate DM immunopathogenesis, non-lesional skin, lesional skin, and circulating immune cells from DM patients were analyzed using single-cell RNA-sequencing. Samples were analyzed in parallel with lesional and non-lesional lupus skin, healthy control skin, and peripheral blood. We demonstrate a pervasive type I interferon (IFN) signature in DM stroma that persists in culture and is distinguished from lupus by upregulation of VEGF and IL-18 signaling in DM keratinocytes. Furthermore, endothelial cells (ECs) in lesional DM exhibit decreased proliferation that was not observed in lupus. Using cell communication networks, we identified a population of DM-specific monocytes interacting with non-proliferating DM ECs. Co-culture of monocytes from DM patients with ECs resulted in increased EC apoptosis inhibited by JAK1 blockade.  JAK1 inhibition also resulted in reversal of DM-stromal and inflammatory signatures. Together, our data provide a comprehensive cross-disease characterization of lesional and non-lesional skin of DM compared to lupus and implicate monocyte-mediated EC dysfunction in DM vasculopathy and support JAK inhibition for refractory skin disease.

overall_design: Patients with dermatomyositis or systemic lupus with active skin lesions were enrolled. Lesional skin biopsies, nonlesional skin biopsies from the upper thigh, and PBMCs were evaluated by scRNA-seq. Healthy controls also underwent skin biopsies of the upper thigh and donated PBMCs for scRNA-seq.

first: Grace A.

last: Osborne


title: Aortic valve calcification is induced by the loss of ALDH1A1 and can be prevented by agonists of retinoic acid receptor alpha: preclinical evidence for drug repositioning

city: Lille

first: Mickael

last: Rosa

address: Boulevard du professeur Jules Leclercq

country: France

institute: Université de Lille

summary: Study the effect of Am80 on osteoblast differentiation

overall_design: Microarray : VIC isolated from control valves treated with control or osteogenic medium treated or not with Am80


title: Aortic valve calcification is induced by the loss of ALDH1A1 and can be prevented by agonists of retinoic acid receptor alpha: preclinical evidence for drug repositioning, 2

summary: Analyse VIC isolated from control and calcified aortic valves

overall_design: Microarray : VIC isolated from 5 control vs 5 calcified aortic valves


title: Blood-borne sphingosine 1-phosphate maintains vascular resistance and cardiac function.

city: PARIS

first: Ilaria

last: Del Gaudio

address: 56 Rue Leblanc

institute: Paris Cardiovascular research center_ InsermU970

summary: Sphingosine 1-phosphate (S1P) circulates in plasma bound to high-density lipoproteins (HDL) and albumin. In mice, isolated deficiency in HDL-S1P and endothelial cell S1P receptor (R)-1 both trigger hypertension, supporting an essential role for HDL-S1P in endothelial function. Physiological roles of albumin-S1P and myocyte S1PRs in the cardiovascular system remain incompletely defined. We report that depletion of all circulating S1P pools induces hypotension and lack of blood pressure increase with age, which contrasts with HDL-S1P deficiency and suggests an essential role for albumin-S1P in cardiovascular homeostasis. Left ventricular contractile function was also reduced but cardiac output preserved in a basal state. Cardiac function and blood pressure was partially or fully normalized by bone marrow transplantation or transfusion of erythrocytes capable of S1P production. Hypotension was accompanied by reduced peripheral resistance, and BSA-S1P, but not S1P complexed to an HDL-like chaperone, dose-dependently increased vascular resistance in isolated perfused kidneys via S1PR2 and S1PR3. Epistatic analysis supported a critical role for S1PR3 in S1P-dependent blood pressure regulation and pointed to a distinct origin of the cardiac phenotype. These observations suggests that albumin-S1P crosses the endothelium in resistance arteries to access contractile receptors, and that myocyte S1PR signaling is essential for vascular resistance and blood pressure maintenance in mice.

overall_design: RNA-seq profiling of hearts from plasma S1Pless (Sphk1f/-:2f/-:Mx1Cre+)  and littermate control male mice

first: Eric

last: Camerer


title: RNA-seq analysis reveals dysregulated pathways in CAFs following NPs treatment.

first: wang

last: zaozao

address: No. 52 Fucheng Rd., Haidian District

department: Key Laboratory of Carcinogenesis and Translational Research

institute: Peking University Cancer Hospital & Institute

summary: Cancer-associated fibroblasts (CAFs) contribute to immunotherapy resistance in colorectal cancer (CRC) by creating physical barriers and fostering an immunosuppressive microenvironment, critically influencing tumor development and metastasis.Nowadays, nanotherapy has been extensively explored in oncology for its dual capabilities in cancer targeted treatment.However, the mechanisms by which nanoparticles (NPs) exert their antitumor effects through targeting and eliminating CAFs remain incompletely understood.In this study,NPs modulated intrinsic signaling pathways in CAFs, leading to altered chemokine secretion profiles. This modification enhanced dendritic cell maturation and promoted CD8+ T cell activation and functionality, ultimately amplifying the anti-tumor immune response to suppress CRC progression.

overall_design: To elucidate the underlying mechanism by which NPs influnence CAFs, RNA sequencing analysis was performed to explore regulated pathways in CAFs after NPs treatment compared to control cells.  Each experimental group includes three biological replicates

first: Shuren

first: Zaozao


title: FACT Complex Recruitment and the Role of H2A.Z in Transcriptional Regulation

city: Yangling

first: Su

middle: Ying

last: Pei

state: Shaanxi

address: No. 3 Taicheng Road

department: College of Life Sciences and Institute of Future Agriculture

institute: Northwest A&F University

summary: The FACT complex (FAcilitates Chromatin Transcription) plays a key role in chromatin remodeling during transcription, enhancing DNA accessibility. It is believed to alter chromatin by temporarily displacing histones, enabling RNA polymerase II (Pol II) to engage, and then reinstating the original chromatin structure after transcription is complete. In this study, we show that FACT complex subunit ssrp1 undergoes neddylation in vivo, which might be important for its subcellular localization and its interaction with Pol II. This, in turn, promotes the recruitment of the FACT complex to actively transcribed chromatin, establishing a positive feedback loop. In addition, the FACT complex mediates H3K4me3 while not influencing the transcriptional rate. Lastly, in contrast to its canonical form, ubiquitinated H2A.Z does not impede FACT's binding to chromatin and may alleviate the transcriptional repression associated with canonical H2A ubiquitination.

overall_design: This study performed FLEP-seq in Arabidopsis thaliana to investigate nascent transcription changes associated with chromatin remodeling factors. Three genotypes were included: Columbia-0 (WT), spt16 mutant, and ssrp1 mutant.

first: Israel

last: Ausin

first: Yafei

first: weiye

last: Qian

first: Chao

last: Xu


title: Luspatercept with Immunosuppression Reducess Inflammation in Patients with Severe Aplastic Anemia by Inhibiting Monocyte Pyroptosis [scRNA-Seq]

first: Rong

summary: Aplastic anemia (AA) is a bone marrow failure disorder caused by diverse etiologies. AA pathogenesis involves aberrant immune activation and an imbalanced inflammatory bone marrow microenvironment. Previous studies have shown that inhibition of transforming growth factor-β (TGF-β) signaling in patients with AA can improve multilineage hematopoietic recovery and immune balance. This study is the first to demonstrate the synergistic mechanisms of TGF-β inhibitor luspatercept in combination with Cyclosporine and Eltrombopag for the treatment of severe aplastic anemia (SAA) by acting on monocytes. Single-cell RNA sequencing revealed increased inflammatory cytokine levels and elevated expression of pyroptosis-related genes in monocytes after luspatercept withdrawal. Mechanistic investigations further showed luspatercept suppressed pyroptosis in monocytes, reshaping the immune microenvironment, and attenuating pro-inflammatory cytokine secretion and cytotoxic molecule expression in CD8+T cells. This groundbreaking study uncovers that Luspatercept can reduce inflammation and pyroptosis through multi-target immune modulation, which provides a novel therapeutic strategy for AA.

overall_design: Single-cell sequencing was performed on effective nodes and relapse nodes after discontinuation of Luspatercept in a 40-year-old female patient with SAA.

first: Zining

last: Wang

first: Jiaming


title: Adipogenic Transcriptional Regulation Mediated by PARP7 Through NAD+ Sensing Mechanism [CUT&RUN]

city: Dallas

first: W. Lee

last: Kraus

state: TX

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

summary: The process of differentiating from a preadipocyte into a mature, fat storing, adipocyte (adipogenesis) is a complex and tightly regulated process vital to human health. The molecular mechanisms regulating adipogenesis are incompletely understood, although key facets of the signaling and regulatory pathways have been defined. Here we have identified a mono(ADP-ribosyl)transferase (MART), PARP7, that plays a pivotal role in adipogenesis. ADP-ribosylation – the process whereby specific members of the poly(ADP-ribosyl)polymerase (PARP) family facilitate the covalent transfer of  ADP-ribose moieties from NAD+ to substrate proteins – has been shown to control multiple components of the adipogenic regulatory machinery. Herein we have found that PARP7 is required for modulation of the adipogenic transcriptional program during adipogenesis, and that the loss of PARP7 results in a decrease of the adipogenic process. Contrary to previous studies, the ability to modulate the adipogenic transcriptional program is independent of PARP7 catalytic activity. However, the catalytic activity of PARP7 plays a vital role in regulating protein stability, in a time and space specific manner, which is required for modulation of the adipogenic transcriptional program. This study has found a novel pathway which utilizes NAD+ compartmentalization to stabilize PARP7 at a specific time during the adipogenic process allowing for the regulation of adipogenic genes, through modulation of the well-known adipogenic transcription factor C/EBPß, in a time sensitive manner. Therefore, acting as another check and balance to the adipogenic differentiation process.

overall_design: 3T3-L1 cells were cultured and treated as described above in 15 cm diameter plates.  The cells were transfected with siRNAs targeting Parp7 or a universal control 48hrs before the addition of the differentiation cocktail. The cells were then differentiated for 24hrs

first: MiKayla

last: Stokes

first: Yoon Jung

last: Kim

first: Sneh

last: Koul

first: Josue

last: Zuniga

first: Shu-Ping

last: Chiu

first: Tulip

last: Nandu

first: Kraus

last: W Lee


title: Adipogenic Transcriptional Regulation Mediated by PARP7 Through NAD+ Sensing Mechanism [ChIP-Seq]

overall_design: 3T3-L1 cells were exposed to various treatments and culture conditions for the experiments described herein.  For treatment with MG-132 (10 μM, Sigma, M7449), the cells were grown as described above, cells were then treated with 10 µM MG-132 for 6 hours before collection.  For treatment with RBN2397, the cells were grown as described above upon differentiation of 3T3-L1 cells using differentiation cocktail the cells were treated with 400 nM RBN2397. The treatment continued every other day with media changes until specified collection time.  For PARP7 MAR immunoprecipitation assays, the cells were treated with RBN 2397 for 16hrs


title: Adipogenic Transcriptional Regulation Mediated by PARP7 Through NAD+ Sensing Mechanism [RNA-Seq]

overall_design: 3T3-L1 cells were seeded in 6-well plates and treated as described above. The cells and tissues were collected, and total RNA was isolated using Trizol Reagent (Invitrogen) according to the manufacturer's protocols. Total RNA was reverse transcribed using oligo (dT) primers and MMLV reverse transcriptase (Promega) to generate cDNA. The cDNA samples were subjected to qPCR using gene-specific primers, as described below. For the reverse transcription quantitative real-time PCR (RT-qPCR) analyses, “relative expression” was determined in comparison to a value of the control sample.


title: The effect of TASL knockout on murine B cells following TLR9 stimulation

city: Oxford

first: Julia

last: Johnstone

address: Kennedy Institute of Rheumatology, Roosevelt Drive

institute: University of Oxford

summary: TLR signalling and the IRF5 pathway play a critical role in the activation of inflammatory pathways in B cells. The recently identified innate immune adaptor, TASL, plays an essential role in this pathway, enabling the phosphorylation of IRF5 and thereby the activation of downstream inflammatory pathways. We here identify the role of TASL in primary ex vivo murine B cells, finding that in the absence of TASL, key Interferon stimulated genes (ISGs) and genes involved in cytokine production are downregulated after stimulation by the TLR9 ligand, CpG ODN.

overall_design: RNA-seq profiling of splenic B cells isolated from WT or TASL-KO mice, stimulated in vitro with 100nm CpG.

first: Alexander

last: Clarke


title: Shotgun metagenomic profiling of human fecal microbiota before and after aerobic exercise intervention

status: Public on Dec 23 2025

first: xinyuan

last: ge

address: Longmian Road 818

institute: Nanjing Medical University School of Public Health

summary: Lean nonalcoholic fatty liver disease (NAFLD) is increasingly recognized as a distinct clinical phenotype with limited evidence for effective non-pharmacological interventions and unclear mechanistic pathways. Aerobic exercise is recommended for NAFLD management; however, its effects and the gut microbiota–associated mechanisms in lean NAFLD remain incompletely understood. This dataset was generated from a randomized controlled trial (ClinicalTrials.gov identifier: NCT04882644). Participants assigned to the aerobic exercise intervention group provided fecal samples at baseline and after the 3-month intervention. A total of 33 paired fecal samples were included in this dataset. Gut microbiota profiles were generated using shotgun metagenomic sequencing. The dataset includes processed and de-identified species-level relative abundance tables derived from fecal samples collected before and after the intervention. These data were used to characterize exercise-induced alterations in gut microbial composition and interindividual variability in microbiota responses to aerobic exercise in lean NAFLD. The data support integrative analyses with clinical phenotypes and circulating metabolomic profiles to explore gut microbiota–associated mechanisms underlying the metabolic benefits of aerobic exercise.

overall_design:
Fecal samples were collected from participants in the aerobic exercise intervention group at baseline and after the intervention. Shotgun metagenomic sequencing was performed, and species-level relative abundance profiles were generated for downstream analyses.

***************************************************************
Raw files for human/patient samples were not submitted to GEO due to concerns about submitting personally identifiable sequence data for open access.
***************************************************************

first: Ci

last: Song

first: Chengxiao

last: Yu

first: Xin

first: Zhibin

last: Hu


title: Adipogenic Transcriptional Regulation Mediated by PARP7 Through NAD+ Sensing Mechanism [ATAC-seq]


title: Targeting mTORC2-Dependent AKT/FOXO1/RNF125 Signaling Exploits a Therapeutic Vulnerability in c-MET-Activated and β-catenin-Mutated Hepatocellular Carcinoma

city: Honolulu

first: Xue

state: HI

address: 701 Ilalo Street

department: Cancer Biology Program

institute: University of Hawaii Cancer Center

summary: Background and Aims: Approximately 10% of human hepatocellular carcinomas (HCC) exhibit concurrent c-MET activation and β-catenin gain-of-function mutations, representing a clinically relevant HCC subtype. This study aimed to investigate the role of mTORC2/AKT signaling in this subtype and identify potential therapeutic targets. Approach and Results: The mTORC2/AKT cascade was activated in c-Met/β-cateninΔ90 HCC lesions. Genetic ablation of Rictor, the essential mTORC2 subunit, strongly suppressed c-Met/β-cateninΔ90-dependent hepatocarcinogenesis. Mechanistically, both the TSC2/mTORC1 axis and FOXO1 transcription factors functioned as critical downstream effectors of mTORC2/AKT in this model. We further identified RNF125 as a direct transcriptional target of FOXO1. RNF125 overexpression significantly inhibited tumorigenesis in the c-Met/β-cateninΔ90 model and suppressed liver cancer cell growth in vitro. Notably, using an in vivo doxycycline-inducible system, we found that inducing RNF125 expression in established c-Met/β-cateninΔ90 HCC suppressed tumor progression, suggesting that activation of RNF125 may have translational implications for HCC treatment. Conclusions: Our study, for the first time, established the mTORC2/AKT/FOXO1/RNF125 axis as a critical driver and therapeutic vulnerability in c-MET-activated/β-catenin-mutated HCC. Our study filled a critical gap by defining the tumor-suppressive role of FOXO1 specifically in this HCC subtype. Furthermore, our results positioned RNF125 as a promising therapeutic target for this aggressive HCC subtype.

overall_design: RNA-seq profiling was performed on pInducer20-RNF125 HepG2 cells treated with or without 2 μM doxycycline hydrochloride (Dox) for 48 hours. The experiment aimed to assess gene expression changes upon RNF125 induction.

last: Chen


title: Adipogenic Transcriptional Regulation Mediated by PARP7 Through NAD+ Sensing Mechanism

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

overall_design: Refer to individual Series


title: Adult leptomeningeal vestigial neural crest-derived multipotent cells promote vascular repair after stroke.

first: Marcin

last: Tabaka

address: Kasprzaka 44/52

institute: International Centre for Translational Eye Research

summary: We collected cerebral cortex at days 3, 7, 14, 28 after dMCAO (distal middle cerebral artery occlusion) and sham.

overall_design: Cerebral cortex 17 samples (sham n=3, D3 n=3, D7 n=4, D14 n=3, D28 n=4)

first: Ji

last: Park

first: Wilber

last: Quispe


title: Isw2-dependent chromatin remodeling at the CRZ1 promoter governs azole tolerance in Candida albicans

city: Montreal

first: Adnane

last: Sellam

address: 5000, rue Bélanger

country: Canada

institute: Universite de Montreal

summary: Here, we conducted a quantitative analysis of transcription factor deletion mutants in Candida albicans to identify novel modulators of azole tolerance. We found that loss of ISW2, which encodes the catalytic subunit of an ATP-dependent chromatin-remodeling complex, markedly increased azole tolerance, establishing Isw2 as a negative regulator of this phenotype in C. albicans. By integrating RNA-seq and ChEC-seq analyses, we defined the Isw2 regulon and discovered that this remodeler binds and modulates nucleosome dynamics at the promoter of CRZ1, a transcription factor that acts downstream of the calcineurin pathway and is a key regulator of azole tolerance. Consistent with this, CRZ1 transcript levels were elevated in the isw2 mutant, supporting a model in which Isw2 modulates antifungal tolerance by directly restricting CRZ1 transcription.

overall_design: In this study, we identified transcripts that were differentially regulated in the isw2 mutant, which lacks the chromatin remodeler Isw2. The transcriptional profile of isw2 cells grown in the synthetic complete medium supplemented or not with the antifungal amphotericin B (0.45 µg/ml) was compared to that of the wild-type (WT) strain grown under the same conditions. For ChEC-seq, DNA cleavage profiles from Isw2-MNase cells (C-terminal MNase-tagged ISW2 at the native locus) were normalized to those from MNase-free control cells (WT cells with ectopic MNase expression).

first: Antony T.

last: Vincent

first: Maria Juliana

last: Mantilla

first: Faiza

last: Tebbji

first: Andrew

last: Chatr-aryamontri


title: ScRNAseq analysis of chicken embryonic pituitary reveals cell heterogeneity and a cell type co-expressing Gh and Pomc

city: College Park

first: Tom

last: Porter

state: Maryland

address: 8127 Regents Drive

department: Animal and Avian Sciences

institute: University of Maryland

summary: Gene expression profiles and the heterogeneity among hormone-producing pituitary cells remain poorly characterized in most vertebrates, especially in chicken embryos. Using single-cell RNA sequencing, the transcriptomes of 4,346 basal and 10,835 corticosterone (CORT)-treated embryonic day 11 chicken pituitary cells were sequenced. Classical endocrine cell clusters were identified, and some were shown to express previously unreported marker genes. A cluster of uncommitted cells was identified that expressed markers for multiple endocrine cell types, with ∼30% co-expressing Gh and Pomc mRNA. We named this population of cells the cortico-somatotrophs. The existence of cortico-somatotrophs were confirmed at both the mRNA and protein level. We further characterized the cortico-somatotrophs by utilizing the known effect of CORT to increase somatotroph abundance. Identification of cortico-somatotrophs challenges the prevailing view that corticotrophs and somatotrophs develop from distinct cell lineages.

overall_design: Embryonic day 11 chicken pituitary cells were collected and dispersed, then treated with or without corticosterone (CORT). Through scRNAseq, different hormone-producing cell types were identified and characterized.

first: Kuan Ling

last: Liu


title: From blood to pluripotency: Fibrocytes as a reprogrammable somatic cell source for bovine iPSCs

city: Ithaca

first: Vimal

last: Selvaraj

state: NY

address: 204 Morrison Hall

department: Animal Sciences

institute: Cornell University

summary: Fibrocytes represent a distinct somatic cell type derived from peripheral blood leukocytes, first described as spindle-shaped adherent cells with dual hematopoietic and mesenchymal features.  Although fibrocytes were identified in early descriptive studies across several mammalian systems, most of this work predated modern molecular approaches, and the cells remain incompletely defined at the molecular level and have not previously been derived or characterized in cattle. Seeking somatic cells that could be collected aseptically and reproducibly under field conditions for reprogramming to pluripotency, we recognized fibrocytes as a practical and previously unexplored candidate population. Here, we establish a reproducible method for fibrocyte derivation and expansion from adult bovine blood and define their molecular identity using transcriptomic and network analyses. Principal component and differential expression analyses revealed extensive immune, inflammatory, metabolic, and stress-responsive pathways that distinguished fibrocytes from fibroblasts. Upstream regulator analysis identified a fibrocyte-restricted transcriptional network governed by SPI1, IRF5/IRF7, NFKBIZ, PRDM1, CIITA, and MAFB, supporting a monocyte-derived origin and indicating some retention of hematopoietic lineage memory despite acquisition of mesenchymal features. Optimized fibrocyte medium (FbC; dexamethasone, ascorbate, PDGF-BB, EGF, A83-01, CHIR99021) supported stable proliferation and selectively enhanced cytoskeletal and matrix-constructive programs while attenuating inflammatory tone. When reprogrammed with polycistronic OCT4-SOX2-KLF4-cMYC and SV40 large T antigen, fibrocytes generated induced pluripotent stem cell (iPSC) colonies exhibiting defining molecular and morphological features of pluripotency. These findings establish fibrocytes as a field-adaptable, stably expandable, and reprogrammable somatic cell type with practical applications in induced pluripotent stem cell generation, genetic preservation, and reproductive biotechnology.

overall_design: Bovine fibrocytes isolated and cultured in two different mediums -  fibroblast and fibrocyte medium to identify suitable culture cunditions that support decreased inflammatory response and proliferation.

first: Hannah

last: Sylvester

first: Prasanthi

middle: P

last: Koganti


title: Sex-specific effects of exogenous asparagine on colorectal tumor growth, 17β-estradiol levels, and aromatase

city: NEW HAVEN

first: Oladimeji

last: Aladelokun

state: Connecticut

department: Environmental Health Sciences

institute: YALE UNIVERSITY

summary: Sex-related differences in asparagine metabolism are associated with cancer prognosis. However, the effect of exogenous asparagine on colorectal cancer (CRC) growth in men and women remain unclear. This study aims to understand the relationship between exogenous asparagine supplementation and 17β-estradiol levels and to elucidate mechanisms underlying sex-dependent signaling during CRC development. We administered asparagine intraperitoneally to tumor-bearing immunodeficient male and female Rag2/Il2RG (R2G2) mice. Asparagine supplementation caused a significant increase in tumor asparagine levels in both the tumor-bearing male and female R2G2 mice but increased serum estradiol levels and suppressed tumor growth in female R2G2 mice only. Additionally, we combined transcriptome, metabolome and immunochemical analyses and found that intraperitoneal asparagine treatment induced sex-dependent intra-tumoral metabolic changes to asparagine, aspartate, glutamine and glutamate levels in CRC cells. We observed that in females, exogenous asparagine exerts a negative feed-back effect on de novo asparagine synthesis and is associated with the activation of a sub-population of macrophages that may secrete 17β-estradiol via an aromatase or cytochrome P450 family 19 (CYP19)-dependent mechanism, resulting in improved tumor-specific survival. Conversely, in male mice, asparagine treatment augments tumor growth and is related to decreased numbers of macrophages, reduction in CYP19-mediated 17β-estradiol secretion leading to worsened tumor-specific survival. Overall, our results reveal a novel and sex-specific role for exogenous asparagine during cancer progression and underscores the importance of understanding mechanisms that control asparagine biosynthesis.

overall_design: Thirty (30) R2G2 (n = 15 female, n = 15 male) mice were randomly separated into 6 groups of 5 for a tumor-specific survival experiment. HCT116 cancer xenograft establishment was confirmed as palpable tumors in all 30 mice. In group 1, female R2G2 mice received vehicle or control: PBS solution. Groups 2 and 3 represent female mice that were administered 1 mg/kg and 10 mg/kg asparagine respectively. In group 4, male R2G2 mice were administered PBS solution. In groups 5 and 6, male mice received 1 mg/kg and 10 mg/kg asparagine respectively. One mouse in the female PBS control group became severely moribund before study endpoint. RNA-sequencing was conducted on xenografts from n = 4 tumors/sex/group. Libraries were prepared with total RNA using the Total RNA TruSeq mRNA Stranded Library Prep Kit (Illumina, San Diego, CA, USA) as previously described [20]. Briefly, mRNA pulldown was performed using an oligodT primer attached to magnetic beads. The libraries were quantified using the Qubit dsDNA HS assay kit (Thermofisher Scientific, Waltham, MA, USA). Pooled library was sequenced on an efficient ultra-high-throughput sequencer using the NovaSeq 6000, an instrument with a patterned flow cell technology which provides the highest throughput across multiple applications (Illumina) according to the manufacturer’s protocol.

first: Katherine

last: Benitez

first: Yuying

last: Wang

first: Abhishek

last: Jain

first: Domenica

last: Berardi

first: Georgio

last: Maroun

first: Xinyi

last: Shen

first: Jatin

last: Roper

first: Joanna

last: Gibson

first: Kaelyn

last: Sumigray

first: Sajid

middle: A

last: Khan

first: Caroline

last: Johnson


title: Gene expression data from SW13 cells infected with Orthonairovirus hazaraense

city: Wakayama

first: Keisuke

last: Ohta

address: 811-1 Kimiidera

department: Microbiology

institute: Wakayama Medical University

summary:
Orthonairovirus hazaraense (Hazara virus: HAZV) is a surrogate model for Orthonairovirus haemorrhagiae (Crimean-Congo hemorrhagic fever virus: CCHFV). Nucleoprotein of these viruses are multifunctional, and is thought to have a great influence on gene expression profiles of host cells.
We used microarray to investigate the effects of HAZV infection on gene expression profiles. Especially, we focused on nucleoprotein using SW13 cells which constitutively express HAZV nucleoprotein (SW13/N).

overall_design: SW13 cells and SW13/N were infected with or without HAZV. Four types of cells (mock SW13, HAZV-infected SW13, mock SW13/N, and HAZV-infected SW13/N) were obtained. Each type of cells were prepared from three independent experiments.

first: Machiko

last: Nishio