title: Targeted Transcriptional Repression by Induced Proximity

city: Basel

first: Fabian

last: Wu

department: Biomedical Research

institute: Novartis Pharma

summary: Most cancer-driving proteins remain “undruggable” due to the absence of ligandable pockets and their reliance on intrinsically disordered or protein–DNA/protein–protein interactions. Transcription factors, which orchestrate oncogenic gene expression programs, are particularly challenging: they turnover rapidly, evade durable pharmacological inhibition, and resist even emerging targeted protein-degradation strategies. Here, we describe a new induced-proximity therapeutic modality, Transcriptional Repression via Active Chemical Epigenetic Reprogramming (TRACER), that enforces locus-specific transcriptional silencing by recruiting endogenous corepressor complexes to transcription factor binding sites. We developed small-molecule TRACERs that tether methyl-CpG binding domain protein 2 (MBD2) and the Nucleosome Remodelling and Deacetylase (NuRD) complex to transcription factor–directed ligands. An estrogen receptor (ER) TRACER potently suppressed ER transcriptional activity in breast cancer cells, downregulated canonical ER target genes, and required MBD2 and histone deacetylase (HDAC1/2) for activity, confirming on-target epigenetic repression. Extending this approach to prostate cancer, an androgen receptor (AR) TRACER transcriptionally repressed both full-length AR and the drug-resistant truncation variant AR-V7, achieving >90% inhibition of AR transcriptional activity in androgen-independent prostate cancer cells with locus-specific gene repression. We further show that TRACERs can be modularly reprogrammed to recruit alternative repressors, including PRC2. Collectively, these findings establish TRACERs as a generalizable modality to pharmacologically silence undruggable transcription factors through targeted epigenetic reprogramming, offering a powerful new strategy for treating cancers refractory to existing therapies.

overall_design:
ATAC-seq was performed to assess chromatin accessibility in T47D cells following treatment with E2 or CS-1-103, with each condition generated in biological triplicates.
CUT&RUN profiling of estrogen receptor (ER/ESR1) binding sites in T47D cells using an anti-ESR1 antibody, performed in biological triplicates.

first: Christian

middle: E

last: Stieger

first: Xinru

last: Chen

first: Dustin

last: Dovala

first: Daniel

last: Fuller

first: Andreas

middle: O

last: Frank

first: Mikias

last: Woldegiorgis

first: Megan

last: Bruce-Smythe

first: Nicolas

last: Pizzato

first: Jeffrey

last: McKenna

first: Cory

last: Johannessen

first: Barna

last: Fodor

first: Markus

last: Schirle

last: Nomura


title: The Inv(16) Oncogene CBFB::MYH11 is Required for the Rurvival of Leukemia Cells in the Blood and Spleen, but not the Bone Marrow

status: Public on Aug 13 2026

city: Omaha

first: Kate

last: Hyde

state: NE

address: 985802 Nebraska Medical Center

country: USA

institute: University of Nebraska Medical Center

type: Expression profiling by high throughput sequencing

summary: Inversion of chromosome 16 [inv(16)] generates the fusion gene CBFB::MYH11 (CM) and is one of the most common chromosomal rearrangements in Acute Myeloid Leukemia (AML). Expression of CM is required for leukemia initiation. Patients with inv(16) at diagnosis invariably have the rearrangement at relapse, leading to the assumption that CM is also required after leukemic transformation. However, a role for CM in leukemia maintenance has yet to be shown experimentally. To address this, we used an inducible CM knockdown (KD) mouse model and found that decreased CM eliminated leukemia cells from the peripheral blood and spleen, but not the bone marrow, despite all populations exhibiting significantly decreased CM mRNA and protein. The surviving CM KD cells in the bone marrow showed decreased apoptosis and proliferation, and increased expression of autophagy related genes. Surprisingly, with prolonged KD of CM, ~40% of mice re-established disease despite maintaining decreased CM. Our work indicates that CM is required for leukemia survival in the spleen and peripheral blood, but in the bone marrow CM KD leukemia cells can survive and re-establish disease independent of the fusion protein. These findings imply that targeting CM alone has potential to reduce leukemic burden but not cure the disease.

overall_design: Mouse leukemia cells expressing CBFB-MYH11 and GFP were transduced with a Doxycycline inducible shRNA construct against MYH11. These cells were transplanted into congenic recipient mice. After leukemia engraftment, mice were given doxycycline (3mg/ml, 5% sucrose) in their drinking water, or control water (5% sucrose). After 7 days of treatment, leukemia cells were harvested from the bone marrow or spleen, sorted for GFP, and sent for whole transcriptomic sequencing. To generate samples with secondary disease, a separate cohort of mice were transplanted as above, then treated with doxycline or control water until they showed signs of fatal disease. Leukemia cells were then harvested, sorted for GFP, and sent for whole transcriptomic sequencing, as above.

first: Sipra

last: Panda

first: Peng

last: Xiao

first: Yiqian

last: Wang

first: Rahul

last: Dogiparthi

first: Michelle

last: Becker

first: Arjun

last: Dhir

first: Calvin

last: Lam

first: Cecilia

last: Rivas

first: Lemlem

last: Alemu

first: Lisa

last: Garrett

first: Sanantha

last: Swenson

first: Kyle

last: Hewitt

first: Katherine


title: The Inv(16) Oncogene CBFB::MYH11 is Required for the Survival of Leukemia Cells in the Blood and Spleen, but not the Bone Marrow

first: Venkatasai Rahul

address: 985805 Nebraska Medical Center

department: Genetics Cell Biology and Anatomy

overall_design: Leukemia cells were harvested from spleen and bone marrow at day 7 of treatment with control and doxycycline. The leukemic cells were then enriched using the MagniSort Mouse Hematopoietic Lineage Depletion kit (Invitrogen) and the GFP+ cells were confirmed by flow cytometry. Single cell RNA sequencing (scRNA-Seq) was performed using the Seq-well, nanowell-based high throughput platform (Gierahn, et al. (2017, Nat Method).

first: Venkatasai

last: Rahul Dogiparthi


title: Massively parallel characterization of adolescent idiopathic scoliosis risk variants

city: Gainesville

first: Darius

last: Ramkhalawan

address: 1200 Newell Drive

institute: University of Florida

summary:
Adolescent idiopathic scoliosis (AIS) is a common pediatric musculoskeletal disorder characterized by lateral spinal curvature, often leading to chronic pain and deformity. While a significant genetic component to AIS is recognized, the functional impact of most associated genetic variants, particularly those in non-coding regions, remains largely unknown.
Using massively parallel reporter assays, we characterize 1,664 variant positions in linkage disequilibrium with 26 AIS lead variants identified by genome-wide association studies (GWAS) in chondrocytes, a major cell type implicated in AIS pathogenesis. Using a library of 7,173 candidate regulatory sequences we compare the 1,664 reference alleles against 4,708 alternate alleles in two human chondrocyte cell lines (TC28a2 and SW1353). Our analysis identifies 92 variants that exhibit significant differential regulatory activity between their reference and alternate alleles, 79 of which are predicted to disrupt transcription factor binding sites, often correlating with their observed regulatory effect.

overall_design: Functional characterization of genetic variants associated, through GWAS, with adolescent idiopathic scoliosis for differential regulatory activity by lentivirus-based massively parallel reporter assays in human chondrocyte cell lines.

first: Justin

last: Koesterich

first: Anat

last: Kreimer

first: Nadja

last: Makki


title: LINE-1 ORF1p is a Shared and Immunogenic Antigen in Cancer

status: Public on Aug 14 2026

city: Boston

first: Liyang

last: Diao

state: MA

address: 201 Brookline Ave. Suite 1001

institute: Rome Therapeutics

summary: In this study, we identify and characterize LINE-1 ORF1p as a shared and immunogenic cancer antigen. LINE-1 elements are normally repressed genomic sequences that can be reactivated in cancer. We demonstrate that ORF1p, a protein encoded by LINE-1, is selectively expressed in tumors and its peptides are presented on MHC class I molecules across diverse tumor types. Using public and newly generated immunopeptidomics datasets, we detect ORF1p-derived peptides in a tumor-specific manner. Functional assays confirm that these peptides can elicit IFN-γ responses from CD4+ and CD8+ T cells in vitro. These findings highlight ORF1p as a promising candidate for a broadly applicable cancer vaccine.

overall_design: Frozen tissue samples from esophageal squamous cell carcinoma (ESCC) tumors (n=5), matched tumor-adjacent normal tissues (n=5), and healthy esophagus controls (n=5) were obtained commercially. RNA was extracted and sequenced, and transcript abundance was quantified in transcripts per million (TPM).

first: Diao

last: Liyang


title: RNA-seq of glioblastoma stem cells with shRNA-mediated DCPS knockdown

city: Shanghai

first: Zhixin

last: Qiu

address: Dongan Road

country: China

institute: Fudan University

overall_design: RNA-seq of glioblastoma stem cell lines GSC4121 and GSC387 with shRNA-mediated DCPS knockdown (2 replicates each)


title: Multiomic single-cell sequencing of skin and blister fluid from patients with severe cutaneous adverse drug reactions.

city: Perth

first: Andrew

last: Gibson

state: Western Australia

address: Building 390, Discovery Way, Murdoch University

country: Australia

institute: Murdoch University

summary: Severe cutaneous adverse reactions (SCAR) are rare but life-threatening drug reactions mediated by human leukocyte antigen (HLA) class I-restricted CD8+ T-cells. To obtain an unbiased assessment of SCAR cellular immunopathogenesis, we performed single-cell (sc) transcriptome, surface proteome, and TCR sequencing (5' scRNA-TCR-CITE-seq, 10x Genomics) on unaffected skin, affected skin, and blister fluid from diverse SCAR patients.

overall_design: 5' scRNA-TCR-CITE-seq, 10x Genomics

first: Elizabeth

last: Phillips


title: Single-nuclei RNAseq of postmortem brains in schizophrenia

city: Philadelphia

first: Benjamin

middle: C.

last: Reiner

state: PA

address: 125 S 31st St

institute: University of Pennsylvania

summary: We performed single-nuclei RNAseq of human postmortem dorsolateral prefrontal cortex brain samples from 16 schizophrenia and 16 control individuals to identify cellular subtype specific changes in the neural transcriptome.

overall_design: We performed the 10x Genomics 3' gene expression assay (v3.1) on nuclei isolated from frozen human postmortem dorsolateral prefrontal cortex brain samples from 16 individuals with a clinical diagnosis of schizophrenia and 16 control individuals.

middle: C

first: Wade

middle: H

last: Berrettini


title: A functional antagonism between let-7 and miR-17 family members relying on sequences outside the seed

city: Zurich

first: Jonathan

last: Hall

address: Vladimir-Prelog-Weg 1-5/10

country: Switzerland

institute: ETH Zurich

type: Non-coding RNA profiling by high throughput sequencing

summary: The canonical function of miRNAs relies on their ability to recognize and target messenger RNAs (mRNAs) through a mechanism known as seed pairing. The seed is a conserved sequence located at the 5'-end of the miRNA, and its specific pairing with the target mRNA is essential for target regulation. Surprisingly, we observed that miR-106a can bind to targets in place of let-7a despite the entirely different seed sequences. This binding does not depend on the seed sequence of miR-106a but instead relies on the extensive pairing on its 3'-end that shows homology with the let-7a seed sequence. miR-106a binding does not induce direct regulation of the bound targets. It shields them from seed-mediated pairing with let-7 family members, leading to competition for pairing with the same sequence in the target mRNA and resulting in two opposing functional outcomes: target repression by let-7a or target shielding by miR-106a. We conclude that by preventing let -7a from repressing oncogenic targets, the noncanonical binding of miR-106a contributes to cancer development.

overall_design: RNA-Seq and smallRNA-Seq profiling of mRNA and miRNA levels in HEK cells after miRNA single and co-transfections.

first: Anneke

last: Brümmer

first: Alexander

last: Kanitz

first: Artur

last: Laski


title: Rest-phase light disrupts hippocampal clock function and impairs object recognition memory

city: Hong Kong

first: Jin Young

last: KIM

address: 83 Tat Chee Ave, Kowloon Tong

department: Biomedical Sciences

institute: City University of Hong Kong

summary: Light exposure during the circadian rest phase is common during shift work and late-night activity, but its effects on memory remain unclear. Here, we show that 6-day rest-phase light exposure (RPL), which combines mistimed light exposure with enforced wakefulness (EW) during the circadian rest phase, impairs long-term object recognition memory but not short-delay spatial memory. Behavioral testing, single-nucleus RNA sequencing, and ex vivo electrophysiology show that RPL alters SCN clock organization and output signaling, reduces hippocampal clock-gene rhythmicity, disrupts phase-dependent synaptic gene expression in dentate gyrus and CA1 neurons, and reduces CA1 long-term potentiation. Maintaining EW without light exposure preserved object recognition memory and CA1 clock-gene expression, showing that mistimed light exposure is required for both effects in this model. Local hippocampal dexamethasone treatment also restored day–night differences in hippocampal clock-gene expression and preserved memory under RPL, supporting a role for hippocampal clock-related regulation in memory preservation. Together, these findings show that RPL alters clock-related regulation in the SCN and hippocampus and impairs object recognition memory.

overall_design: Brain tissues (the hippocampus and hypothalamus) of C57BL/6J adult (8-14wk-old) young mice under standard light–dark conditions (LD) with free sleep (control) or exposed to rest-phase light (RPL) were harvested during the day or at night. Then, nuclei from the hippocampus and hypothalamus were isolated and analyzed using snRNA-seq.

first: Xuebing

last: Zhang

first: Changwei

last: Yang

first: Wenyi

last: Jin

first: Liang

first: Xingqi

last: Meng

last: Kim

first: Yool

last: Lee


title: Epigenetic repressor TRIM28 coordinates myocardial trabeculation and compaction for cardiac chamber formation [RNA-Seq]

first: Yuze

last: Wang

address: Shanghai Minhang District Dongchuan Road No. 800

institute: Shanghai Jiao Tong University

summary: BACKGROUND: Left ventricular non-compaction (LVNC) is a prevailing subtype of cardiomyopathy manifested with excessive trabeculation and spongy-like ventricular wall. LVNC is associated with severe clinical presentations-including arrhythmias, thromboembolic events and heart failure-yet its etiopathology is heterogenous and remains poorly understood.  METHODS: We generated a cardiomyocyte-specific TRIM28 (Tripartite motif containing 28) knockout mouse (TRIM28nCKO) by crossing TRIM28 flox mouse with NKX2.5-Cre mouse. The LVNC phenotype was assessed by combined histologic assays including H&E and immunofluorescence to calculate the thickness of trabeculae versus compact myocardium. We leveraged the RNA-seq and CUT&Tag epigenomic profiling technology to identify molecular pathway mediated by TRIM28 in the trabecular and compact myocardium of developing hearts. Furthermore, we generated TRIM28 and Hey2 (hes-related family bHLH transcription factor with YRPW motif 2) whole-body single and double heterozygous knockout mice to evaluate their cooperative roles on P21Cip1/Waf1 (Cyclin-Dependent Kinase Inhibitor 1A) repression and myocardial compaction. RESULTS: TRIM28nCKO mouse embryos died before the age of E16.5 and developed a mid-gestational LVNC phenotype manifested by excessive trabeculation and insufficient myocardial compaction. TRIM28nCKO hearts displayed reciprocal proliferative profiles: hyperproliferation in the trabecular myocardium versus hypoproliferation in the compact layer. Mechanically, TRIM28 depletion in the trabecular myocardium promoted the expression of zinc finger transcription factor of EGR1 (Early Growth Response 1) to increase the deposition of subendocardial extracellular matrix (ECM) and induced the trabecular overgrowth. In contrast, TRIM28 in the compact layer cooperated with transcription repressor Hey2 to suppress the expression of cell cycle inhibitor P21Cip1/Waf1 (Cyclin-Dependent Kinase Inhibitor 1A) and ensure the normal compaction, whereas TRIM28 ablation disrupted this mechanism and lead to compact insufficiency by removing the inhibition of p21. These distinct compartment-specific mechanisms collectively drive the defective cardiac chamber morphogenesis underlying left ventricular noncompaction (LVNC) in TRIM28  TRIM28nCKO heats. CONCLUSIONS: Our study identifies TRIM28 and its compartmentalized downstream pathways as the critical epigenetic regulatory axis governing the cardiac chamber development and underlying LVNC pathogenesis.

overall_design: RNA‑seq of hearts from E12.5 wild‑type and TRIM28CKO mice

first: Xing

last: Liu

first: Shasha

first: Juntao

last: Lin


title: Transcriptional consequences of viral and cellular ORF overexpression in hTERT-RPE1 cells

city: Cambridge

first: Yi

middle: Hua

last: Chen-Neumann

address: Whitehead Institute 455 Main St, Rm 639 Weissman Lab

institute: Whitehead Institute

summary: To define the transcriptional programs driven by individual viral and cellular open reading frames, hTERT-RPE1 cells were stably transduced with lentiviral constructs expressing GFP11 (negative control), the human papillomavirus E7 oncoprotein, the Epstein-Barr virus protein BNLF2b, or the cAMP-dependent protein kinase inhibitor alpha (PKIA). After puromycin selection, total RNA was profiled by 3' end counting RNA-seq in four biological replicates per condition. Comparison of each ORF-expressing population against the GFP11 control defines the gene expression changes attributable to that ORF.

overall_design: Sixteen libraries: four ORFs (GFP11 control, HPV E7, EBV BNLF2b, PKIA) x four biological replicates. Stranded single-end 3' end counting RNA-seq with unique molecular identifiers, sequenced on an Illumina NovaSeq X Plus. Raw data were previously deposited in SRA under BioProject PRJNA1506741 (study SRP723758).

first: Yi Hua


title: Single-Cell Spatial Transcriptomics Reveals Rewiring of RPE and Muller Glia Signaling toward Photoreceptors Following Outer Segment Disruption in Prph2C213Y Mice

city: Beijing

first: WEIHONG

last: YU

address: Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College

institute: Peking Union Medical College Hospital

summary: PRPH2 mutations cause inherited retinal dystrophies (IRDs), but how photoreceptor outer segment (OS) disruption reshapes the surrounding retina remains unclear. Using a heterozygous Prph2C213Y/+ mouse model generated by CRISPR/Cas9, we characterized age-related retinal pathology and responses of retinal pigment epithelium (RPE) and Muller glia. Independent age- and sex-matched cohorts were examined at 1, 3, and 6 months by electroretinography, optical coherence tomography, and fundus autofluorescence. Mutant mice showed rod dysfunction from 1 month, RPE dysfunction from 3 months, and cone dysfunction by 6 months, accompanied by progressive outer retinal thinning and hyperautofluorescent deposits. Histological and ultrastructural analyses revealed OS disorganization, shortened RPE microvilli, RPE monolayer remodeling, increased RPE autofluorescence, and reactive Muller gliosis. Single-cell spatial transcriptomics of wild-type and mutant retinas at 6 months resolved nine cell populations and identified RPE cells and Muller glia as prominently perturbed non-photoreceptor populations. RPE cells showed an epithelial-mesenchymal transition-related remodeling state linked to a candidate Nfib-Fstl1 module, whereas Muller glia showed activation of activator protein 1 (AP-1) regulons, including Fos, Fosl2, and Junb, with predicted targets Osmr, A2m, and Stat3. Cell-cell communication analyses indicated coordinated changes in neuroprotective, inflammatory, and matrix-related signaling from RPE cells and Muller glia toward photoreceptors. These findings indicate that PRPH2-associated retinal dystrophy is a multicellular process in which OS disruption drives coordinated RPE and Muller glial remodeling with potentially protective or pro-degenerative effects, and nominate the RPE Nfib-Fstl1 program, Muller glial AP-1 responses with predicted STAT3 involvement, and support-cell-derived growth factor signaling as candidate mutation-independent therapeutic targets.

overall_design: A heterozygous Prph2C213Y/+ mouse model on a C57BL/6J background was compared with age- and sex-matched wild-type controls. Independent cohorts were examined at 1, 3, and 6 months by electroretinography, optical coherence tomography, and fundus autofluorescence; retinal morphology and single-cell spatial transcriptomics were assessed at 6 months. Spatial transcriptomic libraries were generated from fresh-frozen mouse retina using the SeekSpace Single Cell Spatial Transcriptome-seq workflow. The original sequencing files supplied for this submission are labeled T1 and do not contain genotype or biological replicate labels; therefore, T1 is not assigned to wild-type or Prph2C213Y in this metadata draft.

first: Haoxin

last: Guo

first: Linfei

last: Wei

first: Binghan

last: Chen

first: Juan

last: Huang

first: Meijiao

last: Zhu

first: Xieyichang

last: Li

first: Ruiyi

last: Yan

first: Xufeng

last: Zhao

first: Xiaoxu

last: Han

first: Weihong

last: Yu


title: Disruption of dnaK results in transcriptional re-programming of biofilm-associated pathways in Clostridioides difficile

city: Coleraine

first: Megan

middle: Grace

last: Taggart

state: Co. Londonderry

address: Cromore Road

country: United Kingdom

institute: Ulster University

summary: Clostridioides difficile is an opportunistic enteric pathogen posing significant challenges in human and animal healthcare due to the recurrent nature of infections and associated financial burden. The molecular chaperone protein, DnaK (Hsp70), encoded by dnaK, plays a central role in the heat stress response and protein homeostasis. Disruption of dnaK in C. difficile 630Δerm has previously been associated with increased biofilm formation and multiple phenotypic alterations. This study investigated the global transcriptional changes associated with dnaK disruption during planktonic and colony biofilm culture. Colony biofilms of C. difficile strains 630, 630Δerm, and 630Δerm:dnaK were cultured on mixed nitrocellulose ester semi-permeable membranes and examined structurally using low-vacuum scanning electron microscopy. Total RNA was extracted from both planktonic cultures and 24 h colony biofilms, followed by Illumina RNA sequencing. Differential gene expression analysis was performed using DESeq (padj < 0.05). Gene set enrichment analysis (KEGG and Gene Ontology) was conducted to identify significantly enriched metabolic pathways and biological processes. Disruption of dnaK resulted in global transcriptomic remodelling, particularly during biofilm culture, where 72.4% of genes were significantly differentially expressed relative to planktonic culture. A core number of pathways were involved in biofilm formation in all strains including increased sporulation with reduced translation, amino acid biosynthesis, and flagellar assembly. The dnaK mutant exhibited a unique pattern of enrichment of pathways associated with cell division, peptidoglycan synthesis, carbon metabolism, and amino acid biosynthesis, alongside a coordinated reduction of motility and chemotaxis pathways. Therefore, disruption of the dnaK gene appears to link the stress response to biofilm formation through a number of pathways associated with biofilm development. Understanding this link may identify systems relevant to persistent and recurrent infections.

overall_design: Transcriptomic analysis of C. difficile 630, 630Δerm and  630Δerm:dnaK cultured both planktonically at 6h and as 24h colony biofilms to identify gene expressional differences between mutant strains and between growth conditions

middle: G

first: Carla

middle: S

last: Mӧller-Levet

first: William

middle: J

last: Snelling

first: Patrick

last: Naughton

first: Roberto

middle: M

last: La Ragione

first: Barry

last: O’Hagan

first: James

last: Dooley

first: Nigel

last: Ternan


title: The transcription factor BLIMP1 promotes obesity and atherosclerosis by regulating macrophage adaptation to nutritional challenges [scRNA-Seq]

city: Los Angeles

first: Jina

last: Kim

state: CA

address: 8700 Beverly Blvd

institute: cedars-sinai medical center

summary: Functionally altered adipose tissue macrophages (ATM) are key players in metabolic diseases and related complications, but the molecular mechanisms underlying ATM dysfunction remain poorly understood. Here, we uncover a critical role for the transcription factor BLIMP in promoting ATM remodeling and function that impacts systemic lipid handling and obesity associated impairment of glycemic responses. BLIMP1 expression in humans and murine ATM is upregulated during obesity, and genetic ablation of BLIMP1 in murine macrophages led to increased energy expenditure and sex-independent resistance to fat mass accumulation. BLIMP1 orchestrates ATM adaptation to nutritional input by promoting the differentiation of monocytes into maladapted macrophages with poor lipid handling capabilities and inflammatory potential, indirectly supporting obesity-associated adipocyte dysfunction and compromising systemic lipid homeostasis. BLIMP1 deficiency in monocytes and macrophages rescued glycemic responses in hyperphagic obese mice and lowered systemic cholesterol levels, mitigating the development of atherosclerosis in mice prone to hypercholesterolemia. Thus, targeting of BLIMP1-regulated pathways may provide novel therapeutic strategies to mitigate obesity-associated metabolic disorders and cardiovascular complications.

overall_design: Single-cell RNA sequencing (scRNA-seq) was performed on gWAT macrophages from Control (Ctrl) and BLIMP1 Conditional Knockout (CKO) mice fed either a Standard Diet (SD) or a High-Fat Diet (HFD) to analyze ATM subset remodeling and functional changes.

first: Jessica C.

last: Dos Santos

first: Gislâine A.

last: Martins

first: Sungyong

last: You


title: The transcription factor BLIMP1 promotes obesity and atherosclerosis by regulating macrophage adaptation to nutritional challenges

overall_design: Whole genome transcriptomics (bulk RNA-sequencing) was performed on whole adipocytes isolated from the perigonadal white adipose tissue (gWAT) of Standard Diet (SD)-fed male Control (Ctrl) and CKO littermate mice


title: Bacterial effector modifies host messenger RNA to promote virulence

city: Clayton

first: Kathleen

last: McCaffrey

state: VIC

address: 25-31 Wright Street

institute: Hudson Institute of Medical Research

summary:
Bacterial pathogens harbor specialized secretion systems that inject effector proteins into the host cell to
establish infection and disease. While many bacterial effectors post-translationally modify proteins to influence
host responses, the extent to which effectors modify host RNA is currently unknown. Here we performed
RNA-interactome capture (RIC) to isolate effectors bound to host cellular messenger RNA (mRNA)
during Legionella pneumophila infection. RIC identified an uncharacterized effector, FadA (Lpw16921), which
localized to the host-cell nucleus and interacted with host mRNAs at uracil (U)-rich RNA motifs. FadA exhibited
NADPH-oxidase activity that mediated 8-oxo-guanine (oxo8G) modifications of mRNA substrates, resulting
in oxidative damage and inhibition of translation. Infection with L. pneumophila harboring wild-type
FadA, but not a catalytically inactive mutant, increased oxo8G modifications, suppressed cytokine responses,
and promoted bacterial persistence in vivo. Our findings demonstrate the potential for a secreted
Q2 effector to post-transcriptionally modify host mRNA as a mechanism to promote bacterial virulence.

overall_design: To investigate the role of Legionella effector protein FadA on host mRNA expression, THP-1 macrophages were infected with the Legionella pneumophila wild-type strain (WT) or a mutant strain lacking the fadA gene (lpw16921). We then performed comparaitive gene expression profiling of RNA-seq data from WT versus delta-fadA infected cells from three independent experiments. A comparison between cells infection with the parental 130b Legionella strain (130b) and the T4SS-mutant strain (delta-dotA) was also performed to provide a control.

first: Elizabeth

middle: L

last: Hartland


title: Decoding Sequence Recognition Code of Nucleic-Acid Binding Proteins of Human-Infecting DNA Viruses

first: Jian

last: Yan

state: Hong Kong Special Administrative Region

address: 83 Tat Chee Avenue, Kowloon

department: Department of Biomedical Sciences

institute: City University of Hongkong·

summary: We applied high-throughput SELEX (HT-SELEX) to profile the DNA-binding specificity of 106 putative nucleic acid–binding proteins (NBPs) from 103 DNA viruses. Three NBPs derived from viruses whose hosts are not humans (YP_010782993.1, NP_671816.1, and AVM80381.1) were included as negative controls. We identified sequence motifs for 33 proteins.

overall_design: Using HT-SELEX, we profiled the DNA-binding specificity of 103 putative NBPs from 100 human-infecting DNA viruses, alongside three non-human host virus NBPs

last: YAN

first: Ligang

last: FAN

first: Meifang

last: TANG

first: Haiqian

last: MA

first: Shifei

last: YANG


title: Astrocytic NFIX regulates thalamocortical circuits through GABA and Purinergic Signaling

city: HOUSTON

first: Sanjana

last: Murali

state: TX

address: 7600 Kirby Drive

institute: Baylor College of Medicine

summary: Astrocytes support synaptic activity and associated circuit function, including those linked to sleep and memory, though how they coordinate these processes remains poorly defined. Here we show that the transcription factor Nuclear Factor I-X (NFIX) is required to maintain astrocyte function in the thalamic reticular nucleus (TRN), as its deletion results in aberrant thalamocortical oscillations and impaired memory formation. We found that NFIX directly regulates the expression of monoamine oxidase B (MAOB) and the purinergic receptor P2RX7. Mechanistically, knockdown of Maob or knockout of P2rx7 in TRN astrocytes results in decreased astrocytic release of the neurotransmitter GABA, reducing tonic inhibition of ventrobasal (VB) relay neurons and impairing memory formation. Altogether, our studies identify region-specific roles for astrocytic NFIX and its gene regulatory network in TRN astrocytes, while further revealing that astrocytes in the TRN couple regulation of thalamocortical circuit dynamics and memory formation through parallel GABA and purinergic signaling pathways.

overall_design: Bulk RNA profiling of FACS sorted astrocytes from Control and NFIXcKO mice from Olfactory Bulb, Cortex, Hippocampus and Thalamus

first: Manuel

last: Pérez

first: Junsung

last: Woo

first: Priyanka

last: Patel

first: Yeunjung

last: Ko

first: Wookbing

last: Kwon

first: Kaitlyn

last: Sanchez

first: Jin

last: Park

first: Henrique

middle: B

last: DaSilva

first: Richard

last: Gronostajski

first: Jeannie

last: Chin

first: Benjamin

last: Deneen


title: Argonaute-2 slicing of Rtl1 promotes skeletal muscle development and postnatal survival [smallRNA-Seq]

city: New York

last: Kleaveland

state: NY

address: 1300 York Ave

department: Pathology and Lab Medicine

institute: Weill Cornell Medicine

summary: Argonaute (AGO) proteins associate with small guide RNAs to bind and repress mRNA targets. AGO2 is the primary AGO slicer in mammals, cleaving RNAs that base-pair extensively to its guide RNA. Disrupting the slicing activity of AGO2 in mice causes neonatal lethality, however, the specific cell types and substrates that contribute to this lethality are not known. Through a combination of genetic, histologic, and molecular approaches, we identify retrotransposon-like-1 (Rtl1) as a key AGO2 slicing substrate in placental endothelium and skeletal muscle, and show that AGO2 slicing in skeletal muscle, but not endothelium, is required for postnatal viability. Loss of AGO2 slicing causes cell-autonomous, pathologic changes in skeletal muscle, characterized by larger fibers, increased central nuclei, prominent central clearings, and induction of transcripts associated with an unfolded protein response. Forced expression of RTL1 in myoblasts induces a similar unfolded protein response, highlighting the importance of preventing excess Rtl1 during muscle development. Taken together, our findings demonstrate a critical role for AGO2 slicing in skeletal muscle development that is, at least in part, due to its repression of Rtl1.

overall_design: To investigate the physiological importance of AGO2 endonuclease (slicing) activity, we generated small RNA-seq libraries from E19–E19.5 diaphragm tissue and performed miRNA expression profiling analyses.The following genotypes were used in this study: Ago2+/- (PN) and Ago2CD/- (CDN).

first: Nickolas

last: Almodovar


title: Placental TRPV2 supports trophoblast function and normal fetal development

city: Leuven

first: Katrien

last: De Clercq

address: Herestraat 49, box 611

country: Belgium

institute: KU Leuven

summary: This study investigates the role of the calcium-permeable ion channel TRPV2 in placental development, with a focus on trophoblast differentiation and syncytiotrophoblast lineage specification. Using a conditional knockout mouse model, we demonstrate that loss of Trpv2 leads to placental abnormalities characterized by impaired labyrinth organization and reduced vascularization. In situ hybridization reveal that Trpv2 is expressed in specific trophoblast subpopulations, including syncytiotrophoblast lineage cells. To assess transcriptional consequences of Trpv2 loss at the tissue level, bulk RNA sequencing was performed on isolated placental labyrinth tissue from control and knockout embryos at mid- and late gestation stages. To complement the in vivo analysis, we generated Trpv2 knockout mouse trophoblast stem cells (mTSCs) using CRISPR/Cas9 and performed bulk RNA sequencing under stem and differentiation conditions. These experiments were designed to identify cell-autonomous transcriptional changes and to assess the role of TRPV2 in regulating trophoblast differentiation programs.

overall_design: Bulk RNA-seq of Trpv2 knockout and control placental labyrinth tissue (E14.5, E16.5) and mTSCs under stem and 3D differentiation conditions with or without CHIR99021 treatment.

first: Vicente

last: Perez-Garcia

first: Amitesh

last: Panda

first: Seppe

last: Gevaert

first: Jill

last: Witvrouwen

first: Pilar

last: Van Mechelen

first: Jorge

last: Lopez-Tello

first: Katarzyna

last: Maksym

first: Anna

last: David

first: Evy

last: Van Den Broeck

last: Luyten

first: Andrei

last: Segal

first: Suresh

last: Poovathingal

first: Marta

last: Wojno

first: Yuki

last: Katanosaka

first: Rudi

last: Vennekens

first: Vicent

last: Pasque

first: Amanda

middle: N

last: Sferruzzi-Perri

first: Thomas

last: Voets

first: Joris

last: Vriens


title: Argonaute-2 slicing of Rtl1 promotes skeletal muscle development and postnatal survival [RNA-Seq]

first: Benjamin

last: Kleaveland

overall_design: To investigate the physiological importance of AGO2 endonuclease (slicing) activity, we generated RNA-seq libraries from E15.5 liver and placenta and E19–E19.5 liver, placenta, heart, lung, and diaphragm tissues and performed RNA expression profiling analyses. The following genotypes were used in this study: Ago2+/+ (PP), Ago2CD/+ (CDP), Ago2+/- (PN) and Ago2CD/- (CDN), ACTA1-cre; Ago2+/fl (PFL), and ACTA1-cre; Ago2 CD/fl (CDFL). To investigate the influence of RTL1 on skeletal myoblasts, we also generated RNA-seq libraries from undifferentiated polyclonal C2C12 cell lines harboring doxycline-inducible Halo, mouse RTL1, or human RTL1 insertions +/- treatment with doxycyline.

first: Nickolas

last: Almodovar


title: ChIP-seq of wildtype Manihot esculenta and transgenic cassava expressing a targeted methyltransferase enzyme

city: Saint Louis

first: Kerrigan

last: Gilbert

state: MO

address: 975 N Warson Rd

institute: Donald Danforth Plant Science Center

type: Genome binding/occupancy profiling by high throughput sequencing

summary: ChIP seq was used to identify H3 and H3K4me3 marks within promoters of interest within the genome of wildtype cassava and a transgenic line expressing a DRM2 methyltransferase targeted to certain loci

overall_design: Five grams of tissue was collected from clonally propagated, six month old plants. Following nuclear isolation, lysates were incubated with an anti-H3 and an anti-H3K4me3 antibody overnight after which the DNA was cleaned and precipitated. Sequencing libraries were prepared with the NuGen Ultralow V2 kit and sequenced on an Illumina NovaSeq X plus sequencer. Two replicates were performed.

first: Rebecca

last: Bart

first: James

last: Carrington


title: Decoding Sequence Recognition Code of Nucleic Acid-Binding Proteins of Human-Infecting DNA Viruses

first: Jian

last: Yan

summary: We applied an in vitro transcription–reverse transcription (ivTRT)-based ssDNA-SELEX workflow to profile the DNA-binding specificities of putative nucleic acid–binding proteins (NBPs) from ssDNA viruses. Translocated in liposarcoma/fused in sarcoma (TLS/FUS), a protein with well-established ssDNA-binding activity, was included as a positive control.

last: YAN

first: Ligang

last: FAN

first: Meifang

last: TANG

first: Haiqian

last: MA

first: Shifei

last: YANG


title: The livebearers platyfish and swordtails partially regenerate their hearts with persistent scarring

city: Fribourg

first: Anna

last: Jaźwińska

address: Chemin du Musée 10

department: Department of Biology

institute: University of Fribourg

summary: Heart regeneration varies among vertebrates, with zebrafish serving as a reference species for efficient cardiac restoration. How this capacity diversified among teleosts is an emerging question, given the recent identification of non-regenerative cardiac repair in medaka and cavefish. Here, we investigate heart restorative capacity following cryoinjury in two livebearers, platyfish and swordtails (Xiphophorus species), belonging to the Poeciliidae family. We demonstrate that their hearts lack the vascularized compact myocardium, which is a ventricular layer implicated in the restorative response in zebrafish. After cryoinjury, both poeciliids failed to rapidly deposit fibrotic tissue that normally reinforces the damaged site. This deficiency led to striking wound protrusion reminiscent of pseudoaneurysm after myocardial infarction in humans. Although the remaining myocardium initially increased cell proliferation, subsequently deposited collagenous scar tissue permanently sealed the interrupted ventricle, preventing complete regeneration. Transcriptomic analysis revealed several divergently regulated pathways between cryoinjured hearts of zebrafish and platyfish, particularly in immune response regulation. This was validated by delayed leukocyte infiltration and prolonged inflammation in platyfish, compared to the rapid, resolved inflammatory response in zebrafish. Our findings demonstrate that Xiphophorus species have evolved hearts with compromised regenerative capacity, characterized by pseudoaneurysm-like protrusion and permanent scarring. These results reveal that evolutionary traits of phylogenetic lineages can fundamentally modulate regenerative competence among teleosts, with important implications for understanding the mechanistic basis of cardiac repair.

sample_organism:
Danio rerio
Xiphophorus maculatus

platform_organism:
Danio rerio
Xiphophorus maculatus

overall_design: RNA sequencing of uninjured and 7-day post-cryoinjury ventricles from adult zebrafish and platyfish.

first: Vincent

last: Hisler

first: Lana

last: Rees

first: Simon

last: Blanchoud

first: Heidi

last: Lischer

first: Rémy

last: Bruggmann


title: Engineering the insulin signal peptide to protect human pancreatic beta cells from autoimmune destruction

city: Paris

first: Farah

last: Kobaisi

address: 123 Bvd Port Royal

country: France

institute: Institute Cochin

summary: The autoreactive T cells that destroy beta cells in type 1 diabetes are largely targeting insulin signal peptide fragments. HLA knockout beta-cells have been proposed to create hypo-immune cells, but this strategy poses significant tumorigenic risks. As an alternative, we hypothesized that insulin signal peptide modification would give rise to beta-cells evading autoimmune recognition while maintaining insulin functionality. Here, we developed human beta-cell lines lacking endogenous insulin that we complemented with insulin carrying signal peptides from different hormones including chromogranin-A. We evaluated insulin synthesis, processing, secretion, activity, and immune evasion. Chromogranin-A signal peptide substitution directed insulin expression, maturation and secretion, maintaining physiological proinsulin/insulin ratios. Secreted insulin remained functional. Crucially, beta-cells expressing insulin with chromogranin-A signal peptide evaded recognition and killing by autoreactive T cells without inducing ER stress or compromising cellular identity. This approach may offer a targeted alternative to systemic immunosuppression to be used in stem-cell-derived therapies by engineering endogenous insulin locus.

overall_design: RNA seq profiling of ECN90 pancreatic beta cells with a knockout of INS gene by CRIPSR cas9 versus wild type cells

first: Masaya

last: Oshima

first: Zhicheng

last: Zhou

first: Delphine

last: Thibaut

first: Abir

first: Barbara

last: Brandao

first: Roberto

last: Mallone

first: Raphael

last: Scharfmann


title: BET inhibition synergizes with Golcadomide by suppressing MYC and E2F pathways in diffuse large B-cell lymphoma [ATAC-Seq]

city: Summit

first: Junfei

last: Zhao

state: NJ

address: 556 Morris Ave

institute: Bristol Myers Squibb

summary: Golcadomide is a potential first-in-class Aiolos/Ikaros-degrading CRBN E3 ligase modulator (CELMoD) agent designed for the treatment of non-Hodgkin lymphoma (NHL) including diffuse large B-cell lymphoma (DLBCL). Aiolos and Ikaros are two critical lineage factors in lymphoid development that sustain lymphoma growth through recruitment of transcriptional complexes to enhancers and promotors of target genes. Through an epigenetic compound library screening, we found that BET inhibitors sensitize DLBCL cells to golcadomide. Using phenotypic assays and a multi-omics approach, we found that the combination treatment led to synergistic inhibition of MYC and E2F target genes, induction of p21, and subsequent cell cycle arrest. Genome-wide analysis revealed co-occupancy of Aiolos, Ikaros and BRD4 at the promoters of MYC and other genes involved in proliferation, as well as MYC-activating enhancers.

overall_design: ATAC-seq was performed in SUDHL4 and WSUDLCL2 diffuse large B-cell lymphoma (DLBCL) cell lines to assess chromatin accessibility changes following treatment with DMSO (vehicle control), BMS-986158 (2.5 nM), CC-99282 (50 nM), or a combination of both compounds.

first: Hsu

last: Chih-Chao

first: Patrick

last: Hagner


title: BET inhibition synergizes with Golcadomide by suppressing MYC and E2F pathways in diffuse large B-cell lymphoma [RNA-Seq]

overall_design: RNA-seq was performed on SUDHL4 and WSUDLCL2 diffuse large B-cell lymphoma (DLBCL) cell lines treated with DMSO (vehicle control), BMS-986158 (1.25 nM or 2.5 nM), CC-99282 (50 nM), or a combination of both compounds. Cells were collected at day 1, day 2, and day 3 post-treatment for transcriptomic analysis.


title: Oncogenic super-enhancer activation of TKT orchestrates metabolic reprogramming and immunosuppressive remodeling in prostate cancer

city: Shanghai

first: Zixian

last: Wang

address: 130 Dong'an Road, Xuhui District, Shanghai

institute: Fudan University

summary: Prostate cancer progression is driven by complex interactions between transcriptional amplification, metabolic adaptation, and immune evasion. Here, we identify the non-oxidative pentose phosphate pathway enzyme transketolase (TKT) as a central effector in this oncogenic axis. Integrative epigenomic profiling of patient-derived tissues and prostate cancer models reveals tumor-specific activation of a distal super-enhancer that engages MYC to drive TKT transcription. Beyond its canonical metabolic role, TKT promotes prostate tumor growth through suppressing interferon-stimulated gene expression by regulating R-loop dynamics. This suppression enhances CXCL6/CXCR2-mediated recruitment of polymorphonuclear myeloid-derived suppressor cells (PMN-MDSCs), thereby establishing a profoundly immunosuppressive tumor microenvironment. TKT depletion abrogates tumor progression in multiple murine models, diminishes PMN-MDSC infiltration, and restores CD8⁺ T cell cytotoxic function. Our findings uncover TKT as a transcriptionally activated metabolic-immunological hub that integrates enhancer hijacking, metabolic rewiring, and immune suppression, offering a compelling therapeutic target for advanced prostate cancer.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: H3K27ac ChIP‑seq was performed on eight flash‑frozen prostate specimens (four tumour + four matched normals, CPGEA cohort) and on three prostate‑cancer cell lines (22Rv1, LNCaP, VCaP); in addition, TKT ChIP‑seq was generated in PC3 cells. All libraries were built with the NEBNext Ultra II DNA kit and sequenced as 150 bp paired‑end reads on an Illumina platform to define super‑enhancer landscapes and TKT binding sites. PC3 prostate‑cancer cells were transfected with two independent TKT‑specific siRNAs (siTKT‑1/2) or a non‑targeting control, each in ≥2 biological replicates; total RNA harvested 48 h post‑transfection was converted to NEBNext Ultra II RNA libraries and sequenced (Illumina PE150) to profile transcriptomic changes elicited by TKT knock‑down. Single‑cell suspensions from prostates of PtenPC−/− and PtenPC−/−; TktPC−/− adult male mice (2 animals per genotype) were processed with the SeekOne® Digital Droplet Single Cell 3’V2.3 workflow and sequenced (illumina Novaseq X plus, PE150), yielding ~10000 cells per sample for  vevaluating how Tkt loss reshapes the tumour immune microenvironment.

first: Qixiang

last: Zhang

first: Xuemei

last: Tong

first: Ying

last: Lu

first: Gong-Hong

last: Wei


title: BET inhibition synergizes with Golcadomide by suppressing MYC and E2F pathways in diffuse large B-cell lymphoma

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

overall_design: Refer to individual Series


title: A comparative multiomic atlas of human immunity to multiple COVID-19 vaccines

city: Palo Alto

first: Dmitri

middle: A

last: Kazmin

address: 240 Pasteur Dr

department: Institute for Immunity, Transplantation and Infection

institute: Stanford University

summary: The rapid development of multiple COVID-19 vaccines, based on mRNA, recombinant adenoviral vectors and adjuvanted proteins, was critical to curtailing the global pandemic, and created a unique opportunity to compare human immunity to distinct vaccine platforms encoding the same antigen. Here, we present a longitudinal comparative analysis of innate and adaptive immune responses to the Matrix-M-adjuvanted Novavax (NX) and chimpanzee adenovirus-based AstraZeneca (AZ) vaccines in 161 healthy South African volunteers across three doses over a 11-month period collected between 2021 and 2022. Prime-boost NX vaccination (~3 weeks apart) elicited significantly stronger binding and neutralizing antibody responses than two AZ vaccine doses administered ~8 weeks apart. A NX booster administered 6–8 months later further increased the antibody titers that persisted for atleast 6 months. Both vaccines stimulated innate antiviral and inflammatory gene expression signatures within two days of vaccination. However, the strongest responses were after AZ priming and NX boosting, coinciding with plasma IFN-a and IFN-g induction, respectively, demonstrating distinct innate immune mechanisms induced by each vaccine. Transcriptional signatures of plasmablast responses that predict the magnitude of antibody responses were significantly induced 7 days after the second and booster but not primary NX vaccination, whereas these responses appeared after primary but not secondary AZ vaccination. Single-cell RNA sequencing revealed a multicellular origin of the innate transcriptional responses. Finally, a meta-analysis integrating immune responses induced by NX and AZ with those induced by the Pfizer-BioNTech mRNA vaccine demonstrated shared interferon-related signatures across all three platforms, while genes expression following mRNA vaccination was uniquely enriched in reactome pathways related to mRNA splicing, ubiquitination and proteasome processing, and class I mediated antigen presentation. Collectively, these data provide a comprehensive multiomic atlas of human immunity across three different COVID-19 vaccine platforms.

overall_design: Whole blood collected in Paxgene tubes at various time points (days 0, 1/2/3, 7) after primary, secondary or tertiary vaccination with the Novavax or AstraZeneca SARS-CoV-2 vaccines were subjected to bulk RNAseq analysis.

first: Prabhu

last: Arunachalam

first: Ana

last: Oliveira


title: Prefoldin is critical for meiotic spindle function, revealing coupling between chromosome segregation and cellular remodeling

city: Berkeley

first: Naohiro

last: Kuwayama

address: 628 Barker Hall

institute: UC Berkeley

summary: Faithful chromosome segregation is essential for producing viable gametes via meiosis which is often described as a specialized version of mitotic segregation. The key specializations known include the addition of that allow two sequential segregation events with no intervening round of DNA segregation. Here, in contrast, we identify the ubiquitously expressed prefoldin subunit Gim3 as a critical regulator of meiotic but not mitotic chromosome segregation. Loss of Gim3 causes pronounced chromosome mis-segregation and reduced spore viability through reduced tubulin protein levels and compromised spindle elongation. GIM3 deletion minimally affects spindle length and chromosome segregation in mitosis, despite similar tubulin levels in both cases, highlighting a previously unrecognized difference between meiotic and mitotic spindles. Beyond chromosome segregation, gim3Δ cells exhibit defects in meiotic cellular remodeling, including increased inheritance of cytosolic aggregates into newly forming spores. Importantly, experimentally induced chromosome mis-segregation disturb cellular remodeling, indicating that chromosome segregation and chromatin-directed remodeling are mechanistically linked processes. Together, our findings establish Gim3 as a key factor for both chromosome segregation integrity and cellular remodeling in meiosis, and reveal a previously unrecognized coupling between these processes.

overall_design: We performed ribosome profiling on WT and gim3Δ cells 4 hours into meiosis.

first: Gloria

last: Brar


title: Characterization of Circulating Neoantigen-Specific T Cell Responses and Their Public TCR Repertoires in Lynch Syndrome Carriers (scRNAseq)

city: Houston

first: Eduardo

last: Vilar-Sanchez

address: 1515 Holcombe Blvd

institute: The University of Texas MD Anderson Cancer Center

summary: Lynch syndrome (LS), a common hereditary cancer syndrome, provides a unique model to study immune surveillance at the earliest stages of tumorigenesis. A hallmark of LS carcinogenesis is the generation of highly immunogenic mutated neoantigens derived from insertion deletions, yet the transcriptomic states of the neoantigen-specific T cells that recognize them remain poorly characterized. Here, we characterized neoantigen-specific T cells from LS carriers using functional assays, single-cell RNA/TCR sequencing, and repertoire integration with existing data sets. Recurrent neoantigens elicited strong immune responses, with neoantigen-specific T cells mediating cytotoxicity against patient-derived tumor organoids. Single-cell analysis revealed oligoclonal expansions spanning effector and memory states with LS cancer survivors showing enrichment for metabolically exhausted subsets and previvor LS carriers retaining polyfunctional effectors. Cross-cohort analyses identified public clonotypes overlapping with tumor-infiltrating repertoire. These findings define the architecture of circulating neoantigen-specific immunity in LS and identify public TCRs as biomarkers for immune monitoring and immunoprevention.

overall_design: To define the phenotypic and transcriptional states of circulating neoAg-specific T cells, we performed single-cell multi-omics on six LS carriers, including three previvors (P1, P5 and P7) and 3 survivors (S2, S8 and S10) with >1% dextramer positivity.


title: IL-1β/IRAK4 Axis Promotes Ovarian Tumor Development at the Mesothelium Injury Sites

city: Rochester

first: Cameron

last: Baker

address: 601 Elmwood Ave

institute: University of Rochester

summary: Epithelial ovarian cancer (EOC) cells seed at mesothelial inflammation or injury sites. Lack of animal models recapitulating tumor cells seeding at inflamed sites in EOC hinders mechanistic studies and therapy developments. Here, we developed a non-surgical MIM (Mesothelium Inflammation/Injury Metastasis) model that recapitulates tumor cell seeding at inflamed sites. This model captures temporal changes in tumor immune microenvironment and tumor growth allowing for deeper mechanistic and preclinical therapeutic studies of EOC in-vivo. We show here that HGS-3 high-grade murine serous EOC cells seed at needle-induced injury sites in mesothelium/peritoneal wall, forming tumors both internally and protruding outward. Using MIM model, we found that deletion of IL1R1 in mice reduced EOC cell seeding at mesothelium injury/inflamed site in WT but not IL1ra-deficient mice. Treatment of MiM mice with a novel IRAK4 inhibitor we recently developed (UR241-2) revealed an essential role for IRAK4 signaling downstream IL-1β/IL-1R1 in fostering an anti-tumor inflammatory environment, and reduced tumor burden. We conclude that IRAK4 inhibitors can be more effective than IL-1/IL-1R1 targeting agents to control metastasis and peritoneal tumors, an unmet medical need in EOC recurrence. Downregulation of extracellular matrix (ECM), upregulation of neutrophil activation genes, reduced cell adhesion and migration exhibit how UR241-2 corrects ECM and immune disorders in EOC, making it less conducive to metastasis and tumorigenesis

overall_design: Two days post tumor cell inoculation, mice were treated with either vehicle or UR241-2 (30mg/kg, 100µL, M-F, IP). DMSO solution of UR241-2 (1µL=200uL, 90mg in 450µL DMSO) was dissolved in formulation made of [H2O (300µL)+PEG6000 (40% in water, 150µL)+EtOH(150µL)] which generates a clear solution after short vortexing. Equivalent volume of the solvent was injected in each animal of the vehicle group. Treatment continued till 44th day. After 45 days, mice were bled via mandibular vein and ~25µL blood was collected for complete blood counts (CBC) and analyzed in EDTA-tubes using ElementHTS+ system. Mice were euthanized soon after and photographed to record the tumors formed at the injury sites. Spleen, omentum and lavages were collected from each mouse. Omentum and spleen weights were recorded and weighed. Spleen was crushed in serum free RPMI1640 medium (Gibco, cat#: 22400-089) and filtered. Tumors/omentum were also crushed similarly. Crushed cells were broken into single cell suspension and analyzed by flow cytometry.

first: Miller

middle: P

last: John

first: Singh

middle: K

last: Rakesh


title: Brain perivascular macrophages regulate endothelial cell function via a cMAF-dependent transcriptional program in mouse and human

city: Stanford

first: Julia

last: Belk

state: California

address: 450 Serra Mall


title: Genomic and transcriptomic feature of HBV integration in treatment-naïve, HBeAg-positive children with chronic HBV infection

city: Chongqing

first: Zhiwei

last: Chen

address: The Second Affiliated Hospital of Chongqing Medical University, 74  Linjiang Road, Yuzhong District, Chongqing

summary: HBV integration represents one of the primary obstacles to achieving HBV cure, however, much remains unknown about HBV integration in children with chronic HBV infection (CHB).We performed probe-based capture strategy and spatial transcriptomic sequencing to analyze HBV integration at both genomic and transcriptomic levels. Our analysis has revealed that HBV integration occurs in CHB children at both genomic and transcriptomic levels, and exhibits patterns similar to CHB adults.Local immune responses to transcriptionally active viral integration were highly age-dependent.

overall_design: Liver biopsy tissues were collected from 30 CHB children and 28 CHB adult. A probe-based capture strategy was employed to analyze HBV integration at genomic level in a subset of 18 pediatric and 28 adult CHB patients. Additionally, spatial transcriptome sequencing was conducted on samples from 12 pediatric CHB patients and 3 adults (from a public database) to analyze HBV integration at transcriptomic levels. Liver biopsy samples from two patients were mounted on a single Visium Spatial Gene Expression Slide for subsequent analysis.

last: Wu

first: Yan

last: Han

first: Jing

last: Tang

first: Jiaying

first: Yingzhi

last: Zhou

first: Yunan

last: Chang

first: Xiaorong

last: Peng

first: Aoxue

last: Tan

first: Yi

last: Xiang

first: Fang

first: Guanhua

last: Zha

first: Zhiling

last: Deng

first: Qingliang

first: Li

first: Xiaohao

first: Wei

last: Shen

first: Peng

last: Hu

first: Mingli

first: Dachuan

last: Cai

first: Xinxin

first: Xuan

last: An

first: Hongmei

last: Xu

first: Hong

last: Ren


title: Methylated eEF1A Selectively Decodes mRNA to Shape Cancer Proteomes

first: Shuo

last: Liu

address: 327 Campus Drive

summary: Differences in mRNA decoding efficiency influence protein synthesis. However, whether the translation elongation machinery harbors an intrinsic mechanism that selectively decodes codons, and how this shapes proteomes in homeostasis and disease, remains unknown. Here we find that METTL13-catalyzed dimethylation of the elongation factor eEF1A at lysine 55 (eEF1AK55me2) enhances decoding of select codons, thereby preferentially increasing synthesis of pro-oncogenic proteins to promote tumorigenesis and targeted therapy resistance. Proteomic profiling and single-molecule imaging reveal that eEF1AK55me2 increases decoding efficiency, particularly for underrepresented codons with weak wobble-position base-pairing. In cancer cells, METTL13 knockdown reduced synthesis of oncogenic proteins, such as KRAS, encoded by genes enriched in eEF1AK55me2-dependent codons; synonymous recoding with eEF1AK55me2-independent codons reversed this effect. Loss of METTL13 inhibited growth of KRASG12C-inhibitor (sotorasib)-resistant syngeneic and patient-derived lung adenocarcinoma (LUAD) xenografts. Further, METTL13 ablation in relapsed autochthonous KRASG12C-driven LUAD tumors mitigated sotorasib resistance, significantly extending survival in vivo. Finally, in clinical trial patients treated with the KRASG12C-inhibitor adagrasib, inferred METTL13 activity was associated with inferior clinical response. These findings identify an eEF1AK55me2-mediated mRNA decoding mechanism that promotes selective oncogenic protein synthesis and suggest that METTL13 targeting may counteract tumor resistance to KRAS inhibitors.

overall_design: RNA-seq profiling of wildtype T3M4 cells and their knockdown derivatives (sgMETTL13) under same treatment conditions for proteomic profiling


title: Precision Nuclear Run-on Analysis of post-mitotic human neurons infected with HSV-1

city: Ithaca

first: Joel

middle: D

last: Baines

address: 235 Hungerfordhill Rd

institute: Cornell University

summary:
These data have been used for the manuscript entitled, "Analysis of Host and Viral Nascent and Steady-State RNA Levels in a Human Neuronal Model of  Herpes Simplex Virus 1 Infection".  This manuscript has the following abstract:
We used precision nuclear run-on with sequencing (PRO-seq) in conjunction with quantitative RT-PCR to map transcription, and transcript abundance in terminally differentiated LUHMES neurons before (mock) and after infection with Herpes Simplex Virus 1 (HSV-1). Initial PRO-seq analysis of cellular transcription demonstrated that the mock-infected differentiated LUHMES neurons expressed genes associated with differentiated neurons. This gene set included transcription of genes related to dopaminergic signaling, cell adhesion, and neuronal cell differentiation. By contrast, epithelial cells transcribed genes involved in cell cycle progression and DNA damage repair. PRO-Seq analysis of HSV-1-infected LUHMES neurons indicated only modest transcription of viral genomes. Additionally, genes of LUHMES neurons maintained RNA polymerase II (Pol II) promoter proximal pausing whereas we previously showed HSV-1 infection decreases promoter-proximal pausing on genes of epithelial cells. PRO-Seq and RT-PCR analysis were then performed during a time course of infection, spanning both acute and latent phases. The results from the acute infection demonstrated slower rates of transcription, viral mRNA accumulation, and viral genome replication compared to undifferentiated, non-neuronal cells. RT-PCR indicated that steady-state transcripts from all viral gene kinetic classes increased in abundance from 1 h to 24 h post-infection. This accumulation correlated with an increase in transcription on the same genes as demonstrated by PRO-seq. In contrast, the latent phase of infection was distinguished by high levels of transcription on all viral genes, but very low viral transcript abundance. These results indicate that viral gene transcription initiation does not correlate with viral transcript abundance during the latent phase, and suggest that blocks to RNA polymerase processivity and other components of the RNA life cycle likely contribute to maintenance of latency in LUHMES neurons.
Importance
Viral latency is a hallmark of all herpesvirus infections and arguably key to its high prevalence in human and animal populations. We found that HSV-1 transcription and viral genome replication is more restricted in LUHMES neurons compared with undifferentiated epithelial cells. Moreover, the latent viral genome is more transcriptionally active than previously appreciated, while overall lytic transcripts are in lower abundance in latency than in acute infection. The latency-associated transcripts, in contrast, accumulate to high abundance during latency, despite only modest increases in transcription.

sample_organism:
Drosophila melanogaster
Homo sapiens
Human alphaherpesvirus 1 strain 17

overall_design: LUHMEs were plated at 40,000 cells/cm2 onto coated dishes and flasks and cells were allowed to proliferate for two days at which time they were switched into differentiation media. At 6 days post-differentiation (8 days post plating), PMNs for the quiescence experiments were pre-treated with 50µM Acyclovir (ACV).   All infections both acute and quiescent were performed with HSV-1 17syn+ at a MOI equal to 3 on day 10 post plating (8 days post differentiation), except for the mock-infected cells which were treated in the same manner as infected cells, just without infectious virus added. The PMNs slated for quiescence were cultured in the presence of ACV for 48 hr after infection, at which time the media was changed without further exposure to ACV. Nuclei were prepared from acutely infected, non-acyclovir treated PMNs at 1, 3, 6 and 24 hr post infection, and the quiesently infected PMNs were collected at 10 days post-infection (8 days post acyclovir removal).  Nuclei were isolated on ice and flash frozen for PRO-seq analysis. There were five independent experiments for the quiescent time points, and two independent experiments for each of the acute infection and mock time points.  Each experiment consisted of five T75 flasks with an approximate number of neurons per experiment totaling 3-3.5x108.  Precision nucelar run on was undertaken as previously described (https://doi.org/10.1128/jvi.00712-24).  Briefly, Frozen nuclei were brought to 37℃, spiked with Drosophila S2 nuclei at a ratio of 1 / 1000 Drosophila / Human nuclei, and pre-warmed run-on reaction buffer (10 mM Tris-HCl [pH8], 300 mM KCl, 1% Sarkosyl, 5mM MgCl2, 1mM DTT, 100 μM biotin-11-ATP, -CTP, -GTP, and -UTP [Perkin-Elmer], and 0.4 U / μL) was added to each sample.  Reactions were incubated at 37℃ with constant shaking for 3 minutes. Reactions were stopped by adding 1.8 mL of Trizol LS (Thermo Fisher). RNA was isolated by adding 520 μL chloroform to each resuspended sample. Incubation times and centrifugation times were performed following the manufacturer’s guidelines. RNA was precipitated with a 2:1 volume of ethanol and the pellets were washed and stored in 700 μL of 75% ethanol before sequencing library preparation. The biotinylated RNA was resuspended in nuclease free water and hydrolyzed with 0.2N NaOH in a final volume of 30 μL. After 20 min, the NaOH was neutralized with the addition of 1M Tris-HCl (pH 6.8), and samples were run through a Bio-Rad P-30 column to remove any unincorporated biotinylated nucleotides. Biotinylated RNA was isolated using streptavidin M280 Dynabeads (Thermo Fisher) following previously published protocols (https://doi.org/10.1038/nprot.2016.086).

first: Claire

last: Birkenheuer

first: Terri

last: Edwards

first: David

last: Bloom


title: KSR2 is novel candidate oncogene in TAL1-positive T-cell acute lymphoblastic leukemia with potential clinical implications

city: Gent

first: Igor

last: Fijalkowski

address: Sint-Pietersnieuwstraat 33

institute: Ugent

summary: T-cell acute lymphoblastic leukemia (T-ALL) is a rare hematological malignancy characterized by substantial molecular heterogeneity and aggressiveness manifested by relatively high incidence of relapse and drug resistance. Despite the growing understanding of T-ALL biology and increasing cure rate of this disease, novel oncogenes with biomarker and therapeutic potential are needed to recognize high-risk patients and improve therapy effectiveness. Here we demonstrate that KSR2 is overexpressed in a subgroup of T-ALL patients and that its expression is linked to TAL1 genetic subtype of this malignancy. We show that the ectopic expression of KSR2 results from demethylation of its regulatory region followed by direct binding of TAL1 transcription factor. We demonstrate that the expression of KSR2 is a potential marker of worse outcome within the TAL1 subtype of T-ALL. We show that KSR2 provides growth advantage in T-ALL in vitro pointing to its oncogenic activity. We demonstrate a dose-dependent cytotoxic effect of APS-2-79, a small molecule inhibitor of KSR2 protein, in T-ALL cell lines expressing KSR2. Finally, we show that KSR2 is involved in metabolic processes, such as glycolysis and biosynthesis of lipids and proteins and that this effect is mediated by supporting AMPK signaling.

overall_design: RNAseq was performed upon inhibition of KSR2 with specific inhibitors (KSRi) and upon deletion of KSR2 using CRISPRi (with two alternative guide RNAs)

first: Monika

last: Drobna-Śledzińska

first: Natalia

last: Maćkowska-Maślak

first: Roman

last: Jaksik

last: Fijałkowski

first: Maria

last: Kosmalska

first: Jakub

last: Czarny

last: Lejman

first: Łukasz

last: Sędek

first: Tomasz

last: Szczepański

first: Agata

last: Pastorczak

first: Katarzyna

last: Derwich

first: Michał

last: Witt

first: Panagiotis

last: Ntziachristos

first: Małgorzata

last: Dawidowska


title: Spatiotemporal transcriptomic niches of complement pathway and serine protease inhibitor activation in aging and infection

city: Saarbrücken

first: Fabian

middle: Michael

last: Kern

state: Saarland

address: Campus E2 1

department: Center for Bioinformatics

country: Germany

institute: Saarland University

summary: Aging is a multifactorial and complex physiological process, affecting every organ with characteristic manifestations. Understanding the molecular mechanisms that drive aging processes is crucial to targeting age-related disorders. Recent reports suggest that severe post-infection syndromes can partially accelerate aging. However, the underlying gene-encoded regulatory interplay, whether being shared or distinct between aging and infection biology are poorly understood. Here, we employed spatial transcriptomics to establish a multi-organ atlas (brain, heart, kidney, liver, lung, and spleen) across the mouse lifespan (4, 17, and 26 months). Dissecting high-quality fresh-frozen tissue samples at unbiased molecular resolution, we found both organ-specific and cross-organ gene dysregulation upon aging. We identified age-related trajectories in gene expression and cell state, some only detectable within their spatial context, and provide validation at subcellular resolution. The most prominent effect was organ-wide immune system activation with spatially variable severity. We therefore evaluated how aging mimics the expression signatures observed in systemic infection, using spatial transcriptomics slices from young mice infected with Plasmodium berghei ANKA. While on the gene level the effect sizes caused by the infection outweighed those of aging, we reveal a shared activation of the early complement pathway (C4b) and serine protease inhibitors (Serpin gene family) within by phenotype distinct spatial niches. We show that this common RNA signature is driven by tissue-specific cell types and eventually affects protein levels in the aged brain, rendering them a target for future mechanistic and drug discovery studies. Taken together, our study provides a coherent in-depth and cross-organ transcriptomics atlas to systematically study aging and infection in the mouse at spatiotemporal resolution.

overall_design:
We first performed spatial transcriptomics experiments using the spot-based 10x Visium platform on a wildtype mouse aging cohort (AC), consisting of up to five mice per timepoint (young: 4 months; middle-aged: 17 months; aged: 26 months) followed by deep sequencing. We processed single sections for the peripheral organs (heart, kidney, liver, lung and spleen) and five sections from the brain (Bregma: –1.7, -2.06, -2.7, -3.52 and -4.72) for each individual mouse (N=111).
To validate the aging brain signatures at the sub-cellular level we performed STOmics Stereo-seq for three mouse brains, processing each at the same five Bregma as for the Visium data set (N=15).
We then repeated the 10x Visium experiments with a completely separate infection cohort (IC), consisting of five young mice infected with the mouse parasite Plasmodium berghei, an animal model for cerebral malaria, and five respective young controls. The IC comprises three peripheral organs (liver, kidney and lung) and two preselected brain regions at bregma –2.06 and bregma 3.89 (the olfactory bulb) per individual mouse (N=42).

first: Viktoria

last: Wagner

first: Vanessa

last: Wahl

first: Nicole

last: Ludwig

first: Simon

last: Graf

first: Jeremy

last: Amand

first: Aulden

last: Foltz

first: Micaiah

last: Atkins

first: Blen

last: Kedir

first: Alexandros

last: Hadjilaou

first: Matthias

last: Flotho

first: Friederike

last: Grandke

first: Philipp

last: Wartenberg

middle: I

last: Hollenhorst

first: Hanna

last: Lotter

first: Rolf

last: Müller

first: Thomas

last: Jacobs

first: Gabriela

last: Krasteva-Christ

first: Ulrich

last: Boehm

first: Oliver

last: Hahn

first: Tony

last: Wyss-Coray

first: Andreas

last: Keller


title: TANGO6 coordinates transcription and translation through nucleocytoplasmic partitioning

city: Barcelona

first: Enrique

last: Blanco

address: Dr. Aiguader 88

department: Gene Regulation, Stem Cells and Cancer

country: Spain

institute: Center for Genomic Regulation (CRG)

summary: Coordinated RNA and protein synthesis is fundamental to cell function and survival. Here, we show that TANGO6, a nucleocytoplasmic RNA-binding protein, is an integral component of the proteostasis control axis, regulating both transcription and translation. In the nucleus, TANGO6 is recruited to gene promoters alongside RNA polymerase II, where it controls the transcriptional activation of essential genes, including those required for G1–S cell cycle progression and cell differentiation. Cytoplasmic TANGO6 associates with polysomes to promote protein synthesis. Under stress conditions, the organization of TANGO6 changes; notably, heat stress triggers its translocation to the nucleus, thereby depleting its cytoplasmic pool. Thus, TANGO6 assists in both transcriptional and translation reprogramming to support cell survival. Overall, the nucleocytoplasmic shuttling of TANGO6 is a central mechanism for controlling the cellular proteome, establishing its essential role in cell viability from homeostasis to stress adaptation.

overall_design: 6 paired-end RNA-seq experiments and 24 ChIP-seq experiments (CTR means siRNA randomised (not targeting) and KD means siRNA specific against TANGO6). Heat-shock effect samples: 37 means 37 degrees Celsius (normal temperature) and 43 means 43 degree Celsius (heat-shock temperature). DMSO means control and dTAG means addition of dTAG-13 that leads to TANGO6 degradation

first: Gonzalo

last: Bigliani

first: Cecilia

last: Ballare

first: Luciano

last: Di Croce

first: Vivek

last: Malhotra


title: Transcriptome-Wide M5C Methylation Profiling in NSUN6-Knockdown HepG2 Cells

city: Hefei

first: Fan

last: Wenhu

address: 81 Meishan Road, Hefei, Anhui 230032, China

institute: Anhui Medical University

summary: This study investigates the role of NSUN6 in RNA 5-methylcytosine (M5C) methylation in HepG2 cells. Stable NSUN6 knockdown cell lines were generated using shRNA-mediated RNA interference, validated by qRT-PCR and Western blot. RNA was extracted from knockdown and control cells, treated with bisulfite to convert unmethylated cytosines, and sequenced. Sequencing data were aligned to the human genome (GRCh38) to identify M5C methylation sites. By comparing methylation levels between NSUN6 knockdown and control cells, we aim to map NSUN6-dependent M5C sites and elucidate their roles in regulating gene expression and cellular function. This dataset provides valuable insights into the epigenetic regulation of RNA modifications and the specific contributions of NSUN6 in human cells, with potential implications for understanding disease mechanisms.

overall_design: RNA-seq profiling of wildtype HepG2 cells and their NSUN6 knockdown derivatives (shNSUN6), assessing M5c methylation levels  of RNA processing in knockdown and control cells.

first: Li

last: Xutong

first: Gu

last: hao


title: Lysosomal dysfunction drives a transcriptional and epigenetic signature found in disease-associated microglia in neurodegenerative diseases [scRNA-seq, snRNA-seq]

city: La Jolla

first: Christopher

last: Glass

address: 9500 Gilman Dr.

department: CMM

institute: University of California, San Diego

summary: Lysosomal dysfunction is causally linked to neurodegeneration in many lysosomal storage disorders and is associated with various age-related neurodegenerative diseases. Here, we investigated the question of underlying mechanisms using a mouse model of mucopolysaccharidosis type IIIA caused by deficiency of the lysosomal hydrolase SGSH. Systematic imaging and transcriptomic and epigenetic studies revealed microglia to be the most profoundly impacted cell type in brains of Sgsh-deficient mice. Further investigation identified dominant and context-dependent roles of members of the MITF/TFE family as major drivers of microglia-specific epigenetic and transcriptional changes resulting from lysosomal stress that are dependent on collaborative interactions with AP-1/ATF, C/EBP, and PU.1/ETS transcription factors. Features of the transcriptomic and epigenetic alterations observed in murine Sgsh deficiency were also observed in microglia derived from mouse models of age-related neurodegeneration and in human Alzheimer's disease patients. These findings reveal common and disease-specific transcriptional mechanisms associated with disease-associated microglia phenotypes.

overall_design: Gene expression analyses across brain cell types by single-nucleus RNA-seq and in sorted microglia by single-cell RNA-seq in WT and SgshKO mice, temporal polyA RNA-seq of sorted ex vivo mouse microglia (WT and SgshKO; 3weeks, 4months, 8 months), polyA RNA-seq of sorted ex vivo mouse microglia following in vivo ASO-mediated knockdowns of Mitf, Tfeb, and Tfe3 (WT) or combination of Mitf+Tfe3 (SgshKO), ATAC-seq and H3K27ac-ChIP-seq of mouse microglia, neurons, and oligodendrocytes (WT and SgshKO) at 4- and 8-months of age, and MITF, TFEB, and TFE3 ChIP-seq from microglia (PU.1+) and oligodendrocyte (OLIG2+) in WT and SgshKO nuclei isolated from mouse forebrains.

last: Balak

first: Johannes CM

last: Schlachetzki

first: Addison

last: Lana

first: Elizabeth

last: West

first: Christine

last: Hong

first: Jordan

last: DuGal

first: Yi

last: Zhou

first: Benjamin

last: Li

first: Nathanael

last: Spann

first: Payam

last: Saisan

first: Vishal

last: Sarsani

first: Kilian

last: Kleeman

first: Xiaoming

last: Zhang

first: Martina

last: Pasillas

first: Sydney

last: O'Brien

first: Juliette

last: Bokor

first: Philip LSM

last: Gordts

first: Oleg

last: Butovsky

first: Beth

last: Stevens

first: Fredrik

last: Kamme


title: Lysosomal dysfunction drives a transcriptional and epigenetic signature found in disease-associated microglia in neurodegenerative diseases [RNA-seq]

first: Christopher

last: Glass

last: Balak

first: Johannes CM

last: Schlachetzki

first: Addison

last: Lana

first: Elizabeth

last: West

last: Kleemann


title: Lysosomal dysfunction drives a transcriptional and epigenetic signature found in disease-associated microglia in neurodegenerative diseases [ATAC-seq]

summary: Lysosomal dysfunction is causally linked to neurodegeneration in many lysosomal storage disorders and is associated with various age-related neurodegenerative diseases. Here, we investigated the question of underlying mechanisms using a mouse model of mucopolysaccharidosis type IIIA caused by deficiency of the lysosomal hydrolase SGSH. Systematic imaging and transcriptomic and epigenetic studies revealed microglia to be the most profoundly impacted cell type in brains of Sgsh-deficient mice. Further investigation identified dominant and context-dependent roles of members of the MITF/TFE family as major drivers of microglia-specific epigenetic and transcriptional changes resulting from lysosomal stress that are dependent on collaborative interactions with AP-1/ATF, C/EBP, and PU.1/ETS transcription factors. Features of the transcriptomic and epigenetic alterations observed in murine Sgsh deficiency were also observed in microglia derived from mouse models of age-related neurodegeneration and in human Alzheimer’s disease patients. These findings reveal common and disease-specific transcriptional mechanisms associated with disease-associated microglia phenotypes.

first: Christine

last: Hong

first: Jordan

last: DuGal

first: Yi

last: Zhou

first: Benjamin

last: Li

last: Spann

last: Saisan


title: CD40ag Activated B Cells Elicit Anti-Tumor Immunity - RNAseq

first: Jingting

last: Yu

address: 10010 N Torrey Pines Rd

institute: Salk Institute for Biological Studies

summary: We leveraged mouse models of Triple Negative Breast cancer of varying tumor mutation burdens to elucidate ways that direct activation of B cells can illiciate an anti-tumor effect. These syngenic tranplant models were treated with CD40 agonist immunotherapy . Primary tumors of both treated and nontreated conditions were profiled by RNA-SEQ. These tumors that have been profiled describe the impact that B cell acitvation has on CD40 agonist immunotherapy  treatment and tumor progression.

overall_design: Primary tumors and draining lymphnodes were isolated from tumor bearing mice and subsequently flash frozened. Total RNA isolation was then performed using Qiagen Rneasy mini kit following the purification of total RNA from animal tissues protocol. The resulting isolated RNA was then made into libraries for sequencing by the Salk Institutes Next Genereation Sequencing Core.

first: Kendrick

last: Nguyen

first: Monika

last: Ramos

first: Daniel

last: Hollern


title: Effects of overexpression on miRNA isoforms and the targetome

first: Fabian

last: Kern

summary: Translational inhibition or degradation of messenger RNAs by microRNAs represent core regulatory mechanisms with a high grade of complexity proposed by experimental and computational approaches. One proposed important factor is isoforms of mature microRNAs (isomirs), adding numerous potential targets and functions. For a set of miRNAs (mir-34a, mir-129, mir-873, mir-133b, mir-7), we characterized the impact of their overexpression in cell culture models (HeLa, HEK293T, LUHMES, SH-SY5Y) on the detection of isomiRs. We observed an astonishing heterogeneity of isomiRs between cell lines, emphasizing a significantly increased isomiR repertoire following artificial overexpression with up to 832 different isoforms per miRNA. Performing a dilution and a time series, we validated a significantly increased isomiR repertoire after 8 hours and for precursor amounts of 0.5 µg. Proteomic analysis further argued for a significant influence of the isomiR repertoire depending on the miRNA amount. While 7mer-m8 sites revealed the highest reduction effect in general, we report an increased frequency but lower amplitude of repression with an increasing number of miR-7-5p isoforms. Our data call attention to interpreting the proposed impact of isomiRs on the targetome, especially using overexpression systems.

overall_design: We compare the number and frequency of isoforms for five commonly investigated miRNA precursors (mir-34a, mir-129, mir-873, mir-133b, mir-7) in four widely used cell culture systems (HeLa, SH-SY5Y, HEK293T, LUHMES). Following systematic overexpression of all miRNAs in all cell culture systems in triplicate, we compared the isoform pattern using deep small RNA-sequencing.

first: Martin

last: Hart

first: Lena

last: Krammes

first: Caroline

last: Diener

first: Ernesto

last: Aparicio-Puerta

first: Pascal

last: Hirsch

first: Nicole

last: . Ludwig

first: Tobias

last: Fehlmann

first: Annika

last: Engel

first: Claudia

last: Fecher-Trost

first: Bastian

last: Fromm

first: Veit

last: Flockerzi

first: Eckart

last: Meese

first: Andreas

last: Keller


title: Unravel the oligodendrogenic program of adult spinal cord neural stem cells

city: montpellier

first: Jean-Philippe

last: Hugnot

address: 141 rue de la Cardonille

institute: Institut de génomique fonctionnelle

summary: The cells of the central canal of the spinal cord constitute a niche of stem cells. A fraction of these cells can give rise to astrocytes and oligodendrocytes in vitro and predominantly produce astroglia in vivo. We explored the molecular mechanisms regulating the formation of oligodendrocyte precursor cells (OPCs) from spinal cord stem cell cultures derived from PDGFRA-GFP mice.

overall_design: To investigate the production of OPC/oligodendrocyte, we use a transgenic mouse PDGFRaGFP where we FACS sorted GFP positive and negative cells.

first: Sandra

last: Joppe

first: Robert

last: Chevreau


title: Curcumin carbon dots promote osteogenic differentiation and exhibit antibacterial activity for peri-implantitis prevention

status: Public on Aug 12 2026

city: Zibo

first: Yu

last: Zhang

address: No. 2018 Jiangmeng Road, Zhoucun District

institute: Qilu Medical University

summary: Peri-implantitis prevention remains a significant challenge in implant dentistry. This study evaluated the dual functionality of a curcumin-carbon dot (Cur-CD) complex in enhancing the osteogenic differentiation of rat bone marrow mesenchymal stem cells (rBMSCs) and exerting antibacterial effects. Primary rBMSCs were isolated and divided into control and Cur-CD-treated groups. After 21 days of osteogenic induction, total RNA was extracted for transcriptome sequencing analysis to investigate the molecular mechanisms underlying Cur-CD-promoted osteogenesis. The results demonstrated that Cur-CD significantly enhanced mineralized nodule formation and up-regulated expression of key osteogenic markers (Runx2, OPN, Osterix, OCN), providing evidence for its potential as a bioactive agent for preventing peri-implantitis.

overall_design: Total 5 samples, consisting of two experimental groups: control group (rBMSCs cultured in osteogenic induction medium) and Cur-CD treatment group (rBMSCs treated with 0.02656 mg/mL curcumin carbon dots in osteogenic induction medium). RNA was extracted after 21 days of osteogenic differentiation. Paired-end mRNA sequencing was performed on Illumina platform to compare gene expression profiles between control and Cur-CD-treated rBMSCs, aiming to identify differentially expressed genes and pathways associated with Cur-CD-promoted osteogenic differentiation.

first: Lingyi

last: Kong

first: Gang

last: Dong

first: Qingqing

last: Du


title: Genome-wide mapping of helicase-generated ssDNA reveals Hrq1 activity at RNA polymerase III-transcribed genes

city: New York

first: Shaili

last: Regmi

address: 100 Washington Sq E

institute: New York University

summary: DNA helicases preserve genome stability by unwinding DNA during replication, repair, recombination, and transcription, yet their sites of action in vivo remain difficult to define. Here, we describe a sequencing-based strategy to map helicase activity genome-wide by coupling helicases to the single-stranded DNA-specific activation-induced cytidine deaminase (AID). Deamination of cytosines exposed during helicase-mediated DNA unwinding generates strand-specific mutational footprints that can be detected by whole-genome sequencing at near-nucleotide resolution. Using the Saccharomyces cerevisiae RecQ4-family helicase Hrq1, a functional homolog of human RECQL4, we generated the first genome-wide map of Hrq1 activity. Hrq1-dependent deaminations were highly enriched at RNA polymerase III (RNAPIII)-transcribed genes, particularly tRNA genes, where they occurred predominantly on the transcriptional template strand. This localization was reproducible using both overexpressed Hrq1-AID fusions and an inducible dimerization system that recruited AID to endogenously expressed Hrq1, and it was markedly reduced by helicase-inactivating mutation, indicating that active DNA unwinding underlies the observed signal. Hrq1 associated with nearly all tRNA genes irrespective of transcription level, replication orientation, or proximity to transposable elements, yet deletion or overexpression of Hrq1 did not detectably alter pre-tRNA abundance or RNA polymerase III recycling under the conditions tested. Application of the same approach to the PIF1-family helicase Rrm3 recovered its established enrichment at a subset of highly transcribed, head-on tRNA genes, validating the method. Together, these findings establish AID-mediated mutational footprinting as a general approach for mapping helicase activity in vivo and reveal an unexpected, widespread association of the RecQ4-family helicase Hrq1 with RNAPIII-transcribed genes.

overall_design: Hrq1 and Rrm3 helicases-generated ssDNA mapping in S. cerevisiae using activation-induced cytidine deaminase.

first: Noof

last: Alsulaiti

first: Daniel

last: Darling

first: Anastasiya

last: Bolgova

first: Bertrand

last: Theulot

first: Spencer

last: Gray

first: Matthew

last: Bochman

first: Duncan

last: Smith


title: Longitudinal single-cell and spatial transcriptomics reveals intratumor heterogeneity, therapeutic response, and comparative value of canine marginal zone lymphoma [scRNAseq data]

city: Minneapolis

first: Grace

last: Walker

state: Minnesota

address: 425 East River Parkway

department: Masonic Cancer Center

institute: University of Minnesota

summary: Diffuse B-cell lymphomas are the most prevalent canine hematologic malignancies, and their clinical presentation resembles that of human B-cell non-Hodgkin lymphomas (NHLs). However, a lack of a clear subtyping framework perpetuates imprecise treatment approaches that fail to address mechanisms of therapy resistance. Here, we employed deep phenotyping via serial sampling and longitudinal transcriptomics to evaluate intratumoral composition and therapy response in a 6-year-old neutered male goldendoodle with stage 5A marginal zone lymphoma (MZL). Following sequential treatment consisting of a single IV dose of oncolytic vesicular stomatitis virotherapy (VSV) and standard CHOP chemotherapy 30 days later, we performed scRNAseq on seven serial lymph node biopsies and spatial sequencing on a resection taken 10 days post-VSV treatment. B cells (>90%) comprised three transcriptionally distinct and temporally stable subpopulations, with specific copy number profiles and robust spatial organization despite disrupted lymph node architecture. Analysis across subpopulations revealed downregulation of the quiescence program including KLF2, suggesting similarity to KLF2-deficient human MZL. While VSV successfully reached target B cells, downstream transcriptional responses were predominantly localized to the T-cell compartment. T cells (≤6%) showed increased proliferation and upregulation of cytotoxicity markers post-VSV administration, enriching for leukocyte-mediated cytotoxicity pathways consistent with an anti-viral immune response. Ultimately, these results provide an in vivo proof-of-concept for the treatment paradigm in canine lymphoma, while emphasizing the need for improved subtyping frameworks and multidimensional treatment strategies targeting intratumoral heterogeneity.

overall_design: Eight longitudinal lymph node biopsies were collected, including a pre-treatment (PreTx) Tru-Cut biopsy (day -4); six fine-needle aspirates (FNAs) (days 3, 7, 10, 28, 49, and 70); and a nodal resection (day 10). All samples except day 70 passed QC and were subjected to single-cell RNA sequencing.

middle: E

first: Marissa

last: Macchietto

first: Kelly

last: Reid

first: Lauren

last: Burt

first: Amber

last: Winter

first: Sara

last: Pracht

first: Michelle

last: Buettner

first: Velia

last: Penza

first: Caitlin

last: Yung

first: Rose

last: Dicovitsky

first: Alana

last: Kuzmik

last: Vallera

first: Kim

last: Demos-Davies

first: Davis

last: Seelig

first: Antonella

last: Borgatti

first: Mike

last: Henson

last: Feiock

first: Jaime

middle: F

last: Modiano

first: Shruthi

last: Naik

first: Aaron

last: Sarver

first: Amy

last: Treeful


title: CpG Hypermethylation and WNT/AP-1 cooperativity Define the Epigenetic Landscape and a Clinical Subgroup of High-Risk Pediatric Adrenocortical Carcinoma

city: Augsburg

first: Victoria

middle: Elisabeth

last: Fincke

address: Stenglinstraße 2

institute: Childens Cancer Center - University hospital Augsburg

summary: Our integrative epigenomic analysis identified four molecularly distinct subgroups based on DNA methylation profiles, each marked by unique transcriptional programs, cellular compositions, and tissue architectures. These molecular subtypes outperformed traditional histopathological classifications in predicting clinical outcomes and addressed the longstanding lack of robust risk markers in pACT.

overall_design: AFFymetrix RNA data for 23 pediatric adrencocortical tumors of the DNA methylation based subgroups.

first: Mauice

last: Loßner

first: Marina

last: Kunstreich

first: Nic

last: Reitsam

first: Irmengard

last: Sax

first: Marlena

last: Mucha

first: Felix

last: Dorn

first: Lorenz

middle: C

last: Helmschrott

first: Maria

last: Hernandez Ramirez

first: Sebastian

last: Dintner

first: Konstantin

last: Okonechnikov

first: Martin

last: Sill

first: Ina

last: Oehme

first: Heike

last: Peterziel

first: Enrique

last: Blanco-Carmona

first: Eva

last: Sipos

first: Stefan

last: Wudy

first: Christoph

last: Slavetinsky

first: Jörg

last: Fuchs

first: Bruno

last: Märkl

last: Jüttner

first: Christian

last: Vokuhl

first: Michael

last: Frühwald

first: Antje

last: Redlich

last: Pfister

first: Matthias

last: Schlesner

first: Rainer

last: Claus

first: Michaela

last: Kuhlen

first: Pascal

last: Johann


title: Human myeloid ontogeny determines inflammatory identity and neurodegenerative potential

city: Austin

first: Anna

last: Warden

address: 2500 Speedway

institute: University of Texas at Austin

type: Methylation profiling by high throughput sequencing

summary: Microglia, the resident macrophages of brain, arise from yolk sac hematopoietic progenitor cells (HPCs) that migrate into the brain during early embryonic development and differentiate in response to microenvironment-specific signals. The resulting spatial and stage-specific programs of gene expression enable microglia to function as key modulators of diverse homeostatic processes that include synaptic pruning, myelination, and neurogenesis throughout the lifespan. Dysregulation of these core microglia functions has been linked to numerous neurodevelopmental and neurodegenerative diseases. Although the CNS is normally a closed myeloid niche, recent evidence suggests that aging involves loss of yolk sac–derived microglia and emergence of peripheral myeloid-derived populations, highlighting the need to define whether human hematopoietic stem cell (HSC)-derived myeloid cells can acquire microglia-like identities and sustain brain homeostasis. To address this, we compared yolk sac–lineage human primary microglia and iPSC-derived hematopoietic progenitor cell (HPC)-derived myeloid cells with peripheral-lineage human HSC- and monocyte-derived myeloid cells in a humanized murine xenotransplantation model. Peripheral-lineage cells efficiently populated the brain and acquired microglia-like features but remained transcriptionally and epigenetically distinct from HPC-derived brain myeloid cells. Compared with HPC-derived cells, peripheral myeloid cells showed heightened interferon signaling, phagocytic programs, and antigen-presentation signatures. Integrative epigenomic analyses identified ontogeny-dependent transcription factor networks underlying these divergent brain myeloid states and correlated with aging related infiltrative myeloid populations. Functionally, global replacement with HSC-derived myeloid cells was associated with astrogliosis, myelin fragmentation, and synaptic loss, indicating neurodegenerative consequences. Together with the accompanying study by Davtyan and colleagues, these findings demonstrate that human peripheral progenitors can partially adopt microglia-like phenotypes but retain pro-inflammatory programs that promote neurodegeneration after global myeloid replacement. This work provides insight into age-associated myeloid replacement in the human brain and informs the risks and therapeutic potential of microglial replacement and bone marrow transplant–based strategies for CNS disorders.

overall_design: snm3C-seq of xenotransplanted human iPS-derived microglia (iMG) or monocytes into the mouse brain

first: Nathan

middle: R

last: Zemke

first: Jing

last: Wang

first: Nicole

middle: G

last: Coufal


title: VEGFR1-Blocking Antibody Improves Endothelial Structure, Kidney Function, and GFR in Diabetic Mice

city: St. Louis

first: Haojia

last: Wu

address: 4523 Clayton Ave, MSB Rm 820

institute: Washington University in St Louis

summary: Diabetic kidney disease remains the major cause of kidney failure. VEGFA neutralizing antibodies also cause kidney disease in normal people. The present studies explored whether endogenous VEGFA deficiency might contribute to DKD.

overall_design: We employed single nucleus RNA-sequencing (snRNA-seq) to a model of murine DKD treated with VEGFA neutralizing antibodies (VEFB1) and the isotype control (Mscb20). We profiled a total of 20 mice from 4 groups, with N=5 mice per group.

first: Jingjun

last: Li

first: Matthew

last: Breyer