title: Fatty Acid Oxidation Fuels Mitochondrial Respiration to Drive Epidermal Stem Cell Fate and Barrier Regeneration

first: Anna

last: Mandinova

address: Charlestown Navy Yard Building 149, 149 13th Street

summary: The skin’s barrier function relies on the epidermis, whose structural integrity is maintained by basal stem cells that continuously renew and differentiate to form the multilayered epidermal architecture. Disruptions in epidermal differentiation underlie numerous hyperproliferative and inflammatory skin disorders. While transcriptional and epigenetic mechanisms are known to regulate the late stages of this process, the molecular events driving the early commitment to differentiation remain elusive. Here, we reveal that early mitochondrial reprogramming, characterized by the activation of oxidative phosphorylation (OXPHOS), is a critical determinant of differentiation initiation. Our findings identify fatty acid oxidation (FAO) as the primary metabolic pathway fueling OXPHOS during this process. Pharmacological and genetic inhibition of FAO, both in vitro and in vivo, disrupts differentiation and compromises the regeneration of the epidermal barrier, causing defective responses to physical insults. Mechanistically, FAO enables ATP production in committed epidermal cells to support the high energy demand of the differentiation process, establishing a direct link between lipid metabolism and epidermal homeostasis. These results uncover a previously unrecognized role for metabolic reprogramming in epidermal stem cell fate and highlight FAO as a novel target for therapeutic interventions to restore barrier function in pathological conditions.

overall_design: RNA-seq profiling from 6 human primary keratinocyte cell lines (3 from male and 3 from female donors) treated with or without Ca2+ to promote the differentiation at several time points (0, 2, 6 and 24h)

first: Kristina

last: Todorova

first: Stefano

last: Sol


title: The Polycomb Protein EED Constrains the SCLC Neuroendocrine Phenotype and Drives Lung Cancer Histological Transformation [snRNA-seq]

status: Public on Aug 05 2026

city: Boston

first: Yixiang

last: Li

address: 450 Brookline Ave

country: USA

institute: Dana-Farber Cancer Institute

type: Expression profiling by high throughput sequencing

summary: Lung cancer is comprised of distinct histological subtypes including lung adenocarcinoma (LUAD) and small cell lung cancer (SCLC). Although histological subtypes of lung cancer are often mutually exclusive, patients can present with combined LUAD and SCLC histology tumors. Moreover, LUADs can histologically transform to SCLC through lineage plasticity as a mechanism of resistance to targeted therapies, which most often occurs in EGFR-Mutant LUAD with concurrent RB1 and TP53 inactivation after treatment with EGFR inhibitors. The mechanisms that promote LUAD to SCLC histological transformation are poorly understood. Expression of genes associated with PRC2 activity increase during LUAD to SCLC histological transformation, but it is unknown whether PRC2 is a causative driver of histological transformation in lung cancer. To study the role of the PRC2 complex in SCLC tumorigenesis, we used CRISPR-based somatic gene editing to make SCLC genetically-engineered mouse models (GEMMs) deficient for PRC2 through inactivation of EED; PRC2’s core scaffolding subunit. Strikingly, EED inactivation caused complete histological transformation from ASCL1-positive SCLC to LUAD through an intermediate NEUROD1-positive/NCAM-positive cell state. Mechanistically, SCLC to LUAD histological transformation is initiated when PRC2 inactivation de-represses bivalent genes marked by both H3K27me3 and K3K4me3 including RAS, PI3K, and MAPK pathway genes as well as NEUROD1. Lastly, we developed an EGFR-Mutant LUAD GEMM with concurrent RB1 and TP53 inactivation where EGFR inhibition can promote SCLC transformation and a metastatic phenotype; both of which are completely abrogated by EED inactivation. Together, these findings show that the PRC2 complex is required to drive ASCL1-positive neuroendocrine SCLC with its loss promoting the LUAD phenotype nominating PRC2 inhibition as a therapeutic strategy to block SCLC transformation.

overall_design: single nuclei RNA-seq profiling of three EED-Mutant RPR2 GEMM tumors.

first: Matthew

last: Oser


title: The Polycomb Protein EED Constrains the SCLC Neuroendocrine Phenotype and Drives Lung Cancer Histological Transformation [scRNA-seq]

overall_design: single cell RNA-seq profiling of EED-Mutant RPR2 GEMM tumors.


title: Genome wide DNA methylation of naive CD4+ T cells from various ages

city: Bunkyo-ku

first: Hiroshi

last: Mutoh

state: Tokyo

address: 7-3-1 Hongo

country: Japan

institute: The University of Tokyo

type: Methylation profiling by genome tiling array

summary: Genome wide DNA methylation profiling of naive CD4+ T cells obtained from cord blood or peripheral blood of healthy individuals.  The Illumina EPIC methylation beadchip array was used to obtain DNA methylation profiles across approximately 850,000 CpG dinucleotide methylation loci in DNA isolated from naive CD4+ T cells. Samples include 32 individuals.

overall_design: Blood samples were collected from 32 healthy individuals aged from neonates to elderly. Age groups were preterm neonates (< 36 gestational ages), term neonates (>37 gestational ages), infants (2-23 months old), children (2-17 years old), younger adults (18-49 years old) and older adults (>50 years old). Mononuclear cells were isolated blood samples by density gradient centrifugation and cryopreserved. Naive CD4+ T cells were sorted by FACS as CD45+ CD3+ CD4+ CD25- CD45RA+ CCR7+ from thawed mononuclear cells. GenomicDNA were extracted from naive CD4+ T cells using Allprep DNA/RNA Micro Kit (Qiagen). DNA methylation was assessed using the Illumina HumanMethylation EPIC array.

first: Tomoko

last: Kawai

first: Hiromi

last: Kamura

first: Kazuhiko

last: Nakabayashi

first: Kohei

last: Kashima


title: Electric Field-Induced Release and Measurement Liquid Biopsy of Urinary Transcriptomics and Key Proteins from Normal and High-risk Pregnant Women

city: los angeles

first: Shubhamoy

last: Ghosh

state: CA

address: 650 Charles E Young  Dr East

department: Pediatrics

institute: University of California Los Angeles

summary: This study aimed to analyze the cell-free transcriptome from the urine of pregnant women diagnosed with various pregnancy-related complications, including gestational diabetes mellitus, preeclampsia, gestational hypertension, and intrauterine growth restriction. The findings were further validated using a liquid biopsy technique to establish non-invasive markers for the quick and early detection of these complications.

overall_design: Cell free mRNA profiling was conducted using the RNA extracted from the urine samples of pregnant women at different trimester.

first: Shanthie

last: Thamotharan

first: Giorgia

last: del Vecchio

first: Carla

last: Janzen

first: Fang

last: Wei

first: Sherin

last: Devaskar


title: Deletion of a Distal IRF4 Element Prevents Inflammation-induced Reprogramming of Human Regulatory T-cell Fate

city: San Francsico

first: Qizhi

last: Tang

address: 513 Parnassus Ave

department: Diabetes Center

institute: University of California, San Francsico

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Adoptive regulatory T cell (Treg) therapy is an emergent treatment paradigm in which ex vivo-expanded Tregs are administered to promote immune tolerance in transplant and autoimmune disease patients. While preclinical models have demonstrated remarkable efficacy, lineage-tracing studies have also revealed that chronic inflammatory exposures can cause a subset of murine Tregs to undergo Foxp3 downregulation and epigenetic reprogramming toward a dysfunctional, proinflammatory state. Despite the potential ramifications for clinical translation, whether human Tregs exhibit a similar susceptibility to inflammatory cytokine-mediated lineage decommitment remains inconclusive. Here, we present an in vitro model of human Treg destabilization characterized by FOXP3 downregulation, Treg-specific demethylated region (TSDR) re-methylation, loss of suppressive activity, and gain of proinflammatory functions. Analysis of single-cell ATAC and transcriptomic profiles from destabilized Tregs revealed a switch in chromatin accessibility between two elements at the IRF4 locus. Excision of the distal IRF4 element enabled Tregs to resist inflammatory cytokine-induced reprogramming, presenting a potential strategy to design more effective Treg therapies.

overall_design: Primary human CD4+CD25+CD127lo/- regulatory T cells (Tregs) were cultured in vitro in the presence or absence of IL-6, IL-1beta, and IL-23 for 16 and 25 days. Cells were stimulated with CD3/CD28 Dynabeads at 1:1 cell:bead ratio on Days 0, 9, and 16 for each media condition.

first: Patrick

last: Ho

first: Wendy

last: Rosenthal

first: Jeffrey

middle: A

last: Bluestone


title: Accurate prediction of central conventional CHondrosarcoma Risk and Outcome using MEthylation profiling: CHROME

city: Leiden

first: Sara

last: Cardoso

address: Albinusdreef 2

department: Pathology

country: Netherlands

institute: Leiden University Medical Center

summary: Chondrosarcomas are malignant cartilage-forming bone tumours with heterogeneous behaviour, making prognostication and clinical management challenging. Histological grading is the primary tool for predicting clinical outcomes in conventional chondrosarcoma. However, its high interobserver variability limits reliable distinction between low- and high-risk patients, potentially leading to suboptimal clinical management. Given the increasing use of DNA methylation profiling as a valuable tool in surgical pathology for tumour classification, we investigated its prognostic value in central conventional chondrosarcoma. We generated methylation data from 69 primary central conventional chondrosarcomas  profiled with Illumina’s Human MethylationEPIC Array (850k sites), and identified methylation sites individually linked to patient outcome. A LASSO Cox regression model was applied to these methylation sites to identify an optimal set of 8 informative sites. With the regression coefficients of these methylation sites, we constructed a risk score that predicts central conventional CHondrosarcoma Risk Outcome from Methylation (CHROME). CHROME stratifies patients into High or Low risk groups for disease recurrence, onset of metastasis and disease-specific mortality. Survival analysis in an independent validation cohort (n=68) demonstrated strong discriminatory performance of CHROME, with complete separation of outcomes and no adverse events observed in the Low risk group. Overview of the clinico-pathological information showed that a low grade (ACT/G1) case with an event was correctly assigned to the High risk group, while 9 high grade cases without events were classified as Low risk. CHROME provides accurate risk stratification in central conventional chondrosarcoma and may represent a valuable tool for improving its prognostication and clinical management.

overall_design: We determined the DNA methylation profiles of 69 primary central conventional chondrosarcomas using Illumina’s Human MethylationEPIC Array (850k) platform.

first: Daniel

last: Baumhoer

first: Noel

middle: F

last: Miranda

first: Judith

middle: V

last: Bovée


title: Gene expression changes in commensal 3D full thickness skin models induced by different skin bacterial mixtures.

city: Berlin

first: Heike

last: Sprenger

address: Max-Dohrn-Strasse 8-10

department: Food Safety

country: Germany

institute: German Federal Institute for Risk Assessment

summary:
Our data indicates that a higher bacterial species diversity is associated with a biologically stable and non-pathogenic co-culture.
We established a commensal human skin model to more accurately emulate healthy skin and facilitate future investigations of microbiome-mediated effects on host health. The system is based on a commercial human full-thickness skin model that can be stably colonized with a defined bacterial community. This community comprises ten different bacterial species that encompass three main phyla, Bacillota, Actinomycetota, and Pseudomonadota, in ratios similar to those found on human skin (BAP). The suitability of BAP for skin colonization was evaluated against combinations of two or one phyla (BA, BP, AP, B, A, and P).

overall_design: Co-cultures consisting of a commercial 3D skin full thickness model and different bacterial mixtures were analyzed by microarrays. In total the study included 36 samples from 6 conditions and 2 different cell types with 3 biological replicates each: control Epidermis and Dermis; Bacillota (B), Actinomycetota (A) and Pseudmonadota (P) mixture Epidermis and Dermis; BA mixture Epidermis and Dermis; BP mixture Epidermis and Dermis; AP mixture Epidermis and Dermis; A mixture Epidermis and Dermis.

first: Maya

last: Kissner

first: Aline

last: Rosin


title: Differential expression analysis in the Drosophila melanogaster midgut from virgin and mated female flies

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

country: United Kingdom

institute: MRC London Institute of Medical Sciences

summary: Adult organs can grow and shrink in response to functional demands. One striking example of such plasticity is the intestine: its length is diet-sensitive in many animals, and it elongates further in females during reproduction. Our current understanding of organ-scale remodelling is centred around the dynamics of epithelial stem cells and their progeny. Here, we show that intestinal muscles resize the entire adult organ. In Drosophila, we find that intestinal muscles differ in their size and structure between the sexes and grow in females during reproduction. Mechanistically, intrinsic sex determinants control myofibril width within muscle cells, whereas hormone-driven changes lead to sarcomere elongation in females during reproduction. Altering the sex or reproductive status of gut muscle cells, we establish that intestinal muscles do not passively respond to changes in the intestinal epithelium: they are actively remodelled in females during reproduction. Such reproductive remodelling increases organ size, sustains reproduction and is deployed beyond flies. Our findings re-define the intestinal muscle as a dynamic responder to specific signals during adult life to adjust organ size and sustain female’s reproductive demands.

overall_design: To investigate the reproductive changes in the intestine of female flies, 30 guts from 8-day-old w1118 virgin and mated (3 days post-mating) female flies were dissected and pooled for each sample.

first: Jake

last: Jakobson

first: Sanjay

last: Khadayate

first: Alessandro

last: Mineo


title: mChIP-seq for high-throughput epigenomic profiling reveals a decoupling of H2A.Z and H3K4me3 in cancer

city: Shenzhen

first: Changbin

last: Sun

address: Dapeng

department: Agricultural Genomics Institute at Shenzhen

country: China

institute: Chinese Academy of Agricultural Sciences

summary: Histone variant H2A.Z has multiple roles in regulating gene transcription and its overexpression has been observed in various cancer types. However, the epigenomic characterization of H2A.Z in cancer is unclear. Combining the pool-and-split strategy with sequencing, we developed mChIP-seq, a multiplexed chromatin immunoprecipitation followed by sequencing method to efficiently profile multifactorial epigenetic landscapes of histone marks for multiple samples in parallel. mChIP-seq generates high-quality profiles comparable to standard ChIP-seq but with merits of high efficiency, low cost, and low-input requirement. Using mChIP-seq to profile H2A.Z and 10 H3 histone modifications for 24 cancer cell lines spanning 9 cancer types, we generated 528 epigenomic profiles from two workflows, comprehensively characterized genomic distribution of H2A.Z, and revealed its associations with main histone modifications and gene expression. Moreover, compared with normal cells by integration analysis of public data, we found a decoupling of H2A.Z and H3K4me3 at promoter sites in cancer cells, where the signal intensity of H2A.Z is not in line with the signal intensity of H3K4me3, which further dysregulates gene expression. Altogether, our results demonstrate that mChIP-seq is a powerful technology for epigenomic profiling and reveal abnormal regulatory features of H2A.Z in cancer.

overall_design: Development of mChIP-seq to establish a novel method for high-throughput and low-cost epigenomic profiling.

first: Wei

last: Xu


title: HepG2 ChIP-seq

city: Philadelphia

first: Matthew

middle: C

last: Pahl

state: PA

address: 3615 Civic Center Blvd

department: Center for Spatial and Functional Genomics

institute: Children's Hospital of Philadelphia

summary: HepG2 ChIP-seq data was generated to annotate variants associated with liver relevant traits from genome wide association studies

overall_design: We used histone marks in HepG2 to prioritize putatively causal variants

first: Max

last: Dudek

first: Mitch

last: Conery

first: James

last: Pippin

first: Struan

last: Grant


title: IPSC derived hepatocyte chromatin accessibility

summary: IPSC derived hepatocyte regulatory elements atlas to query liver relevant traits

overall_design: ATAC-seq was performed on three replicates of iPSC derived heptaocytes to identify potential cis-regulatory elements


title: Obesity disrupts CtBP2-mediated maintenance of the transcriptional equilibrium in hypothalamic feeding circuitry [POMC KO]

city: Tsukuba

first: Motohiro

last: Sekiya

address: 1-1-1 Tennodai

institute: University of Tsukuba

summary: Feeding behavior, a vital activity in the lives of all captive animals, is orchestrated by a delicate equilibrium between the orexigenic and anorexigenic activities of neurons in the hypothalamus. This exquisite control of neuropeptides governing the feeding behavior can be a focal point in the pathogenesis of obesity, and unraveling of the intricate transcriptional systems behind this may offer clues to develop approaches for better management of obese subjects. The transcriptional corepressor, C-terminal binding protein 2 (CtBP2), has been reported to be a metabolite-sensor inactivated in liver tissues and pancreatic β-cells in obesity. Here we describe a transcriptional system regulated by CtBP2 in hypothalamus. Our global mapping of CtBP2 binding sites by ChIP-seq reveals the recruitment of CtBP2 to the promoters of those neuropeptides as well as other key genes involved in the maintenance of hypothalamic neuronal activities. Whereas the expression of CtBP2 is not altered in obese mouse models, the recruitment of CtBP2 to the promoters of those neuropeptides is diminished in obesity, suggesting allosteric inactivation of CtBP2 in the metabolic milieu in obesity in this tissue. Exogenous expression of CtBP2 in hypothalamic cells decreases NPY gene promoter activity, and loss of CtBP2 in hypothalamic neurons in mice increases expression levels of orexigenic neuropeptides. These findings illustrate a sequential event where obesity promotes orexigenic behavior through metabolic inactivation of CtBP2. Our findings underscore a previously unexplored layer within the redundant transcriptional systems that regulate the hypothalamic feeding circuitry.

overall_design: RNA-seq analyses of mouse hypothalamic tissues to obtain transcriptome data for POMC neuron-specific CtBP2 knockout (ACKO) and their controls.


title: Obesity disrupts CtBP2-mediated maintenance of the transcriptional equilibrium in hypothalamic feeding circuitry [AgRP KO]

overall_design: RNA-seq analyses of mouse hypothalamic tissues to obtain transcriptome data for AgRP neuron-specific CtBP2 knockout (ACKO) and their controls.


title: Obesity disrupts CtBP2-mediated maintenance of the transcriptional equilibrium in hypothalamic feeding circuitry [ChIP-seq]

overall_design: ChIP-seq to determine CtBP2 recruited regions in normal mouse hypothalamic tissues


title: Epigenetic Analysis of SLE Disease Activity in Resting Naive (rN) and Transitional (T1T2) B cells

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

summary: Resting naive (rN) and transitional (T1T2) B cells were FACS separated from PBMC samples of human patients diagnosed with systemic lupus erythematosus (SLE) belonging to one of two groups: Active (defined by a SLEDAI score > 4) and Inactive (SLEDAI <=4) as well as matched healthy control.

overall_design: ATAC-seq performed on resting naive and transitional B cells isolated from human blood samples

first: Christopher

middle: D

middle: R

last: Rose

first: Jeremy

middle: M

last: Boss


title: Transcriptomic Analysis of SLE Disease Activity in Resting Naive (rN) and Transitional (T1T2) B cells

overall_design: RNA sequencing performed on resting naive and transitional B cells isolated from human blood samples


title: Epigenomic profiles of SLE resting and transitional B cells

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

overall_design: Refer to individual Series


title: Arabidopsis chloroplast genome breaks during development and environmental stimuli (ssDRIP-Seq)

city: Hefei

first: Wenjie

last: Wang

state: Anhui

address: No. 130, Changjiang West Road

institute: Anhui Agricultrual University

summary: Exposures from the external and internal environments lead to the modification of genomic DNA and even DNA breaks. The landscapes of DNA breaks in eukaryotic nuclear genomes have been extensively studied, while the frequencies and genomic loci of DNA breaks in endosymbiotic organelle are enigmatic. Here, we utilize DEtail-seq, a deep sequencing-based assay, to profile the DNA breaks in the Arabidopsis plastid genome. We find that the plastid DNAs (ptDNA) in cotyledons and true leaves are relatively stable during the juvenile stage but intensively broken in old age. The break level in seeds is much less than those in leaves. Overall, the rDNA regions suffer more breaks with a preference for template strands. Further, we determinate the variation of ptDNA break pattern in response to temperature and photoperiod stimulus. The wild-type plants are capable of maintaining genome integrity under most conditions we tested, while the ptDNA damage repair mutant atrnh1c is not. Moreover, reducing the photoperiod could relieve the ptDNA breaks in Col-0 and more obviously in atrnh1c. Our study provides a systematic and refined view of ptDNA breaks enabling a better understanding of endosymbiotic organellar genome damage and repair.

overall_design: ssDRIP-Seq

first: Chengxia

last: Zheng

first: Kuan

last: Li

first: Qianwen


title: Arabidopsis chloroplast genome breaks during development and environmental stimuli


title: Arabidopsis chloroplast genome breaks during development and environmental stimuli (DEtail-Seq)

overall_design: First, the chloroplasts were isolated from tissues and embedded in an agarose plug, and lysed. Then, the ssDNA adaptor was ligated to the 3’ overhangs of DSBs in situ. After denaturation and sonication, the DEtail-seq library was prepared following an ssDNA library protocol.


title: Peripheral glia drive the initiation of cutaneous squamous cell carcinoma

city: Zurich

first: Khanh

last: Huynh

address: Winterthurerstrasse 190

country: Switzerland

institute: University of Zurich

summary: Although tumor innervation is known to promote cancer progression, underlying mechanisms remain poorly understood and have mostly been linked to axonal signaling. Here, we identify peripheral glia as critical drivers of cutaneous squamous cell carcinoma (cSCC), the second most common skin cancer in humans. Tumor-associated glial cells (TAGs) resemble embryonic Schwann cell lineage stages, are abundant in the stroma of premalignant lesions and established murine and human cSCC, and are essential for tumor formation. TAG activation in premalignant lesions is triggered by UV-induced anti-inflammatory macrophages, which in turn are polarized by TAGs into pro-tumorigenic FcεRIα⁺ macrophages, key components of the cSCC microenvironment. Consequently, TAG depletion reduces FcεRIα⁺ macrophages, cancer-associated fibroblasts, and epithelial-mesenchymal transition in keratinocytes, thereby impairing cSCC initiation by disrupting intercellular communication required for tumor development. As most solid tumors are innervated and harbor peripheral glia, our findings reveal TAGs as previously unrecognized regulators of tumor initiation with relevance beyond skin cancer.

overall_design: To understand how TAGs affect the cellular landscape of cSCC, we performed scRNAseq on the UV-irradiated skin of CTRL (Krt14-HPV8(E6); Plp1-CreERT2; tdTomato) and Glia cKO mice (Krt14-HPV8(E6); Plp1-CreERT2; Sox10lox/lox; tdTomato) (in duplicates).

last: Huỳnh

first: Adrian

last: Salas-Bastos

first: Salome

last: Stierli

first: Lukas

last: Sommer


title: Machine learning of genome-wide 5-hydroxymethylcytosines in blood identifies prognostic models for survival outcomes in multiple myeloma

city: Chicago

first: Zhou

last: Zhang

state: IL

address: 680 North Lake Shore Drive, Suite 1400

department: Preventive Medicine

institute: Northwestern University

type: Methylation profiling by high throughput sequencing

summary:
Background: Aberrant epigenetic modifications play an important role in the progression and aggressiveness of multiple myeloma (MM). The MM-specific hydroxymethylome has been associated with MM cell proliferation and a lower global 5-hydroxymethylcytosines (5hmC) level is associated with inferior overall survival of MM. To date, no study has quantitatively investigated genome-wide 5hmC signatures in circulating cell-free DNA (cfDNA) for its prognostic significance in MM.
Methods: Genome-wide 5hmC profiles were obtained in 321 plasma cfDNA samples collected at the time of diagnosis from newly diagnosed patients with MM between 2010-17 at the University of Chicago Medical Center with a median follow-up of 70.48 months. Deaths were ascertained using the National Death Index. Treatment data (types and transplantation) and outcomes (response, progressive disease, relapse, etc.) were collected from electronic medical records. The Cox proportional hazards model was used to identify 5hmC features associated with overall survival (OS) and progression-free survival (PFS) associated with 5hmC features, followed by pathway analysis and modeling using the elastic net regularization.
Results: Cellular deconvolution showed monocytes as the major source of DNA in cfDNA. The 5hmC profiles in cfDNA reflected the 5hmC in genomic DNA from CD138+ tumor cells from bone marrow and differed by validated clinical prognostic indices. Altered 5hmC features (gene bodies) involving calcium signaling and neuroactive ligand-receptor interaction were found to be associated with OS. A weighted prognostic-score (wp-score) model comprising 18 5hmC modified genes was trained using machine learning, showing a hazard ratio (HR) of 2.9 (95% confidence interval [CI]: 1.7-4.9; log-rank test p<0.0001) for OS and HR of 1.8 (CI: 1.3-2.5; p=0.00014) for PFS in the validation set. Time-dependent receiver operating characteristic (ROC) analysis showed that the wp-score maintained its predictive capacity for OS and PFS at 24, 48, and 72 months of follow-up. The 5hmC-based prognostic model also outperformed known prognostic factors for MM, including ISS stage, LDH level, and treatment types.
Conclusions: Genome-wide 5hmC profiles in patient-derived cfDNA samples reflected specific epigenetic signatures associated with survival outcomes. We demonstrated the feasibility of using non-invasive 5hmC biomarkers for the prognosis of patients with MM.

overall_design:
The 5hmC-Seal, a selective chemical labeling technique was used to profile genome-wide 5-hydroxymethylcytosines (5hmC), an emerging class of cytosine modifications, in patient-derived circulating cell-free DNA (cfDNA). Using 5hmC-Seal and next-generation sequencing (NGS), we comprehensively profiled genome-wide 5hmC in circulating cell-free DNA (cfDNA) from plasma in 342 patients with MM (n=294), SMM (n=18), and MGUS (n=30). We used a machine learning approach to develop an integrated ancestry score that reflected the population-specific epigenetic landscape among AA and EA patients, followed by systematic comparisons of 5hmC modifications between MM and its precursors.
Genome-wide 5hmC profiles were obtained in 321 plasma cfDNA samples collected at the time of diagnosis from newly diagnosed patients with MM between 2010-17 at the University of Chicago Medical Center with a median follow-up of 70.48 months. Deaths were ascertained using the National Death Index. Treatment data (types and transplantation) and outcomes (response, progressive disease, relapse, etc.) were collected from electronic medical records. The Cox proportional hazards model was used to identify 5hmC features associated with overall survival (OS) and progression-free survival (PFS) associated with 5hmC features, followed by pathway analysis and modeling using the elastic net regularization.

***Submitters' note: At this time, we are not able to publicly release detailed treatment or outcome data due to data use agreements and patient confidentiality constraints. However, we are happy to share relevant de-identified clinical information upon reasonable request to the corresponding author once the related manuscript is published***

first: Brian

last: Chiu

first: Wei


title: Gene expression profiling of catfish after treatment with copper sulfate and exposure to Flavobacterium columnare

city: Auburn

first: Jason

last: Abernathy

state: AL

address: 990 Wire Road

institute: USDA-ARS

summary: Catfish farming remains number one among U.S. aquaculture production. Flavobacterium columnare, the causative agent of columnaris disease, produces substantial mortality during the production of freshwater farmed finfish species. F. columnare is ubiquitous in the aquatic environment, and outbreaks of disease are often triggered during the spring and summer months of the catfish production cycle. As food fish production continues to increase, the frequency of columnaris disease will only continue to rise within the aquaculture industry and thus new preventative measures will be required. Copper sulfate is the most common algaecide used in aquaculture. Copper sulfate has also been suggested as a therapeutant for columnaris disease, as we have previously discovered copper sulfate treatment effects the survivability and gill histology of channel catfish during an infection with F. columnare. Therefore to evaluate the functional effects of treatment with copper sulfate on columnaris disease, we performed RNA sequencing on gill samples from control and copper sulfate-treated catfish either immediately (more susceptible) or 24 hours after (more resistant) copper treatment followed by a challenge with F. columnare. We evaluated the differential gene expression patterns over the time-course of infection between groups with a focus on identifying functional differences in immune function.

overall_design: Channel catfish were spawned and reared at the Stuttgart National Aquaculture Research Center. For this study, catfish averaged 7.3 g. There were a total of five treatment or control groups, as follows. Group1: Catfish were exposed to 2.1mg/mL copper sulfate and then immediately challenged with Flavobacterium columnare. Gill tissue from individual fish (n=6) were sampled at 1 h, 4 h, and 24 h after bacterial challenge. Group2: Catfish were exposed to 2.1mg/mL copper sulfate and held statically for 24 h. Then fish were challenged with Flavobacterium columnare. Gill tissue from individual fish (n=6) were sampled at 1 h, 4 h, and 24 h after bacterial challenge. Group3: Catfish were exposed to 2.1mg/mL copper sulfate and then gill tissue from individual fish (n=6) were sampled. Group4: Catfish were exposed to 2.1mg/mL copper sulfate and held statically for 24 h. Then gill tissue from individual fish (n=6) were sampled. Group5: Gill tissue from individual fish (n=6) were sampled at zero hour immediately prior to either copper sulfate and/or Flavobacterium columnare challenge to serve as no-treatment controls.

first: Miles

last: Lange

first: Bradley

last: Farmer

first: Benjamin

middle: H

last: Beck

first: David

middle: L

last: Straus


title: CT26 multi-tissue RNA-seq under immunotherapy combinations

status: Public on Aug 04 2026

city: Cambridge

first: Richard

middle: Lee

last: Gieseck III

state: MA

address: 1 Portland St.

institute: Pfizer, Inc.

summary: Bulk RNA-seq profiling of CT26-bearing BALB/c mice across spleen, tumor, and tumor draining lymph node under multiple treatment regimens (Isotype, PD1, CYTO, PD1/CYTO, TS/CYTO, TS/PD1/CYTO) at study days 16 and 23.

overall_design: One sample per library; paired-end polyA-enriched stranded mRNA-seq. Sample-level metadata includes tissue, treatment, day, RIN, and tumor volume.

last: Gieseck

first: Zhang

last: Ying


title: CYP1B1-Mediated Metabolic Reprogramming Drives Immune Dysregulation in Sepsis: A Single-Cell Transcriptomic and Therapeutic Exploration

city: Hangzhou

first: Jinyan

last: Xie

address: No.866 Yuhangtang Road

institute: zhejiang university

summary: Sepsis, a life-threatening condition characterized by dysregulated immune responses, poses significant clinical challenges due to high mortality and limited therapeutic strategies. Emerging evidence highlights immune-metabolic dysregulation, particularly in monocytes and macrophages, as a critical driver of sepsis pathogenesis. Here, we performed single-cell RNA sequencing (scRNA-seq) on peripheral blood mononuclear cells (PBMCs) from patients with sepsis and healthy controls, revealing significant alterations in immune cell composition. Sepsis patients exhibited increased myeloid cells and decreased T, NK, and B/plasma cells. CD8+ T cells displayed enhanced activation, while macrophages showed disrupted amino acid metabolism, with upregulated tryptophan pathways (e.g., CYP1B1, HADHA) and downregulated arginine and proline metabolism. In vitro, lipopolysaccharide (LPS)-stimulated macrophages exhibited elevated CYP1B1 expression, and its inhibition by (E)-2,3',4,5'-tetramethoxystilbene (TMS) suppressed pro-inflammatory cytokine production (IL1B, TNFA). In a murine sepsis model, TMS administration reduced systemic inflammation, attenuated organ damage, and decreased myeloid cell infiltration. These findings identify CYP1B1 as a novel metabolic checkpoint in sepsis-associated hyperinflammation and demonstrate the therapeutic potential of TMS in rebalancing immune dysregulation. Our study provides insights into precision immunometabolic interventions for sepsis management.

overall_design: 3 patients with sepsis and 3 healthy control volunteers (HC) were recruited from the Department of Intensive Care Unit at Sir Run Run Shaw Hospital affiliated with Medical College of Zhejiang University. The enrollment was performed according to the following inclusion criteria: (1) Admission to ICU, (2) Age ranged from 25 to 60, (3) Confirmed infection, (4) Sequential organ failure assessment (SOFA) score ≥ 2. All three patients had a definitive diagnosis of sepsis according to the Sepsis-3 criteria, based on confirmed infection and a SOFA score increase of ≥2 points. Blood samples for our study were collected during the acute phase of sepsis, within 24 hours following clinical diagnosis and prior to the full effect of targeted antimicrobial therapy. All patients had intra-abdominal infections as the primary source of sepsis, but with distinct pathogens.

first: Yinshan

last: Wu

first: Feng

last: Guo


title: Eliglustat-Induced Remodeling of Sulfo-Glycosphingolipid Metabolism and Gene Expression in hepatocellular carcinoma cells

city: Milan

first: Italia

last: Bongarzone

state: Milan

address: Via Amedeo, 42

department: Department of Diagnostic Innovation

country: Italy

institute: IRCCS Istituto Nazionale dei Tumori

summary: Dysregulation of glycosphingolipid (GSL) metabolism contributes to cancer progression by altering membrane organization, signaling pathways, and cellular adaptation. Sulfated glycosphingolipids (Sulfo-GSLs), including sulfated lactosylceramide, are elevated in several malignancies and have been implicated in tumor cell adhesion and metastasis. We previously identified elevated Sulfo-GSL levels in hepatocellular carcinoma (HCC) HepG2 cells, suggesting that targeting GSL biosynthesis may represent a potential therapeutic strategy. Here, we investigated the molecular consequences of UDP-glucose ceramide glucosyltransferase (UGCG) inhibition by eliglustat in HepG2 by integrating MALDI mass spectrometry-based lipid profiling with RNA sequencing. Eliglustat treatment induced dose-dependent remodeling of the cellular lipid profile, characterized by marked reduction of Sulfo-GSL species and a concomitant increase in selected phosphatidylinositol species. Lipidomic analysis revealed differential sensitivity of Sulfo-GSL molecular species, with preferential depletion of non-hydroxylated forms and relative preservation of hydroxylated species, indicating distinct metabolic responses within the same lipid class. Transcriptomic changes were limited at 20 µM eliglustat, whereas 30 µM induced extensive transcriptional reprogramming involving activation of immediate-early response genes, including EGR, FOS/JUN, and KLF family members, together with enrichment of inflammatory, stress-response, and senescence-associated pathways. Conversely, pathways related to cell-cycle progression, DNA replication, and chromatin organization were suppressed. Genes involved in GSL metabolism were also modulated, suggesting activation of compensatory mechanisms to restore lipid homeostasis. These findings demonstrate that UGCG inhibition induces coordinated lipidomic and transcriptional remodeling in HepG2, revealing both tumor-suppressive molecular features and adaptive responses to metabolic stress providing new insights into the cellular consequences of targeting GSL metabolism in HCC.

overall_design: HepG2 cells were purchased from American Type Culture Collection (ATCC, Manassas, VA, USA; ATCC number: HB-8065) and maintained in Dulbecco’s modified Eagle medium (DMEM; Gibco, Italy) supplemented with 10% fetal bovine serum (FBS; Gibco) at 37 °C and 5% CO2. Lipids from control and eliglustat-treated HepG2 cells were extracted using the Bligh and Dyer method. Eliglustat (Merck) was dissolved in distilled water and added to the culture medium at final concentrations of 10, 20, or 30 µM. HepG2 cells were seeded at a density of 3 × 10⁵ cells/mL, treated with eliglustat 24 h after plating, for 72h, and incubated for an additional 48 h, as previously described by Ghislanzoni et al..

first: Rachele

last: Giannecchini

first: Matteo

last: Niero

first: Fabio

last: Bozzi

first: Federica

last: Padelli

first: Alessia

last: Bertolotti

first: Antonino

last: Belfiore

first: Silvia

last: Ghislanzoni

first: Luca

last: Agnelli


title: Inflammasome Hyperactivation Disrupts  Construction of the Gas Exchange Surface through the NLRP3-IL-18-TNFa Axis [RNA-seq]

city: La Jolla

first: Rongbo

last: Li

address: 9500 Gilman Drive

institute: UC San DIego

summary: Inflammation is a prominent feature of tissue injury, and a driver of chronic disease. However, the precise molecular mechanisms underlying the impact of inflammation remains unclear in many injury settings including in alveolar development to build the gas exchange surface in lung. Here we show that in mice, overexpression of patient-derived activated variants of Nlrp3 (Nlrp3act), a central sensor within the inflammasome, resulted in severe simplification of alveoli. Such histology is accompanied by a striking decrease of cell proliferation and marker expression of secondary crest myofibroblasts (SCMFs) whose contractility is essential for septa formation. Such a drastic effect on lung structure was only observed when the variants were overexpressed in the first two weeks after birth, but not later. While both downstream proinflammatory cytokines IL-1β and IL-18 are upregulated, inactivation of Il18, but not Il1b in the Nlrp3act background reversed simplification. Also unlikely in other tissue settings where Mmp9 is a critical mediator downstream of the inflammasome, inactivation of Mmp9 also did not reverse Nlrp3act phenotypes, suggesting context-dependent mechanisms. scRNAseq followed by validation revealed IL-18-dependent increase of Tnfα in myeloid cells, capable of signaling through its widely-expressed receptors to all structural cells including SCMFs. Addition of recombinant TNFα to mesenchymal cells enriched for SCMFs led to reduced contractile gene expression. Finally, inactivation of Tnfα in the Nlrp3act background led to a robust reversal of simplification. These findings together demonstrate an inflammasome-IL-18-TNFα axis that dictate lung mesenchymal cell states, thereby control the building of the gas exchange surface.

overall_design:
Control, LysMcre;Nlrp3A350V, Il18r1 control, LysMcre;Nlrp3A350V;Il181r+/- and LysMcre;Nlrp3A350V;Il18r1-/- mice lungs were used for bulk RNA-seq.

sample title = column header (in 'LysMcre;Nlrp3A350V;Il18r1 Summary.xlsx' file)
Il18r1 control 1 = q1_0
Il18r1 control 2 = q2_0
Il18r1 control 3 = q3_0
Il18r1 control 4 = q4_0
LysMcre;Nlrp3A350V;Il181r+/- 1 = q5_0
LysMcre;Nlrp3A350V;Il181r+/- 2 = q6_0
LysMcre;Nlrp3A350V;Il181r+/- 3 = q7_0
LysMcre;Nlrp3A350V;Il181r-/- 1 = q8_0
LysMcre;Nlrp3A350V;Il181r-/- 2 = q9_0
LysMcre;Nlrp3A350V;Il181r-/- 3 = q10_0
LysMcre;Nlrp3A350V;Il181r-/- 4 = q11_0

LysMcre;Nlrp3A350V;Il181r+/- = 'Mt' group (in 'Mt & Rescue' spreadsheet)
LysMcre;Nlrp3A350V;Il181r-/- = 'Rescue' group (in 'Mt & Rescue' spreadsheet)

first: Xin

last: Sun


title: A Transcriptomic Biomarker to Classify Chemical-Induced Histone Deacetylase Inhibition in Human HepaRG Cells

city: Ottawa

first: Matthew

last: Meier

state: Ontario

address: 251 Sir Frederick Banting Driveway

department: Health Canada

country: Canada

institute: Government of Canada


title: Exploring the m6A modification profile after METTL16 overexpression in BEAS-2B cells.

city: Nanjing

first: Tingting

last: Xu

address: Guangzhou Road 303

institute: The first affiliated hospital of Nanjing Medical University

summary: Allergic asthma is a common disease. We aimed to investigate the role of METTL16, an N6-methyladenosine (m6A) writer, in allergic asthma and epithelial homeostasis. Here we show that pulmonary METTL16 expression was decreased in patients with allergic asthma and in a murine model of allergic asthma, particularly in airway epithelial cells. Genetic depletion of Mettl16 enhanced type 2 cytokine production and exacerbated epithelial-to-mesenchymal transition (EMT), whereas lung-specific METTL16 overexpression attenuated allergic airway inflammation and remodeling. Mechanistically, METTL16 promoted epithelial arginine biosynthesis and thereby suppressed IL-1β production. Furthermore, loss of Mettl16 impaired m6A modification of Ass1 mRNA, and increased Ass1 expression was associated with arginine biosynthesis. Our findings identify METTL16 as a critical regulator of allergic asthma and suggest it as a potential therapeutic target.

overall_design: m6A modification in BEAS-2B cells transfected with control or METTL16 overexpression.

first: Mingshun

last: Zhang

first: Ningfei

last: Ji

first: Mao

last: Huang


title: T-bet and Runx3 orchestrate effector CD8 T cell differentiation and lineage fidelity through cooperative and distinct chromatin regulatory mechanisms [Multi-omics]

city: Suzhou

first: Qiang

last: Shan

address: No. 100, Chongwen Road

institute: Suzhou Institute of Systems Medicine

summary:
Effector CD8+ T cells must rapidly acquire cytotoxic functions while maintaining lineage fidelity and suppressing alternative fates. T-bet and Runx3 are key transcription factors that drive this process, yet their integrated regulatory logic has remained unclear due to the lack of comprehensive binding and chromatin accessibility data. Here, we systematically dissect the cooperative and distinct roles of T-bet and Runx3 in shaping the transcriptional and epigenetic landscape of antiviral CD8+ T cells. Using CUT&RUN, ATAC-seq, RNA-seq and scRNA-seq across single and double knockout models, we reveal that T-bet and Runx3 coordinate effector differentiation through both chromatin remodeling-dependent and -independent mechanisms. T-bet preferentially binds promoters and restrains Th17-like programs, while Runx3 targets distal elements to suppress Tfh-associated genes and sustain cytotoxic identity. Our findings uncover a cis-regulatory logic wherein these factors act combinatorially to balance activation of effector programs with repression of alternative lineages, ensuring functional precision during antiviral responses. This work establishes a comprehensive framework for understanding lineage enforcement by transcription factors in effector T cells.

This SuperSeries is composed of the SubSeries listed below.


title: TSPAN8 a plasticity marker is transcriptionally regulated through DUSP19 BRD4 crosstalk in Prostate Cancer cells

city: Clermont-Ferrand

first: Joris

last: Mordier

address: 28 place Henri Dunant Faculté de médecine, BP38

country: France

institute: iGReD

summary: To identify upstream regulators of TSPAN8 transcription, we screened a library of 298 phosphatases using a GFP reporter under the control of the TSPAN8 promoter in PC3 cells. DUSP19 emerged as the strongest negative regulator. Unexpectedly, DUSP19-mediated regulation of TSPAN8 was independent of its canonical JNK pathway: pharmacological JNK inhibition with SP600125 did not affect TSPAN8 expression, and pJNK/JNK levels were unchanged by siDUSP19. RNA-seq combined with promoter binding-site analysis identified BRD4 as the candidate effector linking DUSP19 to TSPAN8 transcription, and pharmacological BRD4 inhibition (AZD5153) reversed the siDUSP19-induced TSPAN8 upregulation at both mRNA and protein levels. Additionally, TSPAN8 accumulation is significantly higher in biopsies SYNAPTOPHYSIN+.

overall_design: PC3 cells were seeded in 6-wells plates at 100000/ml density per well. One day later, the transfections and/or treatments (DMSO 0.5 %, AZD5153 1µM, SP6 20µM) were applied in OPTIMEM medium for 48 Hours. We used RNAiMAX according to the manufacturer's guidelines for siRNA transfection. mRNA was extracted utilizing the NucleoSpin RNA II kit (Macherey Nagel EURL, Hoerdt, France).


title: Acoustic Cavitation-Enhanced Remodeling of Lymph Node Microenvironment Enables Deep Infiltration for Potent Cancer Vaccination

first: Bihan

last: Wu

state: other

address: 88 Jiefang Road

institute: Zhejiang University

summary: The efficacy of peptide-based tumor vaccines is often constrained by the size-exclusion barrier of the subcapsular sinus (SCS), which restricts infiltration of macromolecules into the lymph node (LN) parenchyma essential for T-cell priming. Here, inspired by the clinical contrast agent Sonazoid, we developed an ultrasound-assisted vaccine platform with tunable phase-transition behavior for active modulation of the LN microenvironment. The system integrates phosphoserine-decorated lipid chemistry to promote cell-mediated LN trafficking, a covalently conjugated adjuvant–antigen construct for synchronized immunostimulation, and liquid-state perfluorocarbon nanodomains programmed for ultrasound-triggered liquid–gas transition. Upon localized ultrasound irradiation, the chemically programmed phase transition triggers cargo release, while the resultant acoustic cavitation generates transient openings in the SCS endothelium. This process enables deep parenchymal infiltration of vaccine components that would otherwise be excluded. Beyond the physical barrier disruption, RNA sequencing reveals that acoustic stimulation drives both structural and immunological reprogramming of LN into an immune-permissive niche. By synergizing mechanical stimulation with biological modulation, this strategy induces benign and persistent LN expansion, amplifies anti-tumor T-cell responses, and establishes durable immunological memory, resulting in both prophylactic and therapeutic outcomes. This approach is versatile across both model antigens and neoantigens, offering a bio-inspired, two-stage LN-targeted delivery strategy that serves as a framework for designing more effective therapeutic vaccines.

overall_design: RNA-seq profiling of tumor-draining lymph nodes (PBS-treated, IPSPlipo-treated, and IPSPlipo+US-treated) at day 18 from female C57BL/6J mice bearing B16F10-OVA tumors

first: Xiaodan

first: Peile

last: Jin

first: Yijie

last: Chen

first: Xia

last: Fang

first: Yue

last: Song

first: Guowei

last: Wang

first: Jiajia

last: Zhou

first: Huaimin

first: Pintong


title: Spatial transcriptomic atlas of intestinal segments from KM mice

city: Guangzhou

first: Xiaodong

address: No. 111 Dade Road, Yuexiu District

institute: Guangdong Provincial Hospital of Chinese Medicine

summary: This study generated spatial transcriptomic profiles of ileum, cecum, and colon from specific pathogen-free (SPF) and germ-free (GF) Kunming (KM) mice using the BGI Stereo-seq platform. The dataset captures spatial organization and segment-specific immune niches in the absence of microbiota.

overall_design:
Spatial transcriptomics was performed on ileum, cecum, and colon from SPF and GF KM mice using the BGI Stereo-seq platform. Libraries were sequenced on the DNBSEQ-T7 platform.

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Due to storage expiration, the original raw fastq files for this study are no longer retrievable.
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first: Tailiang

last: Chai

first: Yang

first: Weiming

last: Liang

first: Ruizhen

last: Zhao

first: Yifei

last: Sheng

first: Fuhua

last: Lu

first: Fangxiao

last: Dong


title: Gene duplication of SNAPC1 generates transcription factors for snRNAs and sex-specific piRNAs [ChIP-Seq]

city: Baltimore

first: John

last: Kim

state: MD

address: 3400 Charles Street

department: Department of Biology

institute: Johns Hopkins University

summary: Piwi-interacting RNAs (piRNAs) are small non-coding RNAs essential for transposon silencing and germline integrity across metazoans. In many species, piRNA expression is sexually dimorphic, yet the molecular mechanisms underlying this sex specificity remain poorly understood. In Caenorhabditis elegans, sexually dimorphic piRNA expression is regulated at the transcriptional level. We previously identified SNPC-1.3, a paralog of the small nuclear RNA (snRNA) activating protein complex (SNAPc/SNPC) subunit SNAPC1, as a male-specific piRNA transcription factor. However, the factors governing female piRNA expression remained elusive. Here, we identify SNPC-1.2, a second SNPC-1 paralog, as a female-specific piRNA transcription factor. SNPC-1.2 interacts with the core piRNA transcriptional machinery, binds female piRNA loci, is required for female piRNA expression, and promotes hermaphrodite fertility. In contrast, a third paralog, SNPC-1.1, retains the ancestral SNAPc function in snRNA transcription and is dispensable for piRNA biogenesis. Together, these findings reveal how gene duplication and functional specialization within the snpc-1 gene family generate specificity factors that direct the core SNAP complex to distinct genomic targets, providing a molecular mechanism for sexually dimorphic piRNA expression while maintaining canonical snRNA transcription.

overall_design: ChIP-seq of SNPC-1.1, SNPC-1.2, and SNPC-4 from wild-type C. elegans and snpc mutants.

first: Lars

middle: K

last: Benner

first: Margaret

last: Starostik

first: Rebecca

middle: J

last: Tay

first: Ayaka

last: Inoki

first: Mindy

last: Clark

first: Suhua

last: Feng

first: Michael

last: Schatz

first: Steven

middle: E

last: Jacobsen


title: Single-cell transcriptomic validation of B cell, T cell, and myeloid subsets in colon from C57BL/6 mice

first: Xiaodong

last: Fang

summary: This dataset serves as a validation cohort for single-cell transcriptomic changes observed in germ-free (GF) and specific pathogen-free (SPF) mice. Single-cell RNA sequencing was performed on B cell, T cell, and myeloid subsets isolated from the colon of C57BL/6 mice. The dataset captures immune heterogeneity in the absence of microbiota and enables direct comparison with the KM mouse cohort.

overall_design:
Single-cell RNA sequencing was performed on colon samples from SPF and GF C57BL/6 mice at 4 weeks of age. B cell, T cell, and myeloid cell subsets were extracted and analyzed as separate Seurat objects for validation of immune cell responses.

***************************************************************
Due to storage expiration, the original raw fastq files for this study are no longer retrievable.
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last: Chen


title: Single-cell transcriptomic atlas of intestinal segments from KM mice

summary: This study generated a single-cell transcriptomic atlas of multiple intestinal segments (jejunum, ileum, cecum, and colon) from specific pathogen-free (SPF) and germ-free (GF) Kunming (KM) mice. The dataset captures immune heterogeneity and segment-specific transcriptional programs in the absence of microbiota.

overall_design:
Single-cell RNA sequencing was performed on jejunum, ileum, cecum, and colon from SPF and GF KM mice. Cells were processed using the Dnbelab C series single-cell library preparation kit and sequenced on the DNBSEQ-T7 platform.

***************************************************************
Due to storage expiration, the original raw fastq files for this study are no longer retrievable.
***************************************************************

first: Tailiang

last: Chai


title: MiR-31 regulation of human cardiomyocyte differentiation

city: Indianapolis

first: Lei

last: Yang

state: IN

address: 1044 W Walnut Street

institute: Indiana University School of Medicine

summary: This project aims to investigate the imapct of mir-31 on human cardiomyocyte differentiation from iPS cells.

overall_design: CRISPR-cas9 was used to knockout miR-31 in human iPS cells, followed with cardiomyocyte differentiation by forming monolayer cell cutture. After differentiation, cardiomyocytes were enriched for whole mRNA-seq.

first: Juli

last: Liu

first: Sheng

first: Jun

last: Wan


title: Single-cell transcriptional analysis of irradiated skin reveals changes in fibroblast subpopulations and variability in caveolin expression

city: Stanford

last: Januszyk

address: 257 Campus Dr

institute: Stanford University

summary: Background Radiation-induced fibrosis (RIF) is an important late complication of radiation therapy, and the resulting damaging effects of RIF can significantly impact reconstructive outcomes. There is currently a paucity of effective treatment options available, likely due to the continuing knowledge gap surrounding the cellular mechanisms involved. In this study, detailed analyses of irradiated and non-irradiated human skin samples were performed incorporating histological and single-cell transcriptional analysis to identify novel features guiding development of skin fibrosis following radiation injury. Methods Paired irradiated and contralateral non-irradiated skin samples were obtained from six female patients undergoing post-oncologic breast reconstruction. Skin samples underwent histological evaluation, immunohistochemistry, and biomechanical testing. Single-cell RNA sequencing was performed using the 10X single cell platform. Cells were separated into clusters using Seurat in R. The SingleR classifier was applied to ascribe cell type identities to each cluster. Differentially expressed genes characteristic to each cluster were then determined using non-parametric testing. Results Comparing irradiated and non-irradiated skin, epidermal atrophy, dermal thickening, and evidence of thick, disorganized collagen deposition within the extracellular matrix of irradiated skin were readily appreciated on histology. These histologic features were associated with stiffness that was higher in irradiated skin. Single-cell RNA sequencing revealed six predominant cell types. Focusing on fibroblasts/stromal lineage cells, five distinct transcriptional clusters (Clusters 0–4) were identified. Interestingly, while all clusters were noted to express Cav1, Cluster 2 was the only one to also express Cav2. Immunohistochemistry demonstrated increased expression of Cav2 in irradiated skin, whereas Cav1 was more readily identified in non-irradiated skin, suggesting Cav1 and Cav2 may act antagonistically to modulate fibrotic cellular responses. Conclusion In response to radiation therapy, specific changes to fibroblast subpopulations and enhanced Cav2 expression may contribute to fibrosis. Altogether, this study introduces a novel pathway of caveolin involvement which may contribute to fibrotic development following radiation injury.

overall_design: scRNA-seq of unsorted cells from human radiated and non-radiated skin samples

first: Lionel

last: Kameni


title: A Lactic Acid-Chac1 Axis Regulates Ferroptosis-Associated Cell Death and Tumor Progression [A549_LAC RNA-seq]

city: chendu

first: lilan

last: he

address: yulin

institute: Sichuan University

summary: Tumor metabolic reprogramming plays a critical role in cancer progression, yet the direct involvement of lactic acid in regulating tumor cell death remains incompletely understood. In this study, we identified lactic acid as a previously underappreciated regulator of tumor cell fate and investigated whether lactic acid induces ferroptosis-associated cell death in tumor cells. Lactic acid suppressed tumor cell viability in a dose-dependent manner across multiple tumor cell lines and triggered cell death with both apoptotic and non-apoptotic features. Transcriptomic analysis revealed significant enrichment of ferroptosis-related pathways, accompanied by glutathione depletion, Gpx4 downregulation, and increased oxidative stress. Pharmacological inhibition using Ferrostatin-1 and genetic modulation of Slc7a11 supported the involvement of ferroptosis in lactic acid-induced cytotoxicity. Mechanistically, we identified Chac1 as an important mediator linking lactic acid-induced metabolic stress to ferroptosis-associated tumor cell death, as Chac1 knockdown attenuated cytotoxicity in vitro while promoting tumor growth and metastasis in vivo. Furthermore, Chac1 deficiency was associated with enhanced metastatic progression, suggesting that suppression of ferroptosis may facilitate tumor progression, at least in part, potentially associated with alterations in tumor immune cell infiltration. Collectively, these findings uncover a previously unrecognized link between lactic acid and ferroptosis, establish Chac1 as a critical regulatory node, and highlight the therapeutic potential of targeting the lactic acid-Chac1-ferroptosis axis in cancer treatment.

overall_design: Bulk RNA-seq was performed on human A549 lung adenocarcinoma cells. Cells were treated with 20 mM lactic acid added directly to the culture medium for 24 h (three biological replicates) or with an equal volume of PBS for 24 h as the control (three biological replicates). Total RNA was extracted using TRIzol reagent and submitted to a commercial sequencing service for poly(A)-selected, paired-end RNA sequencing.

first: Lilan

last: He

first: Aaron

middle: Q

last: Zhang

first: Rui

last: Wu

first: Shitong

last: Zhong

first: Jiali

first: Bin

last: Shao

first: Siyu

first: Jingyuan

last: Lu

first: Fan

last: Hu

first: Jiayun

last: Yu

first: Hanwen

last: Li


title: Single-nucleus transcriptomic profiling of adult male Japanese medaka brain following parental benzo[a]pyrene exposure

city: Corpus Christi

first: Nonnie

last: Cook

state: Texas

address: 6300 Ocean Drive

department: Life Sciences

institute: Texas A&M University-Corpus Christi

summary: Benzo[a]pyrene (BaP) is a polycyclic aromatic hydrocarbon associated with developmental and neurobehavioral toxicity. This study examined whether parental BaP exposure produces transcriptional changes in the brains of unexposed adult first filial generation (F1) Japanese medaka. Adult parental fish were exposed to solvent control or 1 µg/L BaP for 21 days; eggs were collected after exposure and F1 offspring were reared in clean water. Whole brains from three control-lineage and three BaP-lineage adult males were analyzed by single-nucleus RNA sequencing. Fourteen transcriptionally distinct brain cell populations were resolved, and treatment-associated differential expression was evaluated within each cluster.

overall_design: Six biological replicate libraries were generated from individual whole brains of 6-month-old adult male F1 medaka: TAM1-TAM3 were control-lineage samples and TAM4-TAM6 were BaP-lineage samples. The F1 fish were not directly exposed to BaP. Their parents were exposed to solvent control or 1 µg/L BaP for 21 days before egg collection. Nuclei were isolated independently from each brain, 10x Genomics 3' single-nucleus RNA-seq libraries were prepared, and R1, R2, I1, and I2 FASTQ files were generated for each library. Reads were aligned to the Oryzias latipes reference assembly GCA_004347445.1, the six libraries were aggregated, and treatment-versus-control differential expression was calculated within each cell cluster.

first: Cook

last: Nonnie E

first: Lu

last: Yuan

first: Kulesz

last: Hunter

first: Jayarajan

last: Rijith

first: Mozzachiodi

last: Riccardo

first: Seemann

last: Frauke


title: RNA-seq datasets of Blood transcriptomics reveals the value of Hub genes in patients with NTM - PD

city: Shanghai

first: Guoling

last: Yang

address: No. 507 Zhengmin Road

department: Department of Tuberculosis

institute: Shanghai Pulmonary Hospital

summary: To identify and validate peripheral blood mRNA signatures as non-invasive diagnostic biomarkers for nontuberculous mycobacterial pulmonary disease (NTM-PD), we performed an integrated transcriptomic analysis combining scRNA-seq and bulk RNA sequencing (RNA-seq), followed by experimental validation. Peripheral blood samples were collected from a total of 8 participants, including 3 patients with Mycobacterium avium complex pulmonary disease (MAC-PD), 3 patients with Mycobacterium abscessus pulmonary disease (MAB-PD), and 2 healthy controls (HC). All samples were subjected to scRNA-seq to dissect the single-cell transcriptomic landscape of peripheral blood, and paired bulk RNA-seq was conducted simultaneously to achieve comprehensive transcriptomic profiling. Integrated analysis of scRNA-seq and bulk RNA-seq datasets revealed that eight core genes were significantly upregulated in NTM-PD patients compared with HCs. Notably, this gene signature exhibited superior specificity relative to other candidate gene combinations, highlighting its potential as a diagnostic biomarker for NTM-PD.

overall_design: Bulk RNA sequencing was performed on peripheral blood samples from 5 Mycobacterium avium complex (MAC)-PD patients, 5 M. abscessus (MAB)-PD patients, and 10 healthy controls (HC). A discovery cohort (3 MAC-PD, 3 MAB-PD and 2 HC) subjected to single-cell RNA sequencing (scRNA-seq) and a validation cohort (23 MAC-PD, 27 MAB-PD and 35 HC) was established for quantitative reverse transcription PCR (qRT-PCR) analysis of core gene expression.

first: Li

last: Wang

first: Xubin

last: Zheng

first: Lan

last: Yao

first: Jianxia

last: Chen

first: Peng

first: Wei

last: Sha


title: Bulk RNA-seq, small RNA-seq, and miRNA pulldown profiling of H19 RNA editing and miR-675-3p retargeting in mouse hematopoietic cells

city: Tianjin

first: Shuangshuang

last: Pu

state: China

address: 288 Nanjing Road

institute: State Key Laboratory of Experimental Hematology National Clinical Research Center for Blood Diseases Institute of Hematology

type: Non-coding RNA profiling by high throughput sequencing

summary: Adenosine-to-inosine RNA editing can alter RNA structure, processing, and target recognition, but its physiological functions during hematopoietic stem cell development remain incompletely understood. This study investigates how developmental editing of the imprinted long noncoding RNA H19 regulates hematopoietic stem cell quiescence through the biogenesis and target specificity of miR-675-3p. The deposited datasets comprise conventional bulk RNA sequencing, small RNA sequencing, and biotinylated miRNA pulldown RNA sequencing from mouse hematopoietic stem and progenitor cells and related cell-line models. Bulk RNA-seq was performed in 32D-LV-H19 cells expressing empty vector, wild-type ADAR1 p110, or catalytically inactive ADAR1 p110 E861A; primary mouse c-Kit-positive cells expressing empty vector, wild-type editable H19-A, the H19-G edited mimic, or the editing-resistant H19-T allele; poly(I)-treated Ki67-eGFP-negative LT-HSCs carrying H19-A, H19-G, or H19-T alleles; and steady-state Ki67-eGFP-negative and Ki67-eGFP-positive LT-HSCs. Small RNA-seq was used to quantify miRNA production in 32D-LV-H19 and primary c-Kit-positive cells under the corresponding ADAR1- and H19-dependent experimental conditions. In parallel, biotinylated miRNA pulldown RNA-seq was performed in 32D cells transfected with scrambled-control, unedited wild-type miR-675-3p, or edited miR-675-3p mimics. Input and pulldown fractions were sequenced to identify transcripts preferentially associated with each miRNA species. Together, these datasets enable integrated analysis of H19 editing-dependent transcriptional changes, miR-675-3p biogenesis, and editing-induced miRNA target retargeting in hematopoietic cells.

overall_design: The study contains 69 sequencing libraries divided into three related experimental components. First, conventional bulk RNA-seq was performed on 36 samples. These included nine 32D-LV-H19 cell samples expressing empty vector, wild-type ADAR1 p110, or catalytically inactive ADAR1 p110 E861A, with three biological replicates per condition; twelve primary mouse c-Kit-positive cell samples expressing empty vector, wild-type editable H19-A, H19-G edited mimic, or editing-resistant H19-T, with three biological replicates per condition; nine poly(I)-treated Ki67-eGFP-negative LT-HSC samples carrying H19-A, H19-G, or H19-T alleles, with three biological replicates per genotype; and six steady-state LT-HSC samples separated into Ki67-eGFP-negative and Ki67-eGFP-positive populations, with three biological replicates per population. Second, biotinylated miRNA pulldown RNA-seq was performed using 12 libraries. Mouse 32D cells were transfected with biotinylated scrambled-control, unedited wild-type miR-675-3p, or edited miR-675-3p mimics. For each miRNA condition, total input RNA and biotin-miRNA-associated pulldown RNA were collected in two biological replicates. The paired input and pulldown design was used to distinguish changes in transcript abundance from miRNA-specific target enrichment. Third, small RNA-seq was performed on 21 libraries. Nine libraries were generated from 32D-LV-H19 cells expressing empty vector, wild-type ADAR1 p110, or ADAR1 p110 E861A, with three biological replicates per condition. Twelve libraries were generated from primary mouse c-Kit-positive cells expressing empty vector, H19-A, H19-G, or H19-T, with three biological replicates per condition.

first: Jiabin

first: Hui

last: Cheng


title: Targeting ERO1A enhances antitumor immune response by recruiting CD8+T cells and synergizing with PD-L1 blockade in liver cancer

city: Nanchang

first: Jing

last: Mao

address: No. 566, Xuefu Avenue

institute: The Second Affiliated Hospital of Nanchang University

summary: Despite the availability of various treatment modalities for liver cancer, its mortality rate remains high. Immunotherapy represents an emerging approach for liver cancer. However, the response rate to single-agent immune checkpoint blockade therapy is suboptimal. Endoplasmic reticulum oxidoreductase 1-alpha (ERO1A), a potential therapeutic target associated with endoplasmic reticulum (ER) stress, is implicated in impeding protective antitumor immunity. In this study, we found that targeting ERO1A in liver cancer, while activating the PERK/EIF2α/ATF4/CHOP-mediated apoptosis and autophagy signaling, downregulated ADORA1 and inhibited the cGMP/PKG pathway, thereby promoting the expression and secretion of CCL4. This led to an increased infiltration of CD8+T cells into the immune microenvironment, enhancing the antitumor immune response. Furthermore, targeting ERO1A in liver cancer also upregulated type I interferon synthesis, activated the JAK-STAT pathway, and promoted programmed cell death ligand 1 (PD-L1) and MHC-Ⅰ expression. Using liver cancer animal models, we demonstrated that combination treatment with ERO1A inhibitor and PD-L1 inhibitor increased CD8+T cell infiltration and enhanced their function within the tumor microenvironment, resulting in synergistic antitumor effects. Therefore, ERO1A represents a promising therapeutic target in liver cancer, potentially suitable for combination with immune checkpoint inhibitors to improve patient outcomes.

overall_design: Lentiviral vectors for ERO1A knockdown were designed and synthesized. Hepa1-6 cells were seeded in 6-well plates at a density of 5×105 cells per well. Diluted lentiviral supernatant and polybrene were added to the culture medium. After 24 hours of transduction, the medium was replaced with fresh medium. Cells were selected using puromycin at various concentrations to establish stably transduced cell lines.Total RNA was extracted from shERO1A and shNC Hepa1-6 cells using TRIzol reagent. Standard reference transcriptome sequencing was performed.


title: T-bet and Runx3 orchestrate effector CD8 T cell differentiation and lineage fidelity through cooperative and distinct chromatin regulatory mechanisms

first: Qiang

last: Shan

summary: Effector CD8⁺T cells must rapidly acquire cytotoxic functions while maintaining lineage fidelity and suppressing alternative fates. T-bet and Runx3 are key transcription factors that drive this process, yet their integrated regulatory logic has remained unclear due to the lack of comprehensive binding and chromatin accessibility data. Here, we systematically dissect the cooperative and distinct roles of T-bet and Runx3 in shaping the transcriptional and epigenetic landscape of antiviral CD8⁺ T cells. Using CUT&RUN, ATAC-seq, RNA-seq and scRNA-seq across single and double knockout models, we reveal that T-bet and Runx3 coordinate effector differentiation through both chromatin remodeling–dependent and –independent mechanisms. T-bet preferentially binds promoters and restrains Th17-like programs, while Runx3 targets distal elements to suppress Tfh-associated genes and sustain cytotoxic identity. Our findings uncover a cis-regulatory logic wherein these factors act combinatorially to balance activation of effector programs with repression of alternative lineages, ensuring functional precision during antiviral responses. This work establishes a comprehensive framework for understanding lineage enforcement by transcription factors in effector T cells.

first: Xiaoyu

last: Lin


title: Transcriptomic profiling of mouse aging soleus muscles and drug interventions

city: Singapore

first: Weihan

last: Huai

address: 10 Medical Dr

country: Singapore

institute: NUS

summary: Here, we performed bulk RNA sequencing on soleus muscles of both male and female mice at four different life stages (6, 12, 20, and 28 months). We showed that aging soleus muscle mice follows and shift on gene expression pattern during aging. Network analysis showed that modules enriched in mitochondria showed a down-then-up trend during aging, resembles the expression pattern of longevity-associated modules in C.elegans. We also associated expression of conserved module with frailty and found that the expression of the mitochondria/ribosome module is positively associated with frailty at 28 months in male mice. In addition, we treated mice with four different compounds from 20 months to 28 months, recorded their frailty change over time and performed RNA-seq on their soleus muscles. We found that aKG treatment in male mice significantly reduced frailty index and exhibted an decrease in expression of mitochondria/ribosome modules. Together, we represent a large transcriptomic cohort of aging and drug interventions on mouse soleus muscles. Our study showed the sex-specific beneficial effects on compounds that identified conserved co-expression modules during aging that are associated with longevity.

overall_design: 6- and 12-months old C57Bl/6 mice (Invivos, Singapore) and 20-months old C57Bl/6 mice (Jackson laboratory, USA) were brought in and allowed to acclimatize 2 months prior to start of experiment. Mice are kept in the standard 12/12 light-dark cycle with control feed (Teklad 2918, Envigo, USA) and water ad libitum. Mice were then humanely euthanized, and soleus was immediately placed in RNALater for 24hours, removed and immediately frozen until RNA extraction. A separate group of mice were brought in at 17 months old and allowed to acclimatize for 3 months before being randomized into control and respective geroprotective compounds. All feed was provided ad libitum. Frailty Index scoring was performed at baseline and every other month. Mice were humanely euthanized at endpoint, and soleus was immediately placed in RNALater for 24hours, removed and immediately frozen until RNA extraction.

first: Jasinda

last: Lee

first: Shivaanishaa

last: Raventhiran

first: Brian K

last: Kennedy

first: Esther

last: Wong


title: Long-term immune and extracellular matrix remodeling in the mouse cornea after open-field blast injury

city: Columbia

first: Rajiv

last: Mohan

state: Missouri

address: 1520 East Rollins University of Missouri

department: Department of Veterinary Medicine and Surgery

institute: University of Missouri

summary: Open-field blast injury (OFBI) can produce long-term ocular surface abnormalities, but the chronic molecular response of the cornea remains poorly defined. In this study, awake, non-sedated C57BL/6J mice were exposed to a single open-field blast generated by detonation of 350 g Composition C-4 explosive at a 3 m standoff distance. Corneas were collected 12 months after blast exposure and compared with age-matched naïve controls using bulk RNA sequencing. Differential expression analysis identified persistent transcriptomic remodeling in OFBI corneas, with clear separation from naïve controls by principal component analysis and hierarchical clustering. The data analysis demonstrated that OFBI induces durable corneal transcriptomic remodeling 12 months after injury.

overall_design: OFBI was induced in awake, non-sedated mice using a single open-field blast generated by detonation of 350 g of Composition C-4 explosive at a 3 m standoff distance. Corneas were collected 12 months after blast exposure. For RNA sequencing, three biological replicates were generated per group, with each replicate consisting of pooled corneas. Total RNA was extracted from corneal tissues, and RNA-seq libraries were prepared and sequenced on an Illumina NovaSeq 6000 platform.

first: Rajnish

last: Kumar

first: Nishant

last: Sinha


title: Arabidopsis NAC103 (AT5G64060) ChIP-seq and DAP-seq data

city: Jinan

first: Pengcheng

last: Li

address: 23788 Gongye North Road

institute: Shandong Academy of Agricultural Sciences

summary: To elucidate the molecular landscape of NAC103-mediated transcriptional regulation in Arabidopsis, we combined chromatin immunoprecipitation sequencing (ChIP-seq) and DNA affinity purification sequencing (DAP-seq) to capture the comprehensive cistrome of NAC103. In this project, we employed the transgenic plants of 35S:NAC103-GFP as the material for ChIP. For DAP-seq, NAC103 protein tagged with Halo (NAC103-Halo) was expressed using Promega’s wheat germ system. These results indicate that NAC103 can directly target promoter regions of ANTHRANILATE SYNTHASE ALPHA SUBUNIT 1 (ASA1, AT5G05730) and Acetyl-coenzyme A Carboxylase 2 (ACC2, AT1G36180).

overall_design: ChIP assays were performed using 5-day-old 35S:NAC103-GFP seedlings. Under normal growth conditions, NAC103 protein accumulation is relatively low due to proteasome-mediated degradation. To enhance immunoprecipitation efficiency, seedlings were treated with 20 µM MG132 for 24 h before harvest. For DAP-seq, total genomic DNA was extracted from 5-d-old Arabidopsis seedlings.


title: Targeting the splicing factor hnRNP M with an endogenous circular RNA aptamer suppresses cancer metastasis [shhnRNPM]

city: chengdu

first: PAN

last: YiTong

address: Wangjiang Street

summary: Alternative splicing (AS) is a key regulatory mechanism that expands transcriptomic diversity and is frequently hijacked by cancer cells to drive epithelial-mesenchymal transition (EMT), thereby promoting invasion and therapy resistance. However, therapeutic strategies to reprogram pathological AS networks remain limited. Here, we identified a circular RNA, MASCOT (hnRNP M-ASsociated Circular RNA Of TGFβ), that functions as an endogenous aptamer targeting the splicing factor hnRNP M, a central regulator of EMT-related AS reprogramming. As an endogenous repressor of hnRNP M, MASCOT maintains the epithelial status of cancer cells and suppresses tumor metastasis. Conversely, its downregulation by TGFβ releases hnRNP M to initiate EMT-associated splicing changes. Restoring MASCOT expression significantly reduces metastatic burden in mouse models. Mechanistically, MASCOT scaffolds hnRNP M to nucleolin within the nucleolus, spatially sequestering hnRNP M away from the spliceosome. Our findings reveal a novel regulatory circuit that controls EMT-linked splicing and identify MASCOT as a promising RNA-based therapeutic candidate against metastatic progression.

overall_design: To assess the global contributions of the hnRNP M on alternative splicing during EMT, we performed RNA-seq on A549 cells expressing shRNAs targeting hnRNP M, with or without TGFβ stimulation. In the SCR cells, TGFβ induced 13,726 AS events (|ΔPSI| > 0.1), which were defined as “TGFβ-responsive AS events”.  Consistently, hnRNP M depletion attenuated the TGFβ responsiveness of nearly half of these AS events (Supplementary Fig. 2b, |ΔPSI| < 0.1), with 4,131 AS events commonly affected by two hnRNP M-targeting shRNAs (defined as TGFβ/hnRNP M-regulated AS events).

first: Jiawei

last: Guo

first: Yitong

last: Pan


title: Multi-platform genomic analysis of matched well- and dedifferentiated liposarcomas identify novel risk and progression determinants [aCGH]

city: New York

first: Bic

last: MSKCC

state: NY

address: 1275 York Ave.

institute: Memorial SLoan-Kettering Cancer Center

type: Genome variation profiling by genome tiling array

summary:
To define mechanisms that regulate biological behavior in well- and dedifferentiated liposarcoma (WD/DDLS) subsets, we describe an integrative analysis of DNA sequence, copy number and gene expression in 9 paired WDLS and DDLS samples with validation cohorts and in vitro studies. Amplification of 12q13-15 was common to all WDLS; 6q23-25 amplifications were observed 18% of WDLS and were associated with increased TAB2 and higher local recurrence risk versus non-6q-amplified WDLS. TAB2 knockdown decreased MDM2 protein expression and induced markers of cellular senescence in 6q23-25-amplified WDLS cells but not in non-amplified WDLS of amplified DDLS cells. Amplification of 6q23-25 was not associated with DDLS recurrence risk or progression from WDLS to DDLS. Instead, pathogenic ATRX mutations, recurrent losses in 13q and gains in 8q12-21 accompanied dedifferentiation. Downregulation of the 13q-encoded genes MYCBP2 and IRS2 was observed in DDLS versus WDLS; in vitro, these genes were essential for WDLS cell differentiation. Taken together, this study defines a copy number-driven model of liposarcoma initiation, progression, and differentiation.
Array comparative genomic hybridization (aCGH) was performed using Agilent 244K or 1M arrays and analyzed using the RAE pipeline as previously reported (Barretina J, et. al, Nat Genet. 2010;42(8):715-21, PMC2911503 and Crago AM, et. al, Clin Cancer Res. 2012;18(5):1334-40, PMC3294014)

overall_design: A total of 186 array comparative genomic hybridization (aCGH) samples were profiled, representing patient samples from various clinical subtypes. No biological or technical replicates were included. Each array is a two-color (two-dye) hybridization, with patient genomic DNA co-hybridized against a common reference: Human Genomic DNA derived from blood (buffy coat) (Roche Applied Science), used as the on-chip control for the aCGH assay. Full hybridization conditions are detailed in the hybridization protocol.

first: Aimee

last: Crago

first: Nicholas

last: Socci

first: Samuel

last: Singer


title: Reciprocal, methylation-dependent binding of Zfp57 and Gzf1 safeguards Dlk1-Dio3 imprinting during developmental reprogramming

city: rehovot

first: irina

last: miodownik

address: Herzl 234

country: Israel

institute: Weizmann Institute of Science

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

platform_organism:
Mus
synthetic construct

overall_design: Refer to individual Series


city: Rehovot

first: Yonatan

last: Stelzer

address: Procurement Division 234 Herzl St.


title: Multi-platform genomic analysis of matched well- and dedifferentiated liposarcomas identify novel risk and progression determinants.


title: Single-cell RNA-seq profiling of human bronchial epithelial preparations from non-CF and CF samples

city: Pozzuoli

first: Michele

last: Genovese

address: Via Campi Flegrei 34

institute: Tigem

summary: Single-cell RNA-seq was performed on human bronchial epithelial preparations derived from non-cystic fibrosis and cystic fibrosis samples. The dataset includes untreated BE63 non-CF cells, untreated BE73 CF cells, and BE63 non-CF cells treated with TNFα + IL-17 or IFNα.

overall_design: Single-cell RNA-seq was performed on four human bronchial epithelial samples/conditions. BE63 represents a non-cystic fibrosis bronchial epithelial preparation derived from a non-CF individual, whereas BE73 represents a cystic fibrosis bronchial epithelial preparation derived from a CF patient. The dataset includes two untreated samples, BE63_NON_CF_NT and BE73_NT, which differ by CF status, and two treated BE63 non-CF samples: BE63_NON_CF_TNFa_IL17, treated with TNFα + IL-17, and BE63_NON_CF_IFNa, treated with IFNα. BE63 and BE73 are independent biological samples/preparations. Each treated condition is represented by one biological sample. Raw FASTQ files and processed feature-barcode matrices are provided for each sample.

first: Alessandro

last: Giordano


title: Targeting the splicing factor hnRNP M with an endogenous circular RNA aptamer suppresses cancer metastasis

overall_design: To assess the global impact of the MASCOT/hnRNP M interaction on alternative splicing during EMT, we performed RNA-seq on A549 cells expressing either wide-type MASCOT or its hnRNP M-binding-deficient variant (mhM), with or without TGFβ stimulation. In mhM-overexpressing cells, 9,544 AS events were identified (|ΔPSI| > 0.1) and defined as “TGFβ-responsive AS events” . In contrast, wild-type MASCOT expression attenuated the responsiveness of 4,149 out of these 9,544 events (43.5%; |ΔPSI| < 0.1) . Because mhM cannot bind hnRNP M, these 4,149 events, whose responsiveness was lost upon wild-type MASCOT expression, are likely regulated through MASCOT-hnRNP M interaction and were therefore defined as MASCOT/hnRNP M interaction-dependent AS events.


title: L-2-Producing Tfh Cells Sustain Treg Homeostasis and Immune Tolerance in the Gut

city: Bethesda

first: Tom

last: Hill

state: Maryland

address: NIHBC 10 - CLINICAL CENTER BG RM 11N244A, 10 CENTER DR

institute: NIAID

summary: T follicular helper (Tfh) cells are well known for their role in supporting B cell responses. Here, we identify a critical B cell-independent function for Tfh cells in sustaining regulatory T (Treg) cells within gut-associated lymphoid tissues (GALT). We demonstrate that Tfh cells produce IL-2 at the T-B border and within interfollicular (IF) regions, and that this localized IL-2 is required to maintain GALT Treg homeostasis and restrain the expansion of pathogenic effector T cells. Mice selectively lacking IL-2-producing Tfh cells develop colitis and fatal multiorgan inflammation, driven by impaired GALT Treg responses and uncontrolled effector T cell activation. Broad-spectrum antibiotic treatment alleviates both intestinal and extraintestinal pathology, indicating that loss of tolerance to commensal-derived antigens is a key driver of disease. Together, these findings define a spatially restricted Tfh-derived IL-2 niche critical for GALT Treg stability and uncover an unexpected immunoregulatory role for Tfh cells in maintaining gastrointestinal tolerance beyond B cell help.

overall_design: single cell sequencing and antibody sequencing of mus musculus PBMCs, WT and mutant

first: Shivangi

last: Dave

first: Holly

last: Bachus

first: Nathan

last: Santiago

first: Audrey

last: Meloun

first: Margery

last: Smelkinson

first: Jeremy

last: Foote

first: Christopher

last: Fucile

first: Alexander

last: Rosenberg

first: Andre

last: Ballesteros-Tato


title: Human-specific morphoregulatory signatures in basal radial glia characterise neocortex evolution [atac_gorilla]

city: Dresden

first: Mareike

last: Albert

address: Fetscherstr. 105

department: Center for Regenerative Therapies TU Dresden

institute: TUD Dresden University of Technology

summary: As the seat of our cognition, the human neocortex is an object of immense fascination. Human neocortex expansion during evolution has been attributed to an increase in the proliferative capacity of neural progenitor cells during development, particularly basal radial glia. Despite their evolutionary relevance, the genomic changes driving human basal radial glia biology remain uncharacterized. We used comparative chromatin and transcriptional profiling of neural progenitor cells isolated from gorilla, chimpanzee and human cerebral organoids to identify cis-regulatory elements that have gained activity in humans. Focusing specifically on basal radial glia, we discovered that morphoregulatory enhancer activity and gene expression signatures distinguish human basal radial glia from other great apes. Functional analysis of the morphoregulatory genes FAM107A and CNGA3 in human organoids revealed that these genes contribute to the morphological complexity of human basal radial glia. Taken together, our inter-species comparison of basal radial glia suggests that human-specific morphoregulatory signatures characterise neocortex evolution.

overall_design: Fluorescence-activated cell sorting of apical radial glia (aRG), basal radial glia (bRG), basal intermediate progenitor cells (bIP) and neurons (N) of gorilla cerebral organoids at week 8 of culture for bulk ATAC-seq

first: Theresa

last: Schütze

first: Silvia

last: Vangelisti

first: Boyan

last: Bonev


title: Human-specific morphoregulatory signatures in basal radial glia characterise neocortex evolution.

sample_organism:
Gorilla gorilla gorilla
Pan troglodytes

platform_organism:
Gorilla gorilla gorilla
Pan troglodytes


title: Human-specific morphoregulatory signatures in basal radial glia characterise neocortex evolution [rna_gorilla]

overall_design: Fluorescence-activated cell sorting of apical radial glia (aRG), basal radial glia (bRG), basal intermediate progenitor cells (bIP) and neurons (N) of gorilla cerebral organoids at week 8 of culture for bulk RNA-seq


title: Chronic TGFβ1 Signaling Drives Dysplastic Alveolar-Basal Metaplasia through a KRT17-Stratifin migratory complex

city: New York City

first: Jaymin

last: Kathiriya

address: 1425 Madison Ave

department: Pulmonary

institute: Icahn School fo Medicine at Mount Sinai

summary: Chronic fibrotic disorders like idiopathic pulmonary fibrosis (IPF) are characterized by dysplastic alveolar regeneration and severely limited treatment options. Identification of the mechanisms driving aberrant epithelial repair can lead to new viable therapeutic targets. Using integrated single nucleus ATAC- and RNA-sequencing on human lungs and an in vitro model of dysplastic repair, we identify two distinct regenerative trajectories for alveolar type 2 (AT2) cells: a resolvable euplastic repair trajectory and a persistent non-resolving dysplastic repair trajectory, which is governed by a spatially restricted ITGB6/TGFβ1/SMAD3 signaling axis in fibrotic regions of IPF lungs and murine lungs characterized by chronic epithelial remodeling. Mechanistically, SMAD3 directly regulates DTC markers, including KRT17 and Stratifin. We show that TGFβ1 signaling promotes a physical interaction between KRT17 and Stratifin at the leading edge of migrating dysplastic transitional cells in vitro and in vivo, which is essential for their migratory capacity. These findings collectively define the molecular regulation of AT2-driven dysplastic regeneration and identify TGFβ1-induced KRT17-Stratifin axis as a central driver of pathological epithelial remodeling in chronic fibrosis, which can be targeted therapeutically to tilt the balance in favor of euplastic regeneration.

overall_design:
Single cell suspension of all cells prior to library prepration
10X Genomics Multiome Library Prep
Active Motif CUT&RUN kit

first: Isha

last: Sahasrabudhe


title: CXCL10 contributes to female-specific pathological progression in tauopathy model mice

city: Nagoya

first: Ryohei

last: Uenishi

state: Aichi

address: 1 Kawasumi, Mizuho-cho, Mizuho-ku,

department: Neurocognitive Science

institute: Nagoya City University

summary:
Neuroinflammation plays a central role in the progression of tauopathy via the glial activation and T cell accumulation in the brain parenchyma. However, the key molecular mediators that link these processes to tau pathology remain poorly understood.
Here, we identify C-X-C motif chemokine ligand 10 (CXCL10) as a critical inflammatory mediator that is markedly upregulated in the brains of P301S-mutant tau transgenic mice and associated with regions of severe tau pathology. Spatial transcriptomics revealed that CXCL10 is mainly expressed by disease-associated astrocytes, defining an astrocytic CXCL10-rich inflammatory niche within the tauopathy brain.
Genetic ablation of Cxcl10 significantly attenuated soluble and insoluble tau accumulation selectively in 9-month-old female mice, whereas no attenuation of tau accumulation was observed at 11–12 months of age. In addition, Cxcl10 deficiency significantly prolonged survival specifically in female tauopathy mice. Although Cxcl10 deficiency reduced the number of parenchymal T cells in both sexes, this reduction did not explain the female-specific effects. Furthermore, Cxcl10 deficiency did not alter neurodegeneration and motor dysfunction, suggesting that downstream sex-dependent regulatory mechanisms govern tauopathy progression. Moreover, CXCL10-dependent inflammatory activation within the local microenvironments was observed in both sexes. Although the molecular mechanisms underlying the sex-dependent effects of CXCL10 remain unclear, these findings suggest that CXCL10 contributes to tau pathology through multiple inflammatory pathways.
In summary, our findings identify CXCL10 as a key inflammatory mediator of sex specific tau-associated pathology.

overall_design: To investigate the role of CXCL10 in the progression of tauopathy, we performed RNA-seq using four mouse genotypes: (1) Wild type, (2) Cxcl10 knock out, (3) Tau transgenic, and (4) Tau Tg; Cxcl10 knock out. All mice used were 12-month-old males. Each group consisted of three biological replicates.

first: Masanori

last: Hijioka

first: Takashi

last: Saito


title: Human-specific morphoregulatory signatures in basal radial glia characterise neocortex evolution [atac_chimp]

overall_design: Fluorescence-activated cell sorting of apical radial glia (aRG), basal radial glia (bRG), basal intermediate progenitor cells (bIP) and neurons (N) of chimpanzee cerebral organoids at week 8 of culture for bulk ATAC-seq


title: Human-specific morphoregulatory signatures in basal radial glia characterise neocortex evolution [rna_chimp]

overall_design: Fluorescence-activated cell sorting of apical radial glia (aRG), basal radial glia (bRG), basal intermediate progenitor cells (bIP) and neurons (N) of chimpanzee cerebral organoids at week 8 of culture for bulk RNA-seq


title: SLC38A2 mediates selective L-serine influx across the blood-brain barrier and controls brain D-serine and excitatory synapse development

city: haifa

first: Herman

last: Wolosker

address: 1 Efron St

department: Biochemistry

institute: Technion-Israel Institute of Technology

summary: L-Serine is essential for brain metabolism, serving as a precursor for the synthesis of the neuromodulator D-serine, glycine, and lipids. Contrary to the prevailing view that brain L-serine is derived exclusively from local synthesis, our findings demonstrate that dietary L-serine is required to maintain brain L-serine levels and the production of its downstream metabolites. Sphingolipidome analysis indicates that dietary restriction of serine/glycine leads to the formation of neurotoxic 1-deoxysphingolipids and affects the expression of circadian and endothelial cell genes in the hippocampus. We identified the glutamine transporter SLC38A2 as a selective L-serine transporter at the BBB that mediates the influx of circulating L-serine to the brain.  Endothelial-selective Slc38a2 knockout (Slc38a2-cKO) decreased in vivo blood-to-brain L-serine influx and selectively lowered hippocampal L-serine and D-serine in mouse pups. Isotope tracing experiments confirmed reduced incorporation of L-serine into the brain of Slc38a2-cKO pups but revealed normal incorporation of L-glutamine, indicating that SLC38A2 does not use L-glutamine at this age. Serine-to-glycine conversion in Slc38a2-cKO pups was preserved, while the de novo synthesis of glycine from glucose was higher in the cerebral cortex. Slc38a2-cKO pups exhibited ultrastructural defects at excitatory synapses, including reduced synaptic vesicle cluster size and decreased postsynaptic density area. Immunoelectron microscopy demonstrated that SLC38A2 is localized to both the luminal and abluminal endothelial membranes, supporting a dual role for this transporter at the BBB. Luminal SLC38A2 appears to serve as a selective route for L-serine transport across the BBB during early postnatal development and is required for excitatory synapse maturation. In contrast, abluminal SLC38A2 is more consistent with a role in the equilibrative efflux of brain-derived SLC38A2 substrates. SLC38A2 inhibition may be beneficial for limiting D-serine accumulation in the brain, particularly in conditions with pathologically elevated D-serine levels, such as traumatic brain injury, epilepsy, and neurodegenerative disorders.

overall_design: 1-RNA-seq profiling of hippocampi isolated from 3-week-old mice fed a serine/glycine-deficient diet (-SG also called RD) for 10 days and compared with littermates receiving an amino acid-defined control diet (CD) Slc38a3 (Slc38a3-cKO) in endothelial cells. 2- P11 pups from WT and Slc38a2-cKO were analyzed by bulk RNAseq of the hippocampus


overall_design: To investigate CXCL10- and CXCR3-expressing cell types in a tauopathy mouse model, we performed Xenium-based spatial transcriptomic analysis using four 12-month-old mice: (1) a male wild-type mouse, (2) a male Tau transgenic mouse, (3) a female wild-type mouse, and (4) a female Tau transgenic mouse.


title: Combining ASCL1 and NEUROD1 reprograms human RPE into neurons of distinct lineages

city: Seattle

first: Thomas

middle: A.

last: Reh

state: WA

address: 1959 NE Pacific Street

department: Neurobiology and Biophysics

institute: University of Washington

summary: There are currently few promising approaches for treatment of photoreceptor pathologies: for example, gene therapy to augment or replace mutated genes, has proven successful in preclinical studies, and some of these therapies are moving towards the clinic. Another approach aims to unlock the inherent stem-cell potential of non-neuronal retinal cells to regenerate neurons in situ. This line of research is based on the discovery that some vertebrates can restore even severely damaged retina from RPE with all the necessary cell types to regain full functionality. In this study we first established a robust in vitro culture system based on isolated fetal human RPE. We then employed a barcode-multiplexed, single cell RNAseq based screen to find factors that would reprogram human RPE into a photoreceptor-like state. With this approach we were able to identify NEUROD1 as a complimentary factor to ASCL1. Their combined overexpression together with a treatment with bFGF and Activin A inhibitor produced RPE-derived neuronal cells with expression patterns characteristic of different lineages.

overall_design: Primary human fetal RPE was cultured. Cultures were infected with lentiviruses delivering overexpression cassettes for different factors for the purpose of RPE to neuron reprogramming.

first: Lew

last: Kaplan

first: Abby

last: Greeen

first: Jaz

last: Pang

first: Marina

last: Pavlou

first: Juliette

last: Wohlschlegel