title: Effects of EGCG, resveratrol and their combination on gene expression

city: Huntington

first: James

last: Denvir

state: WV

address: One John Marshall Drive

department: Biochemistry and Microbiology

institute: Marshall University School of Medicine

summary: Natural products available in vegetables, fruits and spices have drawn great deal of attention because of their chemopreventive potential. The purpose of this RNASeq experiment is to investigate the effect of two natural compounds EGCG and reveratrol and their combination on gene expression. Head and neck cancer cell line MDA686TU was treated with 40 μM EGCG, 15 μM resveratrol and their combination for 24 h. Total RNA was used for RNASeq. RNASeq libraries were sequenced in a 2 × 50 paired-end design on an Illumina HiSeq1500. Raw reads were imported from the Illumina HiSeq1500 using bcl2fastq2 v2.17.1.14 (Illumina) and trimmed to remove adapter content and low-quality base calls, with reads trimmed to a length of less than 25 bases removed from further analysis using Trimmomatic v0.36. Quality of reads was assessed before and after trimming using FastQC v0.11.5 (Babraham Institute, Cambridge, England). Reads were aligned to the human reference genome GRCh38 using HISAT2 v2.0.4, and the resulting bam files were sorted and indexed using SAMtools v 1.3.1. DESeq2 was used to identify differentially expressed genes (DEG) with a False Discovery Rate (FDR) threshold of 0.1.

overall_design:
Head and neck cancer cell line MDA686TU was treated with 40 μM EGCG, 15 μM resveratrol and their combination for 24 h. Total RNA was used for RNASeq.
Six replicates per group

first: Arm

middle: R

last: Amin

first: Denvir

last: James


title: Splicing Isoforms Associated to TGFβ-Induced Myofibroblast Activation

status: Public on Apr 22 2026

city: Sherbrooke

first: Sherif

middle: Abou

last: Elela

state: Québec

address: 3201 Jean Mignault

department: Département de microbiologie et infectiologie

country: Canada

institute: Université de Sherbrooke

type: Expression profiling by high throughput sequencing

summary: Myofibroblast differentiation is a key process in developmental biology and involved in numerous physiopathology. The gene expression program orchestrating fibroblast to myofibroblast differentiation as well as its recapitulation by TGFβ stimulation in vitro is relatively well characterized. Intriguingly, it is known that the splicing isoform EDA+FN1 is a marker and driver of myofibroblast differentiation but the alternative splicing landscape of myofibroblast is unknown. Here, we performed a high-throughput transcriptomic approach by RNA-Seq in a primary skin fibroblast line and uncover more than 250 splicing isoforms associated to TGFβ-induced myofibroblast using two different bioinformatic pipelines. This splicing profile highlights a distinct layer of regulation when compared to the global gene expression profile of myofibroblast. Surprisingly, TGFβ do not induce an EDA+FN1 splicing shift, although it stimulates global fibronectin expression. A 5 alternative splicing event (ASE) signature was further validated by ddPCR and AS-PCR and retrieved in publicly available RNA-Seq datasets describing other TGFβ-stimulated lung and skin fibroblasts. Thus, we conclude that the 5 ASEs signature may be used as putative universal myofibroblast markers and be of functional significance to myofibroblast formation and biology.

overall_design: The primary skin fibroblasts GM05386 were TGFb-treated or left untreated for 2 days in 6-well plates in biological triplicates (different cell passage). Samples were processed for RNA-Seq and analyzed for differential gene expression (DESeq2) and alternative splicing changes (rMATS, UdeS pipeline) comparing TGFb-treated vs untreated samples.

first: Opeoluwa

last: Alli-OKE

first: Danny

last: Bergeron

first: Philippe

last: Thibault

first: Jean-Philippe

last: Brosseau


title: Thyroid hormones maintain parvalbumin neuron functions in mouse neocortex

city: Lyon

first: Frédéric

last: Flamant

state: France

address: 46 allée d'Italie

department: IGFL

country: France

institute: ENSL

summary: Parvalbumin-expressing (PV) GABAergic interneurons play a key role in maintaining the excitation-inhibition balance in the mammalian neocortex. Here we investigate the function of thyroid hormones in PV neurons in the mouse neocortex. To this end, Cre/loxP recombination system was used to express a dominant negative mutated receptor of thyroid hormones only in PV neurons. We analyzed the neocortical phenotype of these mice, in which thyroid hormone signaling is selectively disrupted in PV neurons, by combining genomics, histology, electrophysiology, sleep recordings and behavioral analysis. In the mutant mice, gene expression analysis revealed a decreased expression of key perineuronal net components of PV neurons. PV neuron excitability was decreased, leading to behavioral hyperactivity and increased susceptibility to seizures. Additionally, sleep analysis revealed that mutant mice spent more time awake, and a delayed transition to sleep, suggesting impairments in sleep regulation mechanisms. Electrophysiological recordings further demonstrated altered gamma oscillations in the somatosensory cortex. These results highlight that thyroid hormones are not only required for the differentiation of PV interneurons, but also for the maintenance of their inhibitory function after the onset of parvalbumin expression.

overall_design: The Cre/loxP recombination system was used to restrict the expression ofa transgene which drives the expression of a nuclear fluorescent protein.  . A Cre driver additionnal transgene was used to restrict the expression to parvalbumin neurons (Pv-Cre). Four groups of mice were prepared. Group3 mice were treated with PTU for 2 weeks to decrease the circulating levels of thyroid hormones.  Group 1 mice are untreated controls, with wild-type Thra alleles (Ctrl). Group 2 mice are littermates with the ThraAMI floxed allele -(Mut). These mice express the dominant negative thyroid hormone receptor TRalpha1L400R. Group 3  were treated with PTU for 2 weeks to lower the circulating levels of thyroid hormones (PTU). Group4 mice  were treated with PTU for 2 weeks and received an injection of thyroid hormones 24h before cortex dissection (PTU+TH). Fluorescent nuclei were sorted from the cerebral cortex of adult mice. RNA was extracted from the sorted nuclei and libraries were prepared for RNA-seq.

first: Juan

last: Ren

first: Suzy

last: Markossian

first: Romain

last: Guyot

first: Denise

last: Aubert

first: Jiemin

last: Wong

first: Dong Dong

last: Li

first: Fabrice

last: Riet

first: Bruno

last: Cauli

first: Thierry

last: Galopin

first: Sabine

last: Richard


title: Transcriptome profiling of protein-coding RNAs in AGS following ANXA2P1 knockdown

city: Guangzhou，China

first: Jide

last: Wang

state: Guangdong ，China

address: 11838 Guangzhou Avenue North

department: Department of Digestive Medicine

country: China

institute: Nanfang Hospital, Southern Medical University

summary: ANXA2P1 was found to be significantly overexpressed in gastric cancer. To identify protein-coding RNAs regulated by ANXA2P1, we performed mRNA sequencing in AGS after ANXA2P1 knockdown.

overall_design: AGS cells were treated with either negative control or ANXA2P1 knockdown, with three biological replicates per group.


title: IL-33 promotes transcriptional and metabolic adaptations of tissue-resident Th2 cells

city: Baltimore

first: Immunometabolism

last: Department

state: Maryland

address: 1650 Orleans Street

department: Immunometabolism

country: USA

institute: Johns Hopkins University

summary: The polarization of naïve CD4+ T cells into Th2 cells is initiated in lymphoid organs and completed as the cells become tissue resident, where they express ST2, the receptor for the alarmin IL-33, which may be a key signal for tissue integration.  Cellular metabolic requirements associated with this transition remain poorly understood. To address this, we compared the response of lymphoid tissue (LT) Th2 cells from helminth parasite-infected mice to stimulation by IL-33 versus through the T cell receptor via anti-CD3/CD28. We found that IL-33, but not anti-CD3/CD28, induced the development of tissue-resident like Th2 cells expressing ST2. This was associated with IL-33 induced changes in arginine metabolism linked to mTORC1 activation and polyamine synthesis, which were required for the development of tissue-resident like Th2 cells. Furthermore, IL-33 induced transcriptional changes in genes involved in chemotaxis and cell adhesion that may be critical for tissue integration. Our findings provide insights into adaptations of Th2 cells responding to tissue-integration cues

overall_design: 4get mice were infected with Hpoly and sacrificed two weeks later. CD44+GFP+ (IL4+) Th2 cells were FACS isolated from pooled spleen and lymph nodes at D0 and five days after in vitro culture with IL2, IL2 and IL-33, or CD3/CD28 under Th2 polarizing conditions. The cells were sorted directly into RLT buffered snap frozen. RNA extraction, library preparation using SMART-Seq® v4, and Illumina sequencing were performed at Admera Health.

first: Anna

last: Kania

first: David

middle: E

last: Sanin


title: Single-Cell Profiling Reveals Mediators of Immune-Vascular Crosstalk in Mouse Models of Relapsing and Progressive Multiple Sclerosis

city: Wuhan

first: feng

last: zhang

address: jiefang avenue no.1277

department: neurology

institute: wuhan union hospital

summary: Multiple sclerosis (MS) is a chronic inflammatory and neurodegenerative disease of the central nervous system (CNS) with heterogeneous clinical courses. While current therapies can modulate the immune system, their efficacy in halting progressive neurodegeneration remains limited, underscoring the need for novel interventions that address both immune and vascular dysfunction. To investigate the mechanisms underlying these processes, we employed the myelin oligodendrocyte glycoprotein (MOG₃₅–₅₅)-induced experimental autoimmune encephalomyelitis (EAE) model, utilizing C57BL/6 mice, which develop a relapsing-remitting MS-like course, and NOD/ShiLtJ mice, which exhibit a secondary-progressive MS-like course. We performed single-cell RNA sequencing (scRNA-seq) on lumbar spinal cord tissues from these EAE models at the disease peak. Our analysis revealed distinct, cell-type-specific transcriptomic landscapes associated with relapsing and progressive pathologies. We identified critical mediators of immune-vascular crosstalk that were dysregulated across both disease phases, pinpointing conserved pathways and cell populations involved in disease perpetuation. Functional validation confirmed that targeting these key pathways can suppress pro-inflammatory immune cell activity, restore vascular integrity, and ameliorate clinical symptoms in both EAE models. This study provides a high-resolution resource of the immune and vascular interactions in relapsing and progressive MS models. Our findings uncover novel mechanisms sustaining neuroinflammation and highlight promising therapeutic targets for modulating both relapsing and progressive forms of MS.

overall_design: MOG₃₅–₅₅-induced EAE models were established using two mouse strains: C57BL/6 (to mimic RRMS-like acute EAE) and NOD/ShiLtJ (to mimic SPMS-like progressive EAE). A total of four experimental groups were set up, including C57BL/6 EAE group, C57BL/6 healthy control group, NOD/ShiLtJ EAE group, and NOD/ShiLtJ healthy control group. For each group, lumbar spinal cord tissues were collected from 6 age-matched mice, and single-cell suspensions were prepared by pooling the tissues of the 6 mice to form one sample, ensuring sufficient cell yield for subsequent experiments. At the peak of EAE disease (determined by clinical scoring; C57BL/6 mice: day 17-19 post-immunization; NOD/ShiLtJ mice: day 55-65 post-immunization), CD31⁺ endothelial cells and CD3⁺ T cells were FACS-sorted from the pooled single-cell suspensions of each group. High-quality sorted cells were used for scRNA-seq. Sequencing libraries were constructed using standard protocols and sequenced on a high-throughput sequencing platform. The resulting scRNA-seq data were processed to obtain clean single-cell transcriptomes, with a total of 16,365 high-quality cells captured, including 14,142 endothelial cells and 2,223 T cells. Subsequent bioinformatic analyses included cell clustering, cell type annotation (based on canonical markers such as Pecam1 for endothelial cells and Cd3 for T cells), differential gene expression analysis, and gene set enrichment analysis.

first: Feng

last: Zhang

first: Si-Bo

last: Yang

first: Yan

last: Luo

first: Xiao-Di

last: Sun

first: Bo-Hao

last: Chang

first: Da-Qiang

last: Zhou

first: Jun-Jie

last: Jiang

first: Ya-Nan

first: Jie-Hong

last: Wu

first: Hui-Juan

last: Jin

first: Hang

last: Hu

first: Yi-Fan

first: Bo


title: miR-4711-5p suppresses the cancer stemness, proliferation and invasion activity in pancreatic cancer

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

summary: Background/Aim: Pancreatic cancer is a highly malignant neoplasm and current treatment options have only shown minimal efficacy. Therefore, pancreatic cancer continues to have a poor prognosis, with the lowest 5-year survival rate and the development of efficient cancer therapeutics is desired. MiRNAs are involved in post-transcriptional regulation of gene expression and expected as a next generation cancer therapy. Here, we investigated the anti-tumor effects of miR-4711-5p in pancreatic cancer cells. Materials and Methods: We investigated the effects of miR-4711-5p treatment on cell proliferation, cell cycle, apoptosis, cancer stemness, and invasion in pancreatic cancer cell lines. We also explored the novel target genes of miR-4711-5p in RNA sequencing and in silico analysis. Results: We showed that miR-4711-5p suppressed cancer stemness, cell proliferation, and invasion and induced cell cycle delay and apoptosis in pancreatic cancer cells. MET, CASTA, and ANO1 were identified as potential target genes of miR-4711-5p. Conclusion: miR-4711-5p are potential therapeutic miRNAs in pancreatic cancer cells.

overall_design: RNA-sequencing analyses were performed in BxPC-3 cell line in three different conditions (no treatment, negative control treatment, miRNA treatment).

first: Yuhki

last: Yokoyama

last: Okuzaki

first: Hirofumi

last: Yamamoto


title: Male voles Arvicola terrestris scherman escaping to seasonal breeding: an example of a disturbance likely induced by environmental change

city: clermont ferrand

first: yoan

last: renaud

address: place henri dunand

institute: igred

summary: The work was initiated to characterize the testicular gene expression profile of winter and summer males to better understand the physiological changes of these seasonnal breeders. It revealed that a subpopulation of males did not have a seasonnal behavior and were active during the winter, however with a particular gene expression profile. These males may be at the origin of the spring peaks of reproduction, causing outbreaks of the vole populations. We hypothesize that climate change, offering warmer winters and better acces to food supply may at the origin of the dysregulation of the circannual biological clocks of these pest rodents.

overall_design: RNAs were extracted from testis of wild Arvicola terrestris males captured in winter or summer. RNAseq analysis was performed and the two groups were compared.

first: Fabrice

last: SAEZ

first: Yoan

last: RENAUD


title: RIP-seq analysis of RNA-binding protein in gastric cancer cells

first: Jide

last: Wang

summary: HNRNPF is an important RNA-binding protein. To investigate its role in gastric cancer cells, RIP-seq was performed to identify RNAs interacting with HNRNPF. RNA–protein complexes were immunoprecipitated using an anti-HNRNPF antibody, followed by RNA purification and high-throughput sequencing. This study aims to uncover how HNRNPF interacts with and regulates downstream RNAs in gastric cancer cells.

overall_design: RIP-seq was conducted in AGS cells using anti-HNRNPF antibodies to identify HNRNPF-bound RNAs.


title: Expression profiling of human gastric cancer cells after  glucose deprivation

state: Guangdong

address: 1838 Guangzhou Avenue North

type:
Non-coding RNA profiling by array
Expression profiling by array

summary: Glucose deprivation is a common feature in tumors. To investigate the differential expression of ncRNAs and protein-coding genes under glucose-deprivation conditions, human gastric cancer cells were cultured in low-glucose or normal-glucose medium and analyzed using the Agilent Human ceRNA Microarray.

overall_design: Human gastric cancer cells AGS were treated with either low-glucose or normal-glucose medium, with four biological replicates per condition. Total RNA was extracted from each sample and subjected to microarray profiling using the Agilent Human ceRNA Microarray 2019 (Design ID: 086188).


title: Progression of Nipah virus infection in African green monkeys: role of macrophages and dendritic cells in early virus spread

city: Galveston

first: Jacquelyn

last: Turcinovic

state: TX

address: Galveston National Laboratory, 301 University Blvd.

department: Microbiology and Immunology

institute: University of Texas Medical Branch

summary: Nipah virus (NiV) infection causes severe respiratory disease and encephalitis in humans and nonhuman primates with high case fatality rates.  While end-stage disease in primates has been well studied, particularly in African green monkeys (AGM), little is known about the development of NiV disease. Here, 12 AGM were infected with NiV and examined sequentially over 5 days to investigate the pathological and immunological events of NiV infection leading to death. DC-SIGN-positive immature dendritic cells in tonsil and alveolar macrophages were identified at 3 days postinfection (DPI) as early targets of NiV, implicating their important role in the spread of NiV to other tissues.  By 5 DPI, NiV spread to other tissues and cell types, including endothelium of medium caliber vessels and respiratory epithelium. Multifocal regions of fibrin deposition in small and medium caliber vessels and into alveolar spaces were also noted at 5 DPI. NiV antigen was not detected in cells of central nervous system tissues from any AGM at 3-5 DPI, indicating that neuroinvasion is a late event in untreated primates.  NiV infection elicited a biphasic host response characterized by early loss of anticoagulant factors followed by robust induction of interferon-stimulated cytokines, chemokines, and endothelial activation markers, revealing a tightly coupled inflammatory-coagulatory cascade underlying disease progression. RNA-seq analyses of tonsil and lung identified a robust, complement-driven immune response in tonsil but a muted, interferon-driven response in lung. The sequence of pathogenetic events identified here may provide insight into developing new therapeutic interventions and optimizing lead candidate antivirals.

overall_design: Time series NanoString data from African green monkeys challenged Nipah virus

first: Thomas

middle: W

last: Geisbert


title: Enhanced efficacy of a specific HDAC3 inhibitor in combination with 5-Azacitidine against diffuse large B-cell lymphoma [OCI_ly7_RNAseq_Day5]

city: Nice

first: Pilar

middle: M

last: Dominguez

state: Provence-Alpes-Côte d'Azur

address: 151 Route de Saint-Antoine

institute: Centre Méditerranéen de Médecine Moléculaire: C3M

summary: Diffuse large B-cell lymphoma (DLBCL) refers to an aggressive lymphoma that arises from germinal center (GC) B-cells, which differentiate into plasma cells (PC) to produce high affinity antibodies. 40% of DLBCL patients relapse or are refractory to the conventional immunochemotherapy treatment, usually with fatal consequences. DLBCL is characterized by profound alterations in the epigenome, which is correlated with poor survival. The abnormal epigenetic landscape of DLBCL tumors is associated with a blockade in GC exit and differentiation programs, which are regulated by the transcription factor BCL6. This aberrant repression of BCL6-target genes is mediated by 1) increased DNA methylation and 2) loss of acetylation of the lysine 27 of histone 3 (H3K27ac)-through recruitment of histone deacetylase 3 (HDAC3). Thus, we investigated the efficacy against DLBCL of the hypomethylating agent (HMA) 5-Azacitidine (5-Aza) and a specific HDAC3 inhibitor (HDAC3i). We found that treatment with 5-Aza plus HDAC3i had a potent synergistic anti-tumor activity in vitro and in vivo, which was superior to the effect of each single drug or 5-Aza combined with non-specific HDACi and, importantly, was not associated with toxicity in normal cells. We also demonstrated that the combined 5-Aza and HDAC3i treatment induced the epigenetic remodeling of DLBCL cells, which resulted in a more potent re-expression of PC differentiation genes, including XBP1 and ATF4, compared to each drug used as single agents. Our results highlight the importance of specifically targeting multiple layers of the epigenome to maximize the efficacy of epigenetic-based therapies.

overall_design: OCI-Ly7 lymphoma cells were treated with  5-Azacitidine (or vehicle) daily for 5 days, with a HDAC3 inhibitor (or vehicle) added at day 2 and 4. Cells were analyzed at day 5 (3 replicates per group).

first: Emilio Manuel

last: Serrano-Lopez

first: Corinne

last: Menigot

first: Killian

last: Guiraud


title: Whole-blood transcriptomic response to whole-body hyperthermia in participants with major depressive disorder

city: Boulder

first: Pei-San

last: Tsai

state: CO

address: 354 UCB

department: Integrative Physiology

institute: University of Colorado Boulder

summary: Depression is the leading cause of global disability according to the World Health Organization, and Major Depressive Disorder (MDD) makes up a majority of these cases. Current pharmacological interventions suffer from significant limitations and side effects, highlighting a need for novel therapeutic approaches. Whole-body hyperthermia (WBH) has been identified as a promising avenue of treatment; however, a comprehensive understanding of the mechanisms responsible for the antidepressant effects of WBH remains elusive. In this study we utilized high-throughput RNA sequencing (RNA-seq) to compare the whole-blood transcriptomic response, 30 minutes post intervention, of participants with MDD exposed to WBH or sham WBH. Briefly, 34 individuals with moderate to severe MDD (HDRS score > 16) were randomized to a WBH (n = 17) or sham WBH (n = 17) condition. Of 34 participants who were randomized, 22 participants provided blood samples (13 WBH and 9 sham WBH) that were available for sequencing, and 18 participants provided blood samples (9 WBH [33% female] and 9 sham WBH [44% female]) that were included in final RNA-seq analysis. Through differentially expressed gene (DEG) analysis with a false discovery rate (FDR) adjusted p-value (q-value) < 0.01 we identified 17 upregulated DEGs including multiple genes encoding heat-shock proteins (e.g., HSP70 [HSPA1A, HSPA1B, HSPA4], HSP90 [HSP90AB1, HSP90AA1], and HSP110 families [HSPH1]). Resulting log-fold changes and unadjusted p-values for all genes were used in Gene Set Enrichment Analysis (GSEA), which identified enriched (family-wise error rate-adjusted p-value < 0.05) biological processes (BPs) including “chaperone mediated protein folding”, “chaperone cofactor dependent protein refolding”, “cellular response to heat”, “positive regulation of response to cytokine stimulus”, “B cell receptor signaling pathway”, “peptide antigen assembly with MHC protein complex”, “positive regulation of type I interferon production”, and “positive regulation of interferon beta production”. These data identify novel genes and BPs that warrant further investigation as potential mediators of the antidepressant effects of WBH.

overall_design: Bulk RNA-seq profiling of whole-blood samples from participants with major depressive disorder immediately post-exposure to a whole-body hyperthermia (WBH) or sham WBH condition.

first: Tyler

middle: N

last: Akonom

first: Mary

middle: A

last: Allen

first: Tommy

middle: K

last: Begay

first: Charles

middle: L

last: Raison

first: Christopher

last: Lowry


title: Spatially resolved subtype progression reveals metabolic vulnerabilities in pancreatic ductal adenocarcinoma

city: Göttingen

first: Lena-Christin

last: Conradi

address: Robert-Koch-Straße 40

department: Department of General, Visceral and Pediatric Surgery

country: Germany

institute: University Medical Center Göttingen

summary: Pancreatic ductal adenocarcinoma (PDAC) exhibits profound molecular heterogeneity and poor prognosis, necessitating novel tailored therapies. The basal and classical subtypes - driven by glycolysis versus lipid metabolism - have distinct prognostic implications. We mapped PDAC molecular subtype heterogeneity, capturing spatially-resolved gene expression signatures and generating a comprehensive high-resolution dataset of 42,035 spatial spots. Subtype assignments were validated via multiplex immunofluorescence and quantitative analyses in patient-derived organoids. Our analysis resolved cancer cell signatures, deconvoluted intra-tumoral heterogeneity, and delineated a classical-to-basal trajectory. We identified metabolically ‘hot’, high-grade tumor niches characterized by concurrent enrichment of glycolysis and lipogenesis across both subtypes, nominating them as subtype-agnostic therapeutic targets. Preclinical models demonstrated that despite the basal subtype’s glycolysis dependence, both classical and basal tumors are susceptible to glycolysis inhibition. This work challenges the dogma of subtype-specific therapeutic silos and demonstrates highly adaptable energetic niches as reservoirs to drive tumor progression.

overall_design:
RNA-seq profiling of 8 untreated PDOs generated from PDAC tissue from 8 different patients.

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due to patient privacy concerns, we are not able to upload raw data but hope that submission
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title: Encephalopathy-linked UFM1 variants impede neuronal protein translation, development and function

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

summary: Genetic variants that hinder post-translational protein modifications by UFM1, UFMylation, cause encephalopathies. UFMylation regulates endoplasmic reticulum (ER) homeostasis, but how UFMylation-deficiencies cause selective neurological defects is unknown. Using Ufm1 knock-out mice, we investigated two types of UFMylation pathologies, UFM1 loss and expression of a pathogenic UFM1-R81C variant. We found that UFM1-deficiency confounds neuron development and synapse function. Mechanistically, UFM1 loss is associated with induction of ER stress, activation of the PERK-UPR pathway, and reduced protein translation. These defects are rescued by wild-type UFM1, but only partially by UFM1-R81C. UFM1-deficient and UFM1-R81Cexpressing neurons display distinct responses to ER stress, indicating that UFM1-R81C is not merely a loss-of-function variant. Exploring therapeutic options, we show that the PERK-UPR inhibitor Trazodone restores protein translation solely in UFM1-R81C-expressing neurons, and increases synapse number. Our study unveils a pivotal role for UFMylation in neuronal development, provides a molecular understanding of the signaling mechanisms altered in UFM1- associated encephalopathies, and offers important insights into potential treatments for these Genetic variants that hinder post-translational protein modifications by UFM1, UFMylation, cause encephalopathies. UFMylation regulates endoplasmic reticulum (ER) homeostasis, but how UFMylation-deficiencies cause selective neurological defects is unknown. Using Ufm1 knock-out mice, we investigated two types of UFMylation pathologies, UFM1 loss and expression of a pathogenic UFM1-R81C variant. We found that UFM1-deficiency confounds neuron development and synapse function. Mechanistically, UFM1 loss is associated with induction of ER stress, activation of the PERK-UPR pathway, and reduced protein translation. These defects are rescued by wild-type UFM1, but only partially by UFM1-R81C. UFM1-deficient and UFM1-R81C-expressing neurons display distinct responses to ER stress, indicating that UFM1-R81C is not merely a loss-of-function variant. Exploring therapeutic options, we show that the PERK-UPR inhibitor Trazodone restores protein translation solely in UFM1-R81C-expressing neurons, initiating an increase in synapse number. Our study unveils a pivotal role for UFMylation in neuronal development and provides a molecular understanding of the signaling mechanisms altered in UFM1-associated encephalopathies, offering valuable insights into potential treatments for these disorders.

overall_design: RNA-seq analysis of DIV13 primary hippocampal neurons WT and KO for UFM1 via infection at DIV1 with either RFP-expressing virus (WT) or Cre-expressing virus (KO)

first: Catarina

last: Perdigão

first: Josefa

last: Torres

first: Helge

last: Magnussen

first: Janina

last: Koch

first: Elena

last: Rudashevskaya

first: Frederieke

last: Moschref

first: Fritz

last: Benseler

first: Sally

last: Wenger

first: Tanja

last: Nilsson

first: Sabine

last: Beuermann

first: Silvio

last: O. Rozzoli

first: Yogesh

last: Kulathu

first: Olaf

last: Jahn

first: Benjamin

last: H. Cooper

first: Mateusz

last: C. Ambrozkiewicz

first: JeongSeop

last: Rhee

first: Nils

last: Brose

first: Marilyn

last: Tirard


title: Spatially resolved subtype progression reveals metabolic vulnerabilities in pancreatic ductal adenocarcinoma II

first: Lena-Christin

last: Conradi

overall_design:
RNA-seq profiling of 8 PDO lines generated from primary PDAC tissue from 8 different patients untreated and treated with 40 µM PFKFB3-inhibitor KAN0438757 for 24 h

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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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title: A conserved logic for the development of cortical layering in tetrapods [St_55]

city: New York

first: Maria

middle: ANTONIETTA

last: Tosches

address: 1212 Amsterdam Ave

institute: Columbia University

summary: The evolutionary origin of the cerebral cortex, a brain region classically defined by the presence of neuronal layers, remains elusive. We find that the salamander dorsal pallium is layered: superficial and deep-layer neurons have distinct birthdates, transcriptomic identities and projections. Using lineage tracing and scRNA-seq, we uncover evolutionarily-conserved principles of cortical development, including temporal patterning in multipotent radial glia progenitors, and the deployment of intermediate progenitor cells. We also describe the transcriptomic divergence of neuronal differentiation programs across species, suggesting that evolutionary diversification of cortical neuron types stems from changes in gene regulation after cell cycle exit. Our findings challenge long-held assumptions on the development and evolution of the cerebral cortex, and suggest that the mammalian neocortex evolved through modifications of a conserved developmental framework.

overall_design: scRNAseq of larval salamander (Pleurodeles waltl) brains from stage 30-55. Whole Cells were dissociated using papain. All dissociated cells were multiplexed using 4 distinct Cell Multiplexing Oligos (10x Genomics 3’ CellPlex Multiplexing kit) per stage, prior to GEM formation.

first: Astrid

last: Deryckere

first: Saket

last: Choudhary

first: Connor

last: Lynch

first: Lian Kirit

last: Limperis

first: Pauline

last: Affatato

first: Jamie

last: Woych

first: Elias

last: Gumnit

first: Alonso

last: Ortega Gurrola

first: Rahul

last: Satija

first: Christian

last: Mayer

first: Maria Antonietta


title: Effects of overexpression of HKDC1 on gene expression in two colon cancer cells.

city: Taipei City

first: KuoHsing Chen

last: Chen

address: No.57, Ln. 155, Sec. 3, Keelung Rd.

country: Taiwan

institute: National Taiwan University Cancer Center

summary: Dysregulation of cellular metabolism is one of the hallmarks of cancer. Tumor cells would enhance glycolysis to fuel the phenotypes of rapid proliferation and invasion. This study aims to explore epigenetic reprogramming of glycolysis pathway in colorectal cancer (CRC). CRCs and the adjacent normal colon tissues were profiled by using a comprehensive methylation array (Illumina Methylation EPIC Beadchips) to comprehensively analyze the methylation alterations in the glycolysis pathway. Differentially methylated genes (DMGs) were identified by using β value difference (≧ 0.2 or ≦ -0.2) and Wilcoxon rank-sum test (p < 0.05), and the common DMG in open datasets (GSE42752, GSE25062 and TCGA). Pyrosequencing was executed to validate the DMGs. Hexokinase domain containing 1 (HKDC1), the major hypomethylated gene we found, was overexpressed in colon cancer cells. Cells were treated with an HKDC1 inhibitor to elucidate the role of HKDC1. We found hypomethylation of HKDC1 was the only shared hypomethylated DMG in glycolysis pathway after comparing our methylation profiles of CRC to 3 public datasets. The RT-qPCR study in our cohort supported HDKC1 expression is methylation-regulated. Overexpression of HKDC1 in colon cancer cells resulted in increased proliferation of colon cancer cells and decreased cytotoxicity by an HKDC1 inhibitor. RNA sequencing revealed significant up-regulation of glycolysis and cell cycle pathways and their targets in HKDC1 overexpressed cells. In summary, hypomethylation of HKDC1 is common in CRC and may regulate cellular metabolism to promote proliferation of colon cancer cells through upregulation of glycolysis and cell cycle pathways.

overall_design: We performed RNA sequencing in COLO320DM and SW480 cells after pCMV6-HKDC1 or pCMV6-entry transfection to explore gene expression that could potentially contribute to promoting cell proliferation.

first: Kuo-Hsing

first: Chia-Lang

last: Hsu


title: Single-cell RNA sequencing of microglia/macrophages in zebrafish pde6c mutant eyes

city: Onna-son, Kunigami-gun

first: Ichiro

last: Masai

state: Okinawa

address: 1919-1 Tancha

institute: Okinawa Institute of Science and Technology

summary: We performed single-cell RNA sequencing of microglia/macrophages from eyecups of zebrafish pde6c mutant and their siblings at two time points, 5 days post fertilization and 4 weeks post fertilization using the 10x Genomics platform. These data allow (i) detailed study of microglia biology and heterogeneity in the zebrafish eye under normal conditions as well as (ii) microglial response to onset of chronic photoreceptor degeneration (5 days post fertilization) and start of Müller glia-mediated regeneration (4 weeks post fertilization) in the pde6c mutant zebrafish.

overall_design: Zebrafish pde6c mutant and their siblings carrying the mfap4:tdTomato-CAAX transgene to label microglia/macrophages were reared to 5 days post fertilization and 4 weeks post fertilization, respectively. Eyecups were dissected and mechanically homogenized to generate single-cell suspensions. Mfap4:tdTomato-CAAX positive cells were sorted through fluorescence-activated cell sorting (FACS) and subsequently analyzed through scRNA-seq.

first: Darshini

last: Ravishankar

first: Yuki

last: Takeuchi


title: DEVELOPMENTAL LANDMARKS AND CELLULAR TRANSITIONS DURING EXTRAVILLOUS TROPHOBLAST CELL DIFFERENTIATION [bulk_rna_seq_kds]

city: Kansas City

first: Michael

last: Soares

state: KS

address: 3901 Rainbow Blvd

department: Pathology

institute: University of Kansas Medical Center

summary: Human trophoblast stem (TS) can be captured, maintained in vitro under specific conditions, and differentiated into extravillous trophoblast (EVT) cells. The regulatory mechanisms that govern the self-renewal and differentiation of human TS cells into EVT cells are largely unknown.  In this study, bulk RNA-sequencing (RNA-seq) and single cell RNA-seq (scRNA-seq) were performed on human TS cells maintained in the stem state and on cells progressing from the stem state into EVT cells (differentiation days 3, 6, and 8). Distinct bulk and single cell transcript profiles were identified for each day of analysis. Day 3 of EVT cell differentiation represented a striking transition point and was readily distinguished from stem state and days 6 and 8 of EVT cell differentiation. Analysis of scRNA-seq led to the identification of several unique cell populations. Trophoblast cell developmental state-specific regulons and trajectories. We elucidated functional roles of key regulators of EVT cell development: cyclin B1, CCAAT/enhancer-binding protein beta, and ADAM metallopeptidase with thrombospondin type 1 motif 20. Collectively, we have defined developmental landmarks and transitional cell populations during EVT cell differentiation. These findings provide a valuable resource and foundation for future investigations into regulatory mechanisms controlling TS cell differentiation into the EVT cell lineage

overall_design: CT27 Trophoblast stem (TS- Okae et.al.) cell transduced with control shRNAs (shCTR) were used as a control or  shRNAs targeting CEBPB (shCEBPB), ADAMTS20 (shADAMTS20) or CCNB1 (shCCNB1 )were used as treatment. RNA-seq was performed in control and treatment cells after 8 days of differentiated into extravillous trophoblast (EVT) cells. 3 biological replicates each conditions.

first: Ayelen

last: Moreno-Irusta

first: Malay

last: Basu

first: Esteban

last: Dominguez

first: Thomas

middle: S

first: Sawyer

middle: H

last: Smith

first: Kaela

last: Varberg

first: Hiroaki

last: Okae

first: Takahiro

last: Arima

middle: J


title: Transcriptomic profiles of Huh7 and HLF hepatocellular carcinoma cells under 2D and 3D culture conditions

city: Hangzhou

first: Shuting

last: Xue

state: zhejiang

address: 866 Yuhangtang Road

institute: Zhejiang University

summary: This study investigates transcriptomic changes in human hepatocellular carcinoma (HCC) cell lines (Huh7 and HLF) cultured under different microenvironmental conditions, including 2D monolayer, 3D Inject-Embed, and 3D Mix-Embed cultures. RNA-seq was performed on total RNA using Illumina NovaSeq 6000 with paired-end 150 bp reads. Raw sequencing reads were aligned to the Homo sapiens reference genome (GRCh38/hg38) using STAR, and gene-level quantification was performed using featureCounts. The dataset includes raw FASTQ files and processed count and FPKM matrices for each sample. This resource provides insights into the impact of 3D culture on liver cancer gene expression.

overall_design: RNA-seq profiling of Huh7 and HLF liver cancer cell lines under 2D, Inject-Embed, and Mix-Embed culture conditions. Each condition included two biological replicates.

first: Junfang

last: Ji

first: Hanyuan

last: Zhang


title: DJ-1 alleviates high glucose-induced podocyte injury via activating ERK1/2 signaling

city: Jinan

first: Xiaochen

last: Tian

address: Beiyuan Street,

institute: The Second Hospital of Shandong University

summary: Diabetic nephropathy (DN) is one of the most common complications of diabetes. DJ-1 has been reported to participate in the response to renal ischemia/reperfusion (I/R) injury. However, the underlying mechanisms of DJ-1 in the regulation of high glucose-induced renal injury remain obscure. In this study, we performed RNA-seq to explore the function of high glucose on human podocyte cells (HPC), and found that high glucose widely regulated a variety of signaling pathways, including cell growth and death, signal transduction, etc. Furthermore, we found that DJ-1 was decreased in the high glucose conditions and DJ-1 could attenuate the high glucose-induced HPC apoptosis. Mechanically, overexpression of DJ-1 increased the phosphorylation of ERK1/2 (p-ERK1/2) and then mediated the transport of p-ERK1/2 from the cytoplasm to the nucleus. Furthermore, the accumulation of p-ERK1/2 in the nucleus activated the ERK1/2 pathway and enhanced the expression of NF-κB p65 and AP-1, which inhibited the apoptosis of HPC in the high glucose milieu. In conclusion, our study demonstrated that high glucose decreased DJ-1 expression in HPC and that overexpression of DJ-1 attenuated the apoptosis of HPC in high glucose conditions via enhancing the ERK1/2 pathway and the expression of NF-κB p65 and AP-1. Our study provides a novel mechanism by which DJ-1 alleviates high glucose-induced podocyte injury.

overall_design: Total RNA was extracted from podocyte treated with 5.5mM (LG), 15mM (MG) and 30 mM (HG) D-glucos 24h, and was then subjected to RNA-seq analysis by ShenZhen BGl Genomics Co., Ltd.


title: A conserved logic for the development of cortical layering in tetrapods [St_30-53]

first: Maria

last: Tosches

first: Astrid

last: Deryckere

first: Saket

last: Choudhary

first: Connor

last: Lynch

first: Lian Kirit

last: Limperis

first: Pauline

last: Affatato

first: Jamie

last: Woych

first: Elias

last: Gumnit

first: Alonso

last: Ortega Gurrola

first: Rahul

last: Satija

first: Christian

last: Mayer

first: Maria Antonietta


title: Long-Range IgH V(D)J Recombination [ChIP-seq]

city: East Lansing

first: Yu

state: MI

address: 567 Wilson Rd, Biomedical and Physical Sciences Building, Rm 5176

department: Microbiology, Genetics and Immunology

institute: Michigan State University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Cohesin-mediated loop extrusion plays a crucial role in IgH V(D)J recombination, driving D-to-JH rearrangements followed by VH-to-DJH rearrangements.

overall_design: We performed CTCF and SMC3 ChIP-Seq in WT and CTCF N-terminal mutant v-Abl transformed pro-B cells to study the role of cohesin variants in IgH V(D)J recombination

first: FuJung

last: Chang


title: Engineering perfusable vascular networks in organoids-on-chip [bulk RNA-seq]

city: Vancouver

first: Clement

last: Quintard

state: British Columbia

address: 3518 Wesbrook Mall

institute: University of British Columbia

summary: Vascular networks are critical for the development and maintenance of human tissues, as they support metabolism and regulate tissue growth and function. In vitro models such as organoids and organs-on-chip often have a limited capacity to recapitulate in vivo functional vascular networks and their integration within tissues. Most existing systems fail to mimic the structural and functional complexity of native capillary beds, lack physiological flow dynamics, and do not support vascular circulation. Here, we present a fully stem cell-derived microfluidic platform capable of generating perfusable vascular network organoids-on-chip with capillary-scale vessels, endothelial responses to biophysical forces, and physiologically accurate gene expression. Using this platform, we generate vascularized heart organoids-on-chip that replicate the dense capillary architecture of the heart and exhibit organ-specific vascular features and gene expression. These results establish a scalable and physiologically relevant approach for engineering and studying vascularized organoids under dynamic flow, with broad applications in developmental biology, disease modeling, and multi-organ in vitro systems.

overall_design: Vascular network organoids (derived from pluripotent stem cells) and HUVEC-derived networks, cultured under different flow conditions, were analyzed using bulk RNA sequencing.

first: Josef

last: Penninger


title: SP5/8 transcription factors drive primary cilia formation

city: Frederick

first: Francisco

last: Pereira Lobo

address: 1050 Boyles St

institute: National Cancer Institute

summary: Sp5/8 are tissue specific zinc finger transcription factors downstream of Wnt signaling pathway. Sp5/8 null embryos display severe posterior axis truncation resembling mutant phenotypes of Wnt/b-catenin signaling pathway. To address the role of Sp5/8 in gastrulation development, we differentiated R1 Wildtype (WT) and Sp5/8 dko  Embryonic Stem Cells (ESCs) as gastruloids as described previously (Beccari, L. et al, 2018) to evaluate scRNA transcriptome analysis.

overall_design: Gastruloids were initiated from 300 WT (R1) and Sp5/8 dko ESCs in 96 well ultra-low attachment dishes for 48 hours and treated with CHIR (3µM) from D2 to D2.5 for 12hours. Gastruloid spheres were collected at Day 2.5 for single-cell RNA sequencing.

first: Ravindra

middle: B

last: Chalamalasetty

first: Moonsup

last: Lee

first: Terry

middle: P

last: Yamaguchi


title: Engineering perfusable vascular networks in organoids-on-chip

overall_design: Vascular network organoids and vascularized heart organoids, derived from pluripotent stem cells, cultured under different flow conditions, were analyzed using scRNA-seq.


title: Long-Range IgH V(D)J Recombination [HTGTS-V(D)J-Seq]

last: Zhang

overall_design: We performed HTGTS-V(D)J-Seq in v-Abl transformed pro-B cells and their various mutant derivatives to study the differential potential of the two somatic cohesin variants in mediating IgH V(D)J recombination.

first: Fujung


title: Comprehensive Molecular and Functional Analysis of NUTM1-Rearranged Leukemia [iLS-bulkRNA]

first: Masaki

last: Nomura

address: 2-2, Yamadaoka

department: Department of Cancer Pathology

institute: Graduate School of Medicine, The University of Osaka

summary: NUTM1-rearrangement (NUTM1-r) defines a significant subset of B-cell acute lymphoblastic leukemia (B-ALL), particularly in infants lacking KMT2A-rearrangements (KMT2A-r), yet its underlying molecular characteristics remain poorly understood. Here, we establish that NUTM1-r leukemia is a discrete entity characterized by a unique transcriptional and epigenetic landscape, notably featuring global DNA hypomethylation, irrespective of the 5' fusion partner. Functional interrogation of NUTM1 fusions reveals a dual oncogenic role: they drive commitment towards the B-lymphoid lineage while concurrently conferring potent leukemic stem cell properties. Strikingly, expression of a representative fusion, BRD9-NUTM1, is sufficient to induce serially-transplantable prepro-B-like leukemia in vivo, faithfully recapitulating the key molecular and immunophenotypic features of human NUTM1-r B-ALL. Mechanistically, NUTM1 fusions establish an aberrant chromatin state, marked by global enhancement of H3K27 acetylation and the creation of distinctive open chromatin regions that co-opt both B-lineage and stemness-related transcriptional programs, including those involving NF-κB and posterior HoxA genes. In stark contrast to resistant KMT2A-r leukemias, NUTM1-r leukemic cells exhibit a profound sensitivity to chemotherapy. This vulnerability is mechanistically linked to the leukemia's dependence on active transcription. Our findings delineate the unique molecular profile of NUTM1-r leukemias, revealing specific vulnerabilities that rationalize their favorable clinical outcomes and suggest opportunities for modified therapeutic strategies.

overall_design: BRD9-NUTM1 (BN1) iLS cells were sorted by FACS. RNA was extracted, then Poly(A)- selected, and stranded DNA libraries were prepared.

first: Koutarou

last: Nishimura

first: Weijia

last: Zang

first: Masatoshi

last: Takagi

first: Daichi

last: Inoue


title: Homeostatic mature dendritic cells instruct fibroblast specialization via Notch2 to establish T cell niches

city: Epalinges

first: Nagham

last: Alouche

address: Chemin des Boveresses 155

department: Immunobiology

country: Switzerland

institute: University of Lausanne

summary: Secondary lymphoid organs are structurally organized by fibroblastic reticular cells (FRCs), which coordinate immune cell positioning and support adaptive immune responses. However, the mechanisms underlying the differentiation of FRCs into distinct functional subsets remain poorly understood. To investigate the role of Notch2 signaling in this process, we performed single-cell RNA sequencing (10x Genomics) on lymph node immune cells from mice lacking Notch2 expression specifically in FRCs. Our dataset reveals how Notch2 signaling shapes FRC subset differentiation and modulates the composition of neighboring immune cell populations.

overall_design: Lymph node immune cells from two Notch2^fl/fl^ mice and two Ccl19-Cre × Notch2^fl/fl^ mice, all on a C57BL/6 background, were processed for scRNA-seq. Live immune cells were sorted using a MoFlo Astrios EQ cell sorter, with the following final proportions: 20% CD45⁺ CD19⁺, 20% CD45⁺ CD3e⁺, 30% CD45⁺ CD19⁻ CD3e⁻ CD11c⁺ MHCII^hi^, and 30% CD45⁺ CD19⁻ CD3e⁻ CD11c⁻ MHCII^low^

first: Corinne

last: Peter

first: Giovanna

last: Ambrosini

first: Karolina

last: Bojkowska

first: Julien

last: Marquis


summary: Secondary lymphoid organs are structurally organized by fibroblastic reticular cells (FRCs), which support immune cell positioning and adaptive immune responses. However, the mechanisms driving the differentiation of FRCs into distinct functional subsets remain unclear. To investigate the role of Notch2 signaling in this process, we performed single-cell RNA sequencing (10x Genomics) on lymph node FRCs lacking Notch2 expression. Our dataset highlights how this pathway contributes to FRC differentiation.

overall_design: Two experimental batches were performed. The first batch included single-cell RNA sequencing (scRNA-seq) analysis of lymph node fibroblastic reticular cells (FRCs) from Ccl19-Cre x R26R-EYFP mice and non-littermate Ccl19-Cre x Notch2^fl/fl x R26R-EYFP mice, both on a C57BL/6 background. The second batch included Notch2^fl/fl control mice and their littermate Ccl19-Cre x Notch2^fl/fl mice, also on a C57BL/6 background.

first: Isabelle

last: Dupanloup


title: Modeling Masticatory Myalgia to Headache-like Referred Pain Triggers Local Gene Plasticity at Referred Pain Sites

city: SAN ANTONIO

first: YI

last: ZOU

address: 8403 Floyd Curl Drive

institute: UTHSA-GCCRI

summary:
We investigated biological processes associated with referal pain.
Refereal pain was triggered by injection of Collagenase type II into temporal muscle. Bulk RNA sequncing for dura mater samples was perfformed 2d post-injection. Massetr muscle bulk RNA-seq was done 28d post-injection.

overall_design: Gene expression profiling analysis of dura mater and masster muscle RNA-seq data for referred pain model induced by stimulation of temporal muscle with collagenase.

first: Anahit

last: Hovhannisyan

first: Jessica

last: Aldape

first: Jennifer

last: Mecklenburg

first: Jessie

last: Alfaro

first: Yi

last: Zou

first: Zhao

last: Lai

first: Wei

last: Guo

first: Jiale

last: Yang

first: Malin

last: Ernberg

first: Danilo

last: Boada

first: Ke

last: Ren

first: Armen

last: Akopian


title: Comprehensive Molecular and Functional Analysis of NUTM1-Rearranged Leukemia [ChIP-Seq]

city: Suita

first: Masaki

last: Nomura

overall_design: HA-Tagged BRD9-NUTM1 (HA-BN1) expressing human leukemic line K562 cells were sorted by FACS. HA ChIPed DNA libraries were prepared.

first: Koutarou

last: Nishimura

first: Weijia

last: Zang

first: Daichi

last: Inoue


title: Targeted gene expression profile of  breast cancer patients' biopsy tumors and after post-radiation surgical resection tumors

city: Oklahoma City

first: Suresh

last: Niture

state: OK

address: 800 NE 10th St, Department Of Radiation Oncology

institute: Department of Radiation Oncology, Stephenson Cancer Center, Oklahoma Unive

summary:
Individualized outcome prediction classifiers were successfully constructed through expression profiling of a total of  758 (BC360 9.15.2023)  and   750 (IO360 9.15.2023) genes in 20 breast cancer  (BC) cases.
Differential expression on Oncologic (BC30) and Immunooncogenic IO360) profiling was performed using nCounter NanoString technology.

overall_design: This BC360 report analyses 19 samples from the Mayo Clinic. Comparisons within the report include: HISTGRD, TLS (0 vs 1+), TILs Status (Low= <10% vs High= >=10%), Ki67 Analysis (Low= <1% vs High= 1% or more) and RCB Class (RCB-I vs RCB-II), Time Series Analysis for all samples and Time Series Analysis for matched samples. Raw and normalized data can be downloaded from the top of the Quality Control tab and annotations can be downloaded from the bottom of the same tab. Signature data per sample can be downloaded on the Single Sample analysis tab. The IO360 report analyses 20 samples from the Mayo Clinic. Comparisons within the report include: HISTGRD, TLS (0 vs 1+ or N/A), TILs Status (Low= <10% vs High= >=10% or N/A), Ki67 Analysis (Low= <1% vs High= 1% or more) and RCB Class (RCB-I vs RCB-II or N/A-pCR).   Raw and normalized data can be downloaded from the top of the Quality Control tab and annotations can be downloaded from the bottom of the same tab. Signature data per sample can be downloaded on the Single Sample analysis tab.

first: Suryakant

first: Danushka

last: Seneviratne


title: circTGFBR2(3-6) acts as an assembly platform for IGF2BP3 protein and TGFBR1 mRNA to enhance breast cancer cell plasticity

city: Leiden

first: Hailiang

last: Mei

address: Einthovenweg 20

department: Sequencing Analysis Support Core

country: Netherlands

institute: Leiden University Medical Center

summary: Transforming growth factor (TGF)-β signaling is a key driver to induce epithelial-to-mesenchymal transition (EMT), a process that enhances cancer cell plasticity and metastatic potential. However, the role of circular RNAs (circRNAs) in TGF-β signaling remains largely unexplored. Here, we identify circTGFBR2(3-6), a circRNA derived from TGF-β receptor 2 (TGFBR2) pre-mRNA, as a critical enhancer of TGF-β/SMAD signaling in breast cancer cells. Depletion of circTGFBR2(3-6) inhibits TGF-β-induced EMT, migration, and in vivo extravasation of breast cancer cells. Mechanistically, circTGFBR2(3-6) acts as a scaffold that facilitates the interaction between the RNA-binding protein insulin-like growth factor 2 mRNA binding protein 3 (IGF2BP3) and TGF-β receptor 1 (TGFBR1) mRNA in an N6-methyladenosine (m6A)-dependent manner, and thereby stabilizes TGFBR1 and promotes its expression. Furthermore, IGF2BP3 knockdown reduces circTGFBR2(3-6)-mediated enhancement of TGF-β/SMAD signaling and TGF-β-induced EMT and migration. Our findings identify circTGFBR2(3-6) as a novel enforcer of TGF-β/SMAD signaling at the receptor level and highlight IGF2BP3 as a critical m6A reader that mediates circTGFBR2(3-6)-driven breast cancer cell plasticity.

overall_design: circTGFBR2(3-6) is ectopic expressed in MDA-MB-231 cells. RNA from cells transduced with the empty vector was set as a control. Three biological replicates were included in each group.

first: Qian

last: Wang

first: Rayman

middle: T

last: Tjokrodirijo

first: Peter

last: van Veelen

last: ten Dijke

first: Chuannan

last: Fan


title: DGAT: A Dual-Graph Attention Network for Inferring Spatial Protein Landscapes from Transcriptomics

city: Pittsburgh

first: Hatice

middle: Ulku

last: Osmanbeyoglu

state: Pennsylvania

address: 5607 Baum Blvd

department: Biomedical Informatics

institute: University of Pittsburgh

summary:
This dataset comprises spatial multi-omic profiling of malignant pleural mesothelioma (MPM) tissue, enabling simultaneous measurement of transcriptomic and protein expression at spatial resolution. To address the lack of spatially resolved proteomic measurements in standard spatial transcriptomics (ST) technologies, we generated this in-house MPM spatial transcriptomics and proteomics dataset and used it to train and evaluate DGAT (Dual-Graph Attention Network), a deep learning framework for imputing protein expression from ST data. DGAT integrates transcriptomic, proteomic, and spatial information using graph attention networks and jointly reconstructs mRNA and protein profiles through multi-task learning. This dataset serves both as a biological resource for understanding the tumor immune microenvironment in MPM and as a benchmark for spatial protein inference. DGAT’s predictions on this dataset enabled improved identification of immune phenotypes and tumor–stroma spatial organization, with implications for biomarker discovery and therapeutic targeting in mesothelioma.
Spatial transcriptomics (ST) technologies provide genome-wide mRNA profiles in tissue context but lack direct protein-level measurements, which are critical for interpreting cellular function and microenvironmental organization. We present DGAT (Dual-Graph Attention Network), a deep learning framework that imputes spatial protein expression from transcriptomics-only ST data by learning RNA–protein relationships from spatial CITE-seq datasets. DGAT constructs heterogeneous graphs integrating transcriptomic, proteomic, and spatial information, encoded using graph attention networks. Task-specific decoders reconstruct mRNA and predict protein abundance from a shared latent representation.

overall_design:
Two formalin-fixed & paraffin-embedded (FFPE) malignant pleural mesothelioma tissue blocks were obtained from National Meosthelioma Virtual Bank. 5 μm sections were taken each for Visium CytAssist.
To evaluate the generalizability of DGAT beyond the tissue types used for training, we applied the pretrained model to six independent in-house spatial transcriptomic datasets encompassing four kidney samples (three from chronic kidney disease and one normal kidney) and two lung samples from chronic lung disease. These datasets represent distinct organ systems and disease contexts not included during model training, providing a robust test of DGAT’s transferability to unseen tissues.

first: Soto Gutierrez

last: Alejandro

first: Florentino

last: Rodrigo M

first: Faccioli

last: Lanuza AP

first: Saavedra

last: Manuel

first: Ma

last: Xiaojun

first: Osmanbeyoglu

last: Hatice


title: Single-cell multi-omic sequencing reveals cell-specific transcriptomic and chromatin accessibility profiles in gut microbiome metabolite butyrate-produced pain modulation

city: Dallas

first: Feng

last: Tao

address: 3302 Gaston Avenue

department: Biomedical Sciences

institute: Texas A&M University College of dentistry

summary: Pain is a predominant symptom of temporomandibular joint (TMJ) disorders, presenting significant clinical challenges due to their complexity and limited treatment options. This study investigated the therapeutic potential of butyrate, a gut microbiome metabolite, in a complete Freund’s adjuvant (CFA)-induced mouse model of TMJ inflammatory pain. Butyrate administration significantly alleviated TMJ pain and restored butyrate levels in mouse feces, plasma, and the spinal trigeminal nucleus caudalis (Sp5C). Additionally, it reversed TMJ pain-induced reductions in acetylation within Sp5C neurons, a critical epigenetic mechanism linked to pain states. Utilizing single-nucleus RNA sequencing (snRNA-seq) and single-nucleus ATAC sequencing (snATAC-seq), we profiled transcriptional and chromatin accessibility changes at the single-cell level.

overall_design: Inflammatory temporomandibular joint (TMJ) pain was induced in mice using CFA (10 μl, 5 mg/ml) or saline injected into the TMJ space. Mice were divided into three groups: CON (saline injection + glycerol via oral gavage), CFA (CFA injection + glycerol via oral gavage), and TB (CFA injection + tributyrin via oral gavage). Sp5C tissues were collected on day 5 post-CFA injection for single-nucleus RNA sequencing (snRNA-seq) and ATAC sequencing (snATAC-seq). Each group included two biological replicates.

first: Ran


title: Suppression of UCP2 alleviates leukemogenesis by enhancing branched amino acids induced oxidative stress via activating PI3K/AKT/mTOR signaling

city: Shanghai

first: Innocent

middle: Okohi

last: AGIDA

state: Shanghai

address: Building 7, 277 South Chongqing Road, Shanghai Jiao Tong University, School of Medicine. Shanghai, China.

department: Biochemistry and Molecular Cell Biology

summary: Although the cellular role of uncoupling protein 2 (UCP2) in tumorigenesis have been reported in various solid tumor models, its role in leukemogenesis remain elusive. Here, we demonstrated that UCP2 was highly expressed in AML, and it is significantly associated with chemoresistance and poor prognosis suggesting that UCP2 can be a potential biomarker for AML treatment. Mechanically, in vitro and in vivo silencing of UCP2 significantly impairs AML cell growth, survival and accompanied with the disruption of mitochondria homeostasis. Interestingly, RNA-seq analysis and metabolic mass spectrometry revealed that silencing UCP2 results in accumulation of branched chain amino acids (BCAA), which in turn induced oxidative stress through activating PI3K/AKT and mTOR signaling pathway. Additionally, lack of BCAA restored leukemic cell growth, cell survival and decreased mitochondria ROS production which is induced by inhibiting UCP2. Notably, supplementation of BCAA enhanced anti-tumor activity of Genipin, a selective inhibitor that targets UCP2, results in significant reduction of AML blasts, increased mice survival and magnified oxidative stress. Taken together, our study elucidates the rationale of targeting UCP2-BCAA-PI3K/AKT/mTOR signaling axis in leukemogenesis and provide a novel strategy for leveraging the metabolic dependencies of leukemic cells.

overall_design: RNA-seq profiling of AML cells and their UCP2 knockdown derivatives (shUCP2 Ctrl, shUCP2 #1, shUCP2#2)

last: Jiao

first: Innocent-Okohi

last: Agida

first: Zizhen

last: Xu


title: Single cell transcriptome analysis of human primary osteoblasts

city: Changsha

first: Kun

last: Liu

state: Hunan

address: 36 Lushan Road

institute: Hunan Normal University

summary: This study collected three femoral head samples, optimized the experimental workflow for osteoblast isolation and conducted single-cell transcriptomic sequencing. During the bioinformatic analysis of the single-cell transcriptomic data, we annotated into 10 cell types: OB, NE, Chondrocytes (CHON), Erythrocytes (ER), Macrophages (MAC), B cells (B), T cells (T), plasma cells (PC), Endothelial cells (EC), Smooth muscle cells (SMC). Using CellChat, we identified distinct ligand and receptor expression patterns across various cell types. These analyses allowed us to identify unique signaling mechanisms for each cell population and uncover functional communication among different cell types.

overall_design:
This study incloud three femoral head samples undergoing hip replacement surgery. The Magnetic-Activated Cell Sorting (MACS) was employed to isolate cells from femoral head samples.

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due to a server malfunction, the original fastq files were lost
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first: Yan

last: Chen

first: Chong

last: Cao

first: Zhengwu

last: Xiao

first: Yu Xin

last: Li

first: Kaizhi

last: Wen

first: Hongwen

last: Deng

first: LiuJun

last: Tan


title: Sperm lacking Protamine 2 fail to support normal fertilization and embryogenesis in mouse

city: New Haven

first: Bluma

last: Lesch

state: CT

address: 333 Cedar Street

department: Genetics

institute: Yale University

summary: Spermatozoan DNA is hypercondensed by protamines, which are essential for sperm motility and function. However, little is known about how protamine-mediated condensation impacts fertilization and the early stages of embryogenesis We performed intracytoplasmic sperm injection (ICSI) with sperm lacking Protamine 2 (Prm2 KO) and tracked preimplantation embryogenesis in mice. We found that ICSI with Prm2 KO sperm leads to fragmentation and zygotic arrest at the 2-cell stage. Prm2 KO sperm DNA is depleted from the oocyte within two hours of fertilization, during the completion of maternal meiosis II, and the resulting zygote has one pronucleus with multiple nuclear abnormalities. Direct induction of DNA damage in wild type sperm did not fully recapitulate the observed defects. Prm2 KO sperm were sufficient to induce these defects even in the presence of co-injected wild type sperm, and the factors inducing zygotic defects are introduced during epididymal maturation, as testicular Prm2 KO sperm supported normal progression to blastocyst. Our results demonstrate that PRM2 is necessary for correct maturation of epididymal sperm, enabling them to form of a functional zygote at fertilization.

overall_design: scRNA-seq from whole testes of Prm2 heterozygous and Prm2 KO mice

first: Shannon

middle: R

last: Rainsford

first: Zachary

middle: D

last: Smith


title: Wounding activates HSFA1 to  promote cellular reprogramming in Arabidopsis

city: Yokohama

first: Duncan

middle: Peter

last: Coleman

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: CSRS

institute: Riken

summary: Mechanical injury is a primary trigger for cellular reprogramming during organ regeneration, yet the transcriptional mechanisms that link wounding to reprogramming remain poorly understood. In this study we identify the HEAT SHOCK FACTOR A1 (HSFA1) class of transcription factors, key regulators of the heat stress response, as a central player in wound-induced callus formation and shoot regeneration in Arabidopsis. Loss of HSFA1 function in the hsfa1abd triple mutants severely impairs cellular reprogramming, reducing callus formation from wounded hypocotyls and shoot regeneration from explants. Conversely, overexpression of a gain-of-function HSFA1d variant markedly enhances regeneration. Time-series RNA-seq and ChIP-seq analyses revealed that HSFA1 directly activates key reprogramming regulators, WOUND-INDUCED DEDIFFERENTIATION 1 (WIND1), PLETHORA 3 (PLT3) and ZINC FINGER OF ARABIDOPSIS THALIANA 6 (ZAT6). Furthermore, we demonstrate that the HSFA1d activity is attenuated by SIZ1-mediated SUMOylation, linking post-translational modification to the regulation of wound responses. Our findings establish HSFA1 as an early transcriptional hub that integrates wound signals to activate a broad gene network that drives cellular reprogramming, thereby providing a mechanistic framework for understanding how stress-responsive transcription factors control regeneration.

overall_design: RNA-seq experiment of WT Col-0 and hsfa1abd-2 mutant hypocotyls explants at T0, 30min, 1h, 3h, and 24 hours after wounding.

first: Coleman

last: Duncan

first: Sugimoto

last: Keiko

first: Kawamura

last: Ayako


title: Multisensory integration predated land plant colonization

city: Madrid

first: Jose M.

last: Franco-Zorrilla

state: Madrid

address: Darwin, 3

department: Plant Molecular Genetics

country: Spain

institute: Centro Nacinal de Biotecnologia-CSIC

summary: Land plant colonization was a pivotal event in the evolution of photosynthetic eukaryotes. The transition from aquatic to terrestrial environments required complex multisensory systems that enabled plants to perceive and integrate a broader range of environmental cues, such as light intensity and temperature. However, it remains unclear whether this ability was a pre-adaptation or an innovation during early plant terrestrialization. Here, we show that the aquatic streptophyte ancestor of land plants could integrate light and temperature through a complex regulatory network. A conserved regulatory nexus, comprising phytochromes and transcription factors, was active in the last common ancestor of land plants, allowing the first terrestrial colonizers to adapt and flourish on the harsh terrestrial surface of our planet. Thus, we propose that the multisensory integration that enables extant plants to achieve perceptual disambiguation and fine-tune growth in various ecological niches was a pre-adaptation encoded in the genomes of ancestral land plants.

sample_organism:
Marchantia polymorpha
Arabidopsis thaliana

overall_design: DAP-seq experiments

first: Bruno

last: Catarino

first: Fernando

last: Rodríguez-Marín

first: Cristina

last: Úrbez

first: Christina

last: Arvanitiou

first: Eva

last: Álvarez

first: Federico

last: Valverde

first: José

middle: M

first: Francisco

last: Romero-Campero

first: Miguel

last: Blázquez


title: The use of New Approach Methodologies (high-throughput transcriptomics) to study nanoagrochemicals - mechanisms of toxicity of a commercial copper oxychloride

city: Aveiro

first: Susana

middle: Isabel Lopes

last: Gomes

address: Campus Universitário de Santiago, Departement of Biology, University of Aveiro

department: Biology

country: Portugal

institute: CESAM & University of Aveiro

summary: Nanoagrochemicals have been developed aiming increased safety and sustainability, representing an alternative to conventional agrochemicals, mainly pesticides. Given its infancy, the risk-benefit analysis for nano-enabled agrochemicals remains unresolved, especially compared to the conventional precursors. New Approach Methodologies (NAMs), e.g. omics, are high on the agenda, to move beyond standard hazards. The investigation of their mechanisms of toxicity will deliver valuable information to understand the risks. NUCOP–M®, a Cu-based commercial formulation containing nano-features, was previously assessed (OECD 220) in Enchytraeus crypticus (Oligochaeta), impacting survival and reproduction (28 days LC50=890 and EC50=300 mg Cu /kg soil of NUCOP-M®). The aim of the present study was to understand the mechanisms of toxicity of NUCOP–M® at sublethal concentrations (0, 100 and 500 mg Cu/kg soil of NUCOP-M®) in short and longer exposure (2, 21 days). A high-throughput gene expression microarray (NAMs) was used. Results showed that a high transcriptomic response after 21 days of exposure (compared to 2 days), although after 2 days there was an indication of increase in intracellular transport. At 21 days, enchytraeids exhibited a gene expression profile compatible with effects on embryo development (down-regulation of hemicentin 2 and serine/threonine protein kinase 25), which might be linked to reproductive effects observed at organism level at 28 and 56 days of exposure. Several of the genes found up-regulated points towards mitochondrial stress, and activation of mechanisms to cope with oxidative stress. This study is a key contribution to a knowledge gap, the mechanisms of toxicity of nanoagrochemicals, particularly concerning non-target species.

overall_design: Gene expression profile of Enchytraeus crypticus was analysed after 2 and 21 days of exposure to NUCOP, a nanoenabled commercial fertilizer, in three different concentrations: 100, and 500 mg Cu/kg soil of NUCOP. The exposure was performed in LUFA 2.2 soil. Three biological replicates per test treatment and control (un-spiked soil) were used.

middle: I

first: Janeck

last: Scott-Fordsmand

first: Mónica

last: Amorim


title: scRNA-seq of periodontal granulation tissue and periodontally inflamed gingiva

city: Hong Kong

first: Tianfan

last: Cheng

address: 34 Hospital Road, Sai Ying Pun

department: Faculty of Dentistry

country: Hong Kong

institute: The University of Hong Kong

summary: Periodontal granulation tissue is formed during the wound healing process and contributes to subsequent repair or regeneration. However, periodontitis causes the presence of unwanted mass of persistently inflamed granulation tissues in periodontal osseous defects, are routinely eliminated and discarded for anticipated better treatment outcomes. Nevertheless, the emerging evidence of microbiome and histological profiles strongly encourages further studies on this considerable issue and the potential clinical implications. Here, we collected the granulation tissues from pocket wall via excision (PT) and osseous defect (GT) during periodontal surgery, and those attaching on the extracted root surfaces (RT) and remaining in the extraction sockets (ST) during tooth extraction. Subsequently, these samples were used for histological assessment, 16S rRNA sequencing of intra-tissue microbiome and single-cell sequencing (scRNA-seq). The origin-based distinguishment of granulation tissue was well reflected by the clinical and biological characteristics. Conceivably, the periodontal parameters at the involved teeth of RT and ST were more deteriorated than those of GT and PT, which was also reflected with the enrichment of genera of periodontopathogens like Porphyromonas and the depletion of commensals such as Rothia and Neisseria in RT and ST. Further scRNA-seq revealed higher proportion of mesenchymal stem cells and fibroblasts while fewer natural killer cells in GT than those in both PT and ST, in line with elevated wound healing scores and decreased inflammatory response scores. Pseudotime trajectory analysis demonstrated the apparent differentiation of stroma cells among these tissues. Histological examination exhibited a less extent of inflammatory infiltration and CD4+ and NKG2D+ immunoreaction in GT, as compared to other tissue types. Collectively, these findings show the salubriousness of osseous GT and deleteriousness of socket-originated RT and ST in terms of clinical, microbiome and cellular attributes. This work could facilitate the development of novel strategies for potentiating and enhancing periodontal treatment outcomes.

overall_design: Single cell suspensions were generated using the Tumor Dissociation Kit, human (Miltenyi Biotec) on a gentleMACS™ Dissociator (Miltenyi Biotec). For PT, the ‘h_skin_01’ program was selected and performed at 37℃, 45min, while for other tissues, the ‘h_tumor_01’ was selected with the same temperature and time settings. A total of three samples for GT, PT and ST (one sample/tissue) from different patients was included in the study. The single-cell suspensions were filtered through the Falcon® 40 µm Cell Strainer (Corning, USA), counted and examined for viability (>80%) using a hemocytometer. Single cells were encapsulated into GEMs (Gel Bead in Emulsion) on a Chromium™ Controller using the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (10× Genomics, USA), with following cell lysis and reverse transcription to 10×-barcoded cDNA inside. After post-GEM-RT cleanup, cDNAs were purified using SPRIselect Bead-Based Reagent (Beckman Coulter, USA) and amplified on an Applied Biosystems SimpliAmp Thermal Cycler (Thermo Fisher, USA). The products were further fragmented, end-repaired, A-tailed, ligated with adapters, amplified with sample index PCR and SPRIselect-purified. The final libraries, containing barcode, UMI and cDNA, were sequenced on the DNBSEQ-G400 (BGI, China). Raw data were preprocessed with Cell Ranger v5.0.1 analysis pipeline (Zheng et al. 2017) (https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome) for demultiplexing, barcode processing, genome alignment (GRCh38 v2020-A) and single-cell 3’ gene counting (UMI counts). The sequencing was achieved with >340 million reads per sample.

first: Tsz Yung

last: Wong

first: Tianle

last: Li

first: George

last: Pelekos

first: Lijian

last: Jin


title: Dasatinib and quercetin senolytic treatment delays progression of disc degeneration in SM/J mice

city: Philadelphia

first: Emanuel

middle: José

last: Novais

state: PA

address: 1025 Walnut St., Suite 511 College Bldg.

department: Department of Orthopaedic Surgery

institute: Thomas Jefferson

summary: Genetic background is a major determinant of disc degeneration, a leading cause of chronic back pain and disability. Herein, we demonstrate that premature disc cell senescence contributes to early-onset degeneration in SM/J mice and test two systemic senotherapeutic strategies to mitigate it: Navitoclax (Nav.) and a cocktail of Dasatinib and Quercetin (DQ). While Nav. treatment did not improve severe degeneration in SM/J mice, DQ-treated mice showed lower grades of degeneration and decreased levels of senescence markers p19ARF and p21. DQ promoted disc cell viability, phenotype retention, and limited fibrotic remodeling of the NP tissue. Transcriptomic analysis showed disc compartment-specific effects of the treatment, but cell cycle regulation and JNK signaling were commonly affected across tissue types. Additionally, comparison with previously reported C57BL/6N mice treated with DQ identified Junb and Zfp36l1 signaling as targets of DQ ameliorating intervertebral disc degeneration in mice. This study reinforces the positive role of senolytic treatments in mediating local senescence and intervertebral disc fibrosis. Moreover, these findings suggest that Junb and Zfp36l1 are mediators of this effect.

overall_design:
We used microarrays to explore the transcriptomics of differentially expressed genes between aged disc compartments and dorsal root ganglion across aging: 4 weeks AF SM/J vs 17 weeks Veh AF SM/J; 4 weeks NP SM/J vs 17 weeks Veh NP SM/J; 17 weeks AF SM/J DQ vs 17 weeks Veh AF SM/J; 17 weeks NP SM/J DQ vs 17 weeks Veh NP SM/J.
NP and AF tissue were dissected from lumbar discs from mice (n=4-6 per group). RNA extraction and hybridization on Affymetrix microarrays.


title: Childhood obesity impairs muscle growth and function via altered myogenic and adipogenic factors

city: Hangzhou

first: Senjie

last: Wang

address: No. 866, Yuhangtang Road, Sandun Town

institute: Zhejiang University

summary: Background: Childhood obesity is a critical public health issue that detrimentally affects muscle growth and function. Although the condition is widely prevalent, the specific mechanisms through which obesity induces these muscular impairments, as well as effective prevention strategies, remain insufficiently explored. Methods: We conducted a cross-sectional analysis of 155 children, categorized into obese and normal-weight groups, to evaluate the relationship between obesity and muscle health parameters. Concurrently, we established a murine model of obesity by exposing 3- and 8-week-old mice to a high-fat diet (HFD) to investigate the underlying mechanisms behind obesity’s effects on muscle mass, structure, and function. Additionally, vitamin C supplementation was explored as a potential preventative strategy against HFD-induced muscle impairments. Results: In juvenile mice, a HFD significantly increased both body and intramuscular fat while decreasing relative muscle mass and strength, mirroring the patterns observed in obese children. The diet downregulated key myogenic regulatory factors (MRFs) and myosin heavy chains (MHCs) in muscle tissue, alongside an upregulation of adipogenic pathways, contributing to impaired muscle growth and function. Notably, these adverse effects persisted into adulthood despite subsequent weight loss, underscoring the long-term impact of early dietary interventions. In contrast, adult mice did not exhibit significant muscular impairments after 4 weeks of HFD, suggesting age-specific dietary responses. Vitamin C supplementation effectively ameliorated these HFD-induced impairments in juvenile mice, enhancing muscle function and modifying gene expression related to muscle growth and fat metabolism. Conclusion: These results demonstrate that childhood obesity impairs muscle growth and function by altering myogenic and adipogenic pathways, effects which vitamin C supplementation can mitigate. Further research is needed to explore how a HFD induces these impairments, potentially through mechanisms such as fat accumulation and inflammation.

overall_design: We established a murine model of obesity by exposing 3- and 8-week-old mice to a high-fat diet (HFD) to investigate the underlying mechanisms behind obesity’s effects on muscle mass, structure, and function. 3-week-old and 8-week-old C57BL/6J wild-type mice were fed the chow diet or HFD for 4 weeks and separated into four groups: Juvenile-NCD group, Juvenile-HFD group, Adult-NCD group and Adult-HFD group. Fresh tibial anterior muscle tissue was obtained from mice and immediately frozen in liquid nitrogen. Each sample was from one mouse. RNA extraction and bulk RNA sequencing were performed.

first: Wei

last: Zhang

first: Zhewen

last: Qin

first: Rahim

last: Ullah

first: Junfen

last: Fu


title: Effect of MIEN1-Based Peptide LA3IK on Gene Expression in EGF-Induced PC3 Prostate Cancer Cells at 0h, 30 Minutes, 1h, and 6h Time Points

city: West haven

first: Antariksh

last: Tyagi

address: 830 West Campus Dr

summary: This RNA-seq dataset investigates the effect of the MIEN1-based peptide LA3IK on the gene expression patterns of EGF-induced PC3 prostate cancer cells at four distinct time points: 0h (untreated), 30 minutes, 1 hour, and 6 hours. EGF stimulation was used to activate key signaling pathways involved in cell proliferation and survival, mimicking conditions associated with cancer progression. The LA3IK peptide, designed to target MIEN1, was introduced to evaluate its modulatory effects on the transcriptomic response to EGF over time. By capturing the gene expression changes at these intervals, this study seeks to identify the specific molecular pathways and gene networks influenced by LA3IK, providing insights into its potential therapeutic role in modulating EGF-driven oncogenic processes in prostate cancer. The data will contribute to a better understanding of how LA3IK might disrupt tumor-promoting signals and its possible application in cancer therapy.

overall_design: PC3 prostate cancer cells were serum-starved for 24 hours and then treated with EGF and the MIEN1-based peptide LA3IK in media containing 0.1% FBS. RNA was collected at 0h, 30 minutes, 1h, and 6h post-treatment, with three biological triplicates for each time point. Total RNA was extracted, and RNA-seq libraries were prepared and sequenced on Illumina NextSeq 550 sequencing system for 75-bp paired-end reads.To process the sequencing data, raw files were subjected to adapter trimming and quality filtering using Fastp . The reads were mapped to the hg38 reference genome using HISAT2. For differential gene expression analysis, Deseq2 tool was used.This design assesses how LA3IK modulates gene expression over time in EGF-stimulated cells.

first: Amit

middle: K

last: Tripathi

first: Jamboor

last: Vishwanatha


title: Proteostasis sustains T cell differentiation potential and tumor-infiltrating lymphocyte function [RNA-seq]

city: La Jolla

first: Ananda

middle: W

last: Goldrath

state: CA

address: 9500 Gilman Drive

department: Molecular Biology

institute: University of California, San Diego

summary: CD8+ tumor-infiltrating lymphocytes (TIL) often fail to restrain tumor growth due to differentiation to T cell exhaustion. In healthy tissues, tissue-resident memory T cells (TRM) survey tissues and sustain protective capacity for years, and tumors that contain TIL with TRM-features are associated with better patient prognosis. We identified protein homeostasis (proteostasis) significant in distinguishing TRM and progenitor-exhausted TIL (TPEX) from terminally-exhausted TIL (TEX) by identifying multiple E3 ubiquitin ligases that maintain T cell differentiation potential. Sustained ligase-expression in TIL enhanced T cell accumulation, preserved stem-like TCF1+ populations, and improved anti-tumor function, whereas ligase loss-of-function impaired TIL and altered T cell differentiation in acute infection. TEX experience a loss of proteostasis, marked by unfolded protein accumulation despite functional proteasomes. Enforced ligase expression rescued this unfolded protein accumulation in TIL and improved immunotherapy responses, demonstrating the role of proteostasis in maintaining differentiation potential and identifying new avenues for advancing cancer immunotherapies.

overall_design: Recipient mice were injected intradermally with 1 × 10^6 MC38-GP33 adenocarcinoma cells. Congenically distinct P14 T cells were activated and transduced to generate EV and Neurl3 OE P14 T cells, which were co-transferred into recipients on d5 post-activation cells were mixed at a 1:1 ratio and a total of 5×10^5 P14 cells was transferred by intravenous (i.v.) injection into CD45 congenic recipients with d6 tumors. The mice were monitored three times per week, and the mice were sacrificed 6 days after the adoptive T cell transfer. For each replicate, cells from 2-3 mice were pooled per tissue and then 5,000 P14 sorted for bulk RNA-seq.

first: Nicole

middle: E

last: Scharping


title: Single-Cell Spatial Mapping of Human Kidney Development Reveals Cellular Niches and Lineage Dynamics [CosMx]

first: Jonathan

last: Levinsohn

address: 3400 Civic Center Blvd, Smilow 12-188

institute: University of Pennsylvania

summary: Organ development is shaped by both cell-autonomous changes and critical environmental cues. While single-cell genomic tools have enabled the characterization of gene expression and regulatory transitions during development, they have not fully captured the influence of neighboring cells. In this study, we combined single-cell spatial transcriptomics with gene expression data to investigate how cellular interactions influence human kidney development. By analyzing a large collection of fetal human kidney samples, we defined cellular differentiation patterns and uncovered two novel differentiation trajectories for parietal epithelial cells, suggesting greater developmental plasticity than previously recognized. Furthermore, using spatial gene expression data we identify novel spatially plausible ligand-receptor interactions that likely mediate differentiation processes. Among these, we highlight the role of WNT, FGF, and RET signaling, which have been classically described in mouse nephrogenesis but are now observed in human kidney development. In examining ligand expression, we estimate and quantify the microenvironment for each cell, enabling us to identify ligands associated with driving differentiation trajectories, and identify microenvironments which predict gene expression within cell types and differentiation status. Using this approach, we identified IGF2-mediated signaling as enriched within the blastema and associated with renewal signals suggesting its role as a niche renewal factor. This finding may explain the alterations in nephrogenesis associated with uncontrolled maternal diabetes, providing new insights how the local cellular environment shapes cellular differentiation in the kidney and potential therapeutic interventions.

overall_design: We examined 3 human fetal kidneys using the CosMx platform for single cell spatial RNA quantification

first: Katalin

last: Susztak


title: Proteostasis sustains T cell differentiation potential and tumor-infiltrating lymphocyte function [CITE-seq]

overall_design: Congenically distinct P14 T cells were activated and electroporated with complexed tracrRNA, Cas9, and crRNA to generate CRISPR control and KO P14 T cells, which were co-transferred into recipients then infected with LCMV Armstrong. On day 5 of infection, P14 T cells from IEL, liver, and spleen, were profiled by CITE-seq.

first: Maximilian

last: Heeg

first: Alexander

last: Monell

first: Giovanni

last: Galletti


title: A novel histone H3K27 reader, CBFA2T2, inhibits H3K27me3 demethylation and tumor growth by regulating metabolic genes and metabolite levels [RNA-seq]

first: Rui

last: Guo

address: 131 DongAn Road

institute: Institutes of Biomedical Sciences, Fudan University

summary: Histone H3.1/3.2K27M and H3.3K27M mutation are driver mutations frequently identified in diffuse midline glioma (DMG). However, the precise mechanism by which H3K27M mediates tumorigenesis remains incompletely understood. By carrying out bait Protein-Protein Interaction followed by genome-wide screening (bPPI-seq) in H3.3WT and H3.3K27M mouse NSC models, we identified a novel histone reader CBFA2T2, which recognizes non-mutated or un-modified histone H3K27. Importantly, CBFA2T2 binding to H3K27, mediated by the NHR2 domain, is abrogated by the H3K27M oncogenic mutation. In H3.3 wildtype cells, CBFA2T2 represses transcription of genes involved in carbon metabolism and TCA cycle through its binding to H3K27. This alters the α-KG/Succinate (alpha-ketoglutarate/ Succinate) ratio and indirectly impacts H3K27me3 level, possibly through affecting the H3K27me3 demethylases. CBFA2T2 does not bind the H3.3K27M decorated chromatin in vivo, thus the K to M mutation, partially compromises the CBFA2T2 repressive function. However, over-expressing CBFA2T2 rescues the low H3K27me3 level in H3.3K27M mNSC and H3.3K27M DIPG cells, thus suppressing the H3.3K27M tumor growth. Our findings suggest a new mechanism, which may contribute to the low H3K27me3 level observed in the H3K27M cells, and provide a new strategy for H3K27M therapy through manipulation of CBFA2T2.

overall_design: To generate H3.3WT and H3.3WT Cbfa2t2 knockout (KO) cells, we first knocked out H3f3a in a p53-deficient neuronal stem cell line, NE-4C (referred to as H3f3a KO). Subsequently, we knocked out Cbfa2t2 in the H3f3a KO cells, resulting in H3f3a/Cbfa2t2 double knockoutcells.We then stably expressed HA-tagged wild-type H3.3 in both H3f3a KO and H3f3a/Cbfa2t2 double knockout cells. To generate H3.3K27M cells, we stably expressed HA-tagged H3.3K27M in H3f3a KO cells. Finally, we performed RNA-seq in these three cell lines.

first: Shengfei

last: He


title: A novel histone H3K27 reader, CBFA2T2, inhibits H3K27me3 demethylation and tumor growth by regulating metabolic genes and metabolite levels [ChIP-seq I]

overall_design: We performed CBFA2T2 and K27M ChIP-seq in a human H3.3K27M DMG cell line (SHSMU-DIPG-01).

first: Wenyun

last: Weng

first: Yujie

last: Tang


title: Clofazimine induced changes in the host immune system

city: Zürich

first: Johannes

last: Nemeth

address: Rämistrasse 100

department: Department of Infectious Diseases and Hospital Epidemiology

institute: University Hospital Zurich

summary: Clofazimine (CLO), an antibiotic drug has been in use as such for more than 50 years to treat Mycobacterium leprosae and MDR Mycobacterium tuberculosis infections in humans. Long suspected and proven during the COVID pandemic the drug also has a secondary function as a modulator of the host immune system. We want to measure changes in the transcriptome of cells (bulk RNAseq) treated with CLO at t=6h where we see the onset of phenotypic changes in these cells without the typical cell death induced at higher CLO concentrations over a longer period of time.

overall_design: We will use conditionally immortalized cells (CIMs) originally generated from mouse bone marrow, differentiated into Macrophages for 5 days in R10 + 50 ng/ml mCSF in a 96 well plate.  Cells will be treated for 6h with 1 ug/ml CLO or 1% DMSO (vehicle control) with 3 replicates per condition, after 6h cells will be washed with PBS and detached for RNA isolation. A second set of condition is cells that after CFZ treatment subsequently will be infected mit an MOI10 with live MTB (H37RV) for 6 hours before RNA isolation

first: Rebekka

last: Wolfensberger

first: Cédric

last: Dollé

first: Edoardo

last: Sarti

first: Gwendal

last: Graenicher

first: Terence

last: Tutumlu

first: Luca

last: Baroncini

first: Doris

last: Russenberger

first: Roberto

middle: F

last: Speck

first: Peter

last: Sander


title: Homeostatic mature dendritic cells instruct fibroblast specialization via Notch2 to establish T cell niches

city: Epalinges

first: Nagham

last: Alouche

address: Chemin des Boveresses 155

institute: University of Lausanne

summary: Secondary lymphoid organs are organized by fibroblastic reticular cells (FRCs), which direct immune cell positioning and support adaptive immunity. However, the mechanisms driving FRC subset differentiation remain unclear. To uncover signaling pathways involved in this process, we performed ATAC-seq on lymph node FRCs lacking Notch2. Our data reveal chromatin remodeling changes in the absence of Notch signaling.

overall_design: We performed ATAC-seq analysis on fibroblastic reticular cells (FRCs) isolated from brachial, axillary and inguinal lymph nodes of Ccl19-Cre x Notch2^fl/fl mice and their Notch2^fl/fl littermate controls, all on a C57BL/6 background.

first: Allison

last: Burns

first: Julien

last: Marquis

first: Corinne

last: Peter


title: Thyroid hormones act as a timer for the postnatal maturation of parvalbumin neurons in mouse neocortex [RUN54]

city: Lyon

first: Frédéric

last: Flamant

state: France

address: 46 allée d'Italie

department: IGFL

institute: ENSL

summary: A finely tuned balance between excitation and inhibition is essential for proper brain function. Disruptions in the GABAergic system, which alter this equilibrium, are a common feature in various types of neurological disorders. Understanding GABAergic neuron maturation processes is thus currently a major challenge in basic neuroscience. Thyroid hormones (THs) are required for proper maturation of parvalbumin-expressing GABAergic interneurons in the mouse neocortex. However, the timeline of this TH action has yet to be elucidated. Here, we used several mouse models expressing dominant negative mutations of the TH nuclear receptor α1 (TRα1), to better define the time window during which THs promote the postnatal maturation of parvalbumin neurons. Histological observations revealed that the action of TH during the first three postnatal weeks was necessary to initiate the expression of parvalbumin and the elaboration of a specialized extracellular matrix called the perineuronal net. By contrast, after the third postnatal week, TH action on parvalbumin neuron maturation appeared to be somewhat dispensable. Transcriptome analysis of neocortical GABAergic neurons two weeks after birth identified a small set of putative target genes for TRα1. These genes are at the origin of the postnatal remodeling of the repertoire of ions channels and the elaboration of perineuronal nets. These data suggest that THs act as a timer to define the temporal boundaries of the critical period of heightened cortical plasticity, which plays a fundamental role in the development of neuronal circuits.

overall_design: The Cre/loxP recombination system was used to restrict the expression of two transgene: one is a reporter which drives the expression of a nuclear fluorescent protein. The other drives the expression of a mutation of the Thra gene, encoding a dominant negative nuclear receptor for thyroid hormone. A Cre driver additionnal transgene was used to restrict the expression to GABAergic neurons. Two groups of mice were prepared, one with the Thra mutation, the other without it as control. Fluorescent nuclei were sorted from the cerebral cortex of juvenile mice. RNA was extracted from the sorted nuclei. 8 libraries were prepared for RNA-seq (4 controls, 4 with Thra mutation).

first: Juan

last: Ren

first: Suzy

last: Markossian

first: Romain

last: Guyot

first: Denise

last: Aubert

first: Jiemin

last: Wong

first: Sabine

last: Richard


title: Long-Range IgH V(D)J Recombination [3C-HTGTS]

city: East Lansing

first: Yu

last: Zhang

address: 567 Wilson Rd, Biomedical and Physical Sciences Building, Rm 5176

institute: Michigan State University

summary: Cohesin-mediated loop extrusion plays a crucial role in IgH V(D)J recombination, driving D-to-JH rearrangements followed by VH-to-DJH rearrangements.

overall_design: We performed 3C-HTGTS in v-Abl transformed pro-B cells and their various mutant derivatives to study the role of cohesin variants in IgH V(D)J recombination

first: FuJung

last: Chang


title: Thyroid hormones act as a timer for the postnatal maturation of parvalbumin neurons in mouse neocortex [RUN125]

overall_design: The Cre/loxP recombination system was used to restrict the expression of a reporter transgene which drives the expression of a nuclear fluorescent protein to GABAergic neurons. Two groups of mice were prepared: 1) One group of hypothyroid juvenile mice, generated by treating gestating females with propyl-thio-uracy (PTU group). 2) One group of hypothyroid mice which received a intraperitoneal injection of thyroid hormone 24h before brain collection (PTU+TH group). Nuclei were isolated from the cortical GABAergic neurons with a cell sorter. RNA was extracted from the sorted nuclei. 8 libraries were prepared for RNA-seq (4 hypothyroid, 4 hypothyroid +TH)


title: Comprehensive Molecular and Functional Analysis of NUTM1-Rearranged Leukemia [cKitChIP-seq]

city: Suita

first: Masaki

last: Nomura

state: Osaka

address: 2-2, Yamadaoka

institute: Graduate School of Medicine, The University of Osaka

summary: NUTM1-rearrangement (NUTM1-r) represents a significant subset of infant B-ALL, particularly prevalent in cases lacking KMT2A-rearrangements (KMT2A-r). However, the underlying molecular mechanisms for the characteristic leukemia have not been fully elucidated. Our comprehensive analysis reveals that NUTM1-r infant leukemia is characterized by a unique transcriptomic and epigenetic landscape with global hypomethylation, delineating a discrete leukemia entity. Functional interrogation of the BRD9-NUTM1 fusion demonstrates its dual role in promoting B-lineage commitment while conferring leukemic stem cell properties. Strikingly, single transduction of BRD9-NUTM1 is sufficient to induce serially-transplantable pro-B-like leukemia in vivo, recapitulating key features of human NUTM1-r B-ALL, including NUTM1 overexpression, skewed B cell transcriptional programs, and low CD34 expression. Mechanistically, BRD9-NUTM1 expression gives rise to distinctive open chromatin regions with global enhancement of H3K27Ac, particularly at loci associated with Myc, NF-κB, and posterior Hoxa genes. Notably, BRD9-NUTM1 leukemic cells responded robustly to cytarabine, in contrast to the relative resistance observed in KMT2A-r leukemias. Interestingly, our findings highlight a discrepancy observed in the clinical behavior of NUTM1-r leukemias, where the transformed cells display characteristics of stemness, yet tend to lose these properties under chemotherapy due to the dependence on active transcription. Our findings delineate the unique molecular profile of NUTM1-r leukemias, suggesting opportunities for targeted therapies that exploit these specific vulnerabilities.

overall_design: BRD9-NUTM1 (BN1), MLL-AF9 (MA9) and MLL-ENL (ME) murine leukemic cells were sorted by FACS. H3K27ac ChIPed DNA libraries were prepared.

first: Koutarou

last: Nishimura

first: Weijia

last: Zang

first: Daichi

last: Inoue


title: Comprehensive Molecular and Functional Analysis of NUTM1-Rearranged Leukemia [ATAC-Seq]

overall_design: BRD9-NUTM1 (BN1), MLL-AF9 (MA9) and MLL-ENL (ME) murine leukemic cells were sorted by FACS. Sorted cells were processed by a transposition reaction and prepared the ATAC DNA library