title: Primate gut microbiota induce evolutionarily salient changes in mouse neurodevelopment

city: Bethesda

first: Alex

last: DeCasien

address: 9000 Rockville Pike

department: LNG

summary: Multiple primate species, including humans, evolved brains that are exceptionally large relative to their body sizes. These large brains coevolved with metabolic adaptations that enhance cerebral energy supply, including increased circulating glucose levels. While the gut microbiota (GM) is known to influence host metabolism, its potential role in primate brain evolution remains unclear. To investigate this, we inoculated germ-free mice with the GMs of primate species selected to separate the effects of brain size (encephalization) from phylogenetic relatedness: humans (large-brained, Catarrhini), macaques (smaller-brained, Catarrhini), and squirrel monkeys (large-brained, Platyrrhini). We first show that differences in brain gene expression between mice inoculated with human versus macaque GMs resemble those observed between actual human and macaque brains. Comparing the effects of the different primate GMs on mouse brain gene expression further revealed that, despite greater evolutionary distance, the GMs from the two larger-brained species (humans and squirrel monkeys) similarly upregulated genes associated with energy production. Notably, human GMs specifically increased the expression of genes involved in oxidative phosphorylation, and these gene expression changes correlated with increased abundances of GM metabolic pathways related to glucose metabolism and gluconeogenesis. Human GMs also downregulated evolutionarily conserved genes implicated in neurodevelopmental disorders such as autism. Although these are findings based on a small sample of primate species and must be interpreted as preliminary, they suggest that species differences in GM composition can influence brain metabolism and raise the possibility that the GM could have played a supporting role in primate encephalization.

overall_design: Bulk brain RNAseq data: 11,359 detectably expressed genes (excluding ribosomal genes) from the infralimbic/prelimbic frontal cortices (FC; corresponding to areas 25 and 32, respectively) of N=32 mice that were inoculated with the GMs of humans (Homo sapiens; N=12), squirrel monkeys (Saimiri boliviensis; N=8), or macaques (Macaca mulatta; N=12).

first: Jacob

last: Arnoff

first: Elizabeth

last: Mallot

first: Sahana

last: Kuthyar

first: Sriram

last: Chitta

first: Brian

last: Layden

first: Maria

last: Savo Sardaro

first: Stanton

last: Grey

first: Lawrence

last: Williams

first: Emma

last: Leichty

first: Hyo

first: Won

first: James

last: Curly

first: Christopher

last: Kuzawa

first: Katherine

last: Amato


title: Response of gingival keratinocytes challenged with Selenomonas sputigena

status: Public on Dec 08 2025

city: Richmond

first: Daniel

last: Miller

state: Virginia

address: 1101 E. Marshall St. Sanger Hall 5-009

country: USA

institute: Virginia Commonwealth University

summary: NanoString nCounter analysis using the human Host Response Panel was used to determine the expression of 618 genes involved in host response to infection from telomerase immortalized gingival keratinocytes (TIGKs) incubated with the oral pathogen Selenomonas sputigena ATCC 35185 compared to untreated control cells.

overall_design:
RNA was collected from 3 biological replicates from both the untreated control group and the S. sputigena treated group. The entire experiment was performed in duplicate, yielding 6 total samples from each treatment group. For treated cells, they were infected with 100 bacteria per TIGK cell for 4 hrs before RNA was isolated.
All samples were analyzed using the nCounter Host Response Panel to determine the expression of 618 human genes.

middle: P


title: Escape from X inactivation is directly modulated by Xist non-coding RNA [in vivo]

status: Public on Dec 09 2025

city: Solna

first: Jasper

last: Panten

address: Tomtebodavägen 23

country: Sweden

institute: SciLifeLab

type: Expression profiling by high throughput sequencing

summary: X-chromosome inactivation silences one copy of the X-chromosome in female cells, but a number of genes escapes XCI. We asked whether increased levels of Xist RNA, the molecular actor driving X-inactivation, impacts expression levels of escapees. We tested whether dox-mediated Xist-overexpression affected the expression levels of escapees during mouse early embryonic development.

sample_organism:
Mus
Mus musculus

platform_organism:
Mus
Mus musculus

overall_design: To investigate the effect of Xist overexpression on escape levels in early embryos, Xist was overexpressed via doxycycline induction in early mouse embryos carrying an inducible Xist allele on the inactive X. Embryos were derived from natural mating between C57BL/6 TX males Xptet/Y; R26rtTA/WT with wild type JF1 females. Embryos were harvested at E2.5 and E3.5 and cultured in vitro in the presence of Doxycycline for 24 hours. Embryos were harvested for RNA-Sequencing using the Smart-Seq2 protocol and allele-specific expression was determined for X-linked genes.

first: Edith

last: Heard

first: Agnese

last: Loda

last: Kneuss


title: Single-cell RNA-seq of endothelial and pericyte populations in the mouse cochlear stria vascularis

city: Portland

first: Xiaorui

last: Shi

address: 3250 SW Sam Jackson Park Rd

department: OHRC

institute: Oregon Health & Sciences Univers

summary: The cochlear stria vascularis (SV) maintains the endocochlear potential and relies on specialized vascular endothelial cells and pericytes. To characterize the transcriptional profiles of these vascular populations at single-cell resolution, we performed single-cell RNA sequencing (scRNA-seq) on SV tissue from reporter mice. SV was microdissected from temporal bones of 1–3 month-old Tie2-GFP (endothelial reporter) and NG2-DsRed (pericyte reporter) mice, enzymatically dissociated to obtain single-cell suspensions, and, when applicable, subjected to FACS enrichment for Tie2-GFP–positive endothelial cells or NG2-DsRed–positive pericytes. Viable cells were loaded onto the 10x Genomics Chromium platform for single-cell capture and 3′ barcoded library preparation. This dataset contains two independent batches corresponding to SV endothelial cell–enriched and pericyte-enriched preparations and enables analysis of vascular heterogeneity within the mouse stria vascularis.

overall_design: Two independent single-cell RNA-seq batches from the 1-3 months mouse cochlear stria vascularis were isolated by Fluorescence-activated cell sorting (FACS) and analyzed using scRNA-seq. Batch 1. Endothelial cell–enriched batch (Tie2-GFP) Batch 2. Pericyte-enriched batch (NG2-DsRed)

first: Zhiqiang

last: Hou

first: Yunpei

last: Zhang

first: Jinhui

first: Pingting

last: Wang


title: BACH2 regulates T cell lineage states to enhance CAR T cell function [Cut & Run]

city: St. Louis

first: Nathan

last: Singh

address: 660 S Euclid Ave

institute: Washington University School of Medicine in St Louis

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Nearly all chimeric antigen receptors (CARs) signal in the absence of antigen, referred to as “tonic signaling”. Tonic signaling of CARs containing the CD28 costimulatory domain has been shown to driveT cell exhaustion; in contrast, we found that tonic signaling of 41BB-containing CARs enhances T cell function. Using a panel of CARs targeting CD22, we identified that tonic 41BB signaling activatesBACH2, a transcriptional regulator that directs stem and memory programs. Overexpression of BACH2 prevented tonic CD28-driven exhaustion but locked CAR T cells in quiescent states. To overcome this, we linked BACH2 to a degradation domain and found that tuning BACH2 expression enhanced long-term efficacy of exhaustion-prone CAR T cells targeting liquid and solid tumors. Through interrogation of CAR products, we also found an association between BACH2 activity and clinical outcomes in patients with leukemia. These data identify a central role for BACH2 in regulating CAR T cell efficacy.

overall_design: CUT&RUN of primary human CAR T cells with an antibody against cJUN. Two different CARs targeting CD22 were sequenced (CD28 or 4-1BB-costimulatory domain with CD3z stimulatory domain. scFvs contain a Short (S) linker). 28s+BACH2 denotes CD28 costimulatory domain, short linker, and BACH2 over expression vector. All samples in technical triplicate.

first: Tien-Ching

last: Chang

first: John

middle: M

last: Warrington

middle: A


title: Profiles and roles of N6-methyladenosine modification in bovine oocyte maturation [MeRIP]

city: Hefei

first: TC

last: H

address: 130 Changjiang West Road

country: China

institute: AAU

summary: The quality of bovine oocytes is crucial for in vitro embryo production technology, thus it is essential to study the mechanisms of oocyte maturation. N6-methyladenosine (m6A) modification plays a key role in gametogenesis and embryonic development. However, the dynamic landscape and functional roles of m6A modification during bovine oocyte maturation remain unclear. We conducted transcriptome-wide m6A landscape analysis on bovine oocytes at the GV and MII phases using MeRIP-seq and RNA-seq technologies. We identified a total of 6,323 differential m6A peaks in the two groups of oocytes, with 4,422 m6A peaks being significantly upregulated and 1,901 m6A peaks significantly downregulated. The combined analysis of MeRIP-seq and RNA-seq identified 262 genes with significant differences in both methylation modification and transcriptome levels. GO and KEGG enrichment analyses of these genes revealed significant enrichment in biological processes and signaling pathways such as endocytosis, thermogenesis, ribosome, cellular metabolism, Apelin signaling pathway, and HIF-1 signaling pathway. Finally, we examined the roles of m6A modification in bovine oocyte maturation. The results showed that inhibition of m6A modification affects nuclear and cytoplasmic maturation of oocytes. Our results reveal the m6A modification profile during bovine oocyte maturation. Furthermore, we found that inhibition of m6A modification leads to meiotic failure. These results provide a theoretical basis for studying the function of RNA modification in oocyte maturation.

overall_design: GV stage and MII stage bovine oocytes cultured in vitro were collected for MeRIP-seq and RNA-seq

first: Tiancang

last: Han

first: Zhichao

first: Xinqi

last: Gan

first: Zhiyuan

last: Yang

first: Wenzhuo

first: Kunlong

last: Hu

first: Ruiqing

last: Zhu

first: Yunsheng

last: Li

first: Yunhai

first: Zubing

last: Cao


title: Differentially expressed miRNAs in the temporal cortex of Alzheimer’s disease patients and their association to tau pathology.

city: Brussels

first: Siranjeevi

last: Nagaraj

address: Route de Lennik 808 B-1070 Bruxelles

country: Belgium

institute: Université Libre de Bruxelles, Brussels, Belgium

type: Non-coding RNA profiling by high throughput sequencing

summary: Alzheimer's disease (AD) is a major contributor to dementia in the elderly, characterized by progressive impairments in memory and behaviour. AD is marked by pathological hallmarks: amyloid plaques and neurofibrillary tangles (NFTs). Despite extensive efforts to understand these hallmarks, there is still a lack of efficient therapeutic approaches due to limited knowledge of the fundamental cellular mechanisms underlying the disease. One potential avenue of research involves the investigation of the roles of non-coding RNAs, particularly, microRNAs (miRNAs), which bind to the 3' UTRs of target mRNAs to suppress expression. In our study, we analysed the temporal superior T1 isocortex of control and AD patients, identifying differentially expressed miRNAs using next-generation sequencing (NGS). To validate these findings, we utilized an additional technique, RT-qPCR. Overall, our study confirms the previous findings  on the dysregulation of miR-129-5p, miR-132-3p, and miR-146b-5p, while also providing novel insights into the dysregulation of miR-151a-5p and miR-1-3p. Importantly, the expression levels of miR-129-5p, miR-146b-5p, miR-132-3p, and miR-151a-5p were significantly correlated with the neuropathological Braak stages and with biochemically quantified tau phosphorylation levels in brain homogenates. Additionally, we found that miR-146b-5p and miR-151a-5p significantly modulated tau seeding in tau biosensor cell model, highlighting their potential roles in tau pathology.

overall_design: microRNA sequencing profile of postmortem brain samples (temporal superior T1 isocortex) from control and Alzheimer's diseases patients

first: Karelle

last: Leroy

first: Carolina Quintanilla

last: Sanchez

first: Kunie

last: Ando

first: Lidia Lopez

last: Gutierrez

first: Yannick

last: Gansemans

first: Emilie

last: Doeraene

first: Andreea-Claudia

last: Kosa

first: Emmanuel

last: Aydin

first: Filip

last: Van Nieuwerburgh

first: Jean-Pierre

last: Brion


title: A Titin Missense Variant Causes Atrial Fibrillation

city: Chicago

first: Mahmud

middle: Arif

last: Pavel

email: gmmahmud@uic.edu, arvindsr@uic.edu

state: Illinois

address: 840 South Wood Street, Suite 920S

department: Medicine/Cardiology

institute: University of Illinois at Chicago

summary: A single TTN point mutation- a missense variant ( TTN-T32756I) can impair sarcomere integrity and lead to atrial electrical remodeling, increasing AF- A link that needs investigation

overall_design: We performed an unbiased global transcriptomic analysis by RNA sequencing (RNA-Seq) separately on TTN WT and TTN-T32756I- hiPSC-aCMs.


title: Role of SRP/dGATAb in the response of Drosophila S2 Schneider cells to 20-hydroxyecdysone

city: Moscow

first: Nadezhda

middle: E

last: Vorobyeva

address: Vavilova 34/5

country: Russia

institute: Institute of Gene Biology RAS

summary: Background: The tissue-specific response to steroid hormones remains unclear even in model organisms. The mechanism is proposed to be based on the selective binding of nuclear hormone receptors to regulatory sites that are primed by tissue-specific factors. But studies directly describing the cooperative work of nuclear receptors with tissue-specific transcription factors remain sparse. Earlier, GATA family factor SRP/dGATAb was proposed to prime regulatory sites in S2 Schneider cells for their activation by 20-hydroxyecdysone (20E), the main steroid hormone of the Drosophila development. Highly specific expression of SRP/dGATAb in Drosophila tissues makes it a suitable candidate for a factor enabling tissue-specific response to 20E. Results: The role of SRP/dGATAb in the response of S2 Schneider cells to 20E was determined using SRP/dGATAb depletion via RNA interference. Combination RNA-Seq with ChIP-Seq analysis helped identify the primary targets of SRP/dGATAb whose transcription is induced in response to 20E treatment and whose loci contain EcR and SRP/dGATAb binding sites. SRP/dGATAb depletion was found to alter transcription of different 20E-induced genes in opposite ways. For 20E-activated genes whose transcription was decreased upon depletion, SRP/dGATAb was found to control active regulatory sites marked by the H3K27Ac and enriched with SRP/dGATAb motifs. In this group SRP/dGATAb depletion reduced EcR binding level at sites co-bound with EcR and SRP/dGATAb, demonstrating a priming role for GATA family protein. In contrast, for 20E-activated SRP/dGATAb-suppressed genes whose transcription was increased upon SRP/dGATAb depletion, SRP/dGATAb and EcR co-bound sites showed unchanged H3K27Ac levels and EcR binding. The overall level of H3K27 acetylation at the loci of the second group of genes showed increase upon SRP/dGATAb depletion. Conclusions: Obtained data showed a positive role of SRP/dGATAb in 20E-inducible transcription in S2 Schneider cells for some genes. SRP/dGATAb worked as a priming transcriptional factor for 20E-inducible regulatory sites controlling EcR recruitment and chromatin acetylation. But for another group of 20E-inducible genes, SRP/dGATAb had negative impact on transcription. Its recruitment through the protein-protein interactions restrained activity of the regulatory sites.

overall_design: RNA-Seq, FAIRE-Seq, ChIP-Seq experiments were performed on Drosophila S2 Schneider cells treated with 20-hydroxyecdysone for 1 h or sham-treated (DMSO) under SRP/dGATAb-depleted or control conditions (SKi).

first: Aleksandra

last: Evdokimova


title: RNA sequencing of human brain organoids to evaluate sex-specific and opto-FGFR-mediated responses to Simplified 5 Ion GCR Simulation

city: Baltimore

first: Gabsang

last: Lee

state: MD

address: 733 N. Broadway

institute: Johns Hopkins School of Medicine

summary: This study aims to characterize transcriptomic responses to Simplified 5 Ion GCR Simulation  (simGCRsim) in human brain organoids derived from hiPSCs. Two independent RNA-seq experiments were conducted. The first set compared male- and female-derived organoids to evaluate sex-specific transcriptional responses to GCR. The second set assessed organoids derived from i) male hiPSCs expressing optogenetically-controlled FGFR (opto-FGFR) or mock constructs to explore FGFR signaling as a potential countermeasure and ii) one female hiPSC line (SC2131), with or without GCR exposure. Together, these datasets provide insight into both intrinsic sex differences and FGFR-dependent protective mechanisms in human neural tissues in the context of space radiation exposure.

overall_design:
Human brain organoids were generated from hiPSCs and subjected to two independent RNA sequencing experiments. Experiment 1: Organoids were derived from 6 male and 2 female hiPSC lines and matured for 60 days. Organoids from each line were either untreated (control) or exposed to 50 cGy of simGCRsim. RNA was extracted for sequencing to investigate sex-specific transcriptional responses to radiation. Experiment 2: Male hiPSC lines were engineered to express either opto-FGFR or a mock construct, or one female hiPSC line (SC2131), followed by brain organoid differentiation and 60-day maturation. Organoids were then either left untreated or exposed to 50cGy of simGCRsim. RNA was sequenced to assess FGFR-mediated modulation of radiation response or responses of female-derived brain organoids against GCR radiation. Each condition was represented by three biological replicates. Differential gene expression analyses were performed to identify radiation-induced transcriptomic alterations and FGFR-dependent protective mechanisms.

The work was supported by NASA (Grant NNX16AO69A) and TRISH (TSRAD-2020).

first: Eun

last: Ra

first: Han Byeol

last: Kim

first: Wonjin

last: Yun

first: Anjalika

last: Bandaru

first: Micheal

middle: C

last: Anderson

first: Min Seong

first: Hyesoo

first: Yohan

last: Oh


title: Temporal multi-omics gene expression data across human embryonic stem cell-derived polyhormonal cell differentiation [Ribo-seq]

city: New York

first: Marko

last: Jovanovic

state: NY

address: 1212 Amsterdam Avenue

department: Biological Sciences

institute: Columbia University

summary: Human embryonic stem cells (hESCs) provide a powerful in vitro model to study lineage specification and the regulatory programs underlying early human development. Here, we present a high-resolution, temporal multi-omics dataset tracking mRNA, translation, and protein expression dynamics during hESC differentiation into definitive endoderm and subsequent polyhormonal (PH) cells, a key pancreatic lineage. RNA-seq, ribosome profiling, and quantitative mass spectrometry-based proteomics were performed on matched samples collected at ten time points in biological duplicates, allowing detailed characterization of transcriptional, translational, and protein abundance changes over the differentiation timeline. The dataset exhibits high technical quality, with strong reproducibility between replicates and rigorous quality control metrics across all omics platforms. This extensive dataset provides critical insights into the complex regulatory mechanisms driving polyhormonal cell differentiation and serves as a valuable resource for the research community, enabling deeper exploration of mammalian development, endodermal lineage specification, and gene regulation.

overall_design: To comprehensively investigate the gene regulatory mechanisms underlying human embryonic development, we performed genome-wide measurements of mRNA, translation, and protein levels during hESC differentiation. Our experimental design encompassed the generation of all three embryonic germ layers—endoderm, mesoderm, and ectoderm—followed by their directed differentiation into polyhormonal cells, cardiomyocytes, and motor neurons, respectively. In the present study, we focus on the endoderm-to-polyhormonal cell differentiation trajectory. Samples were collected at ten distinct time points, enabling high-resolution tracking of gene expression dynamics over the course of differentiation. Matched samples were measured for mRNA levels by mRNA sequencing (mRNA-seq), for translation level proxies by ribosome profiling (Ribo-seq), and for protein levels by quantitative mass spectrometry-based proteomics. All differentiations and measurements were performed in biological duplicates.

first: Abdurrahman

last: Keskin

first: Hani

middle: J

last: Shayya

first: Achchhe

last: Patel

first: Dario

last: Sirabella

first: Barbara

last: Corneo


title: Rete ridges form via evolutionarily distinct mechanisms in mammalian skin

city: Pullman

first: Sean

last: Thompson

state: WA

address: BLS 240

department: School of Molecular Biosciences

institute: Washington State University

summary: The loss of fur during human evolution has long mystified scientists and the public. Reduced hair density coincides with the acquisition of epidermal rete ridges, whose developmental timing and molecular mechanisms are poorly understood despite their prominence in humans. Examination of human and pig skin development revealed that rete ridges form through an independent mechanism from hair follicles and sweat glands by establishing interconnected epidermal invaginations. We documented rete ridge occurrence across Mammalia, including in grizzly bears and dolphins, and showed that neonatal pig wounds can regenerate them de novo. Multi-species spatiotemporal transcriptomics identified significant signaling interactions between epidermal and dermal cells during rete ridge morphogenesis, particularly through BMP. We also demonstrated that murine fingerpad skin forms rete ridges and functionally requires epidermal BMP signaling. We propose that evolution of rete ridges in mammalian skin involved replacement of the molecular program for formation of discrete microscopic appendages, including hair follicles and sweat glands, with a distinct program for the interconnected appendage network. Broad epidermal activation of BMP is required for the development of rete ridge networks organized around underlying dermal pockets. Understanding rete ridge mechanisms may enable the development of therapeutic approaches to regenerate epidermal appendages lost during wounding or disease in humans.

sample_organism:
Homo sapiens
Sus scrofa
Mus musculus

overall_design:
Skin from a E90 fetal pig, P3 neonatal pig, P10 neonatal pig, and 6-month old adult pig was collected under approved protocols and processed to generate a single-cell suspension from the epidermis and dermis in 1:1 ratios for 10x Genomics scRNA-seq. Additionally, we re-analyzed previously published scRNA-seq datasets from Glover et al., 2023; Cheng et al., 2018; Solé-Boldo et al., 2020; Liu et al., 2022 based on their published sequencing files. Finally, skin from P3, P10, and 6mo pigs were processed to generate spatial transcriptomics datasets using Complete Genomics Stereo-seq.

***************************************************************
The table below lists GEO accessions reused/reanalyzed for this study.
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first: Quan

last: Phan

first: Iwona

last: Driskell

first: Ryan

middle: R


title: Fluorescence tracking Treg movement identifies anti-CCR8 and radiation as a therapeutic combination

first: Wesley

last: Rosales

state: OR

address: 4805 NE Glisan St

institute: Earle A. Chiles Research Institute

summary: Using 10X Genomics single-cell RNA sequencing, we investigated the migration of regulatory T cells (Tregs) following radiation therapy (RT). Employing the Kaede photoconvertible mouse model, we tracked Tregs migrating from the tumor-draining lymph node (TdLN) to the tumor within the post-RT tumor microenvironment. This study serves to identify how RT influences the migrating Treg phenotypes change within the tumor in order to better inform and improve thearaputic strategies for targeting Tregs in combination with RT.

overall_design: MC38 tumors established in Kaede mice. On day 14 post tumor innoculation, TdLNs were photoconverted followed by immediate treatment with 12Gy of radiation. Mice were also injected intraperitoneally with FTY720 on day 15. Tumors were harvested on either 24 hours (day 15) or 72 hours (day 17) post-RT. Tumors were processed into single cell suspensions, magnetically enriched for CD8/CD4 TIL, and stained for with viability dye, CD90.2-Alexa Fluor 700, and Totalseq hashtag antibodies. Kaede green or red live CD90.2+ cells were sorted using a Symphony S6 cell sorter. Each experimental condition had 2 replicates each containing 4 tumors pooled from 4 mice. Samples were immediately processed and libraries were constructed using the Chromium GEM-X Single Cell 5’ Reagent v3 protocol. Libraries were sequenced using the Illumina NovaSeq 6000 with the NovaSeq 6000 S1 Reagent Kit (v1.5). All cDNA pools and resulting libraries were measured using the Agilent Fragment Analyzer with the DNF-474 HS NGS Fragment Kit and Qubit High Sensitivity assays.

first: David

last: Friedman

first: Sina

last: Ramin

first: Tiffany

last: Blair

first: Gwen

last: Kramer

first: Shelly

last: Bambina

first: Alejandro

middle: F

last: Alice

first: Jason

last: Baird

first: Terry

last: Medler

first: Kristina

middle: H

last: Young

first: Marka

last: Crittenden

first: Michael

last: Gough


title: NFAT Mediates Pro-Tumorigenic Inflammation in Cancer-Associated Fibroblasts in Pancreatic Ductal Adenocarcinoma [mouse multiome]

city: Stanford

first: Chuner

last: Guo

state: CA

address: 257 Campus Dr

department: Surgery

institute: Stanford University

summary: Pancreatic ductal adenocarcinoma (PDAC) is characterized by a dense stroma, low immunogenicity, and resistance to therapy. Cancer-associated fibroblasts (CAFs) are key stromal cells within the tumor microenvironment (TME) that drive tumor progression. Interleukin-1 (IL-1) promotes fibrosis, pathogenic inflammation, and poor prognosis in PDAC. Using a novel single-cell multiomic approach, we investigate the IL-1 signaling axis in human and mouse models of PDAC, identifying nuclear factor of activated T cells (NFAT) transcription factors as key mediators. IL1R1+ CAFs activate an inflammatory phenotype associated with elevated NFAT motif activity and gene expression. In vivo, NFAT inhibition in a mouse model of PDAC significantly reduces tumor weight and fibrosis, supporting its pro-tumorigenic role. Our findings suggest that NFAT mediates IL-1-induced inflammation in PDAC, highlighting its potential as a therapeutic target. This study demonstrates the power of multiomic analyses to uncover therapeutic targets within the complex tumor microenvironment.

overall_design: To study IL-1 signaling in a mouse model of PDAC, we developed an orthotopic allograft model via pancreatic inoculation of KPC cells following suture ligation at the mid-pancreas. The suture ligation occludes the pancreatic duct and induces pancreatitis, which helps generate an inflammatory response conducive to PDAC induction while preserving adequate blood supply to the distal pancreas via the short gastric and left gastroepiploic vessels. To model IL-1 signaling inhibition, we chose AF12198, a small peptide antagonist of IL1R1. To counteract any potential immunosuppressive effects of IL-1 inhibition and enhance antitumor immunity, we included IL-12, a potent immune activator. We injected KPC cells into the suture-ligated pancreas, waited for 2 weeks to ensure tumor induction, then performed intratumoral injection with saline, AF12198, IL-12, or a combination of AF12198 plus IL-12. Tissues were harvested and analyzed 2 weeks following intratumoral injection

first: Michelle

last: Griffin

first: Annah

middle: G

last: Morgan

middle: T

last: Longaker

first: Jeffrey

last: Norton


title: In vivo CRISPR screening identifies SAGA complex members as a key regulators of hematopoiesis [ChIP]

city: Philadelphia

last: Haney

state: PA

address: 422 Curie Boulevard

institute: University of Pennsylvania, Perelman School of Medicine, Department of Pathology

summary: The biological mechanisms that sustain the vast blood production required for healthy life remain incompletely understood. To search for novel regulators of hematopoiesis, we performed a genome-wide in vivo hematopoietic stem and progenitor cell (HSPC)-based CRISPR knockout screen for regulators of hematopoiesis. We discovered SAGA complex members, including Tada2b and Taf5l, as key regulators of hematopoiesis. Loss of Tada2b or Taf5l strongly inhibited hematopoiesis in vivo, causing a buildup of immature hematopoietic cells in the bone marrow. The SAGA complex deposits histone H3 lysine 9 acetylation (H3K9ac) and removes histone H2B ubiquitination (H2Bub). Loss of Tada2b led to reductions in H3K9ac levels and altered H2Bub enrichment in HSPCs, implicating disruption of SAGA complex activity. This was associated with upregulation of interferon pathway genes, reduced mitochondrial activity, and increased megakaryocyte progenitor cell commitment. Loss of these factors also enhanced the cell outgrowth and the interferon pathway in an in vivo human myelodysplastic syndrome cell line model. In summary, this study has identified the SAGA complex as an important regulator of hematopoiesis.

overall_design: ChiP-seq of HSPCs in vitro including Tada2b KO HSPCs

first: Adam

last: Wilkinson

first: Leonid

last: Olender


title: Genetic alterations of SENP6 disrupt DNA repair and proteostasis conferring sensitivity to proteasome inhibition in multiple myeloma

city: Berlin

first: Uta

middle: Margareta

last: Demel

address: Hindenburgdamm 30

department: Hematology and Oncology

country: Germany

institute: Charité - CBF

summary: Targeting of the ubiquitin-proteasome system (UPS) remains a mainstay in the treatment of multiple myeloma (MM). Hyperactivation of the closely related SUMO pathway is implicated in disease progression and associated with poor prognosis. Here we investigated the functional imbalance of aberrant SUMOylation in MM by analyzing the large CoMMpass dataset for molecular alterations associated with SUMO pathway regulation. SENP6 and SENP7, key SUMO proteases, were significantly downregulated in patients with high SUMO pathway signatures. Recurrent loss of SENP6, a negative regulator of SUMOylation, was directly linked to adverse prognosis across all disease stages. SENP6 reconstitution markedly reduced cellular growth kinetics in SENP6-deficient MM, indicating a functional role for SENP6 as a tumor suppressor. Mechanistically, SENP6 loss resulted in the accumulation of DNA damage and misfolded proteins, thereby activating the unfolded protein response, increasing reliance on proteasomal degradation, and driving synthetic lethality to therapeutic proteasome inhibition. Together, we establish SENP6 as a biologically relevant biomarker and provide a mechanistic rationale for the clinical efficacy of proteasome inhibitors in the prognostically unfavorable subgroup of SENP6-deficient MM patients.

overall_design: RNA-seq profiling of NCI-H929 and OPM-2 multiple myeloma cell lines with and without CRISPR-Cas9-mediated SENP6 knockdown.

first: Frederik

last: Herzberg

last: Korenkov

first: Konstandina

last: Isaakidis

first: Chuanbing

last: Zang

first: Matthias

last: Wirth

first: Stefan

last: Müller

first: Ulrich

last: Keller


title: NFAT Mediates Pro-Tumorigenic Inflammation in Cancer-Associated Fibroblasts in Pancreatic Ductal Adenocarcinoma [mouse VIVIT]

overall_design: To test the effects of NFAT inhibition in vivo, we used the orthotopic allograft KPC PDAC model described previously. KPC cells were injected into the suture-ligated pancreas, followed by a 2-week interval to ensure tumor induction. Mice were then treated with intratumoral injections of saline or VIVIT, a small peptide inhibitor of NFAT. Tissues were harvested and analyzed 2 weeks following intratumoral injection


title: Escape from X inactivation is directly modulated by Xist non-coding RNA [multiclone]

first: Jasper

last: Panten

summary: X-chromosome inactivation silences one copy of the X-chromosome in female cells, but a number of genes escapes this inactivation. We asked whether increased levels of Xist RNA, the molecular actor driving X-inactivation, impacts expression levels of escapees. To this end, we performed transcriptomic profiling of X-linked gene expression in clonal neural progenitor cell lines with varying Xist levels.

overall_design: Clonal neural progenitor cell lines were generated by differentiating first generation hybrid embryonic stem cells (from a 129/Sv x CAST/EiJ cross). Clones from 21 cell lines were generated in three independent experiments. RNA-Sequencing was performed for each cell line. Using heterozygous variants between the two strains, allele-specific expression of X-linked genes was quantified together with Xist expression.

first: Edith

last: Heard

first: Agnese

last: Loda

first: Antonia

last: Hauth


title: In vivo CRISPR screening identifies SAGA complex members as a key regulators of hematopoiesis [CRISPR]

first: Michael

overall_design: CRISPR KO screening in HSPCs

first: Haney

last: Michael

first: Archana

last: Shankar


title: Temporal multi-omics gene expression data across human embryonic stem cell-derived polyhormonal cell differentiation [RNA-seq]

first: Marko

last: Jovanovic

first: Abdurrahman

last: Keskin

first: Hani

last: Shayya

first: Achchhe

last: Patel

first: Dario

last: Sirabella

first: Barbara

last: Corneo


title: RNA-seq of Drosophila Glioma Model with Ca-α1T and Slo Knockdowns

city: LLEIDA

first: Judit

last: Herreros

address: Rovira Roure 80 (lab 2.11)

department: Basic Medical Sciences

country: Spain

institute: University of Lleida-IRBLleida

summary: This dataset presents transcriptomic profiles of Drosophila melanogaster glioma model to investigate the effects of Ca-α1T and Slo knockdowns on gene expression. The samples consist of dissected Drosophila heads. The glioma model used were based on the study by Read et al., 2009 (PLOS Genetics), which established a Drosophila model of glioma by co-overexpressing an activated form of dEGFR (dEGFRλ) and dp110 (dp110CAAX) in glial cells (Read et al., 2009). This work was supported by the research project 'Programa Generación de Conocimiento PID2022-138688OB-I00' funded by the Spanish Ministry of Science and Innovation.

overall_design: The dataset includes the following conditions: Control, Glioma, GliomaxCa-α1T-RNAi and GliomaxSlo-RNAi

first: Lía

last: Alza

first: Carles

last: Cantí

first: Sergio

last: Casas

first: Andreu

last: Casali


title: Phosphorylated-Ser807 STAT6 protects macrophages from senescence

city: Beijing

first: Zhao

last: Zhou

state: Beijing

address: No. 5 Yiheyuan road

institute: Peking University

summary: STAT6 play a key role in homeostasis of macrophages. We identified a new modification of STAT6 at Ser807, which may contribute to STAT6 function. Thus, we generated STAT6 point mutant mice (S807A and S807E). We sequenced the mRNA of macrophages from these mutant mice to rule out the function of the specific phosphorylation.

overall_design: Primary Thio-elicited peritoneal macrophages were isolated from WT and mutant mice. After short-term adherent, the PMs were collected for RNA extraction.

first: Yifu

last: Qiu


title: Whole blood transcriptomics characterize molecular phenotypes of pulmonary Mycobacterium avium complex disease

city: TSUKUBA

first: Masashi

last: Matsuyama

state: IBARAKI

address: 1-1-1 AMAKUBO

department: respiratory medicine

country: Japan

institute: Tsukuba university

summary: Pulmonary Mycobacterium avium complex (MAC) disease shows a range of clinical phenotypes and responses to treatment. While Th1 immunity and neutrophils have been implicated in its pathogenesis, the precise mechanisms remain unclear. Furthermore, comprehensive gene expression analysis in this context are scarce.  This study aimed to elucidate the heterogeneity of pulmonary MAC disease by gene expression profiling of whole blood cells. Unsupervised cluster analysis was performed on whole blood gene expression data at 0M. In addition, we also evaluated the variation in gene expression profiles of whole blood cells before (0M) and after starting treatment (1M) with guideline based therapy (GBT; azithromycin [AZM]/clarithromycin [CAM]+ethambutol [EB]+rifampicin [RFP]).

overall_design: We enrolled 100 patients with pulmonary MAC disease requiring treatment according to standard guidelines. Whole blood cells were collected for RNA-sequencing before (0M) and one month (1M) after the start of guideline based therapy (GBT; azithromycin [AZM]/clarithromycin [CAM]+ ethambutol [EB]+rifampicin [RFP]). Unsupervised cluster analysis was performed on whole blood gene expression data at 0M. In addition, gene expressions in whole blood cells was compared between before (0M) and after starting treatment (1M) with GBT.

first: Chio

last: Sakai

first: Masayuki

last: Nakajima

first: Mizu

last: Nonaka

first: Sosuke

last: Matsumura

first: Masafumi

last: Muratani

first: Nobuyuki

last: Hizawa


title: NFAT Mediates Pro-Tumorigenic Inflammation in Cancer-Associated Fibroblasts in Pancreatic Ductal Adenocarcinoma [mouse model]

first: Chuner

last: Guo

overall_design: To study IL-1 signaling in a mouse model of PDAC, we developed an orthotopic allograft model via pancreatic inoculation of KPC cells following suture ligation at the mid-pancreas. The suture ligation occludes the pancreatic duct and induces pancreatitis, which helps generate an inflammatory response conducive to PDAC induction while preserving adequate blood supply to the distal pancreas via the short gastric and left gastroepiploic vessels. To model IL-1 signaling inhibition, we chose AF12198, a small peptide antagonist of IL1R1. To study the effects of IL-1 inhibition in vivo, KPC cells were injected into the suture-ligated pancreas, followed by weekly intraperitoneal injections of saline or AF12198. Tissues from normal pancreas, suture ligated pancreas, control KPC tumors, and KPC tumors treated with intraperitoneal injections of AF12198 were harvested and analyzed at 4 weeks.

first: Michelle

last: Griffin

first: Annah

last: Morgan

first: Michael

last: Longaker

first: Jeffrey

last: Norton


title: Position-independent emergence of neocortical neuron molecular identity, connectivity and function

city: Geneva

first: Sergi

last: ROIG-PUIGGROS

state: Geneva

address: 1 Rue Michel Servet

department: Fundamental Neuroscience

country: Switzerland

institute: University of Geneva

summary: Brain architectures vary widely across species, yet how neuronal positioning constrains the type of circuits that can be made, and their function, remains poorly understood. Here we examine how neuronal position affects molecular identity, connectivity and function by studying Eml1 knockout mice, which exhibit abnormally located (heterotopic) neurons beneath the cortex. Heterotopic neurons maintained their molecular signatures, formed appropriate long-range connections and exhibited normal electrophysiological properties. They organized into functional sensory-processing centers that mirrored their cortical counterparts, with preserved somatotopic mapping and responsiveness to sensory stimuli. Remarkably, cortical silencing did not impair sensory discrimination, revealing that heterotopic neurons were the main drivers of this function. Hence, equivalent circuits can emerge in different spatial configurations, allowing diverse brain architectures to converge on similar functional outcomes.

overall_design: Mouse single-nucleus RNA seq of FAC-sorted P23 SSp cells of Eml1lox/lox and Emx1:Cre; Eml1lox/lox


title: Ascl5 variant disrupts gene expression in developing mandibular teeth and dental arch structures

status: Public on Dec 07 2025

city: Bangkok

first: Thanakorn

last: Theerapanon

address: 34 Henri-Dunant Road, Wangmai, Patumwan

country: Thailand

institute: Faculty of Dentistry, Chulalongkorn university

summary: Lobodontia, a rare dental anomaly marked by supernumerary cusps and a single pyramid-shaped molar root resembling carnivorous teeth, is s linked to variants in the CACNA1S gene. However, the underlying molecular mechanisms remain unclear. Here, we identified a novel heterozygous missense variant in ASCL5 (c.274G>A, p.Glu92Lys) as the primary genetic determinant for lobodontia. Through microsatellite linkage and genome sequencing analysis of six families affected by lobodontia, we identified the ASCL5 c.274G>A variant, located upstream of the previously reported CACNA1S variant, completely segregating with the phenotype. To validate this finding, we generated Ascl5 knock-in mutant mice using CRISPR/Cas9. Ascl5Mut/WT exhibited dental anomalies resembling human lobodontia, while Ascl5Mut/Mut displayed significant defects in tooth and jaw development, underscoring the essential role of ASCL5 in craniofacial patterning. Transcriptomic analysis of E17.5 mandibular teeth and arches revealed a significant differential expression of forty-two genes in Ascl5mut/mut compared to Ascl5WT/WT, including reduced expression of key developmental genes Dlx1as, Dlx2, and Shh. Functional assays showed that ASCL5 promotes transcriptional activity of DLX2, a key regulator of craniofacial development. However, the p.Glu92Lys ASCL5 significantly impaired this activation, providing a mechanistic explanation for the observed phenotype. This study establishes ASCL5 as the primary gene responsible for lobodontia, revising the previously understood genetic basis of this rare condition. Our findings highlight the crucial role of ASCL5 in craniofacial development, opening new avenues for understanding craniofacial anomalies.

overall_design:
Mandibular dental arches from Ascl5Mut/Mut, and Ascl5WT/WT mice at embryonic day 17.5 (E17.5) were dissected for subsequent RNA extraction. The total RNA libraries were constructed using Illumina TruSeq Stranded mRNA LT Sample Prep Kit and sequenced using Illumina NovaSeq platform.
The RNA differential expression compared between Ascl5WT/WT mice as a control group and the Ascl5Mut/Mut mice as a comparison group was analyzed using RNA-Seq Differential Expression program (Illumina Inc., San Diego, CA, USA).

first: Theerapanon

last: Thanakorn

first: Thaweesapphithak

last: Sermporn


title: Ascl5 variant alters gene expression in postnatal maxillary molars through potential gain-of-function effect

summary: Lobodontia is a rare dental anomaly characterized by supernumerary cusps and a single, pyramid-shaped molar root resembling those of carnivorous mammals. Through genetic analysis of six unrelated families, we identified a novel heterozygous missense variant in the ASCL5 gene (c.274G>A; p.Glu92Lys) that segregates fully with the phenotype. To investigate the functional impact of this variant, we generated Ascl5 knock-in mutant mice using CRISPR/Cas9. Heterozygous (Ascl5Mut/WT) mice displayed dental anomalies consistent with human lobodontia, whereas homozygous (Ascl5Mut/Mut) mice exhibited more severe craniofacial abnormalities, highlighting the essential role of ASCL5 in tooth and jaw development. To explore the molecular basis of the dental phenotype, we performed transcriptomic analysis of maxillary first molars from postnatal day 1 (P1) Ascl5Mut/WT and Ascl5Mut/Mut mice, each compared to wild-type controls. Based on a gain-of-function hypothesis for the p.Glu89Lys variant, we focused on genes upregulated in both mutant genotypes. This analysis identified 87 commonly upregulated genes. Pathway enrichment analysis using Metascape revealed 11 significantly enriched biological pathways, including Dmp1, Phex, and Atg4b genes associated with biomineral tissue development. Notably, the regulatory region of Phex contains a conserved E-box motif, a known binding site for bHLH transcription factors such as ASCL5, suggesting it may be a direct transcriptional target.

overall_design: To investigate the impact of the Ascl5 mutation on gene expression, we compared mRNA profiles from maxillary first molars of three mouse genotypes harvested at postnatal day 1 (P1): Ascl5Mut/WT, Ascl5Mut/Mut, and Ascl5WT/WT (control). Total RNA was extracted, and Illumina SMARTer Stranded RNA-Seq Kit was used to construct RNA libraries, which were then sequenced on a NovaSeq platform. Differential gene expression analysis was performed using the RNA-Seq Differential Expression program (Illumina Inc., San Diego, CA, USA) to identify genes whose expression was significantly altered in the mutant genotypes compared to the wild-type control.


title: CRISPR screen of genes encoding protein interactors of MCB-613 in parental and EGFR inhibitor resistant EGFR-mutant NSCLC cell lines

city: Durham

first: Kris

last: Wood

state: NC

address: 450 Research Drive, LSRC C259, PO Box 3813

department: Department of Pharmacology and Cancer Biology

institute: Duke University

summary: CRISPR screen of genes encoding protein interactors of MCB-613 in PC9, GR4, and WZR12 cells

overall_design: PC9, GR4, and WZR12 cells were infected with a CRISPR library targeting genes encoding protein interactors of MCB-613 and carried forward in triplicate for 14 population doublings at 1000X coverage. Genomic DNA was extracted using the QIAamp Blood Maxi Kit (Qiagen). Extracted DNA was amplified using a two-step protocol involving staggered barcode sequences for pooled sequencing. Sequencing was performed on an Illumina NextSeq 500 with 75bp paired-end sequencing and analysis was performed using the Models-based Analysis of Genome-wide CRISPR/Cas9 Knockout (MAGeCK) software analysis pipeline under default conditions.

first: Christopher

last: Bassil

first: Christian

last: Cerda-Smith


title: Streptococcus pneumoniae drives specific and long-lasting memory in NK cells

city: Paris

first: Claudia

last: Chica

address: 25-28 Rue du Dr Roux

country: France

institute: Institut Pasteur

summary: Following lung infection with S. pneumoniae, naive (D21PBSpi NKs) and pre-infected NK cells (D21SPNpi NKs) were sorted and used for scRNAseq. We compared their transcriptional program to identify and characterize a new population of NK cells that acquired memory to  bacteria

overall_design: Comparison of naive (D21PBSpi NKs) and memory NK cells (D21SPNpi NKs) mRNA profiles upon secondary S. pneumoniae infection

first: Tipahine

last: Camarasa

first: Julia

last: Cortada

first: Sébastien

last: Mella

first: Mélamie

last: Hamon


title: Escape from X inactivation is directly modulated by Xist non-coding RNA

city: Solna

first: Jasper

last: Panten

address: Tomtebodavägen 23

institute: SciLifeLab

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

overall_design: Refer to individual Series


title: NFAT Mediates Pro-Tumorigenic Inflammation in Cancer-Associated Fibroblasts in Pancreatic Ductal Adenocarcinoma [human multiome]

first: Chuner

last: Guo

overall_design: Human PDAC specimens were obtained from patients undergoing surgery at Stanford Hospital under a Stanford University approved IRB protocol (#45051). The patients were counseled in the pre-operative area by one of the manuscript authors. The aims of the study were discussed with the patient. Participation was entirely voluntary. Written, informed consent was obtained from all the patients included in this study prior to surgery. Tissue specimens were collected by one of the authors from the pathologist once the PDAC tumor specimen had been inked (from a non-critical part of the tumor), placed directly into sterile saline, and kept on ice for transport. Tumor specimens were dissociated into single nuclei and profiled for gene expression and chromatin accessibility simultaneously from the same nucleus.

first: Michelle

last: Griffin


title: Gene expression profiling of parental and EGFR inhibitor resistant EGFR-mutant NSCLC cell lines treated with MCB-613

summary: RNA-seq analysis in PC9, GR4, and WZR12 cells treated with DMSO or MCB-613 for 24 hours.

overall_design: PC9, GR4, and WZR12 cells were treated with DMSO or 2 µM MCB-613 for 24 hours in biologically independent triplicate. RNA was isolated using the Rneasy Mini Kit (Qiagen) according to the manufacturer's instructions and sent for paired-end RNA sequencing by the Duke Sequencing and Genomic Technologies core facility. Mapped reads were using DESeq2 and assessed for differential expression in vehicle- and MCB-613-treated parental (PC9) and EGFR inhibitor resistant (GR4, WZR12) cells.

first: Jacob

last: Hoj


title: Bulk RNA-sequencing on sorted zebrafish macrophages based on novel irg1-knock-in reporter comparing control versus nlrc3l mutation under baseline and injury conditions

status: Public on Dec 06 2025

city: Chapel Hill

first: Celia

last: Shiau

address: 2159 Genome Sciences Building

institute: UNC Chapel Hill

summary: Using a GFP knock-in zebrafish targeting the irg1/acod1 locus, a gene highly induced in activated macrophages, we isolated macrophages based on high and low GFP levels by FACS to conduct bulk RNA-sequencing. Transcriptome analysis of macrophages showed nlrc3l mutants had constitutively activated macrophages that sustained elevated expression of pro-inflammatory genes, including irg1 and tnfa, and canonical and non-canonical NF-κB pathways genes. Furthermore, transcriptome analysis suggested that wild-type/control macrophages exhibited hybrid M1-like and M2-like characteristics during initial injury response, while nlrc3l mutant macrophages remained locked in a pro-inflammatory state. This analysis supports the rest of the functional experiments to demonstrate that chronic macrophage activation restricts functional plasticity associated with mrc1b deficiency and thereby hinders skeletal muscle repair.

overall_design: Two independent RNA-seq datasets were generated in this study. One dataset (Samples 1-12) corresponds to RNA-seq profiling of macrophages sorted from 3dpf zebrafish embryos that were of either sibling or mutant nlrc3l/st73 genotype based on low or high GFP levels indicating endogenous irg1 transcriptional levels using a GFP knock-in reporter at the irg1 locus. Second dataset (Samples 13-19) corresponds to RNA-seq profiling of macrophages that were similarly isolated based on relative expression of the GFP knock-in reporter for endogenous irg1 from injured (24-hour-post major tail amputation) and non-injured 3dpf zebrafish embryos from control and nlrc3l mutant genotypes.

first: Matthew

last: Hamilton

first: Andrew

last: Burciu


title: Dietary methionine deprivation enhances renal resilience against ischemia-reperfusion injury through modulation of glucose oxidation

city: Hangzhou

first: Xiaofeng

last: Peng

address: Yuhangtang Road 866,Hangzhou,Zhejiang

institute: Zhejiang University

summary: Renal ischemia-reperfusion injury (IRI) is a leading cause of acute kidney injury (AKI) and presents significant challenges during kidney transplantation. Due to the detrimental effects of IRI on kidney function and the lack of effective intervention strategies, we conduct a multi-omics study on surgically induced mouse IRI, revealing a modulatory role for the metabolite S-adenosylmethionine (SAM) in AKI development. Our metabolic analysis of clinical samples establishes a link between various AKI conditions and marked elevations in serum SAM, underlying its potential as a biomarker for diagnosis. Furthermore, we find that short-term dietary methionine deprivation, which reduces circulating methionine and kidney SAM levels, effectively enhances renal resilience against IRI. In vivo isotopic tracing demonstrates that this diet preconditions kidney metabolic programs, enhancing glucose and fatty acid oxidation in preparation for IRI. Particularly, the activation of pyruvate dehydrogenase, which produces acetyl-CoA to fuel the tricarboxylic acid (TCA) cycle, highlights an energy-efficient strategy of glucose metabolism that is essential for the protective effects of dietary methionine deprivation.

overall_design: The experimental design includes transcriptomic sequencing data of kidney tissues from male mice subjected to 30 minutes of ischemia followed by 24 hours of reperfusion (IRI group) and from control mice undergoing sham surgery (Sham group).

first: Xiao feng

first: Hong

last: Jiang

first: Cunqi

last: Ye


title: Metabolic engineering of doxorubicin biosynthesis through P450-redox partner optimization and structural analysis of DoxA

city: Turku

first: Mikko

last: Metsä-Ketelä

address: Tykistökatu 6A

department: Department of Life Technologies

country: Finland

institute: University of Turku

summary: Doxorubicin is a widely used chemotherapy agent produced by Streptomyces peucetius ATCC27952. Key to the biosynthesis is the cytochrome P450 monoxygenase DoxA that catalyzes three consecutive late-stage hydroxylations. However, the final conversion from daunorubicin to doxorubicin is rate-limiting and industrial manufacturing occurs through semi-synthesis from daunorubicin. Here we have discovered three factors that limit catalysis by DoxA. We performed comparative transcriptome analysis to identify the natural redox partners, the ferredoxin FDX4 and ferredoxin reductase FDR3, preferred by DoxA. We show that the vicinal oxygen chelate (VOC) family protein DnrV is a drug-binding protein aiding catalysis by binding doxorubicin and preventing product inhibition of DoxA. Ternary structures of DoxA in complex with ligands and density functional theory calculations revealed that 14-hydroxylation is limited by the preferred anti conformation of the daunorubicin substrate. We employed these findings to convert a daunorubicin over-producing industrial strain to produce 300 mg / L doxorubicin.

overall_design: RNA-Seq profiling of Streptomyces peucetius ATCC 27952 and their mutant derivatives GOO1 and X121 at Day1-6

first: Arina

last: Koroleva

first: Erika

last: Artukka

first: Keith

last: Yamada

first: Sean

last: Newmister

first: Ralph

last: Harte

first: Hannah

last: Boesger

first: Mikael

last: Londen

middle: N

last: Sanders

first: Heli

last: Tirkkonen

first: Matti

last: Kannisto

first: Rosan

last: Kuin

first: Mandy

last: Hulst

first: Rongbin

last: Wang

first: Ester

last: Leskinen

first: Morgane

last: Barillec

first: Jarmo

last: Niemi

first: Gilles

last: van Wezel

first: Jacques

last: Neefjes

first: S

last: Nybo

first: K

last: Houk

first: David

last: Sherman

first: Robbert

middle: Q

last: Kim


title: Screening of differentially expressed genes and microRNAs in rabbits with traumatic proliferative vitreoretinopathy based on high-throughput sequencing

city: nanchang

first: shengxiang

last: zhang

state: Jiangxi Province

address: 463 Bayi Avenue, Donghu District, Nanchang City, Jiangxi Province, China

institute: nanchang university

summary: The retinas of rabbits in the experimental and control groups of traumatic proliferative vitreoretinopathy (PVR) were sequenced by high-throughput sequencing technology, and differentially expressed genes (DEGs) and differentially expressed microRNAs (DEMs) were identified to provide new ideas for the diagnosis and treatment of PVR. Differentially expressed genes (DEGs) and differentially expressed microRNAs (DEMs) were screened to provide new ideas for the diagnosis and treatment of PVR.

overall_design: To investigate the changes in gene expression levels in a rabbit model of proliferative vitreoretinopathy, we performed high-throughput sequencing of retinal tissue from a rabbit model of proliferative vitreoretinopathy

first: Qihua

last: Xu

first: Yujie

last: Tang

first: Shengxiang

last: Zhang


title: Evaluation of clonality in lentigo maligna

status: Public on Dec 05 2025

city: Melbourne

first: Mark

last: Shackleton

state: VIC

address: Level 4, Paula Fox Melanoma and Cancer Centre 545 St Kilda Rd

department: School of Translational Medicine

country: Australia

institute: Monash University

type: Genome variation profiling by high throughput sequencing

summary: Lentigo maligna (LM), a type of in situ melanoma, has a high rate of local recurrence following curative-intent surgical resection. Although recurrences might represent inadequately excised incident LMs, apparent recurrences could be new primary LMs developing from distinct melanocytic clones in the same ultraviolet radiation (UVR)-damaged anatomical region. As distinguishing these possibilities has implications for patient management, we tested genetic relationships between incident and recurrent LMs. Raw files for human/patient samples were not submitted to GEO due to concerns about submitting personally identifiable sequence data for open access.

overall_design:
Incident LMs with histologically clear margins, and their recurrent LMs and invasive lentigo maligna melanomas (LMMs) were laser microdissected for DNA extraction. Tumour and matched germline DNA underwent whole exome sequencing (WES). Clonal relationships between incident and recurrent LMs were tested by elucidating and tracking clones within and across samples.*Raw sequencing reads for human/patient samples were not submitted to GEO due to concerns about submitting personally identifiable sequence data for open access.

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

last: Szeto

first: Peinan

last: Zhao

first: Sophie

last: Lim


title: Distinct genomic identities and transformation trajectories of thymomas

city: Daejeon

first: Young Seok

last: Ju

address: 291 Daehakro

country: South Korea

institute: KAIST

summary: Thymoma is a rare tumor originating from epithelial cells of thymus. Despite previous studies, molecular trajectories underlying thymic tumorigenesis remain largely unknown. In this study, we conducted an integrated analysis of genomes and transcriptomes from 124 thymomas and 13 thymic carcinomas. Additionally, we incorporated single-cell transcriptomes of normal thymic tissues collected at different developmental stages. The efforts identify two mutually exclusive molecular types of thymomas: GTF2I-mutant (GTF2I-type) and copy number-altered type (CN-type). The GTF2I-type has a stable copy number profile with cellular identities of transcription similar to thymic progenitor cells. In contrast, CN-type tumors show cellular identities resembling differentiated thymic epithelium with distinct metabolic and immune features and activation of oncogene IRS4. Genome-wide timing analyses on CN-type reveal that tumorigenic courses of the two types were partitioned from the early stage in the lifetime. Our findings provide deep insights into the origin and tumorigenic processes of thymic epithelial cells.

overall_design: We produced single-cell RNA-seq data from 11-week-old mice (FVB). Thymi of seven mice were dissected to generate the dataset. Leukocytes were stained with CD45 antibody and depleted with autoMACS Pro Separator. The single-cell RNA sequencing library was generated using Chromium Single Cell 3’ Library & Gel Bead Kit v2 (10x Genomics).


title: Eos maintains Treg homeostasis and plays a critical role in the function of recirculating thymic Tregs [ChIP-Seq]

city: Bethesda

first: Tovah

last: Markowitz

address: 10 Center Dr, Building 29B

department: Integrated Data Sciences Section (IDSS)

institute: NIAID

summary: Eos, a member of the Ikaros family of transcription factors, is expressed by T regulatory cells (Tregs) and has been postulated to play a role in Treg suppression and maintenance of Treg stability. We demonstrate that expression of Eos was limited to a subpopulation of thymus-derived, activated Tregs and is undetectable in resting or activated T conventional cells (Tconvs). Eos associates with Helios, Foxp3 and Hdac1 and binds directly to the CD25 locus at a site identical to the Foxp3 binding site resulting in enhancement of CD25 expression. Studies in heterozygous female mice demonstrate that Eos is critical for Treg survival and activation. Eos+ Tregs also represent the major population of recirculating thymic Tregs, in which Eos plays a critical role in regulating their migration and suppression of Treg precursors in the thymus by competing for IL-2 and depleting MHC II from thymic dendritic cells (DCs).

overall_design: Single replicate ChIP-seq of anti-Helios or anti-Eos in WT and EosKO conditions

first: Xuan

last: Xie

first: Ethan

last: Shevach


title: Hormonal rewiring of immunity upholds pathogen control and systemic nutrient homeostasis during dietary restriction

city: New York

first: Charles

last: Carr

department: Medicine

institute: Weill Cornell

summary: Food shortages and infectious diseases were constant threats throughout mammalian evolution and often occurred simultaneously. When food availability is reduced, it is unclear how the host adapts to fuel energy-demanding immune processes while preventing malnutrition. In the context of dietary restriction (DR), we found that glucocorticoids (GCs) are increased and promoted naïve T cell homing to the bone marrow niche, a site that supported their survival at steady-state. In response to a primary infection, DR-induced GCs dramatically rewired innate and adaptive immunity to simultaneously promote pathogen control and prevent hypoglycemia. This was achieved by dampening neutrophil glycolytic metabolism, which paradoxically enhanced their survival, function, and capacity to control pathogens. In parallel to enhancing neutrophils, DR-induced GCs restrained the generation of pathogen-specific effector T cells. This was essential for preventing hypoglycemia while combating a primary infection during DR. Although effector T cell responses were dampened, DR-induced GCs enriched for memory precursor effector cells to optimize memory T cell formation. Altogether, our work reveals a fundamental host adaptation strategy that upholds immediate and long-term pathogen control while maintaining systemic nutrient homeostasis in the setting of reduced food availability. These results redefine GCs as dominant optimizers of organismal fitness that align immunity and metabolic physiology with the nutritional status of the host.

overall_design: Examination of naive and effector CD8+ T cells and whole blood neutrophils of dietary restriction versus normal controls with bulk RNA-seq. Total CD8+ naive (CD44low CD62L+) T cells were sorted from the bone marrow of mice fed ad libitum or on DR for 3 weeks. For effector T cells, effector YopE69-77-specific CD8+ effector T cells were sorted at day 8 post-infection with WT Yptb from the spleen of mice fed ad libitum or on DR for 3 weeks. For neutrophils, cells were sorted from peripheral blood 8 days post-Yptb infection.

first: Luisa

last: Menezes-Silva

first: Mingeum

last: Jeong

first: Seong-Ji

last: Han

first: Nicholas

last: Collins


title: Transcriptome analysis of Drosophila melanogaster intestines upon knockdown of Tachykinin (Tk), the GPCR GulpR (CG32547), and bruchpilot (brp)

city: Boston

first: Paula

last: Watnick

state: MA

address: 300 Longwood Avenue

institute: Boston Childrens Hospital

summary: Tk is a peptide hormone mainly expressed in the Drosophila brain and intestine. Gut-derived Tk is known to impact intestinal lipid metabolism and immunity. We used RNA-seq to determine the impact of Tk and the Tk regulators GulpR and brp on intestinal gene expression and further understand their role in metabolism and immunity. We compare the intestinal transcriptome of Tk knockdown, GulpR knockdown, and brp knockdown flies to control driver flies.

overall_design: Tk> (Tk-Gal4) flies were crossed to TRiP control, Tk RNAi, GulpR RNAi, or brp RNAi flies. Progeny was collected and raised at 26°C for 4-7 days. Female intestines were dissected and processed for RNA isolation. RNA sequencing was performed on these samples and the data were analyzed according to 3 different comparisons: 1. Tk>TRiP and Tk>Tk RNAi flies, 2. Tk>TRiP and Tk>GulpR RNAi flies, and 3. Tk>TRiP and Tk>brp RNAi flies.

first: Daniela

last: Barraza

middle: I


title: Escape from X inactivation is directly modulated by Xist non-coding RNA [Capture Hi-C]

first: Jasper

last: Panten

summary: X-chromosome inactivation silences one copy of the X-chromosome in female cells, but a number of genes escapes this inactivation. Increased levels of Xist RNA, the molecular actor driving X-inactivation, results in silencing of escaping genes. To address how chromosome topology responds to changes in transcriptional activity of escapees, we performed allele-specific Capture Hi-C analysis of clusters of escaping genes on the inactive X chromosome in NPCs. We performed the experiments after 7 and 21 days of Xist induction and upon washout of doxycycline and in presence or absence of Xist’s partner SPEN. We further tested changes in the 3D topology of regions surrounding known constitutive escapees in ESCs upon increased Xist levels.

overall_design: TX1072.G4 first generation hybrid mouse ESCs (from a C57BL6/J x CAST/EiJ cross) were cultured and clonal neural progenitor cell lines were generated from them by in vitro differentiation. All NPC cell lines carry an inactive B6 X chromosome and a doxycycline-inducible transgene on the Xi. Allele-specific Capture Hi-C was performed to characterized the 3D spatial organization of the two X chromosomes in ESC at two regions containing known constitutive escapees (Kdm5c and Kdm6a) and in two NPC lines, E6 and CL30.7, of two clusters of genes that escape X-inactivation (Kdm5c and Hcfc1-Mecp2).

first: Edith

last: Heard

first: Agnese

last: Loda

first: Antonia

last: Hauth

first: Nicolas

last: Servant


title: Eos maintains Treg homeostasis and plays a critical role in the function of recirculating thymic Tregs

first: Tom

last: Hill

state: Maryland

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

overall_design: sc-RNA seq of thymic Tregs

first: Angela

last: Thornton

first: Shalini

last: Tanwar

first: Patricia

last: Korty

first: Alexandria

last: Wells

first: Elisha

last: Segrist

first: Ana

last: Teijeiro

first: Claudia

last: Rivera

first: Danping

last: Wei

first: Xi

last: Chen

first: Jinfang

last: Zhu

first: Asya

last: Khleborodova

first: Margery

last: Smelkinson

first: Juraj

last: Kubat

first: Tibor

last: Veres

first: Owen

last: Schwartz

first: Francisco

last: Otaizo-Carrasquero

first: Paul

last: Gardina

first: Amirhossein

last: Shamsaddini

first: Craig

last: Martens

first: Kyoungin

last: Cho

first: Cheng-Chao

last: Lin

first: Jaspal

middle: S

last: Khillan

first: Yelena

last: Levin

first: Ying

last: Wu


title: Spatial Transcriptomics of Human Fetal Lungs

city: Rochester

first: Soumyaroop

last: Bhattacharya

address: 601 Elmwood Ave Box 703

department: Pediatrics

institute: University of Rochester

summary: Spatial transcriptomic profiles were generated using lung tissue sections obtained from twelve prenatal human lung samples ranging in gestational age from 13 – 20 weeks, of which four were diagnosed with Trisomy 21, with defined hypoplasia.

overall_design: Lung tissue sections were assessed for quality using DV200 criteria, and those with DV200 values greater than 50% were selected for spatial transcriptomics. 5-micron tissue sections from individual samples were placed onto Visium Gene Expression Slides (10X Genomics), stained with H&E using Visium chemistry (v1) and scanned, in two batches. Subsequently, the tissue samples were permeabilized to release ligated probe pairs from the cells, that are bound to the spatially barcoded oligonucleotides present on the spots. The resulting barcoded libraries were sequenced on a NovaSeq 6000 sequencer (Illumina) and aligned to GRCh38-2020-A and quantified using the standard Spaceranger workflow (v2.0.1).

first: Bhattacharya

last: Soumyaroop


title: Castration Increases Aggressiveness of Prostatic Luminal Progenitor Cells in Prostate Cancer Through FosL1/AP-1-Mediated Transcriptional Reprogramming

city: Essen

first: Florian

last: Rambow

department: IKIM

institute: University Hospital Essen

summary: In this study, we show that the castration-tolerance potential of prostatic LSCmed (Lin-/Sca-1+/CD49fmed) cells is not intrinsic but rather results from transcriptomic reprogramming that further enhances their aggressiveness. Using scRNAseq specifically applied to Ptenpc-/- LSCmed cells sorted from intact versus castrated mice, we identified three distinct LSCmed cell clusters and we show that castration favors the emergence of a more stem-like LSCmed subpopulation.

overall_design: The transcriptomes of 384 single cells of murine prostate cancer model  were sequenced (scRNAseq) after FACS sorting.


title: Eos maintains Treg homeostasis and plays a critical role in the function of recirculating thymic Tregs [RNA-Seq]

first: Tovah

last: Markowitz

overall_design: Eos+ Tregs, Eos- Tregs, and Tconvs from thymus, total RNA-seq in quadruplicate

first: Xuan

last: Xie

first: Asya

last: Khleborodova

first: Ethan

last: Shevach


title: Divergent immue responses to commensal Clostridia classified based on motility gene arrangement and flagellin diversity

city: Birmingham

middle: L

last: Maynard

state: AL

address: 1825 University Blvd, SHEL 613

department: Pathology

institute: University of Alabama at Birmingham

summary: Flagella-dependent motility is a defining feature of several species of Clostridia that colonize the intestine. The genomes of these bacteria encode varying numbers of flagellins – the basic subunits of flagella - and the machinery necessary for synthesis, assembly, and function of flagella. Although adaptive immune responses to commensal flagellins are hallmarks of Crohn’s disease, it is unclear whether flagellins themselves drive inflammation, or what defines pro-inflammatory flagellated commensals. Here, we show that the arrangement of motility loci and the diversity of encoded flagellins can separate flagellated Clostridia into at least 2 functionally distinct subgroups. Both subgroups induce tolerogenic responses at homeostasis but possess divergent capacities for TLR5 activation and induction of inflammation. We identify a hypervariable region of the flagellin D0 domain that modulates the capacity for TLR5 activation and demonstrate enrichment of bacteria in the pro-inflammatory subgroup in Crohn’s disease biopsies. Collectively, our study identified a subset of colitogenic commensals and revealed one mechanism whereby these organisms can directly initiate intestinal inflammation.

overall_design: Three groups of untreated mice: 1) gnotobiotic with three select G1 bacteria, 2) gnotobiotic with three select G2 bacteria, and 3) germ-free; three replicates of each group for a total of nine samples.

first: Lennard

middle: W

last: Duck

first: Melissa

last: Jennings

first: Jung-Shan

last: Hsu

first: Covenant

last: Adeboboye

first: Elizabeth

last: Morgan

first: Kiarra

last: Coger

first: Barbara

last: Klocke

first: Dave

middle: D

last: Hill

first: Katie

last: Alexander

first: Alexander

last: Rosenberg

first: Goo

last: Lee

first: Qing

last: Zhao

first: Charles

middle: O

last: Elson


title: Single-nucleus RNA sequencing in the post-mortem thamaus and cortex in bipolar disorder

city: Tokyo

first: Masaki

last: Nishioka

address: Bunkyo-ku Hongo 2-1-1

institute: Juntendo University

summary: We performed high-throughput single-nucleus RNA sequencing (snRNA-seq) using the 10x Genomics Chromium platform on archived postmortem thalamus and frontal cortex (BA10) tissues from patients with bipolar disorder and control subjects to identify cell type–specific differentially expressed genes and compositional changes.

overall_design: Single-nucleus RNA sequencing (snRNA-seq) was performed using the 10x Genomics Chromium platform on cell nuclei extracted from the thalamus and frontal cortex (BA10) of postmortem brain tissue from 20 control subjects and 21 individuals with bipolar disorder. snRNA-seq libraries were prepared with the 10x Genomics Chromium Single Cell 3’ Reagent Kits v3.1 (dual index) and sequenced on the Illumina NextSeq 2000 platform (paired-end). Count matrices were generated with Cell Ranger v7.0.0.

first: Mie

last: Sakashita-Kubota

first: Kouichirou

last: Iijima

first: Naguib

last: Mechawar

first: Gustavo

last: Turecki

first: Tadafumi

last: Kato


title: Dermal fibroblasts respond to interleukin-4 and 13 and promote T-cell recruitment in atopic dermatitis

city: San Diego

first: Tomofumi

last: Numata

address: 9452 Medical Center Drive, Department of Dermatology

department: Dermatology

institute: university of california, SD

summary: Atopic dermatitis (AD) is a chronic inflammatory skin disease characterized by type 2 immune responses. While immune cells and keratinocytes are established contributors to AD pathogenesis, the role of dermal fibroblasts remains less defined. Here, we investigated whether fibroblasts contribute to T cell recruitment by producing chemokines in response to type 2 cytokines. Single-cell RNA sequencing (scRNA-seq) of human AD skin and murine models, including IL-4 receptor-deficient mice, revealed transcriptionally distinct fibroblast clusters, with IL-4Rα-dependent populations expressing high levels of chemokines. In vitro, IL-4/IL-13 synergized with inflammatory cytokines(Inf; TNFa + IL-17A + IL-1b) to induce fibroblast expression of CCR3 ligands, including Ccl8. Conditioned media from stimulated fibroblasts promoted T cell migration in a CCR3-dependent manner. Furthermore, pharmacologic inhibition of CCR3 reduced T cell infiltration and skin inflammation in two AD mouse models. These findings demonstrate that dermal fibroblasts are not passive structural cells but active participants in type 2 inflammation, contributing to the pathogenesis of AD by producing chemokines that facilitate T cell recruitment. Targeting the fibroblast–CCR3 axis may represent a novel therapeutic strategy for AD.

overall_design: Bulk RNA-seq of fibroblasts stimulated in vitro


title: Multiomics analysis of concurrent MASH and atherosclerosis in male and female mice

city: Shreveport

first: Sandeep

last: Das

state: LA

address: 1501 Kings Highway

institute: LSU Health Shreveport

summary: Metabolic dysfunction-associated steatohepatitis (MASH) has reached epidemic proportions with limited therapies available. Surprisingly, the leading cause of death in these patients is atherosclerotic cardiovascular disease. No pharmacological therapy exists to treat MASH and atherosclerosis simultaneously, which is attributed to the lack of translational mouse models, particularly in females. Herein, we have utilized both male and female atheroprone mice, combined with different high-fat diets containing physiologically relevant cholesterol levels, to model concurrent MASH-atherosclerosis. Upon phenotypic characterization using standard histopathology, immunohistochemistry, and biochemical assays on liver, cardiovascular, and plasma samples, we report the first female MASH-atherosclerosis model. Furthermore, we conducted a multi-omics exploration of metabolomic, lipidomic, and transcriptomic profiles altered within these groups, and found metabolic and genomic signatures comparable to the human disease. These models will facilitate future cardiometabolic research to unravel the molecular and metabolic underpinnings at the intersection of MASH and atherosclerosis, which must be pharmacologically targeted.

overall_design: Eight-week-old Ldlr-/- male and female mice were housed under controlled temperature (22±2°C) and humidity conditions (40-60%) on a 12-hour light/dark cycle and fed ad libitum a standard chow diet (LabDiet #5053, 13% of calories from fat). For our dietary model we used established29,42 high-fat and high-cholesterol western diet (WD, Envigo TD.88137, 42 kcal% fat with 0.2% cholesterol), choline deficient with high fat and high cholesterol diet (Research Diets #D22052704, 45 kcal% fat without added choline and 0.2% cholesterol) and modified MASH diet (Research Diets #D22052703, 40 kcal% fat with palmitic acid and trans-fat levels and 0.2% cholesterol) for 24 weeks prior to euthanasia and tissue harvest.

first: Oren

last: Rom

first: Sumit

last: Anand


title: Single-cell RNA-seq analysis of immune cells isolated by FACS from zebrafish embryos after acute muscle injury using a novel irg1 knock-in reporter

first: Celia

middle: E

last: Shiau

summary: The objective of this experiment was to analyze the single-cell transcriptomes of macrophages for molecular profiling of subtypes that emerge during acute muscle injury in zebrafish. This transcriptomic data was used in conjunction with high-resolution live-cell microscopy, in which individual macrophages were tracked to examine both cellular and population-level dynamics. Comparisons were made between baseline (stage-matched, uninjured controls) and distinct phases of injury: the initial inflammatory response at 24 hours post-amputation (hpa) and the resolution phase beginning at 48 hpa of two genotypes, control/wild-type and chronic inflammation mutant (nlrc3l deletion). Single-cell sequencing revealed significant differences in immune cell transcriptome post injury between control and chronic inflammation nlrc3l mutants, and that most irg1 positive cells were macrophages with a fraction of them being altered neutrophils also expressing irg1 after injury particularly in the mutants.

overall_design: Transgenic zebrafish carrying the novel GFP knock-in reporter irg1-KI:GFP were used to isolate macrophages at distinct phases of acute muscle injury response. Specifically, samples were collected at 24 hours post-amputation (hpa), representing the initial inflammatory phase, and at 48 hpa, marking the onset of tissue repair following debris clearance. Uninjured ("uncut") animals served as baseline controls. Responses were compared between wild-type (or control sibling) zebrafish and mutants with a deleterious nlrc3l mutation that causes chronic macrophage activation. To induce acute muscle injury, large tail amputations were performed on 2 days post-fertilization (dpf) zebrafish embryos. This procedure causes significant muscle damage, which fully regenerates within four days, forming a new tail tip. Activated macrophages upregulate irg1, displaying strong GFP fluorescence, while steady-state macrophages express minimal irg1, resulting in faint GFP signal. All irg1-KI:GFP+ cells expressing any detectable level of GFP were isolated using fluorescence-activated cell sorting (FACS) on a BD FACSMelody across four conditions: control uncut, control 24 hpa, control 48 hpa, and nlrc3l mutant 24 hpa. Two biological replicates were collected per condition, each consisting of pooled cells from 90 embryos, resulting in a total of eight samples. To maintain cell viability and quality, embryos were dissociated and sorted in batches of 30, with three such batches pooled to constitute a single sample. Sample collection was interleaved to evenly distribute conditions across the processing timeline. Embryo dissociation was performed in a buffer containing ROCK inhibitor, protease, DNase with gentle mechanical grinding, and a holding solution composed of HBSS (without phenol red), 1% BSA, and ROCK inhibitor. Cells were kept on ice until 10x genomics downstream processing and library preparation.

first: Matthew

last: Hamilton

first: Ethan

last: Bedsole


title: A specific subset of Mesenchymal Stromal Cells identified in poor prognosis pediatric AML favor leukemic stem cells persistence in the bone marrow [scRNA-seq]

city: Lyon

first: Kevin

last: Geistlich

address: 28 rue Laennec

institute: CRCL

summary: Pediatric Acute Myeloid Leukemia (AML) emerge likely from highly complex, dynamic and multiparametric mechanism. The importance of stromal cells from the hematopoietic bone marrow (BM) microenvironment in early steps of pediatric AML (pAML) was explored in this study, based on samples of patients collected at diagnosis from a multicenter cohort (CONECT-AML). BM-Mesenchymal stem cells (BM-MSC) were isolated and characterized. Flow cytometry analysis revealed in more than a third of patients, the presence of a CD117(c-kit)-expressing sub-population of BM-MSC, rarely observed in healthy donors, associated with a higher LSC-17 score and a poor risk patient’s group. Lastly, single cell RNAseq data from pAML leukemic cells cocultured in a robust 3D-BM physio-pathological system built with CD117+ BM-MSC cells, indicate a high level of cell-cell interaction specific of this MSC. Very importantly, the presence of CD117+ BM-MSC significantly protect leukemic cells from chemotherapy killing trough cell-cell contacts. To summarize, we revealed the existence of a BM-MSC population associated with high risk pAML and that protect leukemic cells from treatments.

overall_design: Mesenchymal stroma cells isolated from bone marrow of either pediatric donors or leukemic patients were categorized according to their phenotypic status for the CD117 / c-Kit / Kit marker. One condition was sent to single cell RNA-seq : a mix of endothelial cells, CD117 positive stromal cells, and hematopoietic cells untreated

first: Sylvain

last: Lefort

first: Sophia

last: Bounaud

first: Véronique

last: Maguer-Satta


title: Anti-CSF-1R therapy with combined immuno- chemotherapy coordinate an adaptive immune response to eliminate macrophage enriched Triple Negative Breast Cancers

city: Houston

first: Diego

last: Pedroza

address: One Baylor Plaza

institute: Baylor College of Medicine

summary: Patients diagnosed with metastatic triple negative breast cancer (mTNBC) have limited treatment options, are more prone to develop resistance and are associated with high mortality. A cold tumor immune microenvironment (TIME) characterized by low T cells and high tumor associated macrophages (TAMs) in mTNBC is associated with the failure of standard-of-care chemotherapy and immune checkpoint blockade (ICB) treatment. We demonstrate that the combination of immunostimulatory metronomic Cytoxan (CTX) coupled with anti-CSF-1R antibody targeted therapy (SNDX-ms6352) and anti-PD-1 (ICB), was highly effective against aggressive metastatic syngeneic Trp53 null TNBC genetically engineered mouse models (GEMMs) that present with high macrophage infiltration. Mechanistically, CSF-1R inhibition along with CTX disrupted the M-CSF/CSF-1R axis which upregulated IL-17, IL-15 and type II interferon and elevated B- and T cells. Addition of an anti-PD-1 maintenance dose was necessary to overcome de novo PD-L1 intra-tumoral heterogeneity (ITH) associated recurrence in lung and liver mTNBC.

overall_design: All mice received the final doses 24h prior to euthanasia. Single cell suspensions were processed as previously described and pooled from 3 mice per treatment. Only viable cells were used for single cell analysis as such, isolated single cell suspensions were first stained with Ghost Dye UV 450 (Tonbo Biosciences, 13-0868) for 10 min and sorted via FACS to isolate viable cells. Briefly, primary tumor cells were harvested and resuspended in RBC Lysis Buffer (BioLegend, Inc., 420301) and passed through a 70- µm strainer. Viable single cell suspensions were tagged with 3’ CellPlex barcoding oligos (10X Genomics, PN-1000262) and were quickly subjected for scRNA-seq library preparation by the Single Cell Genomics Core at BCM. Single-cell libraries were prepared following the Chromium Single Cell Gene Expression 3’ v3.1 kit encompassing the multiplex capture CMO barcoding kit (10x Genomics, PN-1000262). Next generation library sequencing was performed using the NovaSeq 6000 (Illumina) following quality control check.


title: TET1-mediated DNA hydroxymethylation controlling ferroptosis resistance in cancer [ChIP-seq]

first: Jun

last: Lu

state: Zhejiang

address: 866 Yuhangtang Road

summary: Ferroptosis, a non-apoptotic programmed cell death marked by iron-dependent lipid peroxidation, is closely associated with cancer. Despite of intensive investigation about the molecular pathways underlying ferroptosis, the mechanism that determines the disparity of cancer cell vulnerability to ferroptosis remains unclear. Here we show that the expression level of TET1, the founding member of the ten-eleven translocation (TET) family of enzymes that mediate DNA 5-hydroxymethylation, determines the susceptibility of cancer cells to ferroptosis. In ferroptosis resistant cells, the expression level of TET1 was remarkably higher than that of the sensitive cells. Cell response to ferroptosis could be affected by interfering TET1 expression. TET1 promoted DNA 5hmC modification at its target gene GCLM, activated both the canonical glutathione (GSH) synthesis, and the non-cannonical γ-glutamyl-peptide accumulation, and thus, protected cancer cells against ferroptosis. Our results uncover the role of TET1 as a ferroptotic defensor in cancer, and suggest the translational potential of targeting the TET/GCLM axis in cancer therapy.

overall_design: Chromatin immunoprecipitation sequencing (ChIP-seq) for TET1 in Kasumi-1 cells transfected with shNC or shTET1 lentivirus.

first: Lingling

last: Yang

first: Xi

last: Jiang


title: A targetable developmental program co-regulates angiogenesis and immune evasion.

status: Public on Dec 04 2025

first: Pietro

last: Berico

address: 550 1st Ave Smilow 305

institute: NYU Langone Health

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: TET1-mediated DNA hydroxymethylation controlling ferroptosis resistance in cancer

institute: Zhejiang University


title: Therapeutic Targeting of Epithelial Mesenchymal Cellular Plasticity in Pancreatic Cancer

first: Colin

last: Weekes

address: 55 Fruit Street

institute: Massachusetts General Hospital

summary: Pancreatic ductal adenocarcinoma (PDAC) cells exist on a spectrum of epithelial (E) and quasimesenchymal (QM) transcriptional states with differences in sensitivity to FOLFIRINOX (FFX). GSK-3b is a key regulator PDAC cell epithelial-to-mesenchymal transition (EMT). Here, we performed in vitro analysis of PDAC cell lines combined with multi-omic analysis of data from GSK-3b inhibitor trial (NCT05077800) to evaluate treatment effects on EMT. These data suggested that GSK-3b blockade synergizes with FFX by modulating PDAC plasticity while promoting the development of a tumor suppressive immune microenvironment.

overall_design: We performed single-nucleus RNA sequencing on matched pancreatic cancer patient biopsy specimens over the course of treatment with modified FOLFIRINOX, elraglusib, and losartan.

first: Eric

last: Lin

first: Priyadarshini

last: Pathak

first: Aileen

last: O'Shea

first: Beatrice

last: Awasthi

first: Ildiko

last: Phillips

first: Joshua

last: Kocher

first: Yuhui

last: Song

first: Michael

last: Raabe

first: Katherine

last: Xu

first: Bidish

last: Patel

first: Nicole

last: Lester

first: Jung Woo

middle: M

last: Bae

first: Lisa

last: Zhang

first: Linda

last: Nieman

first: Lawrence

last: Blaszkowsky

first: Elizabeth

last: Walsh

first: Aparna

last: Parikh

first: Andrea

last: Hansen

first: Joanna

last: Caufield

first: Gordon

last: Newbert

first: Akwi

last: Asombang

first: Brenna

last: Casey

first: Jonah

last: Cohen

first: Brian

last: Jacobson

first: Kumar

last: Krishnan

first: Raul

last: Uppot

first: Ralph

last: Weissleder

first: Nora

last: Horick

first: William

last: Hwang

first: Mukesh

last: Harisinghani

first: David

last: Ting


title: TET1-mediated DNA hydroxymethylation controlling ferroptosis resistance in cancer [5hmC-seq]

first: Jun

last: Lu

overall_design:
Examination of 5hmC modifications in Kasumi-1 and MV4;11 cells.
In order to reveal the regulatory mechanism of TET1 on ferroptosis surveillance, RNA profiles of control and TET1 overexpressed THP1 cells were generated by deep sequencing.

first: Lingling

last: Yang

first: Xi

last: Jiang


title: RBM15B Regulates progression of MLL-rearranged leukemia

city: Guangzhou

first: Wen-Tao

last: Wang

state: Guangdong

address: No. 135, Xingang Xi Road

department: School of Life Sciences

institute: sun yat sen university

summary: We identified RBM15B that promotes progression of MLL-r leukemia. In this study, we preformed the m6A RIP-seq, RNA-seq and RBM15B CUT& Tag sequensing to found that RBM15B selectively regulated m6A modified region in the 5′ UTR and in part of the CDS around the start codon (two wings around start codon (TWINS)) of mRNA transcribed from target genes of MLL-fusion proteins, which is guided by histone modification H3K79me2.

overall_design: 1. epz5676  and  DMSO treated MOLM-13 cells used in the   m6A RIP-seq and RBM15B CUT& Tag sequensing.2. Sh-NC and sh-RBM15 MOLM-13 cells used.

first: Yue-Qin

last: Chen

first: Tian-Qi

first: Shun-Xin

last: Zhu


title: Uncovering genetic dependencies in the DNA repair network after ionizing radiation

city: Boulder

first: Nausica

last: Arnoult

state: CO

address: 1945 Colorado ave

department: MCDB

institute: University of Colorado Boulder

summary: We constructed a combinatorial CRISPR guide library to target ~200,000 pairwise combinations of 461 genes associated with DNA Repair.

overall_design: eHAP-iCas9 cells harboring this library were grown under standard growth conditions as well as an LD30 dose of ionizing radiation to induce global DNA damage. Each condition grew for 14-15 days before being collected and sequenced.

first: Benjamin

last: Nebenfuehr

first: Lynn

last: Sanford

first: Robin

last: Dowell


title: TET1-mediated DNA hydroxymethylation controlling ferroptosis resistance in cancer [RNA-seq]

city: Hangzhou

overall_design: In order to identify the mechanism of TET1 mediated ferroptotic resistance, RNA profiles of ferroptosis-resistant (i.e., Kasumi-1),  –sensitive (i.e., MV4;11), and control and TET1 overexpressed THP1 cells were generated by deep sequencing.


title: ATAC-seq in SKBR3 cells treated with lapatinib + tazemetostat

first: Naiara

last: Perurena

address: 77 Avenue Louis Pasteur

department: Medicine/Genetics

institute: Brigham and Women's Hospital

summary: SKBR3 cells were treated with lapatinib + tazemetostat for 24 h. ATAC-seq was performed to identify accessible chromatin regions.

overall_design: SKBR3 cells were treated with 5 µM tazemetostat starting at day -6. At day -3, cells were split and continued to be treated with tazemetostat. At day -1, cells were seeded at 3.5 million cells per 15-cm plate. At day 0, cells were treated with 100 nM lapatinib and 5 µM tazemetostat. 24 h later (day 1), cells were collected by trypsinization and frozen cells were submitted to the AGCT Core at Cedars-Sinai for ATAC-seq.


title: Spatiotemporal remodeling of chromatin topology architecture and H3K27me3 redistribution underlies vascular pathology in Hutchinson-Gilford progeria syndrome [Hi-C]

city: Ottawa

last: Stanford

state: ON

address: 501 Smyth Rd

country: Canada

institute: Ottawa Hospital Research Institute

summary: Hutchinson-Gilford progeria syndrome (HGPS) is a devastating premature aging disorder driven by the accumulation of progerin, leading to severe vascular pathology. While epigenetic alterations are implicated, the spatiotemporal reorganization of the higher-order chromatin and its functional impact on vascular smooth muscle cell (VSMC) transcription remain poorly defined. Through an integrated multi-omics approach combining in situ high-throughput chromosome conformation capture (Hi-C) and Cleavage Under Targets and Tagmentation (CUT&Tag) profiling of CTCF, SMC1A, H3K27me3, H3K27ac, and H3K36me3 with transcriptomic analyses from control and HGPS iPSC-derived VSMCs, we reveal that global topologically associating domain (TAD) architecture remains largely intact in HGPS. However, the internal chromatin states of TADs undergo dynamic, passage-specific remodeling, characterized by a progressive accumulation of broad H3K27me3-repressed domains. This is accompanied by a loss of A/B compartment segregation, as confirmed by DNA-FISH, indicating a collapse of higher-order chromatin organization in late passage. Crucially, we uncover widespread rewiring of enhancer-promoter (E-P) loops, which is linked to the dysregulation of genes critical for vascular development, extracellular matrix organization, and atherosclerosis. Our study demonstrates that spatiotemporal redistribution of repressive histone marks and reorganization of E-P interactions within a structurally resilient TAD framework underpin widespread transcriptional dysregulation in HGPS vascular pathogenesis. This uncovers a critical dissociation    between higher-order chromatin architecture and epigenetic statehistone modification landscape, providing a mechanistic basis for the failure of vascular homeostasis in progeria.

overall_design: Cleavage Under Targets and Tagmentation (CUT&Tag) profiling of CTCF, SMC1A, H3K27me3, H3K27ac, and H3K36me3 in vascular smooth muscle cell differentiated from patient-derived induced pluripotent stem cells

first: Mzwanele

last: Ngubo

first: Naveen

last: Ahuja

first: Rana

last: Karimpour

first: Amit

last: Shrestha

first: Michael

middle: J

last: Hendzel

first: Theodore

last: Perkins


title: Effects on gene expression of lapatinib and/or GSK126 treatment in SKBR3 cells

summary: SKBR3 cells were treated with DMSO (as control), lapatinib, GSK126 or lapatinib + GSK126 for 24 h to identify genes and pathways differentially upregulated/downregulated by these treatments.

overall_design: SKBR3 cells were treated with DMSO or 5 µM GSK126 starting at day -6. At day -3, cells were split and continued to be treated with DMSO or GSK126. At day -1, cells were seeded at 350,000 cells per 6-cm plate in DMSO or GSK126. At day 0, cells pre-treated with DMSO were treated with DMSO or 100 nM lapatinib, while cells pre-treated with GSK126 were treated with 5 µM GSK126 or 5 µM GSK126 + 100 nM lapatinib. 24 h later (day 1), RNA was extracted using a RNeasy Plus Mini kit (Qiagen) and sequenced in an Illumina NextSeq500 run with single-end 75 bp reads.


title: A vagal sensory-to-sympathetic axis restrains anti-tumor immunity

city: Philadelphia

first: Chengcheng

last: Jin

address: BRB II/III, Room 732-734, 421 Curie Blvd

department: Department of Cancer Biology

institute: University of Pennsylvania

summary: Body-brain communication has emerged as a key regulator of tissue homeostasis. Solid tumours are innervated by different branches of the peripheral nervous system, and increased tumour innervation is associated with poor cancer outcomes. However, it remains unexplored how the brain senses and responds to tumours in peripheral organs, and how tumour-brain communication influences cancer immunity. Here, we identify a previously unrecognized tumour-brain axis that promotes oncogenesis by establishing an immune-suppressive tumour microenvironment (TME). Combining genetically engineered mouse models with neural tracing, calcium imaging and single-cell transcriptomics, we demonstrate that lung adenocarcinoma induces increased innervation, activation and transcriptional alterations in vagal sensory neurons (VSNs), a major interoceptive system connecting visceral organs to the brain. Mechanistically, Npy2r+ vagal sensory nerves transmit signals from lung tumours to brainstem nuclei, driving elevated sympathetic efferent activity in the TME. This, in turn, suppresses anti-tumour immunity via β2-adrenergic signaling in alveolar macrophages. Disruption of this sensory-to-sympathetic pathway through genetic, pharmacological or chemogenetic approaches significantly inhibited lung tumour growth by enhancing immune responses against cancer. Collectively, these results reveal a bidirectional tumour-brain communication involving vagal sensory input and sympathetic output that cooperatively regulate anti-cancer immunity; targeting this tumour-brain circuit may provide new treatments for visceral organ cancers.

overall_design: To understand how lung tumors influence the transcriptome of vagal sensory neurons (VSNs), we performed single cell RNA-sequencing analysis of VSNs isolated from healthy or tumor-bearing mice

first: Haohan

middle: K

last: Wei

first: Chuyue

last: Yu

first: Rui

middle: B

last: Chang


title: RNAseq of 3 and 5 days differentiated C2C12 cells treated with conditioned medium of KPC, 4662, LLC or C26 cells

city: Wageningen

first: Evert

middle: M.

last: van Schothorst

address: De Elst 1

country: Netherlands

institute: Wageningen University

summary: It is well known that tumours can exert direct negative effects on muscle tissue, which can contribute to the development of cancer cachexia. However, the underlying mechanisms and mediators involved in the communication between tumour and skeletal muscle are poorly understood. Cachexia-inducing cancer cell lines are used in both in vivo and in vitro research, they cause cachexia when used in an animal model. In the present study, we investigated the effects of conditioned media (CM) from cachexia-inducing cancer cell lines on differentiating skeletal muscle cells. Muscle-derived C2C12 cells were cultured (3-5 days) under differentiation conditions with CM from KPC, 4662, C26 and LLC cell lines and global gene expression was analysed by RNA sequencing.

overall_design: In vitro experiment

first: Miranda

last: van der Ende

first: Mieke

last: Poland

first: Fleur

last: Jansen

first: Jocelijn

last: Meijerink

first: Sander

last: Grefte

first: Jaap

last: Keijer

first: Renger

middle: F

last: Witkamp

first: Klaske

last: van Norren