title: Single-cell RNA-seq of neutrophils from germ-free and specific-pathogen-free mice reveals gut-microbiota-driven heterogeneity and NETosis in acute pancreatitis

city: Nanchang

first: Yaoyu

last: Zou

state: Jiangxi

address: 17 Yong Waizheng Street, Donghu District

institute: The First Affiliated Hospital of Nanchang University

summary: We performed single-cell RNA sequencing (scRNA-seq) using the 10x Genomics platform to characterize pancreatic immune cell populations in germ-free (GF) and specific-pathogen-free (SPF) mice with cerulein-induced acute pancreatitis (AP). scRNA-seq analysis identified distinct neutrophil subpopulations influenced by gut microbiota presence. SPF mice showed enrichment of pro-inflammatory neutrophil clusters associated with increased neutrophil extracellular trap (NET) formation, whereas GF mice exhibited neutrophil subsets expressing reparative and protective signatures. Our data highlight the role of gut microbiota in shaping immune responses during AP.

overall_design: Following induction of AP by repeated intraperitoneal injection of cerulein (100 µg/kg hourly for 10 doses), pancreatic tissues were harvested from GF and SPF male C57BL/6 mice (7–8 weeks old). Single-cell suspensions of pancreatic immune cells were obtained by enzymatic digestion, and libraries were prepared using the 10x Genomics Chromium Single Cell 3′ v3.1 protocol. Sequencing was performed on an Illumina NovaSeq 6000 (paired-end, 2×150 bp). Raw FASTQ files and processed data (gene-cell count matrices) were deposited in GEO

first: Yin

last: Zhu

first: Jianping

last: Liu

first: Cong

last: He

first: Nianshuang


title: SPATIAL TRANSCRIPTOMICS IDENTIFY HOMOLOGOUS MECHANISMS IN THE PATHOPHYSIOLOGY OF HUMAN AND E4FAD MOUSE CEREBRAL MICROBLEEDS

status: Public on Aug 20 2025

city: Chicago

first: Issam

middle: A

last: Awad

state: IL

address: 5841 S Maryland Avenue MC 3026, J 341 MC 3026, J 341

department: Neurological Surgery

country: USA

institute: University of Chicago

type: Non-coding RNA profiling by high throughput sequencing

summary: INTRODUCTION: Cerebral microbleeds (CMBs) are age-related vascular lesions, predisposing patients to a lifetime risk of stroke and cognitive decline. Little is known about the cellular architecture of the CMB lesional milieu as well as CMB pathobiological mechanisms. Understanding common histopathologic and transcriptomic signatures across heterogenous CMBs can aid in biomarker feature selection.  METHODS: These knowledge gaps were first addressed through the morphological and quantitative assessment of human CMB autopsy tissue and E4FAD mouse CMB tissue for cell types previously implicated in neurovascular diseases. Following, assessment of human and mouse lesional differentially expressed genes (DEGs) and pathway enrichment discovered important common and differential mechanisms in CMB pathogenesis. These findings facilitated identification of circulating proteins, which were quantified and underwent feature selection to identify the strongest diagnostic biomarker candidate molecules. In addition, a circulating DE miRNome found mechanistically-relevant homologous miRNA between human subjects and E4FAD mice as candidates.  RESULTS: Histopathologic studies identified significant increases in normalized counts of astrocytes and macrophages in human CMBs, as well as astrocytes and microglia in E4FAD murine CMBs. Spatial transcriptomics identified 781 human CMB DEGs and 448 mouse CMB DEGs, with 47 common DEGs (p<0.05, FDR-corrected). Pathway enrichment identified 110 common pathways related to vascular permeability, endothelial dysfunction, and inflammation (p<0.05, FDR-corrected). A supervised literature search then found 10 blood circulating proteins that had previously been assessed in CMB patients and healthy controls. Protein levels were assessed, and elastic net feature selection identified 7 circulating protein biomarker candidates. Through miRNome sequencing, two miRNAs (p<0.1, FDR-corrected) were discovered common between human CMB patients and E4FAD mice with mechanistic ties to IPA pathways enriched from the respective transcriptomes.  CONCLUSION: This is the first report to characterize the CMB microenvironment, provide mechanistic insight into its pathobiology, and identify biologically plausible circulating diagnostic biomarker features. Future studies should identify specific mechanisms related to lesion genesis, maturation, and progression to hemorrhagic stroke. In addition, studies aimed at validation of these features, and model validation in large multi-site cohorts are needed. The framework applied here paves the way for biomarker discovery in CMBs and other cerebrovascular diseases across varying contexts of use.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: 12 microRNA samples from mouse blood plasma.Obtained from 6 E4FAD mice (5xFAD+/-; human APOE4+/+, C57BL/6 background) emulating Cerebral Microbleeds (CMB) and 6 wild-type mice (C57BL/6 background).

first: Abhinav

last: Srinath

first: Diana

last: Vera Cruz

first: Dorothy

last: DeBiase

first: Akash

last: Bindal

first: Ying

last: Li

first: Geetha

middle: P

last: Yeradoddi

first: Mannan

last: Bhola

first: Rhonda

last: Lightle

first: Justine

last: Lee

first: Agnieszka

last: Stadnik

first: Kristina

last: Piedad

first: Robert

last: Shenkar

first: Peter

last: Pytel

first: Yuanyuan

first: Sharbel

last: Romanos

first: Thomas

last: Moore

first: Sean

last: Polster

first: Yuan

first: Xiaoxi

last: Zhuang

first: Christopher

last: Gomez

first: Sangram

last: Sisodia

first: Romuald

last: Girard


title: RNA-sequencing of endothelial cells and 3D cardiac microtissues from hiPSCs

city: Leiden

first: Valeria

last: Orlova

address: Einthovenweg 20

country: Netherlands

institute: Leiden University Medical Center

type: Expression profiling by high throughput sequencing

summary: We previously showed that two major cellular components of the human heart, cardiac endothelial cells and cardiomyocytes, could be derived simultaneously from human induced pluripotent stem cells (hiPSCs). In vivo studies in mice have shown these lineages derive from a common MESP1+ mesoderm progenitor. Although this has been investigated using whole transcriptome sequencing, the transcriptional control and dynamics of their segregation from cardiac mesoderm are not yet fully understood. In addition, the same transgenic approach cannot be used in human. Here, we used bulk and single cell RNA sequencing (RNAseq) to investigate EC and cardiomyocytes co-differentiation in hiPSC. We confirmed segregation of these two cardiac lineages from common cardiac mesoderm precursors but more importantly, revealed a critical role of transient expression of the transcription factor ETV2 for endothelial fate specification and showed unexpectedly that functional cardiomyocytes could also originate from ETV2+ progenitors. This dataset contain 10X-based scRNA-seq data human induced pluripotent stem cell derived endothelial cells and 3D cardac microtissues, as well as bulk RNA-seq data of endothelial cells derived from cardiac and paraxial mesoderm.

overall_design: scRNA-seq data: Two batches of  cardiac mesoderm derived endothelial cells (CMEC), two batches of  paraxial mesoderm derived endothelial cells (PMEC),  two batches of  3D cardiac microtissues (MTP) differentiated from hiPSCs. Bulk RNA-seq data:  5-6 batches of CMEC and PMEC on differentiation day 6 and 8 from COUPTF-II reporter hiPSC line, 3 batches of CMECs sorted on differentiation day 6, on day 27 of 2D culture and on 27 of microtissues.

first: Xu

last: Cao


title: Single-Cell RNA Sequencing Defines Developmental Progression and Reproductive Transitions in Pneumocystis carinii

status: Public on Aug 19 2025

city: Newport

first: Aaron

last: Albee

state: KY

address: 17 Youngs Ct

institute: University of Cincinnati

summary: This study presents the first single-cell RNA sequencing (scRNA-seq) atlas of Pneumocystis carinii, generated from isolated organisms recovered from the bronchoalveolar lavage fluid of infected rats to map the life cycle of P. carinii.

overall_design: scRNA-seq profiling of wildtype P. carinii, The filtrates were centrifuged at 2500 x g to pellet fungal cells, which were resuspended in 0.85% ammonium chloride solution at 37°C.  for 10 minutes to lyse red blood cells. After centrifugation, the resulting pellets were maintained in RPMI 1640 medium (Fisher Scientific, Pittsburgh, PA) supplemented with 20% fetal bovine serum (Cytiva, Sweden AB), MEM Non-Essential Amino Acids (Gibco, Pittsburgh, PA), MEM Vitamin Solution (Gibco, Pittsburgh, PA), penicillin-streptomycin (10,000 µg/mL,10,000 µg/mL; Gibco, Pittsburgh, PA), and vancomycin (5 mg/mL; Fisher Scientific, Pittsburgh, PA). Following extractions, incubation at 37°C for 30 minutes in T25 tissue culture flasks facilitated host cell adherence and enabled the enzymatic degradation of extracellular DNA using DNase I (Thermo Fisher Scientific, Waltham, MA). DNase I was applied at a concentration of 100 U/mL for effective DNA removal in cell culture systems. P. carinii organisms were collected from the supernatant, followed by centrifugation at 2500 x g to pellet and resuspended in 1 mL of 2% Ficoll-Hypaque before placement on a Ficoll gradient (38). We used a Ficoll-Hypaque gradient (Ficoll: Millipore, Billerica, MD; Hypaque: Sigma, St. Louis, MO). The gradient was prepared with Ficoll concentrations diluted in 16% sodium diatrizoate, ranging from 2% to 12% increments. Following centrifugation, each layer was collected, and the cells were rinsed with cold Dulbecco’s Phosphate-Buffered Saline (DPBS; Fisher Scientific, Pittsburgh, PA) and pelleted by centrifugation at 2500 × g. To minimize cell clumping, pellets were gently resuspended using a 20-gauge ball-tip gavage needle (Becton Dickinson & Co., Franklin Lakes, NJ) before final centrifugation at 2500 x g. The resulting samples were reconstituted in Mg²⁺ and Ca²-free RPMI 1640 medium (Fisher Scientific, Pittsburgh, PA) supplemented as described above.

first: Aleksey

last: Porollo

first: Melanie

last: Cushion


title: Therapeutic Efficacy of Oncolytic Adenovirus YSCH-01 in Osteosarcoma: Evaluation Using PDX and CDX Mouse Models

city: Shanghai

first: Hanqiang

last: Jin

address: Pujian Road No.160

country: China

institute: Renji Hospital Affiliated to Shanghai Jiaotong University School of Medicine

summary: Abstract Background: YSCH-01, a recombinant L-IFN adenovirus injection, is an oncolytic virus- based anticancer drug with dual anti-tumor effects. In previous studies, we have confirmed the potential of YSCH-01 in the treatment of malignant gliomas. Additionally, YSCH-01 has emerged as a promising candidate for osteosarcoma treatment, exhibiting significant antitumor properties. However, its specific role in osteosarcoma and the underlying mechanisms remain poorly understood. Methods: We evaluated the infectivity and efficacy of YSCH-01 in osteosarcoma cells by collecting clinical samples of osteosarcoma and conducting experiments using osteosarcoma cell lines both in vitro and in vivo. Additionally, we studies the impact of YSCH-01 on interferon overexpression at the RNA and protein levels to highlight its potential antitumor properties. Furthermore, RNA-seq analysis of tumor samples treated with YSCH-01 provided valuable insights into the altered gene expression profiles and signaling pathways, helping to elucidate the molecular basis of its antitumor effects. Results: Our findings demonstrated the dose-dependent infectivity of YSCH-01 in osteosarcoma cells, with varying effects observed across different cell lines. Both in vitro and in vivo studies showed that YSCH-01 effectively inhibited osteosarcoma cell proliferation. In CDX and PDX animal models, YSCH-01 exhibited potent therapeutic effects, particularly in terms of its distant effects. Additionally, IFN-αsignaling pathway was activated in the tumor tissues with YSCH-01 treatment. Conclusions: The initial findings of this study revealed the complex molecular pathways through which YSCH-01 exerts its antitumor effects in osteosarcoma. By elucidating the correlation between key molecular markers in osteosarcoma and patient outcomes, we have identified potential therapeutic targets, presenting a promising avenue for osteosarcoma treatment. Keywords: Osteosarcoma; Oncolytic Virus; YSCH-01; L-IFN.

first: Ruoyu

last: Chen

first: Jin

last: Huang

first: Xue-ping

first: Xian-long

last: Fang

first: Ning

last: Li

first: Kang-jian

last: Zhang


title: Pan organ and time course analysis of T cells in acute LCMV (armstrong) infection (day 60) [I40]

city: Boston

first: Liang

last: Yang

state: MA

address: 77 Avenue Louis Pasteur

department: Pathology

institute: Harvard Medical School

summary: This study is part of the immgenT Open Source Project, specifically from IGT40, which focuses on a pan-organ and time course analysis of T cells in acute LCMV (Armstrong) infection at day 60 post-infection. The dataset includes T cells isolated from multiple organs: spleen, prostate, submandibular gland, bone marrow, mesenteric lymph node, small intestine epithelium, small intestine lamina propria, lung, and mediastinal lymph node. 7-week-old male C57BL/6J mice infected intraperitoneally with 2×10^5 PFU LCMV Armstrong, and T cells were analyzed at 60 days post-infection (dpi). The study includes both endogenous T cells and adoptively transferred P14 and SMARTA TCR transgenic T cells. Mice received IV 100,000 SMARTA (CD45.1.2) and 50,000 P14 (CD45.1) T cells one day before infection.

overall_design: T cells were isolated from individual organs using mechanical dissociation, enzymatic digestion (collagenase I or DTE), and anti-CD45 intravenous labeling to distinguish tissue-resident from circulating cells. Sorted CD3e+ or IV- CD3e+ were profiled using single-cell RNA sequencing (10x Genomics), combined with CITE-seq (TotalSeq C) and paired TCR α/β sequencing. Samples were pooled using hashtags.

first: Giovanni

last: Galletti

first: Sara

last: Quon

first: Nicole

middle: E

last: Scharping

first: Kennidy

last: Takehara

first: Amir

last: Ferry

first: Ananda

last: Goldrath


title: Pan organ and time course analysis of T cells in acute LCMV (armstrong) infection (day 7) [I36]

summary: This study is part of the immgenT Open Source Project, specifically from IGT36, which focuses on a pan-organ and time course analysis of T cells in acute LCMV (Armstrong) infection at day 7 post-infection. The dataset includes T cells isolated from multiple organs: spleen, prostate, submandibular gland, bone marrow, mesenteric lymph node, small intestine epithelium, small intestine lamina propria, lung, and mediastinal lymph node. 7-week-old male C57BL/6J mice infected intraperitoneally with 2×10^5 PFU LCMV Armstrong, and T cells were analyzed at 60 days post-infection (dpi). The study includes both endogenous T cells and adoptively transferred P14 and SMARTA TCR transgenic T cells. Mice received IV 100,000 SMARTA (CD45.1.2) and 50,000 P14 (CD45.1) T cells one day before infection.


title: Integrative analysis of RNA binding proteins identifies DDX55 as a novel regulator of 3’UTR isoform diversity

city: Philadelphia

first: Kristen

last: Lynch

state: Pennsylvania

address: 906 Stellar Chance Labs 422 Curie Blvd

department: Biochemistry and Biophysics

institute: University of Pennsylvania

summary: The 3’ untranslated regions (3’UTRs) of mRNAs play a critical role in controlling gene expression and function because they contain binding sites for microRNAs and RNA binding proteins (RBPs) that alter mRNA stability, localization, and translation. Most mRNA 3’ ends contain multiple polyadenylation sites (PAS) that can be utilized in condition-specific manners, a process known as alternative polyadenylation (APA), however the mechanisms driving the regulation of APA remain poorly characterized. By integrating a large set of over 500 RNA binding protein (RBP) depletion and binding experiments across two cell lines generated by the ENCODE consortium, we uncovered a number of RBPs in each cell type whose depletion leads to widespread alteration of 3’ UTR patterns. These include not only known regulators of APA, but also many putative novel regulators of 3’UTR isoform expression. We focused analysis on the largely unstudied DEAD box RNA helicase, DDX55, and validate its novel role in 3’UTR isoform regulation using molecular assays and targeted 3’ end sequencing experiments (QuantSeq REV V2, Lexogen). Our findings identify DDX55 as a new regulator of APA, particularly at PAS that contain features of RNA secondary structure. Our data also suggest additional previously unrecognized regulators of 3’ UTR processing and differential stability.

overall_design: We preformed targeted 3'end sequencing (QuantSeq REV V2, Lexogen) to determine polyA site usage in HepG2 cells transfected with siRNAs for control non-targeting pool or targeting DDX55, in triplicate. RNA was profiled from whole cell in addition to nuclear and cytoplasmic fractions.

first: Matthew

middle: R

last: Gazzara

first: Michael

middle: J

last: Mallory

first: Yoseph

last: Barash

middle: W


title: Role of CRY1 in DNA end resection

city: Sevilla

first: Pablo

last: Huertas

address: Av.Americo Vespucio 24

country: Spain

institute: University of Sevilla

type: Genome binding/occupancy profiling by high throughput sequencing

summary: CRY1 is a circadian clock core component. Data in our laboratory has linked this factor with controlling the activity of the DNA double strand break repair protein CtIP, affecting the process of DNA end resection.  By using ChIP-seq approaches in the DiVA cell system, we can show that the absence of CRY1 increases DNA end resection, measured as the accumulation of RPA at the sites of cleavage of the enzyme AsiSI. Furthermore, this is due to an increase in the accumulation of the resection factor CtIP.

overall_design: Chromatin inmunoprecipitation (ChIP-seq) of RPA, CRY1, CRY2 and CtIP in AsiSI-ER U2OS cells

first: Amador

last: Romero-Franco

first: Sonia

last: Jimeno

first: Silvia

last: Jimeno-González


title: Isoformic PD-1 impedes B cell activation and function in HIV-1 infection

status: Public on Aug 18 2025

city: Hong Kong

first: Ming

last: Yue

address: 21 Sassoon Road, Pokfulam

institute: The University of Hong Kong

summary: The interaction between PD-1 and PD-L1 inhibits activation of HIV-1-specific CD8+ T cells, yet mechanisms underlying B cell dysfunction in HIV-1 infection remain unclear. Here, we identify a key role for Δ42PD-1, an isoform of PD-1, in human B cells. Chronic HIV-1 infection selectively upregulates Δ42PD-1, but not PD-1, on up to 28% of B cells. BCR stimulation induces Δ42PD-1 expression, resulting in B cell cycle arrest and apoptosis. Mechanistically, Δ42PD-1 recruits SHP1 via its intracellular immunoreceptor tyrosine-based switch motif, leading to AKT1 inhibition and suppression of the AKT1/FOXO1 pathway, thus promoting B cell apoptosis. Notably, targeting Δ42PD-1 with a specific antibody or gene knock-down reduces SHP1 recruitment, restores AKT1/FOXO1 activation, and enhances B cell proliferation and function, including in HIV-1 ENV-specific memory B cells. These findings reveal a novel inhibitory Δ42PD-1-SHP1 axis and support Δ42PD-1 as a therapeutic target to restore B cell responses in HIV-1 infection.

overall_design: Sorted Δ42PD-1+, PD-1+ and double negative B cells at 48 hours after the treatment with α-IgM/G F(ab’)2 and CH34 or isotype control IgG2b.

first: Li

last: Liu

first: Zhiwei

last: Chen


title: Single-Cell RNA-Seq Study Showing the Effect of Healthy and Cencer Cells on HSCs

city: Indiana University

first: Reza

last: Shahbazi

address: 980 W Walnut st

institute: Indiana University

summary: Hematopoietic stem cells (HSCs) are highly sensitive to signals from their surrounding microenvironment, yet the precise effects of healthy versus malignant cells on HSC behavior remain poorly understood. In this study, we applied single-cell RNA sequencing (scRNA-seq) to profile HSCs exposed to either exosomes from healthy primary cells or cancer-derived cells. Our analyses revealed distinct transcriptional programs induced by each condition.

overall_design: Single-cell RNA profiling were performed on primary CD34 cells treated with exosomes.

first: Samaneh

last: Maleknia

first: Sanam

last: Rezaei Benam


title: ProCTLA-4 in anti-tumor immunity

city: Beijing

first: Wenyan

last: Wang

address: Tsinghua Road

institute: Tsinghua

summary: We developed a prodrug of the anti-CTLA4 antibody, named ProCTLA-4. ProCTLA-4 elicits anti-tumor immune responses with reduced toxicity compared to current CTLA4 blockade therapies. Moreover, compared to currently used Probody Therapeutics targeting CTLA-4, ProCTLA-4 offers significant advantages for enhanced efficacy. Thus, our design establishes an alternative paradigm for antibody therapeutics that enables reduction of irAEs while simultaneously increasing therapeutic efficacy.

overall_design: We isolated intratumoral live CD45+ immune cells and investigated the transcriptional signatures at the single-cell level following CTLA-4/ProCTLA-4 antibody treatment.

first: Weian

last: Cao

first: Junfan

first: Yutong

last: Fu

first: Yang-Xin


title: GM-CSF production by immune cells in steady state and autoimmune neuroinflammation mapped using fate-reporting mice

first: Michael

last: Gonzalez

address: 3535 Market St

department: Translational Medicine and Human Genetics

summary: The current study tracked ongoing and past GM-CSF expression in various immune cells from multiple organs, both under steady-state conditions and during autoimmune inflammation of the central nervous system (CNS). RNA sequencing (RNA-Seq) was used to identify differences between naïve and effector memory CD4⁺ T cells with (YFP+) or without (YFP-) a history of GM-CSF expression.

overall_design: Transcriptional analysis for YFP+, YFP− naïve (CD62L+CD44−), and TEM (CD62L−CD44hi) CD4+ T cells from the spleens of Gr/fr mice (n = 3)

first: Javad

last: Rasouli

first: Gholamreza

last: Azizi


title: Synergistic effects of Ret coding and enhancer loss-of-function alleles cause progressive loss of inhibitory motor neurons in the enteric nervous system

city: New York

first: Sumantra

last: Chatterjee

state: NY

address: 435 E 30th Street

department: Center for Human Genetics and Genomics

institute: NYU Grossman School of Medicine

summary: Hirschsprung disease (HSCR) is a congenital enteric neuropathy caused by disrupted migration, proliferation, or differentiation of enteric neural crest-derived cells (ENCDCs), with pathogenic variants at the RET locus accounting for a major fraction of cases. While coding variants in RET are known to impair enteric nervous system (ENS) development, the contribution of non-coding regulatory elements remains incompletely understood. The greatest contribution of this risk is from a common variant (rs2435357) in an ENS-active, SOX10-bound RET enhancer (MCS+9.7) that reduces RET expression in vivo and triggers expression changes in other ENS genes in the human fetal gut. Here, we investigate the role of this enhancer during ENS development using a targeted mouse model by deleting mcs9.7. Single-cell RNA-seq profiling of wildtype and homozygous delmcs9.7/ delmcs9.7 embryos revealed an ~8% decrease in RET expression within ENS clusters, with no gross shifts in ENS cell type composition. Ret expression loss was limited to early differentiating neurons and inhibitory motor neurons, indicating cell-type-specific enhancer control. To identify the Ret functional threshold for normal ENS development, we also generated a compound heterozygous mouse (+/delmcs9.7/;+/CFP) that showed additive reductions in Ret expression in these same cell types and bidirectional feedback between Ret and its upstream transcription factor Sox10. We observed reduced expression of 19 cell cycle genes and significant loss of nNOS+ and VIP+ neurons, consistent with decreased inhibitory neuron network driven by loss of proliferation, a hallmark of HSCR. These findings establish a biphasic, cell-type-specific role for the mcs9.7 enhancer in modulating Ret dosage and reveal how subtle enhancer perturbations alter neural subtype specification without overt aganglionosis. Together, our work uncovers the functional consequences of a common RET enhancer variant offering new insights into gene regulatory mechanisms driving HSCR.

overall_design: single cell RNA seq of dissociated GI tract of E14.5 mouse embryos using 10X genomics platform. This included wildype, dleetion of a partiuclar Hirschsprung disease asscoaited enhancer for the gene Ret ((mcs+9.7) and a double heterzygous mice where both the gene Ret and the enhnacer have been deleted (+/delmcs+9.7;+/CFP). These cells were dissocoaited from teh embryonic gut with accumax and single cell sequencing libraries using Chromium Single Cell technology platform's 3'' RT-based assays


title: RNA sequencing analysis of embryos exposed to nanoplastics: effects on developmental and transcriptomic alteration

city: Jeongeup-si

first: Hyeongju

last: you

state: Jeongeup-si

address: Primate resource center

country: South Korea

institute: KRIBB

summary: The increasing prevalence of nanoplastics (NPs) in the environment has raised concerns regarding their potential risks to ecosystems and human health. NP exposure has been shown to interfere with cellular processes; however, their effects on preimplantation embryonic development remain unclear. Given the critical role of zygotic genome activation and early cell cycle progression, disruption during this period can significantly affect embryonic viability. To investigate the molecular effects of polymethylmethacrylate (PMMA)-NPs on early embryonic development, mouse zygotes were exposed to 0.1 or 1 mg/mL PMMA-NPs, and RNA sequencing was performed on four-cell stage embryos. Differential gene expression analysis revealed that 0.1 mg/mL NP exposure affected genes related to DNA damage repair, transcriptional regulation, and cellular homeostasis while 1 mg/mL NP exposure altered the expression of genes associated with apoptotic signaling, cell cycle arrest, and failure of blastocyst formation, suggesting a concentration-dependent effect on developmental progression. Thus, PMMA-NP exposure disrupts early embryonic development by inducing specific transcriptomic changes that potentially affect genome integrity and developmental competency. This study provides new insights into the molecular mechanisms underlying NP-induced embryo toxicity and elucidate the effect of NPs on preimplantation embryo development.

overall_design: RNA sequencing profiling on mouse 4-cell embryos sampled after treatment with nanoplastics at concentrations of 0, 0.1, and 1 mg/mL.

first: Hyeong-Ju

last: You

first: Yu-Jin

last: Jo

first: Jeongwoo

last: Kwon

first: Seung-Bin

last: Yoon

first: Changsic

last: Youn

first: Yejin

last: Kim

first: Man-Jong

last: Kang

first: Ji-Su


title: Computationally resolved neuroprogenitor cell biomarkers   associate with human disorders

city: Houston

first: Gerarda

last: Cappuccio

address: 1250 Morsund street

institute: Baylor College of Medicine

summary: Adult hippocampal neurogenesis, relies on a rare population of neural stem and progenitor cells (NPCs) within the dentate gyrus complex microenvironment. Discovering the specific genes that define these cells is vital yet challenging due to overlapping expression patterns, limiting detection of rare cell populations using traditional approaches. By employing the computational Digital Sorting Algorithm (DSA) on microarray data we identified 129 genes enriched in murine NPCs.

overall_design: Dentate gyri of mice aged between 4 and 12 weeks (five time points for our study, namely 4, 6, 8, 10 and 12 week-of-age)

first: William

last: Choi


title: Mapping Plasmodium transitions and interactions in the Anopheles female

first: Lisa

middle: H

last: Verzier

address: 677 Huntington Avenue

department: Department of Immunology and Infectious Diseases

institute: Harvard University

summary: Gene expression during the late ookinete and oocyst stages of Plasmodium falciparum (human malaria parasite) development has not been previously described in detail. We used single-cell RNA-seq to map gene expression changes in both parasite and mosquito cells and their interactions at multiple timepoints after an infectious blood meal, and in control (dsGFP-injected) and EcR-depleted (dsEcR-injected) mosquitoes.

sample_organism:
Plasmodium falciparum
Anopheles gambiae

platform_organism:
Plasmodium falciparum
Anopheles gambiae

overall_design: Infected midguts were dissected from 80 dsRNA-injected female mosquitoes (dsGFP or dsEcR) and cellularlized by enzymatic digestion, purified and analyzed by single-cell RNA-seq (10X Genomics). Timepoints were 36 h, 2 d, 4 d, and 7 d post infectious blood meal. On-day old mosquitoes were injected with dsRNA 3 d prior to blood feeding.

first: Yan

last: Yan

first: Elaine

last: Cheung

first: Lisa H.

first: Duo

last: Peng

first: W. Robert

last: Shaw

first: Flaminia

last: Catteruccia


title: The few-celled microspore embryo transcriptome of Brassica napus

city: Amsterdam

first: Charlotte

last: Siemons

address: tt. Vasumweg, 40W7

department: Molecular Biology

institute: Wageningen University & Research

summary: Haploid embryos can be induced from cultured immature pollen following a stress treatment. In Brassica napus (B. napus), application of the histone/lysine deacetylase (HDAC/KDAC) inhibitor trichostatin A (TSA) to pollen cultures enhances the production of differentiated embryos and embryogenic callus when applied together with heat stress (Li et al., 2014). To identify genes associated with the induction of B. napus haploid embryogenesis, we employed fluorescence-activated cell sorting on microspore cultures of the LEAFY COTYLEDON1 embryo reporter line (LEC1:LEC1-GFP, Li et al., 2014) to select for embryogenic structures developing in culture, followed by RNA-sequencing. Our transcriptome analysis of the 3-day-old enriched embryo populations and in vitro cultured pollen revealed different regulatory pathways underlying the early development of embryogenic structures. Comparing FACS-sorted embryogenic transcriptomes from cultures treated with heat stress combined with either a low or a high concentration of TSA allowed us to assign transcription profiles to embryogenic structures that have a low or high potential to develop into histodifferentiated embryos.

overall_design: 10 samples were analyzed (3 different treatments). For each condition, three or four biological replicates were analyzed (1 genotype)

first: Amit

last: Kumar

first: Kim

last: Boutilier


title: The Spontaneous Neoantigen-Specific CD4+ T Cell Response to a Growing Tumor is Functionally and Phenotypically Diverse

status: Public on Aug 17 2025

city: La Jolla

first: Vijayanand

last: Pandurangan

state: California

address: 9420 Athena Circle

institute: La Jolla Institute For Immunology

summary: CD4+ T cells play critical roles in the positive and negative regulation of cellular immunity through the many functional subsets they comprise. The progressive growth of immunogenic tumors in the face of mutation-specific T cells suggests that effective immune control may be avoided or suppressed at the level of the neoantigen-specific CD4+ T cell response. We used a tetramer specific for a validated neoantigen, CTLCH129>Q/I-Ek, to characterize the ontogeny of natural CD4+ T cell responses to an aggressive and poorly immunogenic Major Histocompatibility Complex Class II (MHCII)-deficient tumor, SCC VII, during progressive growth or following therapeutic peptide vaccination. We find that the natural CD4+ T cell response to a growing tumor is phenotypically and functionally diverse, with distinct subsets including type 1 helper (Th1), T follicular helper (Tfh)-like, and regulatory T cell (Treg) lineages appearing as early as 9 days after tumor implantation. Therapeutic vaccination using the CLTCH129>Q peptide in adjuvant plus -PD-1 sharply reduces the frequency of CLTCH129>Q-specific Treg frequency in both tumor and tumor-draining lymph node (tdLN). Single cell transcriptomic analysis of CLTC-specific CD4+ T cells recapitulated and extended the diversity of the response, with TCRs of varying affinity found within each functional subset. The TCR affinity differences did not strictly correlate with function, however, as even the lowest affinity TCRs isolated from Treg can mediate therapeutic efficacy against established tumors in the setting of adoptive cellular therapy (ACT). These findings offer unprecedented insight into the functional diversity of a natural neoantigen-specific CD4+ T cell response and show how immunotherapeutic intervention influences the phenotype, magnitude, and efficacy of the anti-tumor immune response.

overall_design:
To understand the endogenous neoantigen-specific CD4+ T cell response, we harvested tetramer-positive and tetrramer-negative CD4+ T cells from the draining inguinal lymph node of mice bearing SCC VII tumors injected subcutaneously on the left flank 17 days prior to cell harvesting.
Harvested lymph nodes were ground through a 70um filter and the resulting cells were moved into a single cell suspension which was stained, run through sorting, and then used for 10x sequencing.

first: Ryan

middle: Q

last: Griswold

first: Spencer

last: Brightman

first: Karla

middle: S

last: Zavala

first: Manuel

last: Ordaz-Arias

first: Navid

last: Djassemi

first: Rukman

last: Thota

first: Martin

last: Naradikian

first: Hannah

last: Dose

first: Suzie

last: Alarcon

first: Pandurangan

last: Vijayanand

first: Bjoern

last: Peters

first: Aaron

middle: M

last: Miller

first: Ezra

last: Cohen


title: Molecular Pathogenesis of Alzheimer's Disease Onset in a Mouse Model: Effects of Cannabidiol Treatment

city: Loma Linda

first: Erik

last: Behringer

state: CA

address: 11041 Campus St.

department: Basic Sciences

institute: Loma Linda University

summary: Alzheimer’s disease (AD) is a common neurodegenerative condition involving a complex blend of disturbances in synaptic development and maintenance, neurovascular cross-talk, ionic and nutrient transport, and mitochondrial metabolism. The precise molecular profile of AD onset with insight for major pathological contributors remains unclear with corresponding impedances in therapeutic development. The current study sought two objectives, as (i) to resolve the molecular pathogenesis from cognitive impairment to the onset of AD-like neuropathology and (ii) whether the novel agent cannabidiol (CBD), noted for its neuroprotective effects, influences the molecular transition associated with AD onset. Dietary CBD was administered daily (80-100 mg/kg/day) in male 3xTg-AD mice and wild-type B6129SF2/J animals from 4.5 to 6.5 mo of age with inclusion of vehicle controls. RNA sequencing encompassed longitudinal and cross-sectional blood and brain samples respectively. Metabolomics and behavioral analyses examined brain regions (cortex, hippocampus) and associated integrated neurocircuitry. There were >1,000 differentially expressed markers of AD onset, whereby >75% were either eliminated or reversed in the direction of expression in response to CBD. Signaling pathways encompassed synaptic development and plasticity (e.g., Foxp2), neurovascular interactions (Smad9, Angptl6), receptors and ion channels (Gria4, Chrna2, Rgs7/Rgs7bp), mitochondrial genes (Ndufa7, Cox7a2), immunity (Ncr1), oxidation-reduction (Esr1), lipid synthesis (Fasn, ApoE), and carbohydrate metabolism (Mafa, Mlxipl). As potentially addressable with CBD treatment, AD onset represents molecular integration of neurovascular interactions, channelopathies, metabolic disturbances, and aberrations in developmental genes with involvement of major pathological contributors such as inflammation, oxidative signaling, dyslipidemia, and insulin resistance.

overall_design: RNAseq profiling of whole blood of male B6129SF2/J and 3xTg-AD mice at 4.5 and 6.5 months of age with cannabidiol-treated and vehicle control groups using a longitudinal analysis design. Note that RNAseq profiling was also conducted for isolated brain samples of all study groups at 6.5 mo of age for cross-sectional analyses. In addition, note that this study also performed a cross-sectional analysis among blood and brain samples at 6.5 mo of age across study groups as well.

first: Phoebe

last: Chum


title: Differential effects of lithium on metabolic dysfunction in astrocytes derived from bipolar disorder patients

city: Daejeon

first: Dayeon

last: Kim

address: 291 Daehak-ro, Yuseong-gu

institute: KAIST

summary: Metabolic alterations have been observed in the brains of patients with bipolar disorder (BD), a neuropsychiatric disorder characterized by biphasic mood episodes of mania and depression. However, the specific contributions of glial cells to these metabolic changes in BD patients remain largely unknown and have not been extensively studied. Here, we investigate the metabolic characteristics of induced astrocytes (iAstrocytes) derived from induced pluripotent stem cells of BD patients and their responses to lithium treatment. The gene expression profiles of iAstrocytes from BD patients (BD iAstrocytes) indicate dysregulation of metabolic processes in BD iAstrocytes. Compared to iAstrocytes from control subjects, BD iAstrocytes showed decreased mitochondrial respiration, increased glycolysis, and elevated lactate secretion. These changes in metabolic pathways suggest impaired mitochondrial function.  Additionally, we observed reduced protein expression within the oxidative phosphorylation complex and decreased reactive oxygen species production, further supporting the impaired mitochondrial function in BD iAstrocytes. Intriguingly, BD iAstrocytes showed an accumulation of lipid droplets (LDs) in both volume and number, possibly reflecting metabolic stress-induced LD accumulation. Lithium, a commonly prescribed treatment for BD, selectively attenuated LD accumulation exclusively in BD iAstrocytes from lithium responders, while it failed to restore mitochondrial dysfunction and increased lactate secretion. Our findings provide novel insights into understanding the metabolic dysfunction in the brains of BD patients and shed light on molecular mechanisms of lithium action, particularly regarding astrocytes. The LDs in BD iAstrocytes from lithium non-responders may serve as a useful readout for drug screening to identify suitable medications for these patients.

overall_design: To investigate the phenotype of BD astrocyte, control and BD patients' iPSCs were differnetitated into iAstrocytes. Then. we performed total RNA sequencing using the obtained iAstrocytes.

first: Jinju

last: Han


title: Infants with perinatal HIV from the TARA cohort, pre-ART

status: Public on Aug 21 2025

city: Miami

first: Akshay

last: Iyer

state: FL

institute: University of Miami

summary: This study investigated immune correlates of viral control in infants with perinatally acquired HIV prior to initiation of antiretroviral therapy (ART). Peripheral blood mononuclear cells (PBMC) were collected at a pre-ART time point and analyzed by single-cell RNA sequencing to profile immune cell composition and transcriptional states. Infants were stratified into high and low viral load groups based on plasma HIV RNA levels at the time of sampling. Transcriptomic profiles were compared between groups to identify cell types, gene expression programs, and immune pathways associated with lower viral load, with the goal of defining candidate immune mechanisms that may contribute to spontaneous control of HIV replication in early life.

overall_design: Investigate gene expression (GEX), protein expression (FB/ADT), and T-cell/B-cell clonality in PBMC from infants that aquired HIV perinatally  at 1-2 month old prior to starting ART.

first: Lesley

last: De Armas

first: Savita

last: Pahwa


title: Effect of overexpression  different alleles C/G at locus rs149707223 of LINC02449 on gene expression of SK-N-SH cells(Human neuroblastoma cell line)

status: Public on Aug 16 2025

city: Guangzhou

first: 杨

last: 腾飞

address: No.1023,South Shatai Road, BaiyunDistrict

department: Medical Genetics

institute: Southern Medical University

summary: Long non-coding RNA (LncRNA) is a significant epigenetic regulatory factor, and its allele-specific expression (ASE) may play an important role in mental disorders. Therefore, clarifying the relationship between allele-specific expression (ASE) of lncRNA and mental disorders is of great significance for an in-depth understanding of the molecular mechanism of mental disorders. We here report that ASE-driven allelic shift in LINC02449 in Bipolar disorder (BD) and schizophrenia (SZ) contributes to behavioral and synaptic abnormalities in mice. We found that when the alternative allele of LINC02449 was overexpressed in cells and mouse brain regions, the expression of differentially expressed genes would be significantly enriched in mental disorders, mediating enhanced synaptic excitability transmission. Taken together, our data supported that LINC02449 overexpression, driven by the rs149707223 alternative allele, affects the disease susceptibility of BD/SZ.

overall_design: RNA-seq profiling of over-expression the rs149707223 refence and alternative allele of LINC02449, and orresponding empty vector in SK-N-SN cells.

first: Tengfei

last: Yang


title: Effect of overexpression  different alleles C/G at locus rs149707223 of LINC02449 on gene expression in the mPFC of mice

overall_design: RNA-seq profiling of over-expression the rs149707223 refence and alternative allele of LINC02449, and orresponding empty vector in mPFC brain region of male C57BL/6J mice.


title: Transactivation of EGF receptor in intestinal epithelial cells by 2’-fucosyllactose mediates prevention of colitis in adulthood

status: Public on Aug 15 2025

city: Nashville

first: Fang

last: Yan

state: TN

address: 2215 Garland Ave., Light hall, Lab No.  1035

institute: Vanderbilt University Medical Center

summary: 2’-fucosyllactose (2’-FL) is a unique oligosaccharide in human milk. We previously reported that 2’-FL protected intestinal integrity, modulated the gut microbial metabolism, and ameliorated intestinal inflammation in adult mice. This study aimed to elucidate mechanisms underlying the direct effects of 2’-FL on intestinal epithelial cells (IECs) for preventing colitis in adulthood. We found that 2’-FL transactivated EGFR in a colonic epithelial cell line, which required 2’-FL-stimulated release of HB-EGF from the cell membrane. Further, findings of 2’-FL-stimulated ADAM17 kinases activity on the cell surface and docking site of 2’-FL to the metalloprotease domain of ADAM17 suggest that 2’-FL could enhance ADAM17 shedding activity for releasing HB-EGF. Remarkably, apoptosis and disruption of tight junction induced by a proinflammatory cytokine and oxidative stress were mitigated by 2’-FL in wild-type, but not EGFR knock-out cell line and colonoids. By using the murine model of colonic injury and colitis induced by DSS, 2’-FL treatment prevented colitis, decreased epithelial apoptosis, and preserved intestinal barrier in wild-type adult mice. These effects were diminished in mice with EGFR deletion in IECs. This study demonstrates a novel mechanism underlying the direct transactivation of EGFR in IECs by 2’-FL that mediates protection of IECs during intestinal inflammation in adulthood.

overall_design: To elucidate if 2’-FL has direct effects on protecting IECs in colitis in adulthood. Established YAMC cells were treated with 2'-FL at 20 μg/ml for 6 hours.Total RNA was isolated for RNA-seq analysis.

first: Kaur

last: Harpreet

first: Ali

last: SyedAzmal

first: Yan

last: Fang


title: Modulating neutrophil phenotype via mesenchymal stromal cell paracrine signals; insights from human and mouse experiments

city: Bucharest

first: Laudy

last: Cherry

state: Sector 5

address: Strada B.P.Hasdeu nr.8, sector 5, Bucuresti

department: Biology

country: Romania

institute: Institute of cellular biology and pathology

summary: Neutrophils play a central role in the inflammatory and reparative processes following myocardial infarction (MI), and can switch between pro-inflammatory (N1) and reparatory (N2) states, influencing disease outcomes. Mesenchymal stromal cells (MSC), known for their immunomodulatory effects, may hold the key to controlling neutrophil behaviour. In this study, we explored how MSC influence neutrophil states both in vitro and in vivo in an MI mouse model. We developed a reliable system to study neutrophils by differentiating HL-60 cells into neutrophil-like cells (dHL-60). These cells were polarized into N1 and N2 types, showing distinct protein markers and cytokine signatures. When exposed to MSC, pro-inflammatory N1 cells reduced their production of inflammatory signals (TNFα, MCP-1), while N2 cells increased their reparatory signals (IL-10, TGM2). In mice with MI, MSC reduced the number of neutrophils migrating to damaged heart tissue and altered their transcriptomic signatures. Surprisingly, MSC enhanced inflammatory pathways in heart neutrophils while dampening their ability to support tissue repair. These findings underscore the complex role of MSC in modulating neutrophil responses, demonstrating a nuanced impact on inflammatory and reparative pathways in the cardiac microenvironment. While the results highlight MSC' potential to influence immune cell behaviour, they also reveal context-specific effects that warrant further investigation to fully elucidate their therapeutic implications in cardiovascular disease.

overall_design: Gene expression profiling analysis of RNA-seq data from cardiac and blood neutrophils isolated from C57Bl/6J mice with and without MSC treatment, after induced myocardial infarction. Samples were collected 3 days after LCA ligation.

first: Sinziana

last: Popescu

first: Carmen

last: Neculachi

first: Evelyn

last: Nastase-Rusu

first: Maya

last: Simionescu

first: Elena

last: Butoi

first: Alexandrina

last: Burlacu

first: Mihai

last: Preda


title: Epigenetic Programming of Estrogen Receptor in Adipose Tissue by High Fat Diet Regulates Obesity-Induced Inflammation

status: Public on Aug 14 2025

city: Atlanta

first: Jia

last: Jing

state: GA

address: Decatur St. SE

institute: Georgia State University

type: Methylation profiling by high throughput sequencing

summary: Adipose inflammation plays a key role in obesity-induced metabolic abnormalities. Epigenetic regulation, including DNA methylation, is a molecular link between environmental factors and complex diseases. Here we showed that DNA methylation, controlled by DNA methyltransferase 1 particularly, is a key determinant of adipose chemotaxis and inflammation. Whole genome DNA methylation profiling with reduced representative bisulfide sequencing (RRBS) analysis revealed that high fat diet (HFD) feeding induced a dynamic change of DNA methylome in white adipose tissue (WAT) of mice. Among these changes there was a significant increase in DNA methylation at the promoter of estrogen receptor α (Esr1), corresponding to the down-regulation of Esr1 expression during HFD. HFD feeding increased the expression of DNA methyltransferase 1 (Dnmt1) and Dnmt3a as well as the binding of DNMT1 and 3a to the Esr1 promoter in WAT of mice. Mice with DNMT1 deficiency in adipocytes (AD1KO) displayed increased Esr1 expression, decreased adipose inflammation and improved insulin sensitivity upon HFD challenge, while D3aKO mice showed a mild metabolic phenotype. The promoter activity of Esr1 promoter enriched with CpG sites was regulated by DNA methylation. Using a modified CRISPR/RNA-guided system to specifically target DNA methylation at the Esr1 promoter in WAT, we found that reducing DNA methylation at the Esr1 promoter increased Esr1 expression, decreased adipose inflammation and improved insulin sensitivity in mice fed HFD. Our study demonstrates that DNA methylation at the Esr1 promoter plays an important role in regulation of adipose inflammation, which may contribute to obesity-induced insulin resistance.

overall_design: RNA-seq profiling was performed on gonadal fat tissue from floxed control (Dnmt1^fl/fl^) and adipocyte-specific DNMT1 knockout (AD1KO) mice after 18 weeks of high-fat diet feeding. RRBS is aimed at studying adipose tissue DNA methylation changes in mice fed with either a low fat diet or a high fat diet.

first: Bingzhong

last: Xue

first: Hang

last: Shi


title: Transcriptome profiling of FGL2-stimulated enteric neural crest cells to investigate metabolic dysregulation in Hirschsprung disease pathogenesis

city: Jinan

first: Jichang

last: Han

state: Shandong

address: 107 Wenhua Xi Road

department: Department of Pediatric Surgery

institute: Qilu hospital of Shandong University

summary: This dataset comprises bulk RNA sequencing data from primary mouse enteric neural crest cells (ENCCs) stimulated with fibrinogen-like protein 2 (FGL2) or left untreated as controls. ENCCs were isolated from embryonic day 14–15 C57BL/6J mice and cultured under defined conditions to ensure >95% expression of P75 and nestin markers. Following FGL2 stimulation, total RNA was extracted, and sequencing libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina. Paired-end sequencing (2 × 150 bp) was performed on the Illumina NovaSeq 6000 platform. The study aims to identify transcriptional changes and signaling pathway alterations induced by FGL2 in ENCCs, providing insights into the role of FGL2-mediated metabolic dysregulation in the pathogenesis of Hirschsprung disease.

overall_design:
Primary ENCCs were obtained from gut tissues of C57BL/6J mouse embryos at gestational day 14–15. Cells were cultured in complete mouse ENCC medium until reaching 80–90% confluence and confirmed to express P75 and nestin in >95% of cells by immunofluorescence. Cells were randomly assigned to two groups:
FGL2-treated group – ENCCs stimulated with recombinant FGL2 protein.
Control group – ENCCs cultured under identical conditions without FGL2.
Three biological replicates were included per group. Total RNA was extracted using TRIzol reagent, and RNA quality was assessed on an Agilent 2100 Bioanalyzer. Poly(A)+ mRNA was enriched, fragmented, and reverse-transcribed to cDNA. Libraries were constructed using the NEBNext Ultra RNA Library Prep Kit and sequenced (paired-end, 2 × 150 bp) on an Illumina NovaSeq 6000.


title: RNA Sequencing of macrophages harboring redox-diverse Mycobacterium tuberculosis.

city: Bengaluru

first: Amit

last: Singh

state: KARNATAKA

address: Sir CV Raman Road

department: Microbiology and Cell Biology

country: India

institute: Indian Institute of Science

summary: The ability of Mycobacterium tuberculosis (Mtb) to tolerate antibiotics is a major impediment in the treatment of tuberculosis. This antibiotic tolerance is influenced by the host cells in which the bacteria reside, as Mtb senses host cues, and the bacterial response can provide an enhanced ability to withstand anti-TB drugs. Previouslyt, we have shown that Mtb exhibits redox heterogeneity in terms of its mycothiol redox potential (EMSH) giving rise to three broad subpopulations  EMSH-reduced, EMSH-basal, and EMSH-oxidized Mtb specifically inside the macrophages. Among these, the EMSH-reduced Mtb exhibit enahnced tolerance to several anti-TB drugs while the EMSH-basal and EMSH-oxidized subpopulations  are more susceptible. In this study, we explored the transcriptomic level differences between macrophages that harbor the antibiotic tolerant Mtb and those harboring antibiotic susceptible Mtb to get a mechanistic understanding of host factors that influence drug tolerance in intracellular Mtb.

overall_design: RNA-Seq of bone marrow-derived macrophages harboring different Mtb subpopulations 24 hours post infection. The study involves four different subpopulations- uninfected, bystanders, macrophages harboring EMSH-reduced Mtb, EMSH-oxidized Mtb.  All samples are assessed in biological triplicates.

first: Vikas

last: Yadav

first: Sarthak

last: Sahoo

first: Nitish

last: Malhotra

first: Mohit

last: Jolly

first: Aswin Sai Narain

last: Seshasayee


title: RNA Sequencing of Mycobacterium tuberculosis-infected macrophages treated with meclizine.

summary: The ability of Mycobacterium tuberculosis (Mtb) to tolerate antibiotics is a major impediment in the treatment of tuberculosis. This antibiotic tolerance is influenced by the host cells in which the bacteria reside, as Mtb senses host cues, and the bacterial response can provide an enhanced ability to withstand anti-TB drugs. Previouslyt, we have shown that Mtb exhibits redox heterogeneity in terms of its mycothiol redox potential (EMSH) giving rise to three broad subpopulations  EMSH-reduced, EMSH-basal, and EMSH-oxidized Mtb specifically inside the macrophages. Among these, the EMSH-reduced Mtb exhibit enahnced tolerance to several anti-TB drugs while the EMSH-basal and EMSH-oxidized subpopulations  are more susceptible. In this study, we have discovered a novel host-directed therapy molecule- meclizine, which enhances the drug susceptible population and diminishes the tolerant population.

overall_design: Bone marrow-derived macrophages were infected with Mtb expressing Mrx1-roGFP2 and were treated with 20uM meclizine or equivalent amount of DMSO (0.2%). At 24h post-infection, infected macrophages were flow-sorted using GFP as a marker for infection and RNA-Seq was performed for these sorted macrophages.


title: Targeting CyclinD1-CDK6 to Mitigate Senescence-Driven Inflammation and Age Associated Functional Decline

status: Public on Aug 13 2025

first: K. Garrett

last: Evensen

address: 10010 N Torrey Pines Rd

institute: The Salk Institute for Biological Studies

summary: Cellular senescence contributes to aging and age-related diseases by driving chronic inflammation through the Senescence Associated Secretory Phenotype (SASP) and interferon-stimulated genes (ISGs). Cyclin D1 (CCND1), a key cell cycle regulator, is paradoxically upregulated in these non-proliferating cells. We show that CCND1 and its kinase partner CDK6 drive SASP and ISG expression in senescent cells by promoting DNA damage accumulation. This leads to the formation of cytoplasmic chromatin fragments (CCFs) that activate pro-inflammatory CGAS-STING signaling. The tumor suppressor p53 (TP53) and its target p21 (CDKN2A) antagonize this CCND1-CDK6–dependent DNA damage accumulation pathway to suppress the SASP. In aged mouse livers, senescent hepatocytes show increased Ccnd1 expression. Hepatocyte-specific Ccnd1 knockout or treatment with the Cdk4/6 inhibitor Palbociclib reduces DNA damage and ISGs in aged mouse liver. Notably, Palbociclib also suppresses frailty and improves physical performance of aged mice. These findings reveal a novel role for CCND1/CDK6 in regulating DNA damage and inflammation in senescence and aging, highlighting it as a promising therapeutic target.

overall_design: In this study, we collected CosMx spatial transcriptomics data on young, old, and Pten KO mice using the 1,000 plex panel

first: Adarsh

last: Rajesh

first: Peter

middle: D

last: Adams

first: K

last: Garrett Evensen


title: Transcriptomic profiling of aganglionic and ganglionic colon segments from Hirschsprung disease patients

summary: This dataset contains bulk RNA sequencing data from paired aganglionic and ganglionic colonic tissue specimens obtained from three pediatric patients diagnosed with Hirschsprung disease (HSCR, OMIM 142623). RNA was extracted and sequenced to investigate transcriptomic alterations and signaling pathway dysregulation associated with HSCR pathogenesis. Raw paired-end FASTQ files generated by Illumina NovaSeq 6000 sequencing are provided for each sample, enabling downstream analyses of differential gene expression between diseased and unaffected intestinal segments.

overall_design: Colonic tissue samples were collected from three pediatric HSCR patients during surgical resection. For each patient, paired specimens were obtained from the aganglionic segment (designated as “X”) and the ganglionic segment (designated as “K”). The paired samples from patients 1, 2, and 3 are labeled as HSCR-1 (X-1, K-1), HSCR-2 (X-2, K-2), and HSCR-3 (X-3, K-3).  Total RNA was extracted using the Trizol reagent kit (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s protocol. RNA quality was assessed with an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and verified using RNase-free agarose gel electrophoresis. Eukaryotic mRNA was enriched using Oligo(dT) beads, fragmented, and reverse transcribed into cDNA using the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB #7530, New England Biolabs, Ipswich, MA, USA). Purified double-stranded cDNA was end-repaired, A-tailed, ligated to Illumina sequencing adapters, purified with AMPure XP Beads (1.0X), and PCR-amplified.  The resulting cDNA libraries from colon tissue were sequenced using the Illumina NovaSeq 6000 platform (paired-end, 150 bp) by Beijing igeneCode Biotech Co., Ltd. (Beijing, China). Raw data are provided for all six tissue samples to facilitate downstream transcriptomic analysis.


title: Identification of oleic acid-induced transcriptome changes under anaerobic conditions in the yeast Candida albicans

first: Jose

middle: Christian

last: Perez

state: TX

address: 6431 Fannin

institute: UTHealth Houston

summary: Dietary components influence microbial composition in the digestive tract. Although often viewed as energy sources, dietary components are likely to shape microbial determinants of intestinal colonization beyond metabolism. Here, we report that a dietary long-chain fatty acid enhances the yeast Candida albicans colonization of the murine gut partly by eliciting modifications to the fungal cell surface. Mice fed an oleic acid-rich diet were readily colonized by C. albicans and exhibited higher fungal load in feces compared to rodents fed an isocaloric control diet. Surprisingly, β-oxidation, a catabolic process to break down fatty acids for energy production, was dispensable for C. albicans to colonize the high-oleic acid diet-fed mice. RNA-Seq was employed to identify oleic acid-induced transcriptome changes under anaerobic conditions. We identified SOK1 as an oleic acid-induced kinase that dictates cell wall mannan exposure and binding to intestinal mucin under anaerobic conditions. Furthermore, oleic acid induced the expression of several C. albicans transcription factors that positively regulate intestinal colonization via remodeling of the fungal cell surface.

overall_design: Comparison of the transcriptome of the Candida albicans strain AHY940 (= WT) in YNB either with final concentration of 0.2% oleic acid (OE) or 0.02% glucose (dextrose, DX). The strains were grown anerobically at 30°C for 24 hours. RNA purification was performed from cells harvested from liquid cultures. Directional mRNA library preparation (with poly A enrichment) and sequencing using NovaSeq PE150 mode was executed at Novogene Corporation Inc.

first: Musfirat

last: Shubaita

first: Elena

last: Lindemann-Perez

middle: C


title: Identification of SOK1-dependent transcriptome changes under anaerobic conditions in the yeast Candida albicans

summary: Dietary components influence microbial composition in the digestive tract. Although often viewed as energy sources, dietary components are likely to shape microbial determinants of intestinal colonization beyond metabolism. Here, we report that a dietary long-chain fatty acid enhances the yeast Candida albicans colonization of the murine gut partly by eliciting modifications to the fungal cell surface. Mice fed an oleic acid-rich diet were readily colonized by C. albicans and exhibited higher fungal load in feces compared to rodents fed an isocaloric control diet. Surprisingly, β-oxidation, a catabolic process to break down fatty acids for energy production, was dispensable for C. albicans to colonize the high-oleic acid diet-fed mice. We identified SOK1 as an oleic acid-induced kinase. RNA-Seq was employed to identify SOK1-dependent transcriptome changes. We found that SOK1 influences multiple cellular functions and components in C. albicans, including oxidoreductase activity, metabolism, and cell periphery.

overall_design: Comparison of the transcriptome of the two Candida albicans strains SC5314 (= WT) and JCP_1525 (Δsok1) in YNB with final concentration of 0.2% oleic acid (OE). The strains were grown anerobically at 30°C for 24 hours. RNA purification was performed from cells harvested from liquid cultures. Directional mRNA library preparation (with poly A enrichment) and sequencing using NovaSeq PE150 mode was executed at Novogene Corporation Inc.


title: Sex-specific role for 5-HT2A receptor in psychedelic-induced extinction of opioid rewarding properties

city: Blacksburg

first: Chang

last: Lu

state: VA

address: 235 Goodwin Hall, 635 Prices Fork Road, Virginia Tech

department: Chemical Engineering

institute: Virginia Tech

summary: Emerging evidence suggests that classical psychedelics may offer therapeutic potential for opioid use disorder (OUD) by alleviating key hallmarks such as altered reward processing and dependence. However, the mechanisms behind these effects remain unclear. Our data demonstrate that a single administration of the psychedelic psilocybin (PSI) reduces conditioned behavior and withdrawal induced by the opioid oxycodone (OXY) in male mice but not in females, and this effect is mediated via the 5-HT2A receptor (5-HT2AR). We show that the sex-specific attenuation of OXY preference is driven by 5-HT2AR activation in frontal cortex pyramidal neurons projecting to the nucleus accumbens (NAc). Additionally, PSI modulates epigenomic regulation following repeated OXY exposure and induces sex-specific NAc dendritic structural plasticity independently of 5-HT2AR. Notably, female frontal cortex and NAc show fewer changes at gene enhancer regions in response to PSI, repeated OXY, or combined PSI-OXY treatment compared to males, with the frontal cortex exhibiting more pronounced sex differences than the NAc at the epigenomic level. Together, these results provide novel insights into the neural and epigenetic mechanisms of psychedelic-induced plasticity in OUD, while also highlighting sex differences in PSI's modulation of reward pathways and its therapeutic potential.

overall_design: MOWChIP-seq (Zhu et al. Nature Protocols 14 (2019) 3366-3394) was performed on neuronal neclei extracted from mouse frontal cortex (FC) and nucleus accumbens (NAc) to investigate impact of psilocybin (PSI) treatment on epigenomic regulation following repeated oxycodone (OXY) administion in make and female mice. Mice received three separate administrations of OXY (3 mg/kg) or vehicle on consecutive days (days 1-3), with 24-hour intervals between doses, followed by a single dose of PSI (1 mg/kg) or vehicle (day 4), resulting in four distinct experimental groups: VEH-VEH, VEH-PSI, OXY-VEH, and OXY-PSI. On day 5, FC and NAc tissue samples were collected for H3K27ac profiling. Neuronal nuclei were extracted and isolated by FACS, followed by MOWChIP-seq on 10,000 nuclei per sample.

first: Thomas

last: Hadlock


title: Temporal control of human DNA replication licensing by CDK4/6-RB signalling and chemical genetics

city: Geneva

first: Vasilis

last: Dionellis

address: 30, quai Ernest-Ansermet

country: Switzerland

institute: University of Geneva

summary: Cyclin-dependent kinases (CDKs) coordinate DNA replication and cell division, and play key roles in tissue homeostasis, genome stability and cancer development. The first step in replication is origin licensing, when minichromosome maintenance (MCM) helicases are loaded onto DNA by CDC6, CDT1 and the origin recognition complex (ORC). In yeast, origin licensing starts when CDK activity plummets in G1 phase, reinforcing the view that CDKs inhibit licensing. Here we show that, in human cells, CDK4/6 activity promotes origin licensing. By combining rapid protein degradation and time-resolved EdU-sequencing, we find that CDK4/6 activity acts epistatically to CDC6 and CDT1 in G1 phase and counteracts RB pocket proteins to promote origin licensing. Therapeutic CDK4/6 inhibitors block MCM and ORC6 loading, which we exploit to trigger mitosis with unreplicated DNA in p53-deficient cells. The CDK4/6-RB axis thus links replication licensing to proliferation, which has implications for human cell fate control and cancer therapy design.

overall_design: EdUseq data of RPE CDC6d CDT1d clone #1 cells under control conditions or after treatment with ADN and/or Palbociclib

first: Anastasia

last: Sosenko Piscitello

first: Ann-Sofie

last: Nillsson

first: Michael

last: Hawgood

first: Abid

last: Sayyid

first: Sotirios

middle: G

last: Ntallis

first: Pratikiran

last: Bajgain

first: Jiri

last: Bartek

first: Thanos

last: Halazonetis

first: Bennie

last: Lemmens


title: Multi-omic analysis reveals retinoic acid molecular drivers for fibrosis and regenerative repair in skin fibrosis

city: Stanford

first: Jennifer

middle: Brigitta

last: Parker

address: 257 Campus Drive

department: Surgery

institute: Stanford University

summary: In the skin, tissue injury results in fibrosis in the form of scars composed of dense extracellular matrix deposited by fibroblasts. The therapeutic goal of regenerative wound healing has remained elusive, in part because principles of fibroblast programming and adaptive response to injury remain incompletely understood. Here, we present a multimodal -omics platform for the comprehensive study of cell populations in complex tissue, which has allowed us to characterize the cells involved in wound healing using a bleomycin induced ifibrosis model. We employ a bleomycin skin models that recapitulates human tissue repair kinetics. Through integrated analysis of single cell chromatin landscapes and gene expression states, coupled with spatial transcriptomic profiling, we are able to impute fibroblast epigenomes with temporospatial resolution. This has allowed us to reveal potential mechanisms controlling fibroblast fate during migration, proliferation, and differentiation following skin injury, and thereby reexamine the canonical phases of wound healing. These findings have broad implications for the study of tissue repair in complex organ systems.

overall_design: Mouse wound tissue transcriptomes were profiled using single cell RNA sequencing, single cell ATAC sequencing, and Visium spatial transcriptomics. For single-cell RNA sequencing, wound cells were harvested at 3 timepoints over the course of wound healing (POD 12, 21, 28) and normal skin as a control. For single-cell ATAC sequencing and visium similiar time points were harvested. For single cell RNA sequencing, cells treated with a cyp26b1 inhibitor were also assessed referred to as POD 12 + TREATMENT.

last: Januszyk

first: Michelle

last: Griffin


title: Human Dicer hotspot mutation induces both loss and gain of miRNA function [sRNA-seq]

city: New York

first: Seungjae

last: Lee

address: 430 East 67th St.

department: Department of Developmental Biology

institute: Sloan-Kettering Institute

summary: The core miRNA biogenesis enzyme Dicer sustains recurrent mutations in cancer, which specifically compromise catalysis by its RNase IIIb domain. These are proposed to act as selective hypomorphs, since Dicer-RNase IIIb cleaves the 5p arms of pre-miRNA hairpins. However, the lack of knockin models has hindered a full understanding of the consequences of Dicer hotspot mutations for miRNA biogenesis. Here, we generated Dicer-KO and Dicer-S1344L (homozygous and hemizygous) hESCs; the latter is a non-catalytic mutation in RNase IIIa that impairs RNase IIIb activity. Consistent with our previous work, Dicer-KO is cell lethal in hESCs. However, in contrast to the expectation that Dicer hotspot mutations confer cell advantages, Dicer-S1344L knockin hESCs were subviable and also required a conditional genetic strategy for isolation. Small RNA sequencing using spike-in normalization reveals two broad trends: ablation of miRNA-5p species, and selective changes in miRNA-3p species. Curiously, we recognized a directional upregulation of miRNA-3p passenger strands, indicating a broad strand switch. Activity assays and Argonaute profiling of the transcriptome confirm that these confer increased repression capacity. Finally, we used in vitro assays to show 3p arm-nicked pre-miRNAs preferentially load miRNA-3p species into Argonaute, compared to corresponding miRNA/passenger duplexes. Overall, Dicer hotspot mutations have unexpected neomorphic consequences on miRNAs, including both loss- and gain-of-function.

overall_design: To investigate the consequences of the Dicer cancer hotspot mutation, we generated CRISPR-Cas9 engineered Dicer-S1344L homozygous and hemizygous hESCs cells.

first: David

last: Jee

first: Dapeng

last: Yang

first: Robert

last: Rickert

first: Renfu

last: Shang

first: Danwei

last: Huangfu

first: Eric

last: Lai


title: In-utero rescue of neurological dysfunction in a mouse model of Wiedemann-Steiner syndrome [CUT&Run]

city: Reykjavik

first: Tinna

last: Reynisdottir

state: Ísland

address: Sturlugata 8

country: Iceland

institute: University Of Iceland

summary: Wiedemann-Steiner syndrome (WDSTS) is a rare genetically determined cause of intellectual disability primarily caused by heterozygous loss of function variants in the gene encoding the histone methyltransferase KMT2A. Prior studies have shown successful postnatal amelioration of disease phenotypes for several related Mendelian disorders of the epigenetic machinery, including Rett, Rubinstein-Taybi and Kabuki syndromes. To explore whether the neurological phenotype in WDSTS is treatable in-utero, we created a novel mouse model carrying a loss of function variant in between two LoxP sites. Kmt2a+/LSL mice demonstrate core features of WDSTS including growth retardation, craniofacial abnormalities, and hypertrichosis as well as hippocampal memory defects. This mouse model offers a strategy to systematically explore the therapeutic window in WDSTS. The neurological phenotypes show rescue upon breeding to a nestin-Cre, which restores KMT2A levels in-utero. Together, our data provide a novel mouse model to explore the therapeutic window in WDSTS. Our work suggests that WDSTS has a window of opportunity extending at least until the mid-point of in-utero development, making WDSTS an ideal candidate for future therapeutic strategies.

overall_design: To explore the effects of Kmt2a loss and its in-utero malleability on a chromatin level, we performed a CUT&RUN of the H3K4me1 mark in mNPCs.

first: Kimberley

last: Anderson

first: Andrew

last: Brinn

first: Katie

last: Franklin

first: Juan

last: Ouyang

first: Cat

last: Lutz

first: Asbjorg

middle: O

last: Snorradottir

first: Valerie

middle: B

last: DeLeon

first: Aamir

last: Zuberi

first: Hans

middle: T

last: Bjornsson


title: Human Dicer hotspot mutation induces both loss and gain of miRNA function [iCLIP]

first: Seungjae

last: Lee


title: In-utero rescue of neurological dysfunction in a mouse model of Wiedemann-Steiner syndrome

overall_design: To evaluate rescue of transcriptional abnormalities caused by heterozygous Kmt2a-deficiency and in-utero rescue of the effect in a homogenous cell population, we dissected the hippocampus from newborn pups (P0) and cultured mouse neuronal progenitor cells (mNPCs). We performed RNA-sequencing  to identify gene expression changes between Kmt2a+/+ and Kmt2a+/LSL NPCs and the reversal in Nes-Cre+/-Kmt2a+/LSL.


title: Gene Expression of mobPBSC After FVA3-Ang1 Priming

status: Public on Aug 12 2025

city: seoul

first: hyunju

last: seo

address: CMI, 71 Daehak-ro, Jongno-gu, Seoul, Republic of Korea

institute: seoul national niversity

summary: The FVA3-Ang1 priming strategy was evaluated with a dual focus—safety assessment via modifications in cell characteristics and enhancement of therapeutic efficacy through augmented angiogenic potential. Gene expression patterns were analyzed by total RNA sequencing of mobPBSCs collected from patients diagnosed with acute myocardial infarction.

overall_design: RNA sequencing profiling was performed on G-CSF–mobilized PBSCs from myocardial infarction patients, comparing cells treated with FVA3-Ang1 for 1 hour and 24 hours to untreated controls. Three controls and reference samples.


title: Regulation of the oxidative stress response by the E3 ligase TRIP12

city: Berkeley

last: Ingersoll

address: 1951 Oxford St

department: MCB

institute: University of California, Berkeley

summary: Centered on the transcription factor NRF2, the oxidative stress response counteracts reactive oxygen species (ROS) to ensure cell and tissue homeostasis. While unstressed cells constantly degrade NRF2, ROS inhibit the respective E3 ligase, CUL3KEAP1, to stabilize NRF2 and elicit antioxidant gene expression. Following ROS clearance, cells must rapidly reinstate NRF2 degradation, but mechanisms underlying this dynamic regulation are poorly understood. Here, we identify TRIP12, an essential E3 ligase dysregulated in Clark-Baraitser Syndrome and Parkinson’s Disease, as a component of the oxidative stress response. TRIP12 is a ubiquitin chain elongation factor that acts after CUL3KEAP1 to extend K29-linked conjugates for efficient NRF2 degradation. TRIP12 accelerates stress response silencing as CUL3KEAP1 is being restored, but limits NRF2 activation during stress. The need for dynamic NRF2 regulation therefore comes at the cost of less responsive stress signaling, suggesting that TRIP12 inhibition could be exploited to bolster the oxidative stress response in neurodegenerative diseases.

overall_design: To investigate the role of KEAP1 and CCNF on C2C12 myoblast function, cells were siRNA depleted of KEAP1, CCNF, or both to determine which genes were differentially expressed.

first: Devlon

last: McCloud

first: Jenny

middle: Y

last: Hu

first: Michael

last: Rape


title: Epigenetic gene regulation during astrocyte development

first: Inkyung

last: Jung

address: KAIST, 291 Daehak-ro, Yuseong-gu

department: Biological Sciences

institute: KAIST

summary: Numerous literatures report similar time points are important in astrocyte development and transition from neurogenesis to gliogenesis. However, these developmental time points have not been studied in the perspective of chromatin state and the resulting transcriptional changes. In addition, the characteristics of astrocyte in different developmental time point is still unclear. Therefore, we examined the transcriptome and open chromatin regions of astrocytes during its development.

overall_design: Examination of transcriptme and open chromatin regions during astrocyte development. This project contains mouse RNA-seq and ATAC-seq data during astrocyte development.

first: Seongwan

last: Park

first: Junghyun

last: Eom


title: Sex dimorphic impact of maternal Zika infection on offspring neutrophil functions

city: Detroit

first: Gil

middle: G.

last: Mor

state: Michigan

address: 275 E. Hancock

department: C.S. Mott Center for Human Growth and Development

institute: Wayne State University School of Medicine

summary: To investigate the impact of Zika infection during pregnancy on the placenta and offspring immune response

overall_design: Pregnant C57/BL6 mice were exposed to 50PFU Zika virus on E8.5. Placentas were collected on E12.5. And in another cohort, pups were delivered and sacrificed on PND35, bone marrow neutrophils of offspring from Zika-exposed dams were isolated and sent for RNAseq.

first: Jiahui

last: Ding

first: Anthony

last: Maxwell

first: Aditi

last: Singh

first: Grace

last: Loedeman

first: Nicholas

last: Adzibolosu


title: Multi-omic analysis reveals retinoic acid molecular drivers for fibrosis and regenerative repair in skin fibrosis [Spatial transcriptomics]

first: Jennifer

last: Parker

overall_design: Mouse wound tissue transcriptomes were profiles using single cell RNA sequencing, single cell ATAC sequencing, and Visium spatial transcriptomics. For single-cell RNA sequencing, wound cells were harvested at 3 timepoints over the course of wound healing (POD 12, 21, 28) and normal skin as a control. For single-cell ATAC sequencing and visium similiar time points were harvested. For single cell RNA sequencing, cells treated with a cyp26b1 inhibitor were also assessed referred to as POD 12 + TREATMENT.

last: Januszyk

first: Michelle

last: Griffin


title: Multi-omic analysis reveals retinoic acid molecular drivers for fibrosis and regenerative repair in skin fibrosis [scATAC-seq]


title: PDZK1 Protects Against RPE Senescence by Targeting the 14-3-3ε-mTOR Axis to Attenuate Early Diabetic Retinopathy

first: Junbiao

last: Zhang

state: Guangdong

address: No. 183, Zhongshan Avenue West

department: Ophthalmology

institute: The Third Affiliated Hospital of Southern Medical University

summary: In diabetic retinopathy (DR), hyperglycemia induces retinal pigment epithelium (RPE) cell senescence via downregulation of PDZK1. PDZK1 overexpression counteracts senescence by binding 14-3-3ε to modulate mTOR signaling, reducing oxidative stress and enhancing autophagy. Both genetic PDZK1 restoration and pharmacologic senolysis (Nutlin-3a) attenuate retinal senescence and ameliorate early DR pathology, establishing the PDZK1-14-3-3ε-mTOR axis as a therapeutic target

overall_design: Cells are maintained in DMEM with 10 % fetal bovine serum and 1 % penicillin–streptomycin at 37 °C in a humidified 5 % CO₂ incubator. At approximately 50 % confluence, cultures are transduced with PDZK1-overexpressing or control lentivirus (Tsingke) at MOI 10. After 48 h of transduction, 4 μg/ml puromycin is added for stable selection. Control and PDZK1-overexpressing cells are then exposed to 37.5 mM d-glucose for 48 h, after which total RNA is extracted for downstream analysis.

first: Jian

last: Zhao

first: Yanli

last: Liu

first: Lili

last: Wang

first: Chunxi

last: Huang

first: Wei

last: Chi

first: Meixia

last: An


title: Zingerone treats postmenopausal osteoporosis via increased ferroptosis sensitivity by p53-mediated regulation of Sat1 and Gpx4 expression

status: Public on Aug 11 2025

city: Shenyang

first: Fangming

last: Cao

state: Liaoning

address: 155 Nanjing Street

institute: First Hospital of China Medical University/Department of Orthopedics

summary: Zingerone, a component of dried ginger, has known anti-ulcer and bone growth-promoting effects, but its impact on postmenopausal osteoporosis (PO) is unclear. This study investigates the therapeutic potential and underlying mechanisms of zingerone in PO. A concentration-dependent effect identified on osteoclast precursors: at low concentrations, zingerone maintains low ROS levels, enhance proliferation, and facilitates bone remodelling; at high concentrations, it elevates ROS levels, enhances ferroptosis sensitivity, and suppresses osteoclast formation. Zingerone significantly improves bone mass in an ovariectomised mouse model of PO. Metabolomics identifies 869 differential metabolites linked to glutathione and purine metabolism. Transcriptomics highlights pathways including ferroptosis, leukocyte migration, and cell adhesion. In RAW264.7 cells, zingerone modulates p53, enhances ferroptosis sensitivity, increasing ROS and Fe2+, upregulates Sat1, and downregulates Gpx4, suggesting that zingerone may act via p53-mediated ferroptosis, indicating potential clinical utility. Before clinical application, the dose-dependent effects of zingerone on bone remodelling and its underlying mechanisms warrant further investigation.

overall_design: Novogene Co., Ltd. in Beijing, China conducted RNA sequencing analysis on three replicates of mouse femoral tissue. Differential expression analysis was carried out using the DESeq2 R package for two groups, each with three biological replicates. Differential gene analysis was done using the Limma package in R, with a cut-off threshold of abs(log2) > 0.2. Genes with a p value < 0.05 were deemed significantly differentially expressed. Significantly enriched genes among the DEGs were identified based on corrected p values below 0.05. Statistical enrichment of annotated genes was performed using the KEGG pathway database and the clusterProfiler R package. Additionally, Gene Set Enrichment Analysis (GSEA) was conducted utilizing the clusterProfiler R package. Multiplicative changes in gene expression were calculated for group comparisons, leading to the generation of gene lists based on |log2FC| changes. Pearson correlation analysis was undertaken to assess the correlation between genes and metabolites, with statistical significance set at a p value of less than 0.05.

first: Hao

last: Li

first: Dian

first: Lin

last: Tao


title: Pancreatic cells are resistant to KRASQ61L expression due to hyperactivation of ERK/MAPK signaling and induction of apoptosis

city: Charleston

first: Guy

middle: Aaron

last: Hobbs

state: SC

address: 86 Johnathan Lucas, HCC 702

institute: Medical University of South Carolina

summary: The RAS family of small GTPases is among the most frequently mutated gene families in human cancer. In pancreatic ductal adenocarcinoma (PDAC), ~95% of cases harbor an activating KRAS mutation, primarily at codon 12, 13, or 61, with G12D the most common overall (40%). In contrast, the KRASQ61L mutation, though constitutively active, is virtually absent in PDAC patient tumors. This suggests that KRASQ61L may engage in distinct, allele-specific signaling that limits its ability to drive tumorigenesis. Determining the mechanisms that limit the occurrence of this mutation will aid in our understanding of the critical KRAS effectors and pathways that drive tumorigenesis. To investigate these mechanisms, we utilized a tightly controlled doxycycline-inducible KRAS expression system in an isogenic, immortalized pancreatic cell line, enabling direct comparison of KRASQ61L to the common PDAC mutant KRASG12D. Using TurboID proximity labeling alongside RNA sequencing, we mapped early effector interactions and transcriptional responses, revealing that KRASQ61L induces greater hyperactivation of the ERK/MAPK pathway, resulting in increased nuclear translocation of ERK1/2. Finally, pancreatic cells are highly tolerant to overexpression of KRASG12D, but KRASQ61L overexpression leads to impaired proliferation and increased apoptosis. These findings provide experimental support for the long-standing "Goldilocks" model of oncogenic signaling, where too much ERK/MAPK pathway activation is detrimental to tumorigenesis. Our work offers a mechanistic explanation for the relative absence of KRASQ61L in PDAC and contributes to our understanding of KRAS allele-specific vulnerabilities, which can inform future therapeutic strategies targeting KRAS-driven pancreatic cancer.

overall_design: This RNA sequencing experiment was performed to investigate how different KRAS mutations impact transcriptional programs in a human pancreatic ductal epithelial context. We used HPNE (human pancreatic nestin-expressing) cells engineered to express doxycycline-inducible versions of wild-type KRAS (KRASWT), or one of three oncogenic KRAS mutants: KRASG12D, KRASG12R, or KRASQ61L.  Each isogenic cell line (HPNE-KRASWT, HPNE-KRASG12D, HPNE-KRASG12R, HPNE-KRASQ61L) was treated with doxycycline for 48 hours to induce transgene expression.

middle: A

first: Rachel

last: Burge

first: Silvia

last: Vaena


title: RNA-seq of Melanoma cell lines M257, M238, 451Lu, 451LuR treated with PUFA/Fe3+ compared to untreated controls

city: Leuven

first: Sahar

last: Motamedi

address: Herestraat 49, Nieuwstraat

department: Oncology

country: Belgium

institute: KU Leuven

summary: here we assess the effect of PUFA/Fe3+ on gene expression in human melanoma cell lines in 2 time points (18 and 36 H).

overall_design: We performed RNAseq on 4 melanoma cell lines treated with PUFA/Fe3+ or control.


title: Human Dicer hotspot mutation induces both loss and gain of miRNA function [RNA-seq]

first: Seungjae

last: Lee

state: NY

first: David

last: Jee

first: Dapeng

last: Yang

first: Robert

last: Rickert

first: Renfu

last: Shang

first: Danwei

last: Huangfu

first: Eric

last: Lai


title: Metastasis-initiating osteosarcoma subpopulations establish paracrine interactions with both lung and tumor cells to create a metastatic niche

city: Columbus

first: Matt

last: Cannon

state: OH

address: 700 Children's Dr.

department: Center for Childhood Cancer

institute: Nationwide Children's Hospital

summary: Osteosarcoma is an aggressive and deadly bone tumor, primarily afflicting children, adolescents, and young adults. Poor outcomes for osteosarcoma patients are intricately linked with the development of lung metastasis. While lung metastasis is responsible for nearly all deaths caused by osteosarcoma, identification of biologically defined, metastasis-targeting therapies remains elusive because the underlying cellular and molecular mechanisms that govern metastatic colonization of circulating tumor cells to the lung remains poorly understood. While thousands of tumor cells are released into circulation each day, very few can colonize the lung. Herein, using a combination of a novel organotypic metastasis in vitro model, single-cell RNA sequencing, human xenograft, and murine immunocompetent osteosarcoma models, we find that metastasis is initiated by a subpopulation of hypo-proliferative cells with the unique capacity to sustain production of metastasis promoting cytokines such as IL6 and CXCL8 in response to lung-epithelial derived IL1α. Critically, genomic and pharmacologic disruption of IL1 signaling in osteosarcoma cells significantly reduces metastatic progression. Collectively, our study supports that tumor-stromal interactions are important for metastasis, and suggests that metastatic competency is driven, in part, by the tumor cell’s ability to respond to the metastatic niche. Our findings support that disruption of tumor-stromal signaling is a promising therapeutic approach to disrupt metastasis progression.

overall_design: Single cell RNAseq was performed on osteosarcoma patient derived xenografts (PDX) and cell culture models. The pdx models are OS-17 lines and either represent primary tibial tumors or lung metastses.

first: James

last: Reinecke

first: Amanda

last: Saraf

first: John

last: Hinckley

first: Amy

last: Gross

first: Helene

last: Le Pommellette

first: Leyre

last: Jimenez Garcia

first: Maren

last: Cam

first: Matthew

first: Sophia

last: Vatelle

first: Berkley

last: Gryder

first: Ruben

last: Dries

first: Ryan

last: Roberts


title: Improving bulk RNA-seq protocols

city: Martinsried

first: Wolfgang

last: Enard

state: Bavaria

address: Grossshaderner Str.2, Anthropology Human Genomics, AG Enard

department: Anthropology and human genomics

country: Germany

institute: LMU Munich

summary: Bulk and single-cell RNA-seq are powerful tools for transcriptomic analysis, providing insights into many aspects of molecular and cellular phenotypes. Costs constrain the amount of biological insight obtainable within a given budget, and as sequencing prices decline, efficient library protocols have become a decisive factor. In this study, we introduce an approach to systematically optimize the number of usable reads that RNA-seq protocols generate. We applied this ”funnel strategy” to prime-seq, an early-barcoding bulk RNA-seq protocol, by systematically testing critical protocol steps totaling 1080 samples in 49 libraries. This resulted in the optimized prime-seq2 protocol that increases the number of usable reads by 60 % and improves one of the most cost-efficient bulk RNA-seq protocols available. Our study also suggests that monitoring the filtering of usable reads can serve as a valuable quality control for many RNA-seq protocols and sheds light on the complexity of the conditions and interactions that shape RNA-seq library composition and their interpretation.

overall_design: During different experiments various bulk-RNAseq protocol steps were altered and explored for their performance on a read count level.

first: Felix

last: Pförtner

first: Eva

last: Briem

first: Daniel

last: Richter


title: Dual regulatory role of invariant natural killer T cells in the development and progression of hepatocellular carcinoma

city: Vari

first: Mihalis

last: Verykokakis

address: Fleming 34

country: Greece

institute: BSRC Alexander Fleming

summary: Our project aims to examine the role of Invariant Natural Killer T cells (iNKT) in Hepatocellular Carcinoma (HCC) which is not known. HCC is a leading cause of death and accounts for ~80% of cases of liver cancer worldwide. Because there are no biomarkers that allow the early diagnosis, HCC is diagnosed at late stages when the tumor is developed enough and is resistant to chemotherapy. The liver is characterized by an immunosuppressive environment and due to this environment, liver is prone to HCC development. Once HCC is developed, the function of immune cells that fight the tumor such as dendritic cells, natural killer cells, helper and cytotoxic T cells is suppressed while the function of regulatory T cells and myeloid- derived suppressor cells is enhanced. However, the role of Natural Killer T cells (NKT) is not known. NKT cells is a population of the immune system which is largely enriched in the liver, which recognize lipid antigens by CD1d molecule and can rapidly produce large amounts of various cytokines to enhance the function of other immune populations. Here, we investgated the  role of NKT cell in chemical-induced HCC that recapitulates the development of human HCC usiing genetic models that lack or overproduce NKT cells.

overall_design: Hepatic Invariant Natural Killer T  (iNKT) cells, identifed as CD1D-PBS57-tetramer+Tcrb+ cells,  were isolated through FACS sorting from two healthy WT mice (controls) and three WT mice with DEN-induced hepatocellular carcinoma

first: Maria

last: Papanastasatou


title: Depot-dependent effects of subclinical ketosis on visceral and subcutaneous adipose tissue transcriptional cellular diversity in dairy cows

status: Public on Aug 10 2025

city: Lubbock

first: Clarissa

last: Strieder-Barboza

state: Texas

address: ESB II, 1006 Canton Ave.

department: Veterinary Sciences

institute: Texas Tech University

summary: Adipose tissue plays a central role in regulating whole-body metabolic health, facilitated by the variety of cell types and their wide-ranging functions. In addition, depot-specific differences in adipose tissue have been shown to play important roles in different disease states including obesity, diabetes, and metabolic dysfunction in human and animal models. For early postpartum dairy cattle, metabolic dysfunction, triggered by a negative energy balance, is often manifested as subclinical ketosis (SCK). However, the role that subcutaneous (SAT) and visceral (VAT) adipose tissue depots, and their diverse cellular compositions, play in the response to subclinical ketosis conditions is unclear. Flank SAT and omental VAT were collected via laparotomy from five non-ketotic (NK; BHB ≤ 0.8 mmol/L) and five subclinical ketosis (SCK; 1.4 mmol/L < BHB ≤ 2.6 mmol/L) multiparous cows during early lactation. Following collection, nuclei were isolated from the tissue and subjected to single-nuclei RNA sequencing in order to investigate the transcriptional cellular heterogeneity. Distinct clusters of adipocytes (AD), adipose stem/progenitor cells (ASPC), immune cells (IMC), endothelial cells (EC), and pericyte/smooth muscle cells (PE/SMC) were identified in both adipose depots, with a greater abundance of ASPC in SAT compared to VAT. In addition, we identified a VAT-specific AD subtype characterized by higher expression of progenitor-like marker genes. While the abundance of none of the identified cell subtypes were different between SCK and NK, underlying transcriptional changes provided insight into potential effects of SCK. In general, SCK was associated with pro-lipogenic, anti-inflammatory, and pro-angiogenic transcriptional changes, possibly indicating a greater capacity for homeostatic responsiveness in SAT under conditions of enhanced negative energy balance. In contrast, SCK appeared to promote transcriptional changes indicative of impaired adipogenesis, impaired angiogenesis, and increased inflammation in VAT. Uniquely, our study presents novel insight into the cellular heterogeneity of adipose tissue in dairy cattle with subclinical ketosis. Furthering our understanding of the role of adipose tissue in response to this form of metabolic challenge has the potential to enhance efforts aimed at limiting the incidence and impact of subclinical ketosis and improving the health and productivity of dairy cattle.

overall_design: Five non-ketotic cows (NK; n = 5; BHB ≤ 0.8 mmol/L; 3.2 ± 1.6 lactations; 7.4 ± 1.8 DIM; 3.7 ± 0.2 BCS) and five cows with subclinical ketosis (SCK; n = 5; BHB > 1.4 and ≤ 2.6 mmol/L; 3.2 ± 1.2 lactations; 7.8 ± 2.0 DIM; 3.6 ± 0.4 BCS) were selected for adipose tissue sampling. Adipose tissue samples of flank subcutaneous adipose tissue (SAT) and omental visceral adipose tissue (VAT) were collected via laparotomy from each cow, and ~1g of tissue was immediately flash frozen and kept in liquid nitrogen until nuclei isolation.

first: Hunter

middle: R

last: Ford


title: Single nuclei RNA-seq of Ossabaw pig atherosclerotic and healthy aortae

city: Leipzig

first: Olga

last: Bondareva

state: Saxony

address: Philipp-Rosenthal-Straße 27

department: HI-MAG

institute: Helmholtz Zentrum München

summary: Atherosclerosis is a major contributor to cardiovascular diseases. Well-established preclinical models that can accurately recapitulate human atherosclerosis development and progression are necessary for developing new therapeutics. Pig models are extensively used in cardiovascular research due to their physiological similarities to humans. However, their translational efficacy into clinical settings has remained limited. To ensure better translational outcomes, a deeper molecular characterization of atherosclerotic disease mechanisms in swine models is urgently required. Methods: To address this gap, we employed single nuclei transcriptomics to characterize healthy and atherosclerotic aortas in the Ossabaw pig model. We analyzed over 36,000 nuclei from aortas of 5 adult male castrated pigs kept on atherogenic and chow diets. In-depth single-nuclei transcriptomic and cell-cell communication analyses were undertaken to uncover molecular changes in swine atherosclerosis development. Comparisons to human and mouse atherosclerosis were used to establish the veracity of the Ossabaw pig in modeling human disease.

overall_design: Castrate male Ossabaw pigs of 12-month age were put on HF/HFru or chow diet for 9 months. Abdominal aortae were dissected and snap-frozen. Frozen tissues were processed for nuclei isolation followed by snRNA-seq protocol. Single nuclei RNA-seq was performed using 10x Next GEM Single Cell 3 GEM kit v3.1 according to the manufacturers protocol. Separate 10x genomics reactions were used for each sample. Generated libraries were sequenced on an Illumina NovaSeq with >27.5 x 10^3 reads per cell followed by de-multiplexing and mapping to the domesticated pig genome (build Sscrofa11) using CellRanger v5.0. Further analyses were performed using Seurat package v.5.0.


title: PDZK1 Protects Against RPE Senescence by Targeting the 14-3-3ε-mTOR Axis to Attenuate Early Diabetic Retinopathy [MG_HG]

city: Guangzhou

first: Junbiao

last: Zhang

overall_design: Cells were cultured for 48 hours in either control medium containing 5.5 mM D-glucose and 32 mM mannitol, or in high-glucose (HG) medium containing 37.5 mM D-glucose, followed by RNA extraction for sequencing.

first: Jian

last: Zhao

first: Yanli

last: Liu

first: Lili

last: Wang

first: Chunxi

last: Huang

first: Wei

last: Chi

first: Meixia

last: An


title: Epigenetic reprogramming involved in bronchial epithelial cells memory induced by flagellin stimulation

city: Paris

first: Rachel

last: Legendre

address: 28, rue du docteur Roux

department: Research and Resource Center for Scientific Informatics

country: France

institute: Institut Pasteur

summary: Innate immune memory is a new concept describing ability of innate myeloid and lymphoid cells to gain memory characteristics after transient stimulation, resulting in an nonspecific modified response upon secondary challenge. In recent work, we demonstrated that bronchial epithelial cells that are non immune cells, the first immune cells of the lower respiratory tract to encounter pathogens were capable of innate immune memory after pre-exposure to Pseudomonas aeruginosa flagellin. In the present study  we identified chromatin modifications induced by flagellin pre-exposure that sustain reprogramming of transcriptional patterns. We researched chromatin structure modifications responsible for the modulation of gene expression and thus of innate memory induced by the exposure of cells to flagellin.

overall_design: Refer to individual Series

first: Jeanne

last: Bigot

first: Juliette

last: Hamroune

first: Sébastien

last: Jacques

first: Mathieu

last: Legars

first: Loïc

last: Guillot

first: Harriet

last: Corvol

first: Christophe

last: Hennequin

last: Guitard

first: Jean-Yves

last: Coppee

first: Viviane

last: Balloy

first: Claudia

last: Chica


title: Bronchial epithelial cells accessibility upon flagellin stimulation (ATAC-Seq)

summary: Innate immune memory is a new concept describing ability of innate myeloid and lymphoid cells to gain memory characteristics after transient stimulation, resulting in an nonspecific modified response upon secondary challenge. In recent work, we demonstrated that bronchial epithelial cells, non immune cells,  that are the first immune cells of the lower respiratory tract to encounter pathogens were capable of innate immune memory after pre-exposure to Pseudomonas aeruginosa flagellin. In the present study  we identified chromatin modifications induced by flagellin pre-exposure that sustain reprogramming of transcriptional patterns. We researched chromatin structure modifications responsible for the modulation of gene expression and thus of innate memory induced by the exposure of cells to flagellin.

overall_design: 15 samples, 5 conditions in triplicate