title: Somatic deficiency of human E3 ubiquitin ligase CBL in leukocytes  Impairs B cell but not T cell development and function

first: Anna-Lena

last: Neehus

address: 1 Blackfan Circle

institute: Boston Children's Hospital

summary: The casitas B lineage lymphoma (CBL) proto-oncogene promotes positive selection and antigen responses in murine T lymphocytes by ubiquitinating ZAP70. However, CBL and CBL-B are redundant for ubiquitination of SYK and regulation of B cell receptor (BCR) signaling in murine B cells. We studied lymphocyte development, maturation and function in patients with somatic homozygosity for CBL loss-of-function variants in leukocytes. Surprisingly, human CBL is largely redundant for the development and function of human T cells. Conversely, CBL is critical for B cell development and function. Patients with somatic, hematopoietic CBL deficiency have a 10-fold increase in transitional B cells during childhood and are susceptible to bacterial infections. CBL deficiency impairs B cell maturation in a cell-intrinsic manner through reduced apoptosis and dysregulated BCR signaling, thereby reducing the proportions and numbers of memory B cells. Overall, our findings demonstrate that CBL deficiency has two major effects on human B cells. First, B-cell development in the bone marrow is altered at the immature stage, resulting in enhanced survival and differentiation of autoreactive B cell clones and impaired B cell tolerance, manifested as the production of autoantibodies. Second, the generation of antigen-specific B cells is impaired, thereby disrupting the establishment of adaptive immune memory. Thus, our study reveals the critical role of human CBL in B cells and its redundancy in T cells.

overall_design: Umbilical cord blood CD34+ hematopoietic stem and progenitor cells were edited at the AAVS1 safe harbor locus (n=2), the CBL locus (in frame exon 8 deletion; n =2) or base edited use ABEm8 at the PIK3CD locus (n=1) to generate the p.C416R gain-of-function variant. To initiate B cell differentiation, the edited CD34+ cells were co-cultured with MS-5 stroma cells in the presence of IL-7. At day 21 of co-culture (day 24 post editing), the cells were collected from the MS5, sorted for CD19+CD10+CD20dim and subsequently rested for 12 hours in RPMI+10%FBS. RNA was extracted from each sample in duplicates using the Total RNA Purification Micro Kit (Norgen, #35300) according to the manufacturer’s instructions. All samples were treated with DNase I to remove residual genomic DNA.

first: Vijay

middle: G

last: Sankaran


title: In toto imaging reveals intravascular proliferation promotes transmigration of daughter cells during brain invasion of Cryptococcus neoformans

status: Public on Nov 10 2025

city: Shanghai

first: Donglei

last: Sun

address: 800 Dongchuan RD. Minhang District

department: School of Life Sciences and Biotechnology

country: China

institute: Shanghai Jiao Tong University

type: Expression profiling by high throughput sequencing

summary: Cryptococcus neoformans causes lethal cryptococcal meningoencephalitis. Although the mechanism of blood-brain barrier (BBB) transmigration has been widely studied, the predominant route remains unclear due to technical limitations. Here, we developed a whole-organ imaging workflow, termed fTRACE, that enables in toto visualization of individual fungal cells within host tissue. Further labeling of host counterparts revealed in situ host-pathogen interaction in detail. We utilized fTRACE to address the major route of fungal brain invasion and found C. neoformans can proliferate intravascularly within capillaries prior to BBB transmigration. Notably, by distinguishing mother and daughter cells in vivo, we discovered that daughter cells, rather than mother cells, predominantly transmigrate via the paracellular route. We also identified key factors supporting fungal proliferation in serum as mimicry of intravascular environment. RNA sequencing revealed that serum-growing fungi exhibit a markedly altered gene expression profile. In particular, de novo purine biosynthesis is essential for serum and intravascular proliferation. A fluorescent strain deficient in purine synthesis allowed us to trace the fate of non-proliferating fungi during prolonged brain infection. Unlike inert polystyrene beads, fungal cells showed significantly reduced wash-away events from capillaries - a process enhanced by VEGFR inhibition. For those fungi remain in the brain, the majority remained trapped in capillaries, while a smaller portion was able to induced local capillary pruning. Angiophagy, presumably by transcellular pathway, was detectible but at a low frequency. Collectively, this study not only elucidates the major route of brain invasion by C. neoformans, but also set a paradigm for studying host pathogen interactions using in toto imaging approach.

overall_design: RNA-seq profiling of C. neoformans grown in mouse serum versus rich medium(Sabouraud dextrose broth) for 12 hours.


title: Chemoradiation Reprograms Tumor Cells and Immune Microenvironment In Cervical Cancer [scRNA-seq]

city: St. Louis

first: Julie

middle: K.

last: Schwarz

state: MO

department: Radiation Oncology

country: USA

institute: Washington University in St. Louis

summary: Despite advances in screening and prevention, cervical cancer remains a leading cause of cancer-related deaths worldwide, underscoring the need for better treatments. Here, we present a multi-cohort longitudinal study of human cervical tumors and the tumor microenvironment during chemoradiation therapy (CRT). Integrating RNA sequencing, single-cell transcriptomics, and in vivo validation, we define the cellular and molecular programs shaping cell interactions and document how CRT alters them. We identify multiple therapeutic targets in CRT-resistant tumors, notably MDM2, a key mediator of radiation responses in tumor and immune cells. MDM2 inhibition enhanced radiotherapy effects in HPV-positive, TP53 wild-type cervical cancer cells, improved radiation response and reshaped the immune landscape in preclinical models. These findings highlight the potential of combining MDM2 inhibition with CRT to overcome resistance and improve patient outcomes. Our data provides novel insights into therapy-induced changes in tumor and immune compartments, guiding new strategies against treatment-resistant HPV-positive cancers.

overall_design: scRNA-seq of primary tumor samples from 10 cervical cancer patients treated with definitive chemoradiation obtained before treatment (pre-RT), and at 1–2 weeks (on-RT#1) and 2–3 weeks (on-RT#2) after the initiation of chemoradiation

first: Tito

middle: A

last: Sandoval

first: Yize

last: Li

first: Naoshad

last: Muhammad

first: Tresha

last: Desai

first: Reyka

last: Jayasinghe

first: Saman

last: Zeeshan

first: Kay

last: Jayachandran

first: Matthew

last: Inkman

first: Michael

middle: R

last: Waters

first: Naomi

last: Msengi

first: Tyler

last: Mckinnish

first: Ibrahim

last: Hatipoglu

first: Ana

middle: C

last: Paschoalini Mafra

first: Muyassar

last: Anwar

first: Donghua

last: Hu

first: Dhaval

last: Bhatt

first: Varintra

last: Lander

first: R. Jay

last: Mashl

first: Liyun

last: Chen

first: Jessika

last: Contreras

first: Clifford

last: Robinson

first: Sherri

last: Davies

last: Belmar

first: Shunqiang

first: M. Benjamin

last: Major

first: David

last: DeNardo

first: Stephanie

last: Markovina

first: Brian

middle: T

last: Edelson

first: Jin

last: Zhang

first: Li

last: Ding

middle: K


title: Age-dependent immune responses and resident cell dynamics in young mice following pneumonia

city: Philadelphia

first: Sylvia

middle: N

last: Michki

state: PA

address: 3615 Civic Center Blvd

department: Pulmonary & Sleep Medicine

institute: Children's Hospital of Philadelphia

summary: A developmental murine model of pneumonia was used to investigate how lower respiratory tract E. coli infections differentially affects lung immune responses and cell behavior in young mice (neonates; PND5 and juveniles; PND12). Acutely, juveniles recover more quickly than neonates, but alveolar simplification occurred in both groups 6-8 weeks post-infection. Single-cell RNA sequencing revealed transient inflammatory responses in neutrophils, macrophages, and fibroblasts at 48 h post infection in both age groups with a partial return to baseline by 96h. The highly proliferative neonatal alveolar type 2 (AT2) cells showed a modest decrease at 48h post infection, whereas the quiescent juvenile AT2 cells exhibited a proliferative response only post-infection. Neonatal PDGFRα+ fibroblasts had higher expression of inflammatory genes post infection than juveniles and in vitro stimulation of PDGFRα+ fibroblasts with LPS-exposed primary macrophages alone, induced expression of the inflammatory marker SAA3. We conclude that early-life pneumonia alters lung homeostasis in an age-differential manner, potentially affecting lung structure and function in adulthood.

overall_design: Unsorted cells from the lungs of multiple C57Bl/6 WT mice aspirated at either PND5 (neonatal) or PND12 (juvenile) with either PBS, E. coli, or room air and sacrificed at either 48hr or 96hr post-aspiration were loaded into independent lanes of a 10X Chromium GEX 3’ v3 microfluidics chip for 3’-biased scRNA-seq.

first: Benjamin

middle: D

last: Singer

first: Sharon

last: McGrath-Morrow


title: Chemoradiation Reprograms Tumor Cells and Immune Microenvironment In Cervical Cancer [bulk RNA-seq]

first: Julie

last: Schwarz

overall_design: RNA-seq profiling of biopsies of primary cervical tumors from patients treated with definitive chemoradiation collected at pre-treatment and at week 3 of treatment

first: Tito

last: Sandoval

first: Yize

last: Li

first: Naoshad

last: Muhammad

first: Tresha

last: Desai

first: Reyka

last: Jayasinghe

first: Saman

last: Zeeshan

first: Kay

last: Jayachandran

first: Matthew

last: Inkman

first: Michael

last: Waters

first: Naomi

last: Msengi

first: Tyler

last: Mckinnish

first: Ibrahim

last: Hatipoglu

first: Ana

last: Paschoalini Mafra

first: Muyassar

last: Anwar

first: Donghua

last: Hu

first: Dhaval

last: Bhatt


title: The effect of Slc6a6 loss on MSC function.

city: Rochester

first: Cameron

last: Baker

state: NY

address: 601 Elmwood Ave

institute: University of Rochester

summary: RNA sequencing analysis was performed on MSCs isolated from age and sex matched Slc6a6 WT/KO mice.

overall_design: Long bones from TauT WT/KO mice were harvested and CD45- MSC cultures were magnetically sorted and processed for RNA-sequencing.

first: Christina

middle: M

last: Kaszuba

first: Jeevisha

last: Bajaj


title: Monocyte control of organismal energy homeostasis

city: Oeiras

first: Rui

last: Martins

address: Rua da Quinta Grande 6

department: Inflammation

country: Portugal

institute: Gulbenkian Institute for Molecular Medicine

summary: Multicellular organisms rely on inter-organ communication networks to maintain vital parameters within a dynamic physiological range. Macrophages are central to this homeostatic control system, sensing deviations of those parameters and responding accordingly to support tissue function and organismal homeostasis. Here we demonstrate that dysregulation of iron metabolism in parenchyma cells, imposed by the deletion of ferritin H chain, is sensed by monocyte-derived macrophages. In response, macrophages support tissue function, energy metabolism and thermoregulation, as demonstrated in bone marrow chimeric and parabiotic mice. This salutary effect is contingent on a transcriptional program, controlled in macrophages by the transcription factor A mitochondria. This transcriptional response acts in a non-cell autonomous manner to support the mitochondria of parenchyma cells, irrespectively of mitochondrial transfer. In conclusion, monocyte-derived macrophages cross-regulate Fe and energy metabolism to support tissue function and organismal homeostasis.

overall_design: Goal: to assess the transcriptomic landscape of FTH-competent vs FTH-deleted monocytes/macrophages in the liver, white adipose tissue and hearts upon global deletion (or not) of ferritin (FTH) in parenchymal cells (from bone marrow chimeras). Specifically, we performed pairwise comparisons of Fth-competent vs. Fth-deleted macrophages from tdTLysMFthR26Δ/Δ vs. tdTLysMFthLysMΔ/ΔFthR26Δ/Δ chimeras, where FTH is deleted in non-hematopoietic tissues (parenchyma), respectively. In addition, we performed pairwise comparisons of Fth-competent macrophages from control tdTLysMFthfl/fl vs. tdTLysMFthR26Δ/Δ chimeras.

first: Birte

last: Blankehaus

first: Faouzi

last: Braza

first: Pedro

last: Ventura

first: Sumnima

last: Singh

first: Sebastian

last: Weis

first: Miguel

last: Mesquita

first: Maria

last: Pires

first: Sara

last: Pagnotta

first: Qian

last: Wu

first: Sílvia

last: Cardoso

first: Elisa

last: Jentho

last: Figueiredo

last: Faísca

last: Nóvoa

first: Vanessa

last: Alexandra Morais

first: Stefanie

last: Wculek

first: David

last: Sancho

first: Moises

last: Mallo

middle: P

last: Soares


title: Effect of Aiolos on virtual memory T cell differentiation and function [ATAC-Seq]

city: Columbus

first: Ken

last: Oestreich

state: Ohio

address: 460 W 12th Ave, Biomedical Research Tower

department: Microbial Infection and Immunity

institute: The Ohio State University College of Medicine

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Virtual memory CD8+ T (TVM) cells provide rapid bystander protection during an infection despite their antigen naivety. In addition, these cells are also capable of antigen-specific response, making them an intriguing part of both the host innate and adaptive immune repertoire. While the innate and adaptive capabilities of these cells have been well characterized, much remains to be defined regarding the mechanisms governing their differentiation and function. Here, we investigate the role of the Ikaros zinc-finger (IkZF) transcription factor Aiolos in regulating CD8+ TVM generation and function. Using bulk RNA-sequencing and Assay for Transposase-Accessible Chromatin (ATAC)-sequencing, we identify differences in gene expression as well as accessibility profiles of key TVM effectors and regulators in TVM cells isolated from the spleen of control (wild-type) and Aiolos-deficient (Ikzf3-/-) mice. These studies will provide mechanistic insight into the regulation of TVM differentiation and function by Aiolos.

overall_design: ATAC-sequencing of TVM cells isolated from the spleen of specific pathogen free WT and Aiolos-deficient mice.

first: Srijana

last: Pokhrel


title: The transcription factor HHEX and the Androgen receptor (AR) drive the mouse adrenal sexual dimorphism

city: Ann Arbor

first: Antonio

middle: Marcondes

last: Lerario

state: MI

address: 109 Zina Pitcher Place, 1528 BSRB

department: MEND

institute: University of Michigan

summary: Glucocorticoids are cholesterol-derived steroid hormones produced by the adrenal gland and widely known for maintaining glucose homeostasis, modulating the immune system, and orchestrating the circadian rhythm. In this study, we defined HHEX as a key regulator of adrenocortical cell function. By using multiple transgenic mouse models, we demonstrate that HHEX shapes AR-dependent sexual dimorphism in the zF following the onset of puberty. HHEX protects lipid droplets integrity from lipophagy induced by AR signaling and its absence results in glucocorticoid insufficiency in males.

overall_design: CUT&Tag of the histone modification H3K27ac and AR in the male mouse adrenal gland. A total of 6 male mouse adrenals was dissociated and 280 000 nuclei were used per Cut&Tag reaction using the kit CUT&Tag-IT (Active motifi, #53170) and AMPure XP reagent (Beckman Coulter, A63880)

first: Typhanie

last: Dumontet


title: Effect of Aiolos on virtual memory T cell differentiation and function

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

overall_design: Refer to individual Series


title: Effect of Aiolos on virtual memory T cell differentiation and function [RNA-Seq]

overall_design: RNA-sequencing of TVM cells isolated from the spleen of specific pathogen free WT and Aiolos-deficient mice.Also included is naïve WT CD8+ T cells from the spleen of unifected mice.


title: Regulation of ribosomal gene expression and senescence by a PML-mTOR-RONIN nuclear complex in triple-negative breast cancer [ChIP-seq_PML]

city: Montréal

first: Vincent

last: Giguère

state: QC

address: 1160 Pine Ave West, McIntyre Bldg Room 710

department: Goodman Cancer Centre

country: Canada

institute: McGill University

summary: Triple-negative breast cancer (TNBC) is the most aggressive form of breast cancer that associates with poor prognosis and a high risk of relapse with limited treatment options. While the induction of senescence, a state of arrested cell growth, is generally achieved by available anticancer treatments, senescence can adversely promote tumorigenesis through an upheld augmented inflammatory state called senescence-associated secretory phenotype (SASP). Thus, the precise delineation of underlying regulatory mechanisms governing senescence is urgently needed. Herein, we investigated the beneficial anticancer senescence response elicited by silencing of the expression of the promyelocytic leukemia protein (PML) in TNBC, where it exerts an oncogenic role. Functional genomics studies implicated the downregulation of a specific set of ribosomal protein (RP) genes tied to poor clinical outcome. Re-introduction of RPL38 or RPL39L alone but not RPS14, a favorable outcome-associated RP, was sufficient to block the senescence phenotype induced by PML knockdown. RP gene regulation by PML was found to involve the assembly of a previously unrecognized PML-mTOR-RONIN transcriptional complex at their promoters. Furthermore, we show that RONIN levels are elevated in TNBC and that RONIN silencing can recapitulate the senescent phenotype of PML-deficient cells. This work offers new therapeutic insights for TNBC that involve senescence-inducing therapies or senolytics.

overall_design: PML ChIP-seq experiments were performed on TNBC MDA-MB-231 cells with input controls as a reference for peak calling. Duplicate experiments were performed and the sequencing data were merged together.

first: Younes

last: Medkour

first: Mathieu

last: Vernier

first: Catherine

last: Dufour


title: Effect of Hhex and AR deletion on mouse adrenal gene expression

summary: Glucocorticoids are cholesterol-derived steroid hormones produced by the adrenal gland and widely known for maintaining glucose homeostasis, modulating the immune system, and orchestrating the circadian rhythm. In this study, we defined HHEX as a key regulator of adrenocortical cell function. By using multiple transgenic mouse models, we demonstrate that HHEX shapes AR-dependent sexual dimorphism in the zF following the onset of puberty. HHEX protects lipid droplets integrity from lipid catabolism induced by AR signaling and its absence results in glucocorticoid insufficiency in males. Additionally, in both sexes, HHEX supports the inner zF transcriptome, including the expression of Abcb1b, a critical regulator of steroids and xenobiotics cellular levels.

overall_design: RNAseq profiling of wildtype (WT) mouse adrenal and conditional deletion of the transcription factor HHEX and androgen receptor AR in the adrenal gland


title: Regulation of ribosomal gene expression and senescence by a PML-mTOR-RONIN nuclear complex in triple-negative breast cancer [RNA-seq_shPML]

overall_design: RNA-seq was performed on TNBC MDA-MB-231 cells with shRNA-mediated knockdown of PML (shPML) or non-targeting shControl (n=3 per condition).


title: Versatile molecular tools enabling customizable DNA methylation editing in plants [BiSulfite-seq]

first: Li

last: He

address: No. 3888 Chenhua Road

department: Shanghai Center for Plant Stress Biology

institute: CAS Center for Excellence in Molecular Plant Science (CEMPS)

type: Methylation profiling by high throughput sequencing

summary: Tools to edit DNA methylation in a targeted manner are vital for clarifying the causal relationships between DNA methylation and its function, as well as for plant breeding and gene therapy; non-specific tools that induce genome-wide DNA methylation changes are valuable for the creation of novel epialleles and performing large-scale screens. Here, by constructing dCas9 fusions to a panel of effectors and cofactors, we uncovered a range of tools for editing DNA methylation, including five tools for DNA methylation and six tools for DNA demethylation. Our tools show diversity of performance in terms of specificity and efficiency, offering either the capacity to target editing DNA methylation or the ability to edit DNA methylation at the genome-wide level. Remarkably, DNA methylation edited by these tools was inherited in the absence of transgene. These versatile tools pave the way for diverse applications in DNA methylation editing and hold promise for advancing plant epigenetic breeding.

overall_design: 127 WGBS

first: Yao

last: Yao

first: Jian-Kang

last: Zhu


title: Regulation of ribosomal gene expression and senescence by a PML-mTOR-RONIN nuclear complex in triple-negative breast cancer


title: Regulation of ribosomal gene expression and senescence by a PML-mTOR-RONIN nuclear complex in triple-negative breast cancer [ChIP-seq_mTOR]

overall_design: mTOR ChIP-seq experiments were performed on TNBC MDA-MB-231 cells with input controls as a reference for peak calling.


title: Elucidating the effects of volatile organic compounds on the inhibition of the phytopathogen Sporisorium scitamineum

city: Campinas

first: Gabriela

middle: F

last: Persinoti

state: São Paulo

address: Rua Giuseppe Máximo Scalfaro, 10.000

department: Brazilian Biorenewables National Laboratory LNBR

country: Brazil

institute: Brazilian Center for Research in Energy and Materials CNPEM

summary: Sugarcane holds substantial agricultural and industrial importance in Brazil and worldwide, primarily due to its use in biofuel production and for a range of biomolecules of diverse biochemical applications. The drive towards sustainable agricultural practices has fostered the interest in the exploration of bioproducts to reduce the dependence on agrochemicals. In this context, microbial volatile organic compounds (VOCs) have emerged as potential biofungicides, offering several advantages over conventional chemical treatments. This study focused on evaluating their antagonistic potential against Sporisorium scitamineum, the causative agent of sugarcane smut disease, and investigated the molecular mechanisms underlying their inhibitory effects. Two Pseudomonas bacterial strains isolated from sugarcane roots exhibited remarkable antagonistic activity against S. scitamineum. Notably, ITA P2F2 completely inhibited the growth of the phytopathogen and was identified as a novel species within the Pseudomonas genus. A total of 63 VOCs were identified from both bacterial isolates, with eight showing inhibitory activity against the phytopathogen. Transcriptomic analyses revealed significant changes in gene expression of S. scitamineum when exposed to VOCs from ITA P2F2, including the downregulation of genes involved in central metabolic pathways, such as carbohydrate metabolism and fatty acid β-oxidation, and the upregulation of genes associated with DNA repair. Potential DNA damage caused by the VOCs was further evidenced through temporal analysis using Fourier Transform Infrared (FTIR) spectroscopy. Additionally, electron microscopy analysis showed structural damage to the fungal hyphae after VOCs exposure. This multidisciplinary study is the first to investigate the inhibition of S. scitamineum using VOCs. Our findings contribute to the molecular understanding of these signaling molecules and highlight their potential as promising bioproducts to replace conventional agrochemicals in the control of sugarcane pathogens.

overall_design: To investigate changes in the gene expression of S. scitamineum and to identify potential genes involved in its growth inhibition, we conducted transcriptomic analyses using RNAseq. S. scitamineum samples were pre-growth for 5 days at 28°C. The collection of cellular pellets were performed after 2 days of co-culture with ITA P2F2, E coli DH5α, and with no VOC-treatment. We used 4 replicates per treatment. RNA extraction was performed with RNeasy Plant Mini Kit (Qiagen). Twelve libraries were prepared using the TruSeq Stranded mRNA Sample Prep LS Kit (Illumina) using 1.5 micrograms of total RNA as imput and sequenced on the Hiseq 2500 instrument.

first: Mulato

last: Aline Tieppo Nogueira

first: Persinoti

last: Gabriela Félix

first: Oliveira

last: Juliana Velasco de Castro


title: Tumor immunity following radiopharmaceutical + checkpoint blockade varies with treatment sequence, radioisotope, and tumor immunogenicity

city: Madison

first: Zachary

last: Morris

address: 1111 Highland Avenue

institute: University of Wisconsin

summary: Radiopharmaceutical therapy (RPT) enhances tumor response to immune checkpoint inhibitors (ICI) in preclinical models, but the effects of different radioisotopes have not been compared. To evaluate mechanisms of response to RPT+ICI, we used NM600, an alkylphosphocholine selectively taken up by most tumors. Effects of 90Y-, 177Lu-, and 225Ac-NM600 + ICIs were compared in syngeneic murine models, B78 melanoma (poorly immunogenic) and MC38 colorectal cancer (immunogenic). 90Y-/177Lu-/or 225Ac-NM600 delivering 2 Gy mean tumor dose promoted tumor regression and improved survival when combined with ICIs in syngeneic mice bearing B78 or MC38 tumors. Regardless of the administered isotope, this combination was optimized with early ICI administration (days -3/0/3) relative to day 1 RPT. 90Y-NM600+ICI produced the greatest anti-tumor response for MC38, whereas high linear energy transfer (LET) alpha particle radiation from 225Ac-NM600+ICI was most effective against poorly immunogenic B78 tumors. Flow cytometry and single cell RNA and T cell receptor (TCR) sequencing illuminated distinct mechanisms of 90Y- or 177Lu-NM600 in promoting expansion of existing adaptive immunity and of 225Ac-NM600 in promoting immune priming when combined with ICI. Antitumor immune response can be achieved with appropriate application of α- or β- emitting RPT in combination with ICIs in diverse murine tumor models.

overall_design: B78 melanoma tumor-bearing mice received either 2 Gy 90Y-, 177Lu-, 225AcNM600 or EBRT on day 1 + ICI (anti-CTLA4 and anti-PD-L1) on days -3/0/3 or ICI alone. Tumors were harvested on day 15, dissociated, and immune cells were isolated by Ficoll density gradient centrifugation for single cell RNA sequencing analysis. All samples had viability > 90%, and were resuspended at a concentration of 1.2 *106 cells/mL in RPMI-1640 for single-cell RNA sequencing.


title: Versatile molecular tools enabling customizable DNA methylation editing in plants [ATAC-seq]

overall_design: 1 ATAC-seq


title: 3D chromatin-based variant-to-gene maps across 57 human cell types reveal the cellular and genetic architecture of autoimmune disease susceptibility [captureC]

first: Khanh

middle: Bao

last: Trang

department: Human Genetics

summary: The genetic basis for many common autoimmune disorders has been uncovered by genome-wide association studies (GWAS), but GWAS do not reveal causal variants, effector genes, or the cell types impacted by disease-associated variation. We have generated 3D genomic datasets consisting of promoter-focused Capture-C, Hi-C, ATAC-seq, and RNA-seq and integrated these data with GWAS of 16 autoimmune traits to physically map disease-associated variants to the genes they likely regulate in over 50 human cell types. These 3D maps of gene cis-regulatory architecture are highly powered to identify the cell types most likely impacted by disease-associated genetic variation compared to 1D genomic features, and tend to implicate different effector genes than eQTL approaches in the same cell types. Most of the variants implicated by these cis-regulatory architectures are highly trait-specific, but nearly half of the target genes connected to these variants are shared across multiple autoimmune disorders in multiple cell types, suggesting a high level of genetic diversity and complexity among autoimmune diseases that nonetheless converge at the level of target gene and cell type. Substantial effector gene sharing led to common enrichment of similar biological networks across disease and cell type, however, trait-specific pathways representing potential areas for disease-specific intervention were identified. To test this, we functionally validated squalene synthase, a cholesterol biosynthetic enzyme encoded by the FDFT1 gene implicated in MS and SLE, as a novel immunomodulatory drug target controlling inflammatory cytokine production by human T cells. These data represent a comprehensive resource for basic discovery of gene cis-regulatory mechanisms, and the analyses reported reveal mechanism by which autoimmune-associated variants act to regulate gene expression, function, and pathology across multiple, distinct tissues and cell types.

overall_design: To investigate the 3D chromatin conformation landscape of different immune cell types, we performed chromatin contacts profile analysis from Promoter-focused Capture-C of different cell types at different stages.

middle: B

first: Megan

last: Levings

first: Struan

last: Grant

first: Andrew

last: Wells


title: Endothelial cells in sepsis - batch 1

city: Münster

first: Klaus

last: Schughart

address: Von-Esmarch-Str 56

department: Virology

country: Germany

institute: University Münster

summary: Differentially expressed genes were identified in lung endothelial cells of CLP-treated mice compared to sham-treated controls and after treatment with sitagliptin. Sitagliptin strongly reduced the inflamatory response.

overall_design: Sepsis was induced in mice by CLP (Cecal Ligation Puncture). Some mice were treated with sitagliptin. Endothelial cells from the lungs of CLP-treated, CLP plus sitagliptin, sham-treated and untreated mice were isolated and subjected to RNAseq analysis. Analysis was done in two batches, this is batch 1.

first: Nana-Maria

last: Wagner

first: Laura

last: Brabenec

first: Katharina

middle: E

last: Hellenthal


title: 3D chromatin-based variant-to-gene maps across 57 human cell types reveal the cellular and genetic architecture of autoimmune disease susceptibility [HiC]

overall_design: To investigate the 3D chromatin conformation landscape of different immune cell types, we performed chromatin contacts matrix profile analysis from Hi-C of different cell types at different stages.


title: 3D chromatin-based variant-to-gene maps across 57 human cell types reveal the cellular and genetic architecture of autoimmune disease susceptibility [RNA-seq]

overall_design: To investigate the expression landscape of different immune cell types, we performed genes expression profile analysis from RNA-seq of different cell types at different stages.


title: ChIP-seq of Deaf1 in myocytes

city: Cardiff

first: NATHAN

last: HARMSTON

address: Museum Avenue

country: United Kingdom

institute: Cardiff University

summary: We identify DEAF1, a FOXO-regulated transcription factor, as a key upstream activator of mTORC1 in aging muscle. In order identify the targets of Deaf1 in myocytes, we performed ChIP-seq to identify its targets in this system

overall_design: 2 replicates of Deaf1 ChIP-seq in myoblasts differentiated from C2C12 cells

first: Nathan

last: Harmston

first: Hong Wen

last: Tang


title: Axon Regeneration and Functional Recovery from Spinal Cord Injury is Enhanced by Allele-Specific ApoE Neuronal Action through Lrp8

city: New Haven

first: Stephen

last: Strittmatter.

state: Connecticut

address: 295 Congress Ave, BCMM Rm433

department: Neurology

institute: Yale University

summary: Adult CNS trauma frequently causes neuronal disconnection and persistent deficits due to failed axon regeneration. While model system screening has identified candidate neural repair genes, ApoE – LRP8 signaling is unique in being implicated clinically. Here, we show that cortical axon regeneration requires LRP8 and is modified by APOE variants. ApoE2-expressing mice show reparative corticospinal and raphespinal axon growth with greater motor function than controls after spinal cord injury. Distinct from ApoE in other settings, there is no change in inflammation or scarring. After axotomy, ApoE exerts allele_x0002_specific effects on LRP8 localization and signaling in cortical neurons. APOE alleles regulate synaptic organization gene expression by cortical neurons after injury, with little effect on glial gene expression. AAV-mediated overexpression of ApoE2 in mice after spinal trauma increased locomotor recovery and reparative axon growth. Thus, a role for ApoE – LRP8 signaling is supported by preclinical and clinical observations, providing a potential site for intervention.

overall_design: Age-matched adult (12-13 weeks) female mice of ApoE2 or ApoE4 genotype were subjected to a thoracic dorsal-over hemisection (injured) or shame (control) surgery.  All animals received subcutaneous injections of 100 mg/kg ampicillin and 0.1 mg/kg Buprenex twice daily for the first 2 d after surgery and additional injections later as necessary. Eleven days post-surgery, the motor cortices of both SCI-injured and control mice were dissected and processed for single nuclei isolation and RNA sequencing for comparative transcriptomic expression profile analysis.

first: Ramakrishnan

last: Kannan

first: Xingxing

last: Wang

first: LaShae

last: Nicholson

first: Nancy

last: Lin

first: Elisa

last: Howard

first: Atrayee

last: Basu

first: Ines

last: Ingabire

first: Yuichi

last: Sekine

last: Strittmatter


title: REV-ERBα regulates regulatory T cell function in inflammatory bowel disease [CUT&RUN]

city: La Jolla

first: Jingting

last: Yu

state: CA

address: 10010 N Torrey Pines Rd

institute: Salk Institute for Biological Studies

summary: Colonic Rorgt+Foxp3+ Treg cells are critical to maintain intestinal homeostasis and prevent inflammatory bowel diseases by suppressing exuberant innate and adaptative immune responses. In this study, In this study, we found that REV-ERB was highly expressed in colonic RORt+Foxp3+ Treg cells and essential for their differentiation and function. Deletion of REV-ERB in Treg cells lead to diminished colonic RORt+Foxp3+ Treg cell populations even at steady state, and render mice more susceptible to TNBS and/or oxazolone-induced colitis. As a transcriptional repressor, REV-ERB can directly repress the expression of pro-inflammatory cytokines IL-17a and IL-17f, and promote RORt expression through Bhlhe40-c-maf axis in RORt+Foxp3+ Treg cells. Furthermore, REV-ERB also orchestrate RORt genome-wide distributions and co-regulate core signature genes in RORt+Foxp3+ Treg cells, including IL-10, CTLA-4, Icos, c-maf.

overall_design: Cleavage Under Targets and Release Using Nuclease (cut&run) for transcription factors RVBa, Foxp3, RORgt, c-maf and BHLHE40 in induced RORgt+iTreg cells.

first: Xianting

last: Hu


title: Amnion-derived serum amyloid A1 participates in sterile inflammation of fetal membranes at parturition

first: Yikai

state: Shanghai

address: Dongchuan Road, No.800

institute: SJTU

summary: Sterile inflammation of the fetal membranes is an indispensable event of normal parturition. However, triggers of the sterile inflammation are not fully resolved. Serum amyloid A1 (SAA1) is an acute phase protein produced primarily by the liver, which is believed to be implicated in the host inflammatory response to ensure early survival. Emerging evidence indicates that SAA1 can also be synthesized in extra-hepatic tissues including gestational tissues. Moreover, SAA1 synthesis is greatly enhanced in gestational tissues at parturition. Given the inflammatory actions of SAA1, we hypothesized that increased SAA1 synthesis locally in the fetal membranes may act as a humoral trigger of sterile inflammation of the fetal membranes at parturition. Here, by using transcriptomic sequencing and multiplex immunoassay, we found that multiple pathways related to chemotaxis were evoked by SAA1 in human amnion fibroblasts along with upregulation of a series of chemokines, particularly CCL3, CXCL6 and CCL20. Mechanistic studies showed that both toll-like receptor 4 (TLR4) and formyl peptide receptor 2 (FPR2) was involved in the induction of chemokines by SAA1. Moreover, SAA1-conditioned culture medium of amnion fibroblasts was capable of chemoattracting virtually all types of mononuclear leukocytes, particularly monocytes and dendritic cells, which reconciled well with the chemotactic activity of conditioned culture medium of amnion tissue explants collected from spontaneous labor. The infiltration of monocytes and dendritic cells to the fetal membranes at parturition was confirmed both morphologically with immunohistochemical staining and quantitatively with Western blotting. Additionally, SAA1 could also activate monocytes/macrophages and dendritic cells towards a proinflammatory phenotype. Conclusively, increased local SAA1 synthesis may trigger sterile inflammation of the fetal membranes at parturition by stimulating chemokine production initially in local cells resulting in increased chemotaxis of mononuclear leukocytes to the membranes to facilitate their transition towards the proinflammatory phenotype.

overall_design: RNA sequencing of  human amnion fibroblasts with or without SAA1 treatment (50 ng/mL, 24 hours).


title: 3D chromatin-based variant-to-gene maps across 57 human cell types reveal the cellular and genetic architecture of autoimmune disease susceptibility [ATAC-seq]

first: Khanh

last: Trang

overall_design: To investigate the chromatin accessibility landscape of different immune cell types, we performed open chromatin regions profile analysis from ATAC-seq of different cell types at different stages.

first: Megan

last: Levings

first: Struan

last: Grant

first: Andrew

last: Wells


title: N1-Methylpseudouridine Directly Modulates Translation Dynamics

status: Public on Nov 09 2025

city: Rehovot

first: Noam

last: Stern-Ginossar

address: 234 herzel

department: Molecular Genetics

country: Israel

institute: Weizmann Institute

summary: The remarkable effectiveness of mRNA vaccines against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has highlighted synthetic mRNA as a promising technology. A critical feature of this approach is the incorporation of the modified ribonucleotide N1-methylpseudouridine (m¹Ψ), which enhances antigen expression while reducing immunogenicity. However, a comprehensive understanding of how this modification influences translation remains incomplete. Here, we analyze translation at sub-codon resolution using ribosome profiling and demonstrate that m¹Ψ increases ribosome density on synthetic mRNAs. This elevated ribosome load, together with the correlated increase in protein production, occurs independently of intrinsic cellular immunity or eIF2α phosphorylation. Our data reveal that m¹Ψ directly slows ribosome elongation in specific sequence contexts while concurrently enhancing translation initiation. Cryo-electron microscopy shows that m¹Ψ-modified mRNAs alter interactions within the ribosome decoding center, providing a mechanistic basis for slowed elongation dynamics. Furthermore, by introducing synonymous mutations that disrupt modification-mediated changes in elongation, we show that the m¹Ψ-dependent effect on protein output can be modulated, and that its impact is strongest in mRNAs containing non-optimal codons with uridines at the wobble position. Together, these findings demonstrate that m¹Ψ directly modulates translation elongation and initiation, thereby enhancing translational capacity and increasing protein output from synthetic mRNAs in defined sequence contexts.

overall_design: All experiments involved comparing in vitro transcripts (IVTs) synthesized with standard UTP to the same IVTs synthesized with either Ψ or m¹Ψ substitutions at all uridine positions. Two specific IVTs were studied in detail: SARS-CoV-2 and luciferase (in two different nucleotide sequence variants). For these IVTs, we performed RNA-seq, Ribo-seq, and, in the case of luciferase, also a chase experiment.  In addition, we generated a library of luciferase-encoding sequences with varying uridine content. For this library, we performed polysome profiling, followed by sequencing of five gradient fractions as well as the total RNA.

first: Batsheva

last: Rozman

first: Karin

last: Broennimann

first: Aharon

last: Nachshon

first: Tamar

last: Arazi


title: Alternative Splicing And Global Transcriptome Changes Associated with LPS Stimulation in Human Peripheral Blood Mononuclear Cells

city: San Francisco

first: Kord

last: Kober

address: 521 Parnassus Avenue, 3229, Box 0638

institute: University of California San Francisco

summary: Lipopolysaccharide (LPS) is a commonly used stimulant that induces an innate immune response, and serves as a model for studying inflammatory responses. Alternative splicing is key to gene expression and cell function, and is a key layer of gene regulation during disease progression and stress response. Although alternative splicing has been identified to play a role in response to LPS stimulation, a transcriptome wide ex vivo characterization of bulk PBMCs is lacking. Given the role of alternative splicing in the immune response is largely unexplored, understanding the role alternative splicing in the immune response can improve our understanding of gene regulatory processes and identify targets for treatment. The purpose of this study, using deep sequencing, is to evaluate for differential gene expression and alternative splicing associated with LPS treatment in human PBMCs.

overall_design:
Total RNA isolated from peripheral blood mononuclear cells (PBMCs) from 3 healthy subjects treated ex vivo with either lipopolysaccharide (LPS) or PBS at baseline and after 24 hours.

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

first: Esther

last: Chavez Iglesias

first: Anatol

last: Sucher


title: SOX2 is a dispensable modulator of NUT carcinoma oncogenesis in mouse

city: East Lansing

first: Bin

last: Gu

address: 755 Woodlot Drive

department: OBGYN

institute: Michigan State University

summary: NUT Carcinoma (NC) is an aggressive and lethal malignancy driven by BRD4::NUTM1 and other NUTM1 fusion oncogenes, which aberrantly activate transcription factors (TFs) linked to poorly differentiated squamous cell carcinoma (SCC) phenotypes. Among these, SOX2 has been proposed as a critical driver. However, its roles in NC initiation and progression have not been investigated in vivo. Here, using a genetically engineered mouse model (GEMM) that faithfully recapitulates human NC, we performed lineage-specific conditional deletion of Sox2 in both squamous and non-squamous tissues during NC oncogenesis. We found that SOX2 is dispensable for NC initiation and progression, and that tumors lacking SOX2 retain characteristic histological features and expression of key oncogenic drivers, including BRD4::NUTM1, MYC, and TP63. Bulk RNA sequencing revealed only modest transcriptional changes in SOX2-deficient tumors, primarily affecting metabolic and biosynthetic pathways, without disrupting core oncogenic programs. These findings challenge the assumption that SOX2 is universally required for NC oncogenesis and highlight the autonomy of BRD4::NUTM1 in establishing and maintaining the NC phenotype. Our results suggest that SOX2-targeted therapies may have limited utility as monotherapy and provide a refined framework for prioritizing  therapeutic targets for this devastating cancer.

overall_design: RNA-seq profiling of wildtype and Sox2 KO tumors from oral cavity and pancreas

first: Chenxiang

last: Luo


title: Comprehensive long-read transcriptomic analysis reveals multi-level transcriptional alterations mediated by miR-214-3p dysregulation in gastric cancer cells

city: Yinchuan

first: ruijuan

last: Xin

state: Ningxia

address: Zhengyuan South Street

institute: People's Hospital of Ningxia

summary: Long-length sequencing has been widely used in cancer-related research for exploring transcriptome variations in human cancer in recent years. miR-214-3p, a microRNA, has been reported to have abnormal expression and play important regulation roles in diverse cancers. However, information about the genome-wide targets and action mechanisms of miR-214-3p in cancer cells is still limited. Here, long-read sequencing were performed to character the transcriptome variations after disturbing the expression of miR-214-3p in AGS cells, a gastric cancer cell line. The results showed that both miR-214-3p overexpression (OE) and suppression (KD) extensively increased or decreased expression level of a number of genes involved in apoptotic process and transcription at transcript level and gene level. In particular, both miR-214-3p KD and OE could increase or decrease on the expression levels of some target genes at the same direction. Moreover, miR-214-3p broadly regulated the alternative splicing of hundreds of genes with functions of cell division, cellular senescence and transcription regulation. In addition, the changes in the expression level of miR-214-3p can cause changes in the alternative polyadenylation and 3UTR lengths of the transcript. Taken together, these results indicated that miR-214-3p could mediate apoptosis by diverse modes in AGS cells, which adds to the understanding of the critical role of miR-214-3p in cancer cancer.

overall_design: Using Oxford Nanopore Technology (ONT)-based long-read sequencing, we investigated the effects of miR-214-3p overexpression (OE) and knockdown (KD) to elucidate the functional role of miR-214-3p in AGS cells

first: Ruijuan

first: Xiaoqin

last: Ma

first: Min

last: Niu

first: Qian

last: Hao

first: Hongliang

last: Li

first: Shengjuan


title: REV-ERBα regulates regulatory T cell function in inflammatory bowel disease [RNA-seq]

first: Jingting

last: Yu

summary: Colonic Rorgt+Foxp3+ Treg cells are critical to maintain intestinal homeostasis and prevent inflammatory bowel diseases by suppressing exuberant innate and adaptative immune responses. In this study, In this study, we found that REV-ERBa was highly expressed in colonic RORgt+Foxp3+ Treg cells and essential for their differentiation and function. Deletion of REV-ERB in Treg cells lead to diminished colonic RORgt+Foxp3+ Treg cell populations even at steady state, and render mice more susceptible to TNBS and/or oxazolone-induced colitis. As a transcriptional repressor, REV-ERBa can directly repress the expression of pro-inflammatory cytokines IL-17a and IL-17f, and promote RORgt expression through Bhlhe40-c-maf axis in RORgt+Foxp3+ Treg cells. Furthermore, REV-ERB also orchestrate RORgt genome-wide distributions and co-regulate core signature genes in RORgt+Foxp3+ Treg cells, including IL-10, CTLA-4, Icos, c-maf.

overall_design: Gene expression profiling of RNA-seq data for Colon Tregs in TNBS induced colitis (REV-ERB KO and WT).

first: Xianting

last: Hu


title: VGLL1 contributes to both the transcriptome and epigenome of the developing trophoblast compartment [ChIP-Seq]

first: Robert

last: Morey

address: 2880 Torrey Pines Scenic Dr

department: Pathology

institute: UCSD

summary: The trophectoderm (TE), the outer layer of the blastocyst, is the first lineage specified during mammalian development. It initiates attachment and implantation into the maternal endometrium and gives rise to trophoblasts, the epithelial cells of the placenta that support development in utero.  Animal models have identified key signaling pathways, including BMP, WNT, and HIPPO, that regulate extra-embryonic ectoderm development, but species-specific differences in regulatory networks underlying TE specification and placental development emphasize the need for human-specific models. We were the first to previously identify Vestigial-like Family Member 1 (VGLL1), a coactivator of the TEAD family of transcription factors, as a human-specific placental marker highly expressed in first trimester trophoblast progenitors. The HIPPO signaling pathway effector TEAD4 in complex with YAP1 regulates initial TE specification by acting on key TE transcription factors (TEtra factors): GATA2, GATA3, TFAP2A, and TFAP2C. Pluripotent stem cells (PSCs) represent a unique resource to study species-specific genetic and epigenetic mechanisms of TE and trophoblast development. Here, we use a PSC model in which BMP4 treatment and WNT inhibition (via IWP2) induce TE-like cells. We examined BMP4-dependent chromatin accessibility during the transition from PSC to TE-like cells in relation to gene expression and WNT activation. We found that BMP4 drives chromatin remodeling toward a trophoblast identity and that mesoderm genes are only transiently expressed with canonical WNT activation. Using this model, we determined that, while VGLL1 expression activation is temporally downstream of the TEtra factors, it is necessary for complete trophoblast differentiation by regulating EGFR expression and reinforcing GATA3 activation through positive feedback.  We also found that VGLL1 enhanced canonical WNT signaling by directly regulating WNT receptors and effector genes. Furthermore, we identified KDM6B as a direct target of VGLL1. As a chromatin remodeler, KDM6B removes the repressive H3K27me3 at bivalent promoters, enabling the transcriptional activation of TE markers. These findings establish a mechanistic framework that determine the lineage outcomes at the interplay of three developmentally important signaling pathways, HIPPO, BMP, and WNT, positioning VGLL1 at the center of the genetic and epigenetic mechanisms supporting the maintenance and differentiation of human TE and trophoblast cells, key aspects of early placental development.

overall_design: ChIP-seq of VGLL1 and TEAD4 on trophectoderm(TE)-like cells generated from treating WA09/H9 with BMP4 and IWP2 for 4 days.

first: Ruben

middle: I

last: Calderon

first: Nirvay

last: Sah

first: Molly

last: Huang

first: Ryan

middle: H

last: Kittle

first: Walee

last: Shaik

first: Jennifer

last: Chousal

first: Sampada

last: Kallol

first: Tony

last: Bui

first: Alexandra

last: Mitre

first: Norah

last: Fogarty

first: Claudia

last: Gerri

first: Claire

last: Zheng

first: Peter

last: DeHoff

first: Pratik

last: Home

first: Kathy

last: Niakan

first: Heidi

last: Cook-Andersen

first: Kathleen

last: Fisch

first: Soumen

last: Paul

first: Francesca

last: Soncin


title: Transcription factor ZNF263 primes human embryonic stem cells for pluripotency dissolution and early differentiation

city: shanghai

first: shao

last: zhen

address: 320 Yueyang Road

institute: Shanghai Institute of Nutrition and Health

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

overall_design: Refer to individual Series


title: VGLL1 contributes to both the transcriptome and epigenome of the developing trophoblast compartment [RNA-Seq 2]

first: Robert

last: Morey

overall_design: Bulk RNA-seq of WA09/H9 at day 0, day 2, and day 4 of trophectoderm(TE)-like cell differentiation with BMP4 or BMP4/IWP2.

first: Ruben

last: Calderon

first: Nirvay

last: Sah

first: Molly

last: Huang

first: Ryan

last: Kittle


title: A novel non-nad-based PARP1 inhibitor, Japoflavone B, triggered Caspase-3/GSDME-mediated pyroptosis through ROS/p38/p53 pathway in NSCLC

city: Shenzhen

first: haoqiang

last: Wan

address: 1066 Xueyuan Avenue, Nanshan District

institute: shenzhen university

summary: It’s an effective anti-cancer strategy to study natual products for activating GSDME-mediated pyroptosis through targeting PARP-1 in NSCLC. Previously, we found that a novel flavonoid Japoflavone B (JFB) has exhibited an excellent inhibitory activity against cancer cell proliferation in vitro study, but its in vivo and mechanism study are still unknown. Herein, JFB could specifically inhibit the proliferation of NSCLC cells, but not normal lung epithelial cells. JFB induced inflammatory pyroptosis through the activation of caspase-3 and GSDME cleavage. JFB also activated caspase-3/7/9 activities and triggered mitochondria-mediated apoptosis. Its inhibitory activity would be significantly reversed with the caspase-3 or GSDME deficiencies and their specific inhibitors. JFB could targetedly inhibit PARP-1 activity, and promote DNA damage and ROS accumulation. Meanwhile, JFB could significantly promote p-p38 and p53 expression. Then, JFB induced cell cycle G2/M arrest by reprogramming the expression of cyclins, CDKs and CKIs. Moreover, its cytotoxicity could be dramatically reversed with the ROS scavenger and p38 inhibitor. In vivo, JFB exhibited a comparable anti-tumor activity to that of Dox with no significant tissue toxicity. Our data firstly revealed that JFB functions as a selective and non-NAD-based PARP inhibitor with high affinity and low toxicology, which makes it potential to develop as a lead anti-cancer compound. As well, JFB promoted caspase-3/GSDME-mediated pyroptosis through ROS/p38/p53 pathway in NSCLC cells. Our study was further enriched the specific mechanism that PARP inhibitor could trigger caspase-3/GSDME-mediated pyroptosis through ROS/p38/p53 pathway in NSCLC cells.

overall_design: To further reveal the molecular mechanism by which Japoflavone B activated caspase-mediated cell pyroptosis and apoptosis, the changes of gene mRNA expression levels after Japoflavone B treatment for 24h were detected by transcriptome sequencing compared with the control group.

first: Haoqiang

first: Jipeng

last: Wei

first: Xiaobin

last: Zeng

first: Yang

last: Wang


title: Neuronal conversion of pre-labeled astrocyte using adeno-asociated viruses in vivo

city: Toronto

first: Hussein

last: Ghazale

state: Ontario

address: 2075 Bayview Ave, North York

department: Biological Sciences

institute: Sunnybrook Research Institute

summary: Neuronal reprogramming using adeno-associated viruses (AAVs) carrying a GFAP mini-promoter to drive neurogenic transcription factor expression in astrocytes in vivo were refuted due to off-target neuronal expression. Here, we show successful neuronal conversion of pre-labeled astrocytes using AAV-GFAP to express phospho-deficient Ascl1SA6, and demonstrate that miR124 target sites reduce off-target neuronal expression. Finally, single cell transcriptomic and pseudotime trajectory analyses confirmed Ascl1SA6-driven astrocyte-to-neuron conversion, and more limited oligodendrocyte conversion events

overall_design: Following AAV injection into the motor cortex of C57/BL6 male mice, brains were harvested 7 and 50 days post injection. Cortex was microdissected under the microscope and single cell suspension was prepared for single cell analysis using scRNA-seq.

first: Carol

last: Schuurmans


title: Expression data from mouse E15.5 kidneys expressing IlkT173I or IlkWT

first: Norman

middle: David

last: Rosenblum

address: 686 Bay St

department: Developmental and Stem Cell Biology

institute: Hospital for Sick Children

summary:
Mammalian kidney development relies on interaction between three major lineages: the ureteric lineage, the nephrogenic lineage and the stromal lineage. Ilk expression was reported as a regulator of development of the ureteric lineage.
We used microarray to analyze gene expression in the ureteric and non-ureteric cells from mouse kidneys expressing IlkT173I, a missense variant of ILK identified from a human patient with Congenital Anomalies of the Kidney and Urinary Tract (CAKUT)

overall_design: Mouse kidneys expressing IlkT173I or IlkWT with ureteric cells labeled by GFP were dissociated for FAC-sorting to isolate ureteric cells and non-ureteric cells.

first: Xiangyue

last: Hu


title: Licochalcone B alleviates Crohn’s Disease injury by targeting FTO

city: hefei

first: duo

last: ma

address: No.81 Meishan Road, Shushan District

institute: Anhui Medical University

summary: To investigate the mechanism of demethylase FTO in Crohn's disease，We used RNA-seq data from three normal colon samples and three TNBS-induced IBD colon samples of C57 mice for gene expression profiling.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from three normal colon samples and three TNBS-induced IBD colon samples of C57 mice

first: Duo

last: Ma

first: Xinhua

last: Liu

first: Yaling

last: Hong

first: Xingxing

last: Zhang


title: VGLL1 contributes to both the transcriptome and epigenome of the developing trophoblast compartment [RNA-Seq]

first: Robert

last: Morey

overall_design: RNA-seq of WA09/H9 doxycycline inducible VGLL1 with or without IWP2 and DMSO control, and shRNA scramble or shRNA consitutive knockdown of VGLL1 WA09/H9 cells at day 0 and 4 day of TE-like cell differentiation with BMP4/IWP2.

first: Ruben

last: Calderon

first: Nirvay

first: Walee

last: Shaik

first: Jennifer

last: Chousal

first: Sampada

last: Kallol

first: Tony

last: Bui

first: Alexandra

last: Mitre

first: Norah

last: Fogarty

first: Claudia

last: Gerri

first: Claire

last: Zheng

first: Peter

last: DeHoff

first: Pratik

last: Home

first: Kathy

last: Niakan

first: Heidi

last: Cook-Andersen

first: Kathleen

last: Fisch

first: Soumen

last: Paul

first: Francesca

last: Soncin


title: Characterizing Hypoxia-Orchestrated Post-Stroke Changes in Oligodendrocyte Precursor Cells for Improved Stroke Cell Therapy

city: Kyoto

first: Kazuto

last: Tsukita

state: Kyoto

address: 54 Shogoin-Kawaharacho

country: Japan

institute: Kyoto university

summary: Oligodendrocyte precursor cells (OPCs) are traditionally known for their role in differentiating into oligodendrocytes, thereby contributing to myelination. Additionally, it has been increasingly recognized that OPCs actively modify their characteristics in response to the surrounding environment, exhibiting various other functions. However, how and when OPCs change their characteristics after acute ischemic stroke, and the contribution of these changes to post-stroke recovery, are not well understood. In this study, we aimed to transcriptionally characterize the changes in OPCs during acute ischemic stroke and develop therapies to support these changes. For this purpose, we first leveraged mouse single-cell RNA sequencing (scRNAseq) datasets to create a “middle cerebral artery occlusion (MCAO) atlas.” Crucially, we identified the distinct appearance of “angiogenic” OPCs in the subacute phase and “oligogenic” OPCs in the chronic phase after MCAO, contributing to angiogenesis and remyelination, respectively. Furthermore, we successfully induced OPCs ex vivo with similar functional characteristics to “angiogenic” OPCs through severe hypoxic preconditioning. The intravenous transplantation of these hypoxia-preconditioned OPCs more efficiently promoted post-stroke angiogenesis, reduced infarct size, and improved neurological function after MCAO compared to normally treated OPCs. Finally, we demonstrated that mild hypoxia at least partially contributes to the generation of “oligogenic” OPCs. Therefore, following acute ischemic stroke, OPCs sense oxygen levels and undergo phenotypic changes to exhibit functions required at specific times. Importantly, therapies supporting these phenotypic changes hold great promise for improving recovery from damage caused by acute ischemic stroke, for which current available treatments focus on quickly restoring blood flow.

overall_design: To investigate the effect of a mild hypoxic preconditioning on ex vivo POCs, we conducted comparative bulk RNAseq of these mild hypoxic-preconditioned OPCs and normally-treated OPCs.

first: Ken

last: Yasuda

first: Takakuni

last: Maki

first: Yasuhiro

last: Kuwata


title: Endothelial cells in sepsis - batch 2

first: Klaus

last: Schughart

summary: Differentially expressed genes were identified in lung endothelial cells of CLP-treated mice compared to sham-treated controls and after treatment with sitagliptin. Sitagliptin strongly reduced the inflamatory response.

overall_design: Sepsis was induced in mice by CLP (Cecal Ligation Puncture). Some mice were treated with sitagliptin. Endothelial cells from the lungs of CLP-treated, CLP plus sitagliptin, sham-treated and untreated mice were isolated and subjected to RNAseq analysis. Analysis was done in two batches, this is batch 2.

first: Nana-Maria

last: Wagner

first: Laura

last: Brabenec

first: Katharina

last: Hellenthal


title: Comparative Single-Cell Transcriptomics of Immune Profiles in LADA Versus Type 1 Diabetes

city: Moscow

first: Vadim

last: Chechekhin

address: Leninskie gory 1

country: Russia

institute: Lomonosov Moscow State University

summary: Autoimmune diabetes encompasses rapidly progressive type 1 diabetes mellitus (T1D) and indolent latent autoimmune diabetes in adults (LADA), yet the immunological drivers of this kinetic divergence remain unresolved. We performed single-cell RNA sequencing with paired T and B cell receptor profiling on over 400,000 peripheral blood mononuclear cells (PBMCs) from patients with LADA, newly diagnosed T1D, and healthy controls. PBMC composition was comparable across cohorts, indicating that qualitative rather than quantitative immune differences underlie disease heterogeneity. In T1D, pan-lineage activation of NF-kB, EGFR, MAPK, and hypoxia pathways, coupled with a TNF-centered communication hub, enhanced MHC signaling, and disrupted adhesion, promoted systemic inflammation. LADA, by contrast, exhibited global suppression of NF-kB/EGFR activity, retention of moderate JAK/STAT tone, reinforced natural killer cell inhibitory checkpoints via HLA-C-KIR2DL3/3DL1 interaction, and stabilized CD8+ T cell synapses through HLA-C-CD8 binding, collectively restraining effector activation. Single-cell V(D)J analysis revealed polyclonal, patient-unique adaptive repertoires, emphasizing the primacy of signaling context over receptor convergence. These findings define LADA and T1D as endpoints on an inflammatory-inhibitory spectrum and identify the NF-kB/EGFR-JAK/STAT gradient and HLA-C-KIR axis as potential therapeutic targets for preserving residual beta-cell function in autoimmune diabetes.

overall_design: scRNA-seq of PBMCs from patients with type 1 diabetes, latent autoimmune diabetes in adults, and healthy controls


title: The exit of naïve pluripotency contains a metabolism-induced checkpoint for telomere homeostasis.

city: London

first: Veronique

last: Azuara

state: London

address: Institute of Reproductive and Developmental Biology, Hammersmith Hospital Campus

department: Metabolism, Digestion and Reproduction

institute: Imperial College London

summary: During peri-implantation development, the pluripotent tissue of the early embryo undergoes profound cellular and biochemical reprogramming. These transformations are essential for subsequent development, yet how they are coordinated with the preservation of genome integrity remains poorly understood. Here, we uncover a telomere length checkpoint that is elicited by metabolic remodeling as mouse embryonic stem cells (ESCs) transition from the naïve to formative pluripotent state. We show that the exit of naïve pluripotency is marked by accelerated mitochondrial respiration and de novo lipogenesis, fueling lipid droplet accumulation required for tissue remodeling. Unexpectedly, these acute metabolic shifts trigger transient telomere shortening and activate ZSCAN4, a pluripotency-associated regulator of telomeres, followed by telomere re-elongation as cells adopt a more glycolytic metabolic profile. Our findings reveal a feedback mechanism in which metabolism-induced telomere stress engages ZSCAN4 as a protective response, thereby linking metabolic state to telomere homeostasis during early developmental progression.

first: Roshni

middle: A

last: de Souza


title: RNAseq in tail fins of turquoise killifish

city: Cologne

first: David

last: Willemsen

address: Joseph-Stelzmann-Str 9b

department: Valenzano

institute: Max Planck Institute for Biology of Ageing

summary: In this study we investigated gene expression in tail fins of 12 samples. 3 samples from adult red-tailed male fish (MZCS002), 3 samples from adult yellow-tailed male fish (GRZ-BELL) and 3 samples each of the corresponding region in female fish of the same strain.

overall_design: RNAseq of 4 conditions, 3 biological replicates each. Conditions are red tail (MZCS002), yellow tail (GRZ-BELL), female tail (MZCS002), female (GRZ-BELL)

first: Jongbeom

last: Park

first: Dario

middle: R

last: Valenzano


title: Single cell analysis of epidermis from nickel-challenged skin

city: Copenhagen

first: Kelvin

last: Yeung

address: Blegdamsvej 3B

country: Denmark

institute: LEO SIC

summary: In this study, we investigated the consequences of repetitive nickel challenge at previously nickel-challenged skin sites in allergic participants. Repeated challenge with nickel resulted in progressive worsening allergic skin reactions in nearly all participants (11 out of 12). To investigate the immunopathogenesis of nickel in allergic contact dermatitis (ACD), clinically cleared epidermal skin taken 21 days after each challenge was analyzed by immunohistochemistry, flow cytometry and single-cell RNA sequencing (scRNA-seq). Correlating with the worsening skin reactions, an expanding pool of epidermal CD4+ and CD8+ tissue-resident memory T (TRM) cells was seen locally in the challenged skin. Using scRNA-seq a broad subset of TRM cells with various effector phenotypes was identified, which included a predominant population of type 2 T helper (TH2) and KIR+CD8+ TRM cells that expanded with repeated challenge. We observed, broad clonal expansion after nickel challenge with interindividual variations, and clonally related clusters of less differentiated cells which may supply more developed effector TRM cells. Furthermore, repetitive challenge resulted in an increasing population of exhausted regulatory T (Treg) cells that showed lesser clonal expansion. Collectively, our data suggests that repeated challenge to nickel leads to aggravation of eczema and is supported by the increased numbers of effector TRM cells, phenotype differentiation, clonal expansion, and exhaustion of Treg cells in the challenged skin.

overall_design:
Analysis of epidermal skin cells obtained by punch biopsies from preiovusly nickel- or vehicle-challenged clinically cleared skin taken 21 days after each challenge. The exact same skin sites were challenged with nickel for a total of three times with 21 days between challenges.
>>>Submitter declares that raw data are unvailable due to patient privacy concerns<<<


title: Inhibition of microglial SLC2A5 attenuates brain injury following acute ischemic stroke [RNA-Seq]

status: Public on Nov 08 2025

city: Beijing

first: Daosheng

last: Ai

address: Bldg.3, NO.9, YIKE Rd, Zhongguancun Life Science Park, Changping District

institute: Chinese Institute for Brain Research

summary: The Slc2a5 in microglia plays a crucial role in the brain's injury response. In this study, we utilized single-cell RNA sequencing to examine the impact of Slc2a5 knockout on cell type-specific transcription in the brain. Additionally, we employed single-nucleus RNA sequencing to investigate the cell type-specific transcriptional changes in the brain 24 hours after transient middle cerebral artery occlusion (tMCAO) in response to ischemic stroke. Furthermore, RNA sequencing was conducted to analyze the effects of oxygen-glucose deprivation (OGD) conditions on the transcriptional profiles of wild-type and Slc2a5 knockout microglia in vitro.

overall_design: (1)brain cortex were isolated for scRNA-seq from  P35-40 widetype and Slc2a5 knockout mice. (2) Brain samples were harvested from widetype and Slc2a5 knockout mice with 24 hours after tMCAO, followed by library preparation using standard 10x Genomics workflows and snRNAseq (NovaSeq 6000, Illumina). Left and right hemispheres were sequenced separately. Hence, we obtained datasets from the contralateral and ipsilateral to ischemic lesion.(3) brain microglia was isolated by FACS from P35-40 widetype and Slc2a5 knockout mice, and culture them under oxygen-glucose deprivation(OGD) condition with or with 24 hours recovery.The library for sequencing was prepared following the protocol for SMARTer Stranded Total RNA-Seq Kit v2.

first: Wooping

last: Ge

first: Wenzhi

last: Sun


title: VGLL1 contributes to both the transcriptome and epigenome of the developing trophoblast compartment [ATAC-Seq]

first: Robert

last: Morey

overall_design: ATAC-seq of WA09/H9 at day 0, day 2, and day 4 of trophectoderm(TE)-like cell differentiation with BMP4 or BMP4/IWP2.

first: Ruben

last: Calderon

first: Nirvay

last: Sah

first: Molly

last: Huang

first: Ryan

last: Kittle

first: Walee

last: Shaik

first: Jennifer

last: Chousal

first: Sampada

last: Kallol

first: Tony

last: Bui

first: Alexandra

last: Mitre

first: Norah

last: Fogarty

first: Claudia

last: Gerri

first: Claire

last: Zheng

first: Peter

last: DeHoff

first: Pratik

last: Home

first: Kathy

last: Niakan

first: Heidi

last: Cook-Andersen

first: Kathleen

last: Fisch

first: Soumen

last: Paul

first: Francesca

last: Soncin


title: Control of gene output by intron RNA structure

city: Worcester

first: Leonard

last: Schärfen

state: MA

address: 368 Plantation Street

department: RNA Therapeutics Institute

institute: UMass Chan Medical School

summary: Intron removal through pre-mRNA splicing is a central step in gene expression across Eukarya. The process initiates with the recognition of intronic sequence elements (splice sites) by highly conserved RNA-protein components of the spliceosome. Intron sequences themselves are not generally conserved  beyond the splice sites, yet intronic mutations are often associated with genetic disease. Here we systematically test if and how  intron RNA structure formation modulates gene output. We generated intron variant libraries that measure the impact of base pairing at every position across a natural intron. Using a massively parallel reporter assay (MPRA), we find that base pairing involving the splice sites modulates splicing across orders of magnitude. An additional intron region upstream of the branch site was also sensitive to structure, suggesting steric hindrance. Combining thermodynamic structure prediction with libraries designed to sequester splice sites in structures of varying stability, we show that machine learning models can nearly fully explain observed gene output. Informed by this, designed alterations in intron sequence that modulate base pairing are shown to improve inefficient splicing of human β-globin IVS1. Finally, intronic mutations that alter RNA structure emerge rapidly under selection pressure, providing eukaryotes with a simple  evolutionary strategy to fine-tune gene output.

overall_design: We used Sort-seq to assay the gene output of thousands of intron variants. Introns were either designed to form specific structures, or were randomly generated and then integrated in high-throughput into the yeast genome. Yeast libraries were then sorted using FACS into bins of different fluorescence levels. From each bin, genomic dna was isolated and the intron region amplified. This library was then sequenced. Identifying the frequency with which each variant is found in each bin allows us to estimate the original fluorescence value of every intron variant. In addition to Sort-seq for several different library designs, we also performed a selection experiment to estimate mutation rates of yeast clones that survive evolutionary pressure against a stem loop at the 5'SS. We generated amplicon sequencing libraries to measure mutation rates after mutagenesis and selection.

first: Pernille

last: Bech

first: Paulina

last: Podszywałow-Bartnicka

first: Karla

last: Neugebauer


title: Analysis of the Cercospora zeina transciptome in the early, mid and late stages of gray leaf spot disease on maize

city: Pretoria

first: Dave

middle: Kenneth

last: Berger

state: Gauteng

address: Lynnwood  road

department: Dept. Plant and Soil Sciences

country: South Africa

institute: University of Pretoria

summary: Cercospora zeina is a fungal pathogen that causes gray leaf spot (GLS) disease on maize (Zea mays L.) in South Africa. Upon landing on a maize leaf, the pathogen rapidly enters through the stomata and continues to develop asymptomatically for up to 28 days before symptoms are seen. As previous work has yet to adequately determine how the pathogen behaves during its infective period, we used transcriptomics to gain insights about the in-planta development of the pathogen and explore how it uses its effectors to facilitate this process. Samples from B73 maize inbreds infected with C. zeina were harvested in a time course experiment and used for RNA sequencing. We used reads mapped to the C. zeina genome as a proxy for biomass accumulation. At the end of the latent period, C. zeina was found to rapidly accumulate biomass and showed a nearly 50-fold increase in biomass as symptoms appeared. There were two distinct transcriptional waves occurring across the infection period. The first wave showed expression of genes for cellular growth, maintenance and immune avoidance, whereas the second wave was enriched with genes involved in detoxification and carbohydrate catabolism. A total of 140 putative effector genes were differentially expressed over the time-courses, with most up-regulated during the mid stage when the switch to necrotrophy occurs. Transient expression of three of these C. zeina effectors (CzEcp2, CzNis1a, CzNis1b) induced plant immunity in Nicotiana spp. resulting in the development of a hypersensitive response. This suggests that a cohort of C. zeina effectors expressed at this time have functions for which receptors have evolved in non-host species like tobacco. Altogether, this work suggests C. zeina behaves as a latent necrotroph during infection and provides a foundation for future research into the infection biology of C. zeina on maize.

sample_organism:
Zea mays
Cercospora zeina

platform_organism:
Zea mays
Cercospora zeina

overall_design: Infection trials were set up by inoculating B73 maize plants with the C. zeina CMW 25467 strain. Samples were harvested at three timepoints: 23, 30 and 44-days post infection (dpi) with four replicates harvested per timepoint. Mock-inoculated plants inoculated with Tween 20 (0.02%) were used as a control for the experiment.

first: Trystan

last: Nadasen

first: Ingo

last: Hein


title: Inhibition of microglial SLC2A5 attenuates brain injury following acute ischemic stroke [scRNA-Seq]

first: Daosheng

last: Ai

first: Wooping

last: Ge

first: Wenzhi

last: Sun


title: Valine induces testis apoptosis through altering autophagy and nucleic acid methylation in mouse

city: Jingzhou

first: Fang

last: Wang

state: Hubei

address: West Campus of Yangtze University, Jingzhou District

institute: Yangtze University

summary: The branched-chain amino acids (BCAA) are required for animal growth and metabolic health. However, as one kind of BCAA, the effects and molecular signals of valine on male reproduction were unknown. Valine supplementation by drinking water (0.45%) for 21 days unchanged body and testis weight as compared to Control group, but significantly disturbed morphology of sertoli cells and germ cells within seminiferous tubule and enlarged the space inter seminiferous tubules within testis. TUNEL assay and γH2AX immunostaining showed that 0.45% valine supplement induced apoptosis of mouse testis through upregulating the expression of Caspase 3 and Caspase 9. The mRNA levels of autophagy related genes of Atg5 and Lamb3 were significantly reduced in 0.45% valine group as compared to Control group, but protein level of ATG5 was unchanged. The mRNA levels of DNA 5mC methylation related genes of Dnmt1, Dnmt3a, Tet2 and Tet3 were significantly reduced by 0.45% valine supplement, but protein level and localization of Tet2 was without significant difference. 0.45% valine supplement significantly reduced the mRNA levels of RNA m6A methylation related genes of Mettl14, Alkbh5 and Fto, as well as decreased protein level and changed localization of Alkbh5 and FTO. For m6A binding proteins, 0.45% valine treatment significantly decreased the mRNA levels of YTHDF1, YTHDF2, YTHDF3, IGF2BP1 and IGF2BP2, suppressed protein level of YTHDF3. Taken together, valine could disturb the autophagy and the nucleic acid methylation (DNA 5mC and RNA m6A) pathways to induce apoptosis, and therefore change the tissue structure of mouse testis.

overall_design: To explore the effect of valine on testis of male mouse

first: Cai-Xia

last: Yang

first: Zhi-Qiang

last: Du


title: Exploring the potential mechanism of artesunate in intervening with glioma cells with distinct therapeutic effects on the basis of transcriptome sequencing and network pharmacology

city: beijing

first: Li

last: tao

state: beijing

address: dongchen

institute: China Academy of Chinese Medical Sciences

summary: Artesunate possesses the potential of intervening with glioma, however, its pharmacological mechanisms remain unclarified. In this research, we aim to explore the regulatory mechanism of artesunate acting on glioma through constructing the interaction network of therapeutic effects-related genes of artesunate based on transcriptome sequencing data of glioma cells, and then verified by apoptosis staining and molecular docking at cellular level. In vitro cell activity and proliferation assay of two human glioma cell lines indicated that artesunate exerted more obvious inhibitory effects on the cell activity and proliferation of U87 cells than that of U251 cells. It could significantly promote apoptosis in U87 cells (P<0.01), while not in U251 cells (P>0.05), detected by using Hoechst and TUNEL cell apoptosis staining. Further, the differential expression gene sets between artesunate-sensitive and non-sensitive cell line, as well the therapeutic effects-related genes of artesunate were obtained, respectively, by transcriptome sequencing and differential data analysis using the lysis buffer of U87 and U251 cells before and after artesunate treatment. Then, key putative targets that related to therapeutic effects were screened by constructing the interaction network of differential genes of three above comparison groups, and calculating their topological characteristics. Pathway enrichment analysis showed that those key putative targets were significantly enriched in several signaling pathways that were closely associated with the main pathological changes of glioma, among which ATF4-DDIT3-PARP1 signaling axis, that was related with cell apoptosis, was the most enriched in. Molecular docking indicated that artesunate had fine binding affinities with ATF4 and DDIT3. Above all, this study preliminarily revealed that artesunate may induce the apoptosis and inhibited cell proliferation of glioma cells through regulating the abnormal alterations of corresponding proteins in ATF4-DDIT3-PARP1 signaling axis, which provided the novel scientific basis for its potential application in treating glioma.

overall_design: Before and after ART treatment for 24 hours, U87 and U251 glioma cell lysates were centrifuged at 3000 rpm for 15 minutes, and then total RNA was extracted according to the routine procedure. After the quality inspection is qualified, the double stranded cDNA is further purified and reverse transcribed, which is used as a template for PCR amplification to construct a cDNA library. High throughput sequencing was carried out on the illumina NovaSeq 6000 platform and entrusted to Beijing Zhimeiyinuo Biotechnology Co., Ltd. (Beijing, China). Use fastp software to clean and filter the original offline data to obtain high-quality sequences (Clean Reads); Use Hisat2 2.1.0 software to compare Clean Reads with the reference gene (the reference genome version is GRCh 38.91); Stringtie 1.3.3b software was used to compare the results and quantify the transcriptome expression; TMM (trimmed mean of M values) algorithm was used for normalization, and finally FPKM (Fragments PerKilobase Million) value of each gene was calculated, and edgeR 3.30.3 software package was used for differential analysis of gene expression between samples/groups.

first: Tao

last: Li

first: Xia

last: Mao

first: Yanqiong

last: Zhang

last: Lin


title: OncoScan CNV Assay (Thermo Fisher Scientific/Affymetrix) data for 13 cold agglutinin disease samples

city: Oslo

first: Gunhild

last: Trøen

address: Ullernchausseen 70

country: Norway

institute: Oslo University Hospital

summary: We analyzed 13 samples of primary cold agglutinin disease (CAD) for copy number variations (CNVs). In 12/13 cases complete or partial trisomy 3/3q was detected. Most of the cases (9/13) had a trisomy 12 or 18 but never both together. 4 cases had trisomy 12 and 5 case had trisomy 18. In addition there were only small recurrent gains and losses. Our data indicate that trisomy 3 or at least +3q is present in almost all cases of CAD and therefore testing for it could aid diagnosis. In addition, trisomy 12 or 18 or absence of it correlates with response to therapy.

overall_design: OncoScan CNV Assay was performed according to the manufacturer's recommendations. DNA was extracted from clonal B-cells sorted from cryopreserved bone marrow or peripheral blood samples using fluorescence activated cell sorting prior to analysis.

first: Agnieszka

last: Małecka


title: REV-ERBα regulates regulatory T cell function in inflammatory bowel disease

city: La Jolla

first: Jingting

last: Yu

address: 10010 N Torrey Pines Rd

institute: Salk Institute for Biological Studies

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

overall_design: Refer to individual Series


title: RNA-seq profiling in dorsal root ganglian (DRG) after fracture surgery and Protectin DX treatment

status: Public on Nov 07 2025

city: Durham

first: Sharat

last: Chandra

state: NC

address: 3 Genome Court

department: Department of Anesthesiology

institute: Duke University

summary: This study investigates the molecular mechanisms by which Protectin DX (PDX), a specialized pro-resolving mediator derived from docosahexaenoic acid, alleviates fracture-induced postoperative pain through GPR37 receptor signaling. The bulk RNA-sequencing experiment was conducted on L3-L5 dorsal root ganglia (DRG) tissues collected from CD1 mice three days after tibial fracture surgery, comparing gene expression profiles between PDX-treated and vehicle-treated groups. The primary goals are to identify differentially expressed genes regulated by PDX treatment, with particular focus on macrophage/neutrophil signaling, cytokine responses, and neuronal excitability pathways that contribute to pain resolution. This transcriptomic analysis aims to elucidate the molecular basis of PDX's superior analgesic efficacy compared to conventional anti-inflammatory treatments, and to understand how PDX promotes rather than delays the resolution of postoperative pain. The findings have significant clinical relevance for developing safer, non-opioid therapeutic strategies for postoperative pain management, particularly in orthopedic surgery patients, where current treatments often remain inadequate despite multimodal approaches.

overall_design: RNA-seq profiling of L3-L5 dorsal root ganglia (DRG) from vehicle- and PDX-treated CD1 mice at day 3 post-tibial fracture surgery. Sample size: n=6 per group (3 males and 3 females)

first: Yize

first: Sangsu

last: Bang

first: Jasmine

last: Ji

first: Jing

last: Xu

first: Min

last: Lee

first: Charles

last: Serhan

first: Ru-Rong


title: PAD4⁺ Neutrophils Promote Hepatic Stellate Cell Activation and Accelerate MASH Fibrosis Progression via NETs-DNA/TAOK1/MAPK Pathways

city: Nangjing

first: Jiajia

last: shen

address: No.300,guangzhou Road

institute: nanjing medical university

summary: Neutrophils play a pivotal role in the progression of metabolic-associated steatohepatitis (MASH) by mediating inflammatory responses. However, the heterogeneity of neutrophil subsets in MASH and their specific contributions to disease progression remain unclear. In this study, analysis of liver biopsies from 265 patients revealed a strong association between elevated neutrophil counts and MASH severity, particularly fibrosis. Five distinct neutrophil subsets were identified in human liver tissue, with PAD4⁺ neutrophils serving as key drivers in MASH progression. Mechanistically, PAD4⁺ neutrophils generate neutrophil extracellular traps (NETs) and activate hepatic stellate cells via the TAOK1-dependent MAPK signaling pathway. Inhibition of PAD4⁺ neutrophils in vivo attenuated the progression of liver fibrosis without exacerbating liver injury. Collectively, these findings elucidate the pivotal involvement of PAD4⁺ neutrophils in MASH progression and identify them as promising therapeutic targets for mitigating fibrosis and inflammation.

overall_design: RNA-seq dataset of neutrophis and lneutrophil extracellular trapping network intervening in human liver stellate cell LX-2


title: EZH2 directs breast cancer progression through the modulation of epithelial cellular plasticity [RNA-Seq]

city: Montreal

first: William

last: Muller

state: Quebec

address: 1160 Av des Pins O

department: Biochemistry

institute: McGill University

summary: Breast cancer remains a leading cause of death among women, encompassing diverse molecular subtypes with distinct clinical outcomes. The HER2+ subtype is particularly aggressive, with many patients eventually developing resistance to HER2-targeted therapies, underscoring the urgent need for alternative treatment strategies. Enhancer of Zeste Homolog 2 (EZH2), the catalytic subunit of Polycomb Repressive Complex 2, represses the expression of genetic programs crucial for differentiation, control of proliferation, and apoptosis through histone H3 lysine 27 trimethylation (H3K27me3). To investigate the role of EZH2 in HER2+ tumor progression, we crossed a genetically engineered mouse model (GEMM) of HER2-driven breast cancer with a conditional Ezh2 knockout strain. The results showed that Ezh2 is essential for accelerating tumor initiation and metastatic dissemination in HER2-driven breast cancer. Combined bulk and single cell RNA sequencing analyses revealed a significant downregulation of basal cell populations in the absence of Ezh2, characterized by the loss of Tp63 expression, and an upregulation of luminal progenitor cell populations, driven by crucial transcription factors such as Esr1, thereby driving luminal lineage commitment. Further, inhibition of EZH2 in vitro resulted in increased expression of ER in HER2+ human breast cancer cell lines and rendered them susceptible to tamoxifen. Altogether, these findings demonstrate that EZH2 dictates breast cancer plasticity through control of cellular identity and provides rationale for combining EZH2 inhibitors with endocrine therapies to improve outcomes in HER2+ breast cancer.

overall_design: RNA-seq profiling of wildtype EIC/EZH2 tumor cells and  EIC/EZH2 knockout tumor cells obtained from mice, 5 biological samples for each group

first: Linshan

last: Liu

first: Ellie

last: Massey

first: Dongmei

last: Zuo

first: Alain

last: Pacis

first: Mert

last: Demirdizen

first: Jessica

last: Cinkornpumin

first: Yu

last: Gu

first: Elizabeth

last: Podleszanski

first: Hailey

last: Proud

first: Virginie

last: Sanguin-Gendreau

first: Vasilios

last: Papavasiliou

first: Zhengze

last: Jiang

first: Harvey W.

last: Smith

last: Pastor

first: Paolo

last: Ceppi

first: William J.


title: Cannabidiol exerts anti-inflammatory effects but maintains T effector memory cell differentiation: A Single-Cell Study in Humans

city: Indianapolis

first: Michael

middle: T

last: Eadon

state: IN

address: 950 West Walnut Street Room 402 Room 402

institute: Indiana University School of Medicine


title: Cannabidiol exerts anti-inflammatory effects but maintains T effector memory cell differentiation: A Single-Cell Study in Humans [snRNA-Seq]

summary: Cannabidiol is widely available and often used for pain management. Individuals with kidney disease or renal allografts  have limited analgesia options. We conducted a Phase 1 healthy volunteer study to compare the peripheral immune cell  distribution before (pre-cannabidiol) and after exposure to cannabidiol at steady state (post-cannabidiol).  This study included specimens from participants who received oral cannabidiol (up to 5 mg/kg twice daily)  for 12 days. Lymphocytes were isolated and stimulated with anti-CD3/CD28 antibodies, with or without tacrolimus.  Understanding the clinical safety of cannabidiol use is important given the paucity of pain control options available for  immunocompromised transplant populations. Each individual has three conditions that are sequenced for the phase No CD3/CD28, CD3/CD28 and CD3/CD28 +Tacrolimus across two phases: pre-CBD and post-CBD.

overall_design: PBMCs were collected from each participant at Day 1 (pre-CBD) and Day 12 (post-CBD). Cells were cultured ex vivo for 72 h under six conditions that combine T-cell stimulation (±CD3/CD28), cannabidiol (±CBD), and tacrolimus (±TAC). After culture, cells were processed  for single-nucleos RNA-seq using the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression (v.1.0)  workflow and sequenced on an Illumina NovaSeq 6000. In total, 2 libraries (1 condition × 1 time-point × participants) capture transcriptomic effects of CBD, and T-cell activation.

first: Debora

middle: L

last: Gisch


title: Single-cell RNA sequencing (sc RNAseq) of white adipose tissue of aged mice

city: Ann Arbot

first: Raymond

last: Yung

state: Michigan

address: 109 Zina Pitcher Pl

institute: University of Michigan

summary: Aging and obesity are associated with pro-inflammatory changes in adipose tissue. Overlapping mechanisms, such as the infiltration of inflammatory macrophages and T cells into visceral adipose tissue, have been implicated in contributing inflammation. However, a comparative analysis from both states is needed to identify distinct regulatory targets. Here, we performed single-cell RNA sequencing of stromal vascular fractions (SVF) isolated from gonadal white adipose tissue (gWAT) of young mice fed a normal or a high-fat diet, and aged mice fed a normal diet.  Our analysis revealed that physiological aging, more so than high-fat diet induced obesity, was associated with accumulation of phenotypically distinct CD8 T cells resembling virtual memory (VM) CD8 T cells.

overall_design: Stromal vascular fraction from normal diet-fed young, high fat diet-fed young and normal diet fed aged male and female mice (C57BL/6J) was sorted for live cells, and subjected to scRNA sequencing

first: Archit

last: Kumar


title: RhCMV Expands CCR5 Memory T Cells and promotes SIV reservoir seeding in the Gut Mucosa

city: Covington

first: Joseph

last: Mudd

state: LA

address: 18703 Three Rivers Road

department: Division of Immunology

institute: TNPRC

summary: Cytomegalovirus (CMV) is a prevalent β-herpesvirus that persists asymptomatically in immunocompetent hosts. In people with HIV-1 (PWH), CMV is associated with HIV-1 persistence and particular inflammatory-related co-morbidities. The true causative role of CMV in HIV-associated pathologies however remains unclear given that nearly all PWH are coinfected with CMV. In this study, we examined acute phase immune and virological dynamics in cohorts of SIV-infected rhesus macaques (RMs) that were naturally seropositive or -negative for rhesus CMV (RhCMV). We observed prior to SIV, RhCMV expanded a polyclonal population of target CCR5+CD4+ T cells in gut and lymph nodes (LN) that expressed the chemotactic receptor CXCR3 and were largely not specific for RhCMV. Upon SIV infection, RhCMV+ RMs exhibited higher peak viremia and elevated levels of SIV DNA in the upper and lower intestine. Greater seeding of SIV DNA was associated with a maintenance of CCR5-expressing CD4+ T cells that were enriched within the RhCMV+ gut along a CXCR3-CXCL9 chemotactic axis. Overall, the data suggest that RhCMV can promote SIV susceptibility within a diverse, polyclonal pool of CD4 T cells that are not entirely RhCMV-specific.

overall_design: Bulk RNA TCR-seq was performed on sorted CD4+CCR5+ and CD4+CMV-specific T cells from 5 rhesus macaques. CMV-specific T cells were identified and sorted using an activation-induced marker assay following in vitro stimulation with CMV lysate.

first: Chrysostomos

last: Perdios

first: Naveen Suresh

last: Babu

first: Celeste D.

last: Coleman

first: Anna T.

last: Brown

first: Shevon N.

last: Alexander

first: Matilda J.

last: Mostrom

first: Carolina

last: Allers

first: Lara

last: Doyle-Meyers

first: Christine M.

last: Fennessey

first: Lori A.

last: Rowe

first: Brandon F.

last: Keele

first: Amitinder

last: Kaur

first: Michael L.

last: Freeman

first: Joseph C.


title: Multi-Omics Elucidation of KDM5C, KDM6A, and KMT2B Roles in Cancer Epigenetic Dysregulation and Transcriptional Reprogramming [ATAC-seq]

city: Shanghai

first: Tengjiao

last: Li

address: No.800, Dongchuan Road, Minhang District, Shanghai, China Address in Chinese

department: School of Pharmaceutical Sciences

institute: Shanghai Jiao Tong University

summary: Histone-modifying enzymes (HMEs) are critical regulators of tumorigenesis through epigenetic reprogramming. While mutations in HMEs are recognized drivers of cancer epigenome dysregulation, systematic comparative analyses of their mutational impacts and functional divergence across malignancies remain underexplored. This study addresses this gap by investigating three HMEs—KDM5C (H3K4me3 demethylase), KMT2B (H3K4me3 methyltransferase), and KDM6A (H3K27me3 demethylase)—frequently mutated in diverse cancers. Using CRISPR/Cas9 knockout cell lines, we performed integrated multi-omics profiling encompassing genome-wide chromatin accessibility, transcriptomics, and chromatin-bound proteomics. Contrary to expectations that KMT2B loss (H3K4me3 depletion) and KDM5C loss (H3K4me3 accumulation) would induce opposing transcriptional programs, or that KDM6A deficiency (H3K27me3 accumulation) would exhibit distinct regulatory effects, our analyses revealed striking discrepancies between transcriptional outputs and chromatin-associated proteomic states across all three knockouts. Notably, each HME knockout elicited distinct transcriptional regulatory patterns, challenging conventional assumptions about their antagonistic or synergistic functions. These findings highlight context-dependent functional hierarchies among HMEs and underscore the necessity of multi-dimensional profiling to resolve epigenetic regulatory complexity. Our work advances the mechanistic understanding of cancer epigenetics and provides a framework for elucidating tumorigenic vulnerabilities linked to HME dysregulation.

overall_design: ATAC-seq: 50,000 cell nuclei were collected from each cell line. Resuspend cell nuclei in 50 ul of transposition mixture (25 ul 2× TD buffer, 2.5 ul transposase (100nM final), 16.5 ul PBS, 0.5 ul 1% digitonin, 0.5 ul 10% Tween-20, 5 ul H2O) by pipetting up and down 6 times. Incubate reaction at 37°C for 30 minutes in a HUXImixer (HUXI, shanghai) with 1000 RPM mixing. Transposition reactions were cleaned up with a UNIQ-10 Column MicroDNA Gel Extraction Kit (Songon Biotech, shanghai). Libraries were amplified with Illumina Nextera sequencing primers.


title: MeCP2 regulates telencephalic development in human cerebral organoids

first: Alysson

middle: R.

last: Muotri

address: 2880 Torrey Pines Scenic Drive - Room 3005

institute: UCSD

summary: Human cerebral organoids and telencephalic assembloids derived from iPSC lines: isogenic control and harboring MeCP2 variants associated with Rett Syndrome.

overall_design: Expression profiling by high throughput sequencing

first: Miguel

last: Tenreiro


title: Characterisation of human in vitro tumour-associated macrophage models to define translational relevance

city: Barcelona

first: Clara

last: Alsinet

address: Diagonal 615

country: Spain

institute: AstraZeneca

summary: Tumour-associated macrophages (TAMs) are key components of the tumour microenvironment with a demonstrated ability to modulate anti-tumour T-cell responses and immunotherapy outcomes. With increasing realisation that the M1/M2 paradigm does not reflect the complexity of macrophage phenotypes in cancer patients, an urgent need has arisen to develop improved, translatable in vitro models for human TAMs. To address this gap, we have screened conditioned media from a panel of tumour cell lines for their ability to induce suppressive marker upregulation on human monocyte-derived macrophages (hMDMs), as well as active T-cell immunosuppression. We performed secretome characterization of these tumour-conditioned media (TCM) to shed light on cancer cell-derived soluble factors that may contribute to TAM polarisation. Furthermore, we characterized the proteomic and transcriptomic signatures of macrophages exposed to either TCM or primary ascites fluid from ovarian cancer patients and performed bioinformatics analysis to determine the most translationally relevant models of TAMs. In summary, our work provides mechanistic insights on tumour-macrophage crosstalk in the context of establishing suppressive TAM phenotypes and addresses the long-standing gap of defining translationally relevant human in vitro TAM models.

overall_design: RNAseq profiling of in vitro differentiated macrophages from freshly isolated CD14+ monocytes. Monocytes were differentiated for 6 days in 50ng/ml of M-CSF with tumor conditioned media from cancer cell lines cultures or ascites fluid from ovarian cancer patients.

first: Arthur

last: Dyer

first: Rebecca

last: Dudley

first: Shreya

last: Ahuja

first: Pawan

last: Poudel

first: Georgina

last: Bowyer

first: Kalvin

last: Sahota

first: Saly

last: Songvilay

first: Des

last: Jones

first: Matthew

last: Glover

first: Sonja

last: Hess

first: Elina

last: Timosenko

first: Simon

middle: J

last: Dovedi


title: Multi-Omics Elucidation of KDM5C, KDM6A, and KMT2B Roles in Cancer Epigenetic Dysregulation and Transcriptional Reprogramming [RNA-seq]

overall_design: RNA-seq profiling of wildtype HEK293T cells and their knockout derivatives (sgKDM5C, sgKDM6A, and sgKMT2B).