title: Mitochondrial Protein Import Stress Causes Lysosomal Damage and Tissue Atrophy

city: Syracuse

first: Nicholas

last: Brennan

state: New York

address: 766 Irving Ave

department: Biochemistry and Molecular Biology

institute: SUNY Upstate Medical University

summary: Mitochondrial abnormalities are commonly associated with aging-related degenerative disease and the atrophy of tissues including muscle and brain. Whether bioenergetic defect is the sole pathogenic factor has been long questioned. Lysosomal damage is another hallmark of degenerative disease. However, it is unknown whether these two pathogenic pathways affect tissue homeostasis independently, convergently or epistatically. Here, we show that mitochondrial protein import stress, which can be induced by many forms of mitochondrial injuries, causes structural and functional damage to the yeast vacuole and its mouse counterpart, the lysosome. This effect is independent of bioenergetic defects and the production of reactive oxygen species. We found that unimported mitochondrial proteins are targeted to the vacuole for degradation in yeast. Overloading by these proteins causes V-ATPase disassembly, and vacuolar deacidification, fragmentation and membrane permeabilization. In a mouse model of mitochondrial protein import stress and muscle atrophy induced by overloading of the mitochondrial protein ANT1, genes involved in amino acid uptake/biosynthesis, one-carbon metabolism, nucleotide biosynthesis, lysosomal biogenesis and iron homeostasis are activated. These signatures are recapitulated in yeast mutants of severe vacuolar damage. Supporting lysosomal dysfunction, the Ant1-transgenic muscles accumulate glycogens, lipofuscins and poorly processed multiple vesicle bodies. Multiple lysosomal repair and lysophagic pathways are activated. Luminal proteolytic enzymes including cathepsins are released into the cytosol, which likely contributes to imbalanced cellular proteostasis, reduced myofiber size and progressive muscle atrophy. In summary, we show an evolutionarily conserved pathway wherein mitochondrial defect can epistatically cause proteostatic damage to the lysosome thereby leading to tissue atrophy. This finding could help the better understanding of how the mitochondrial and lysosomal pathways of pathogenesis interact to cause degenerative disease.

sample_organism:
Saccharomyces cerevisiae
Mus musculus

platform_organism:
Saccharomyces cerevisiae
Mus musculus

overall_design:
Quadricep skeletal muscle mRNA profiles of 2-month-old wild type (WT) and Ant1-transgenic overexpressing female mice were generated by stranded paired-end RNA sequencing, in quadruplicate, using Illumina NextSeq500.
Yeast cells were grown in YP+2% galactose+ 2% raffinose to mid-log phase of OD600 around 1.0. mRNA profiles of wildtype, vma13, GAL10-AAC2 and vma13_GAL10-AAC2 were generated by stranded paired-end RNA sequencing, in triplicate, using Illumina NextSeq2000.

first: Xiaowen

last: Wang

first: Arnav

last: Rana

first: Sanaea

last: Bhagwagar

first: Jason

last: Horton

first: Patricia

last: Kane

first: Xin Jie

last: Chen


title: Amoeboid-Mesenchymal Transition and the Proteolytic Control of Cancer Invasion Plasticity [scRNA-seq]

status: Public on Feb 01 2026

city: Ann Arbor

first: Stephen

middle: J

last: Weiss

state: MI

address: 210 Washtenaw Ave

country: USA

institute: University of Michigan

type: Expression profiling by high throughput sequencing

summary: Invasion plasticity allows malignant cells to toggle between collective, mesenchymal and amoeboid phenotypes while traversing extracellular matrix (ECM) barriers. Current dogma holds that collective and mesenchymal invasion programs trigger the mobilization of proteinases that digest structural barriers dominated by type I collagen, while amoeboid activity allows cancer cells to marshal mechanical forces to traverse tissues independently of ECM proteolysis. Here, we use cancer spheroid-3-dimensional matrix models, single-cell RNA sequencing, and human tissue explants to identify the mechanisms controlling mesenchymal versus amoeboid invasion. Unexpectedly, collective/mesenchymal- and amoeboid-type invasion programs – though distinct – are each characterized by active tunneling through ECM barriers, with expression of matrix-degradative metalloproteinases. CRISPR/Cas9-mediated targeting of a single membrane-anchored collagenase, MMP14/MT1-MMP, ablates tissue-invasive activity while co-regulating cancer cell transcriptional programs. Though changes in matrix architecture, nuclear rigidity, and metabolic stress as well as the presence of cancer-associated fibroblasts are proposed to support amoeboid activity, none of these changes restore invasive activity of MMP14-targeted cancer cells. While a requirement for MMP14 is bypassed in low-density collagen hydrogels, invasion by the proteinase-deleted cells is associated with nuclear envelope and DNA damage, highlighting a proteolytic requirement for maintaining nuclear integrity. Nevertheless, when cancer cells confront explants of live human breast tissue, MMP14 is again required to support invasive activity. Corroborating these results, spatial transcriptomic and immunohistological analyses of human breast cancers identified MMP14 expression in tissue-infiltrating carcinoma cells that were further juxtaposed with proteolyzed type I collagen fragments, underlining the pathophysiologic importance of this proteinase in directing invasive activity in vivo.

overall_design: Single Cell RNA-sequencing of HT1080 spheroids following 72 hour invasion/incubation in 3D collagen hydrogels in the presence or absence of a 4B4 Beta1-integrin inhibiting antibody.

first: Adam

middle: W

last: Olson


title: Amoeboid-Mesenchymal Transition and the Proteolytic Control of Cancer Invasion Plasticity [RNA-Seq]

overall_design: Bulk RNA-sequencing of control and MMP14-targeted MDA-MB-231 spheroids isolated directly from hanging droplets, following 24-hour incubation in collagen, or following 48-hour incubation in collagen.


title: Mechanistic Modelling of Recessive Disease through Allelic Integration of Variant Effects

city: Edinburgh

first: Grzegorz

last: Kudla

address: Crewe Road

department: MRC HGU

country: United Kingdom

institute: University of Edinburgh

summary: Interpreting variants in recessive diseases is difficult because clinical severity depends on the combined function of both alleles. Deep mutational scanning (DMS) experiments can provide functional measurements at scale, but their scores often relate nonlinearly to true biochemical activity. We developed a general method to infer enzymatic activities for thousands of variants by running two fitness assays at different expression levels and modelling the nonlinear activity–fitness relationship. These inferred activities allow computation of a biallelic pathogenicity score that captures the joint effect of two alleles. We applied this to adenylosuccinate lyase (ADSL), quantifying the effects of >8,000 coding variants in a yeast-based assay. The inferred activities separated pathogenic from benign alleles, and the biallelic score correlated strongly with biochemical measurements from patient-derived cells, outperforming existing predictors. This framework provides a broadly applicable strategy for mechanistic interpretation of variants in recessive enzymes.

sample_organism:
Saccharomyces cerevisiae
synthetic construct

overall_design: A human ADSL variant library was generated using plasmid-based saturation mutagenesis and subsequently barcoded; each variant was associated with one or multiple unique DNA barcodes. Barcode–variant associations were determined by PacBio Sequel II sequencing. The barcoded library was transformed into the yTHC-ADE13 yeast strain, where doxycycline treatment can control expression of the endogenous ADE13 gene and enables measurement of functional complementation by human ADSL. Human ADSL variants were expressed from two distinct promoters to create low- and high-expression conditions. The pooled library was grown for five days under these expression regimes, both with and without doxycycline treatment, with samples collected every 12 hours. Barcode abundances (counts) from the growth assay were quantified on an Illumina NextSeq 2000 platform and used to calculate fitness scores from multiple barcodes per variant. This submission includes two types of sequencing samples: (1) PacBio CCS library-reference samples used to map each barcode to its ADSL variant, and (2) Illumina time-series samples collected during the yeast growth assay. Functional effects of ADSL variants were measured under four conditions reflecting the major variables under investigation: low ADSL expression with ADE13 repressed (dox-treated), low expression with ADE13 active (dox-untreated), high expression with ADE13 repressed (dox-treated), and high expression with ADE13 active (dox-untreated).

first: Hasan

last: Çubuk

first: Marcin

last: Plech

first: Vahid

last: Aslanzadeh

first: Marie

last: Zikanova

first: Vaclava

last: Skopova

first: Stanislav

last: Kmoch

first: Yuxin

last: Shen

first: Joseph

middle: A

last: Marsh


title: A Longitudinal, Multi-omic Atlas Reveals the Emergence of a Spatially Organized Immunosuppressive Ecosystem in Resistant Melanoma [nCounter RNA]

status: Public on Jan 31 2026

city: Hong Kong

first: hongbin

last: lan

address: 34 Hospital Road, Sai Ying Pun, Hong Kong

country: Hong Kong

institute: The University of Hong Kong

summary: This study employed the NanoString nCounter platform to perform targeted, quantitative molecular profiling of longitudinally collected FFPE tumor samples to elucidate molecular mechanisms underlying resistance to anti–PD-1 therapy.  nCounter® Vantage 3D™ Single Nucleotide Variant assay was integrated using a solid tumor panel to screen 104 driver variants across 25 genes frequently mutated in solid tumors. We quantified the expression of 770 cancer-related mRNA transcripts to identify persistently activated oncogenic pathway signatures in non-responders, which were further complemented by quantitative profiling of 27 total and phosphoproteins using antibody–oligonucleotide conjugates for functional validation of pathway activity. To characterize the tumor microenvironment spatially, GeoMx Digital Spatial Profiler analysis was utilized to assess the distribution of 38 proteins across distinct histological regions, revealing an immunosuppressive spatial architecture associated with treatment resistance.

overall_design: We applied the nCounter® Vantage 3D™ RNA:Protein Solid Tumor Assay to a longitudinal cohort of 34 metastatic melanoma tumor samples obtained from 7 patients. To ensure data robustness, technical replicates were performed for expression profiling, yielding a total of 46 analyzable data points, including two tumor samples analyzed in triplicate, eight tumor samples analyzed in duplicate, and the remaining samples analyzed as single measurements.

first: Gao

last: Zhang


title: A Longitudinal, Multi-omic Atlas Reveals the Emergence of a Spatially Organized Immunosuppressive Ecosystem in Resistant Melanoma

summary: The goal of this study is to explore the mechanisms of resistance in melanoma under various immunotherapy treatments, particularly focusing on anti-PD-1 therapy,  through the analysis of RPPA data. The study includes 38 tumor samples from two melanoma patients, with samples collected at pre-treatment, on-treatment, and post-treatment time points.  These two patients were classified as non-responders (NRs). The RPPA data covers more than 300 antibodies targeting key signaling pathways, including hormone receptor signaling, HER family signaling, cell cycle/proliferation pathways, immune checkpoint regulation, DNA repair deficiency, AKT/mTOR/PI3K pathways, apoptosis/autophagy, IGF1R signaling, and RTK pathways. These data will serve as a valuable resource for validating resistance markers and understanding the signaling mechanisms driving tumor progression despite immune checkpoint blockade therapies.

overall_design: This study analyzes RPPA data from 38 tumor samples of two melanoma patients, collected at pre-treatment, on-treatment, and post-treatment time points following anti-PD-1 therapy.


title: Extracellular Matrix Origin Directs Morphogenesis and Gene Regulation in Bioengineered Human Skin

city: Napoli

first: Paolo

middle: Antonio

last: Netti

address: Istituto Italiano di Tecnologia (IIT), Largo Barsanti e Matteucci 53

department: IIT - Center for Advanced Biomaterials for Healthcare

country: Italy

institute: IIT

summary: The cellular microenvironment plays a pivotal role in directing tissue development, repair, and homeostasis through a complex interplay of biochemical and mechanical cues. The extracellular matrix (ECM) serves as a key instructive component, guiding transcriptional programs that determine cell fate, function, and identity. In this study, we investigated the impact of microenvironmental context on the biofabrication of human skin equivalents, comparing constructs based on endogenous versus exogenous ECMs. Our RNA sequencing analyses reveal that ECM origin profoundly influences transcriptional trajectories, highlighting the importance of a native-like microenvironment in supporting appropriate gene expression profiles and morphogenetic processes. Notably, skin equivalents featuring endogenously produced ECMs exhibit physiologically relevant architecture, including a well-organized dermo-epidermal junction (DEJ), whereas constructs based on exogenous matrices—such as animal-derived collagen—display abnormal epithelial expansion and fail to replicate key structural features. These findings underscore the necessity of recapitulating the native ECM to achieve functional tissue constructs in vitro and raise critical considerations regarding scaffold choice in regenerative medicine and tissue engineering applications. We also discuss the implications of these findings for the development of organ-on-chip systems, where the accurate recapitulation of native tissue architecture and function is essential for modeling physiological and pathological conditions in human-relevant experimental assays.

overall_design: Morphological characterization (collagen and elastin quantification) and RNA-Seq profiling (differential gene expression analysis and enrichment analysis) of endogenous and exogenous human skin equivalents to highlight the role of the ECM in guiding the correct production of relevant 3D skin model.

first: Francesco

last: Galardo

first: Giorgia

last: Imparato

first: Costatino

last: Casale

last: Urciuolo

first: Luca

last: Mannino

first: Antonio

last: Federico

first: Dario

last: Greco


title: Single Cell RNA Sequencing Unveils Distinct Cellular Dynamics in Celiac Disease Duodenal Biopsies

city: NEW HAVEN

first: FENGRUI

last: ZHANG

state: Connecticut

address: 1 Gilbert street, TAC S570

department: Immunobiology

institute: Yale University

summary: Celiac disease (CeD) is the most common autoimmune disorder in the U.S., affecting at least 1% of the population. The ingestion of gluten-containing proteins triggers an adaptive immune response, causing intestinal damage and leading to both gastrointestinal and systemic symptoms. Despite a strong genetic predisposition, the mechanistic understanding of CeD remains limited. The lack of approved therapy, other than dietary avoidance of gluten which is difficult and often unsuccessful, underscores the need to identify new mechanisms that can provide insights for developing therapeutics. To gain an unbiased view of the transcriptional landscape of the duodenum, we compared duodenal biopsies showing active CeD to normal controls using single-cell RNA sequencing. We analyzed fresh research biopsies from 4 patients with active CeD, confirmed by diagnostic biopsies from the same endoscopy, as well as 2 healthy control biopsies without specific pathological changes. Our analysis captured every major intestinal mucosal cell type including all subsets of immune cells, epithelial cells and stromal cells. Among these, enterocytes and activated T cells exhibited the most significant differences between CeD biopsies and controls. In CeD biopsies, CD8+TCR αβ and TCR γδ T cells were the primary producers of IFNG, a feature that was largely absent in the control biopsies. Moreover, enterocytes that express villous defining marker APOA4+ showed elevated levels of IFNGR1, suggesting an increased responsiveness to IFNγ produced by CeD T cells. We assessed effects of IFNγ on potential target molecules expressed on enterocytes that could activate and trigger killing by CTL. Bioinformatic ligand receptor analyses showed frequent interactions between intraepithelial CTLs and enterocyte HLA-E or HLA-B, suggesting that IFNγ production by the CTLs likely promotes further CTL recruitment and antigen-dependent killing of the villous epithelium.

overall_design: Duodenal mucosal biopsies for research were obtained with informed consent from 4 patients with CeD with mild villous blunting (Marsh grade 3A) or severe villous blunting (Marsh grade 3C) and 2 patients with normal mucosa undergoing diagnostic endoscopy. All six samples were deidentified prior to transfer to the laboratory under a protocol approved by the Yale Institutional Review Board. Research biopsies were processed for droplet-based single-cell RNA-seq (scRNA-seq) using 10x Chromium GEM technology.

first: Kriti

last: Agrawal

first: Fengrui

first: Esen

last: Sefik


title: A Longitudinal, Multi-omic Atlas Reveals the Emergence of a Spatially Organized Immunosuppressive Ecosystem in Resistant Melanoma [nCounter protein]

overall_design: We applied the nCounter® Vantage 3D™ RNA:Protein Solid Tumor Assay to a longitudinal cohort of 34 metastatic melanoma tumor samples from 7 patients. To ensure robustness of the protein expression data, technical replicates were included, yielding a total of 46 protein measurements for analysis, comprising two tumor samples analyzed in triplicate, eleven analyzed in duplicate, and the remaining samples analyzed as single measurements.


title: A Longitudinal, Multi-omic Atlas Reveals the Emergence of a Spatially Organized Immunosuppressive Ecosystem in Resistant Melanoma [SNV]

overall_design: To detect somatic mutations in metastatic melanomas, we performed nCounter® Vantage 3D™ Single Nucleotide Variant assay in 10 longitudinal tumor specimens from two patients (MP13_674 and G001). The solid tumor panel contains 104 driver variants from 25 genes that are frequently mutated in solid tumors, including Single Nucleotide Variant (SNV), Multi-Nucleotide Variant (MNV), and Insertions or Deletions (InDels).


title: Targeting of a novel interplay between MET Tyrosine Kinase and NRF2 enhances sensitivity to Paclitaxel in Triple Negative Breast Cancer

city: Rome

first: Daniela

last: Barilà

address: Via Cracovia, 90

department: Department of Biology

institute: Università Tor Vergata

summary:
Triple-negative breast cancer (TNBC) is a very aggressive and heterogeneous cancer. The lack of effective targeted therapies and frequency of relapse point to the urgent need for identifying molecular vulnerabilities to overcome resistance to chemotherapy.
Nuclear Factor Erythroid 2-related factor 2 (NRF2) is a transcription factor that plays a central role in response to oxidative stress. Its hyperactivation contributes to metabolic rewiring and resistance to therapy in several tumors including TNBC. Unfortunately, efficient pharmacological approaches that block NRF2 functions are still missing. Protein Tyrosine kinases (PTKs), often overactivated in cancer and influencing several signalling pathways, are promising candidates to explore for their potential impact on NRF2.
The link between Receptor Tyrosine Kinases and NRF2 expression and its impact on the survival probability of TNBC and non-TNBC patients were investigated by bioinformatic analyses using TCGA and GEO databases. MET-NRF2 connection was further confirmed by immunoblotting, immunofluorescence, qRT-PCR and RNAseq experiments through the combinatorial use of murine and human TNBC cellular models. The efficacy of combination treatments with Paclitaxel and specific inhibitors of MET-NRF2 signalling was assessed by viability assays and flow-cytometry analyses on TNBC cellular models as well as on TNBC patient-derived organoids.
Here, we identify a novel interplay between MET and SRC kinases with NRF2 expression and activity and demonstrate that its targeting enhances the sensitivity to the standard Paclitaxel treatment of TNBC cells and patient-derived organoids.
Our study shows that RTKs regulate NRF2 expression and activation in TNBC providing a proof of principle for the ability of Tyrosine Kinase Inhibitors (TKIs) to impinge on NRF2 signalling. Our findings also uncover the value of the MET-SRC-NRF2 axis as exploitable vulnerability in NRF2-hyperactivated TNBC, paving the way for the repositioning of TKIs as modulators of NRF2 signalling.

overall_design: Gene expression profiling through RNA-seq for each biological replicate of MGT-13 cell line with and without PHA-665752 and with and without siNRF2

first: Irene

last: Taddei

first: Claudia

last: Cirotti

first: Fabienne

last: Lamballe

first: Oliver

last: Castellanet

first: Flavio

last: Maina

first: Fabrizio

last: Fierro

first: Francesca

last: De Nicola

first: Maurizio

last: Fanciulli

first: Eleonora

last: Cesari

first: Vanessa

last: Medici

first: Claudio

last: Sette


title: Intraspecific variation in the duration of epigenetic inheritance in wild isolates of C. elegans

city: Paris

first: Germano

last: Cecere

address: Institut Pasteur, 28 Rue Du Docteur Roux, Batiment Monod, 5eme Etage

department: Development and stem cell biology

country: France

institute: Institut Pasteur

summary: Epigenetic inheritance is generally less stable across generations than DNA sequence-based heredity. One common form of epigenetic inheritance, found in plants, fungi, and animals, is the transgenerational memory of gene silencing mediated by small RNAs. These small RNAs can be amplified through RNA-dependent RNA polymerases, thus maintaining the silenced state across multiple generations. Such molecular mechanisms raise questions regarding their natural variation and evolutionary impact. We here ask whether the presence and duration of epigenetic inheritance vary within a species. We use the ability of the nematode Caenorhabditis elegans to silence genes for multiple generations after an initial RNA interference trigger. We find that the duration of silencing memory expressed in number of generations varies across C. elegans wild strains as a quantitative trait. Strikingly, several wild strains show no memory, while some display a longer memory than the reference strain. Natural DNA sequence polymorphisms, such as in the set-24 gene, affect the duration of small RNA inheritance. We further show that the silencing memory duration in wild strains increases with temperature and that memory is retained upon early starvation arrest and passage through dauer diapause. Altogether, these results demonstrate intraspecific diversity in the regulation of small RNA-based heredity, a prerequisite for selection acting on genetic variants affecting epigenetic inheritance duration.

overall_design: small RNA sequencing profiles of natural C. elegans isolate harboring a germline nuclear GFP reporter and subjected to RNAi silencing targeting the GFP reporter or control RNAi.

first: François

last: Frejacques

first: Marie

last: Saglio

first: Mohammed

last: Aljohani

first: Christian

last: Froekjaer-Jensen

first: Almira

last: Chervova

first: Loan

last: Bourdon

first: Lise

last: Frézal

first: Marie-Anne

last: Félix


title: Müller glia-microglia cross talk reprograms the Müller glia transcriptome for cell division-related processes during retina regeneration [scRNA-Seq]

first: Daniel

last: Goldman

address: 109 Zina Pitcher Place

summary: In the zebrafish retina, Müller glia (MG) respond to retinal injury by dividing and producing a multipotent progenitor for retinal repair.  This cell division is regulated by microglia; however, the underlying mechanism remains unknown.  Here we report that MG-derived Il34 attracts microglia to sites of retinal injury where they stimulate MG proliferation via the release of cytokines, like M17, Spp1, Tnfa and Tnfb.  Remarkably, RNaseq analysis of MG’s regeneration-associated transcriptome with and without microglia depletion suggests microglia stimulate MG proliferation by preferentially enhancing the expression of regeneration-associated genes involved in cell division-related processes.  In contrast, genetic ablation of essentially all microglia from early development appears to reprogram MG so they exhibit enhanced injury-dependent proliferation, but their survival is compromised.  Our studies illustrate the profound effects MG-microglia cross talk can have on MG transcriptional programs related to cell division processes.

overall_design: Wild type and csf1ra-Mutant;csf1rb-Mutant double mutant zebrafish were compared in this study.  Retinas were injured by intravitreal injection of NMDA. At 2 days post injury, retinas were isolated and dissociated into single cells for scRNAseq using the 10X Genomics Chromium platform using Chromium Single Cell 3' reagent kit.

first: Soumitra

last: Mitra

first: Sulochana

last: Devi

first: Mi-Sun

last: Lee

first: Aresh

last: Sahu

first: Jon

last: Jui


title: Cellular milieu of the neural retina informs complement immune regulation [Hs]

city: Philadelphia

first: Dwight

middle: Edward

last: Stambolian

state: PA

address: 422 Curie Blvd.

department: Opthalmalogy

institute: University of Pennsylvania

summary:
Purpose: We present a comprehensive map of the human retinal complement expression at a single-cell resolution, spanning 11 cell types.
Methods: Retinal mRNA profiles from were generated by scRNA sequencing (10x Genomics) from a healthy human donor immediately within 4 hours of death. The data was normalized using Seurat.
Results: Using an optimized data analysis workflow, we found novel patterns of complement expression in the retina
Conclusions: Our landmark atlas provides crucial mechanistic insights in complement immunology

overall_design:
Retinal cell mRNA data from a healthy human donor, separated into Macula (mac) and Peripheral (per) retina.
11 cell types:  Amacrine Cells, Cone BCs, Cone Photoreceptors, Endothelial Cells, Horizontal Cells, Microglia, Muller Glia, Pericytes, Retinal Ganglion Cells, Rod BCs, Rod Photoreceptors.

first: Nicholas

last: Dana


title: Transcriptome profiles of male wild-type and IRF8 knockout microglia

city: Bethesda

first: Keita

last: Saeki

state: Maryland

address: 6 Center Drive

institute: NIH/NICHD

summary: The lineage-determining transcription factor IRF8's function in microglia, particularly concerning gender differences, is yet unclear. Our study aims to identify the gender biases in gene expression in WT and IRF8 knockout microglia. This mRNA transcrptome data provides a new understanding of the gender-associated transcriptional programs in microglia.

overall_design: Transcriptome profiles of male WT and IRF8KO microglia were analyzed.

first: Keiko

last: Ozato


title: Integrative analysis of a novel small-cell-positive AVPC model [LYM1]

first: Adam

middle: G.

last: Sowalsky

state: MD

address: 37 Convent Drive Building 37 Room 1062B

department: Genitourinary Malignancies Branch

institute: National Cancer Institute

summary: Prostate cancer translational research has been hampered by the lack of comprehensive and tractable models that represent the genomic landscape of clinical disease. Metastatic prostate cancer patient-derived models recapitulate the genetic and phenotypic diversity of the disease.We sought to establish a representative, preclinical platform of patient-derived organoids that is experimentally facile for high throughput and mechanistic analysis.

overall_design:
Short-read RNA-seq and long-read DNA-seq of the NCI-LYM-1 model.

***************************************************************
Raw files for human/patient samples are being made available in dbGaP (https://www.ncbi.nlm.nih.gov/gap/) (accession ID phs001587) for controlled access to the personally identifiable sequence data.
***************************************************************

middle: G


title: Establishment and characterization of prostate cancer organoids II

overall_design:
Short-read RNA-seq of the PC35 and PC60 patient-derived organoid models.

***************************************************************
Raw files for human/patient samples are being made available in dbGaP (https://www.ncbi.nlm.nih.gov/gap/) (accession ID phs001587) for controlled access to the personally identifiable sequence data.
***************************************************************

first: Kathleen

last: Kelly


title: Single cell profiling reveals three endothelial to hematopoietic transitions with divergent isoform expression landscapes

city: Manchester

first: Georges

last: Lacaud

state: England

address: Wilmslow Raod

department: Stem Cell Biology

institute: Cancer Research UK Manchester Institute

summary: Hemogenic endothelium (HE) is recognized as the origin of all definitive blood cells including hematopoietic stem cells (HSC). However, the mechanisms governing the hematopoietic progenitor versus HSC fate choice within the HE remains unknown. To explore this, we combined differentiation assays with full-length single-cell transcriptome data for extra-embryonic yolk sac (YS) and intra-embryonic aorta–gonad–mesonephros (AGM) region HE populations. We identified and localized three differentiation trajectories, each containing a distinct HE subset and potential: erythro-myeloid progenitor-primed HE in the YS plexus, lympho-myeloid progenitor-primed HE in large YS arteries, and HSC-primed HE in the AGM. Chromatin modifiers and spliceosome components were enriched AGM HE. Nanopore long-read sequencing identified AGM specific, functionally unique, splice variants of stemness-associated factors Runx1, Mecom, and Dnmt3b. Our data indicate that isoform expression changes are associated with HSC generation and provide a unique resource for studying cell fate decisions in HE.

overall_design: Long Read single cell RNA-seq of cells undergoing hemogenic to endothelial transition in AGM at E9.5 and E10.5 and Yolk Sac (YS) at E9, E9.5, E10.5.  To study the HE populations present at different anatomical locations and time points during the mouse development, we used transgenic reporter mouse lines GFI1-GFP and RUNX1B-RFP and performed Oxford Nanopore Long Read Sequencing (single cell RNA seq) on FACS isolated E9.5 and E10.5 AGM HE cells (RUNX1+, KIT-,CDH5+, GFI1+/-, CD41-, CD45-), and E9, E9.5, E10.5 YS HE cells (RUNX1+, KIT+, GFI1+/-, CD31+, CD41-, CD45-). Total 27 cells were used. We selected 9 cells from the middle of AGM_3 and AGM_4 cluster for AGM HE (HE-HSC),  9 cells from the middle of YS_m1 and YS_m2 as YSm HE (HE-LMP) and 9 cells from the middle of YS_b2 and YS_b3 as YSb HE (HE-EMP).

first: Wen

middle: H

last: Neo

first: Muhammad

last: Zaki Hidayatullah Fadlullah

first: Harshangda

last: Bhatnagar

first: Cristiana

last: Barone

first: Giulia

last: Quattrini

first: Filipa

last: Timóteo-Ferreira

first: Joana

last: Carrelha

first: Gianluca

last: Sala

first: John

last: Weightman

first: Wolfgang

last: Breitwieser

first: Natalia

last: Moncaut

first: Roshana

last: Thambyrajah

first: Sten

middle: E

last: Jacobsen

first: Mudassar

last: Iqbal

first: Syed

middle: M

last: Baker

first: Emanuele

last: Azzoni

first: Michael

last: Lie-A-Ling


title: Streptococcus parasanguinis Transcriptomics Data with and without Exogenous Nitrite

city: Birmingham

first: Sara

middle: Elizabeth

last: Edmonds

state: AL

address: 1720 2nd Ave South, BBRB 744

department: Microbiology

institute: University of Alabama at Birmingham

summary: Oral commensal streptococci play a large role in mediating microbial homeostasis. Our published findings have demonstrated that hydrogen peroxide (H2O2) produced by oral commensal streptococci can react with salivary nitrite (NO2) and generate peroxynitrite (ONOO-), a potent antimicrobial. We have shown that the combinatorial antimicrobial effects of NO2 and H2O2 produced from the commensal Streptococcus parasanguinis, inhibit the colonization and pathogenesis of oral pathogens to promote homeostasis. Remarkably, S. parasanguinis is highly resistant to the NO2 and ONOO-. However, it remains unclear how S. parasanguinis copes in the presence of nitrosative stress. The goal of this study was to identify mechanisms used by S. parasanguinis to resist NO2-mediated nitrosative stress using a transcriptomics approach. Transcriptomic analysis showed that the competence response regulator, comE, is upregulated in the presence of NO2. Loss of comE resulted in a decrease in biofilm development, H2O2 production, increased acid tolerance and sensitivity to ONOO- compared to wild-type S. parasanguinis. Our data show that ComE is critical for key aspects of S. parasanguinis physiology and potentially impacts this commensal's ability to colonize and modulate homeostasis in the oral cavity.

overall_design: Wild-type Streptococcus parasanguinis were grown in the presence of 2 mM of Nitrite in Todd-Hewitt Broth to late-exponential phase and RNA was harvested for RNA-sequencing analysis.

first: Hernan

last: Grenett

first: Jessica

last: Scoffield


title: A Longitudinal, Multi-omic Atlas Reveals the Emergence of a Spatially Organized Immunosuppressive Ecosystem in Resistant Melanoma [DSP protein]

first: hongbin

last: lan

overall_design: GeoMx Digital Spatial Profiling (DSP) was performed on longitudinal FFPE tumor specimens collected at pre-treatment, on-treatment, and post-treatment stages of anti-PD-1 therapy. A total of 258 ROIs were selected from 7 patients based on morphological markers (S100B, CD45, and DNA). Each ROI was segmented into tumor (S100B+/Pmel17+) and immune (CD45+) compartments (AOIs) for proteomic quantification.

first: Gao

last: Zhang


title: Asymmetric division in a two-cell-like state rejuvenates embryonic stem cells

city: Guangzhou

first: Qingyang

last: Sun

address: No. 9 XingDaoHuanBei Road, Guangzhou Internation Bio Island

country: China

institute: Guangzhou National Laboratory

summary: An intriguing question in biology is whether all cells age. Embryonic stem cells (ESCs)stand out as rare normal cells capable of indefinite in vitro passage. However, it remains unclear how ESC lineage immortality is achieved and whether individual ESCs are immortal. Using long term live-cell imaging to follow fates of single ESCs, we show here that lineage renewal of ESCs can be attributed to a sporadic state characterized by the expression of markers found in two-cell embryos. During this state, cells undergo asymmetric divisions, giving rise to one dying branch, and one that reverts to the pluripotent state. Importantly, the latter lineage exhibits signs of rejuvenation, including reduced DNA damage and enhanced chimeric efficiency. These findings underscore the crucial role of asymmetric cell division in maintaining the long-term health of the ESC lineage against mounting damage within individual cells.

overall_design: Bulk RNA-seq profiling of mESC labeled with MERVL::DsRed2+/-, and repeat three times each group.


title: Transcriptional Cancer Immune pathways of localized early prostate cancer

city: Ribeirão Preto

first: William

last: Lautert Dutra

state: SP

address: Av. Bandeirantes, 3900

department: Genetics Department

country: Brazil

institute: Universidade de São Paulo

summary: The management of intermediate-risk early prostate cancer (PCa) is challenging due to the difficulty in distinguishing indolent from aggressive tumors. This study explores the impact of genomic alterations on the tumor and its microenvironment (TME). We performed multi-omic profiling in a cohort of 53 localized PCa using targeted sequencing, transcriptional and proteomic spatial profiling. Somatic mutations and copy number alterations in RB1 (21%), PTEN (18%), and TP53 (9%) were identified. Kaplan-Meier analysis revealed that alterations in the RB and Cell Cycle pathways, particularly aberrations in PTEN, TP53, or RB1, were associated with shorter biochemical recurrence-free survival (p < 0.001). Spatial proteomic analysis demonstrated a complex immune landscape in patients with mutations. The tumor compartment demonstrated higher expression of immune checkpoint markers, T-cell activation proteins, and proliferation markers; and a TME that is enriched with CD8+ T cells and antigen-presenting cells, but also with immunosuppressive M2 macrophages, suggesting adaptive immune resistance. Our analysis demonstrates that genomic alterations in PTEN, TP53, or RB1 are not only prognostic for poor outcomes but also actively shape a unique, immunologically active yet suppressed TME.

overall_design: We performed multi-omic profiling in a cohort of 53 localized PCa using targeted sequencing, transcriptional and proteomic spatial profiling. The associated design involved comparison between tumors with BRC and without BRC.  used two commercial expression profiling panels (Nanostring PanCancer and Immune Profile) to examine a primary PCa cohort (n=51) and  identified gene signatures and downstream pathways associated with biochemical recurrence and  increased clinical risk.

last: Lautert-Dutra

first: Camila

last: Melo

first: Luiz

middle: P

last: Chaves

first: Fracisco

middle: C

last: Souza

first: V

last: Talebian

first: Cheryl

last: Crozier

first: M

last: Quintayo

first: L

last: Liao

first: D

last: Dion

first: Fabiano

last: Saggioro

first: Felipe

middle: S

last: Avante

first: Rodolfo

last: dos Reis

first: Jeremy

last: Squire

first: Jane

last: Bayani


title: Multi-omic sequencing reveals distinctive gene expression and epigenetic alterations associated with primary sclerosing cholangitis development in treatment-naïve paediatric ulcerative colitis

city: Dublin

first: Alejandra

last: Rodriguez-Sosa

address: 123 St Stephens Green

country: Ireland

institute: Royal College of Surgeons in Ireland

type: Methylation profiling by high throughput sequencing

summary: Background: Primary sclerosing cholangitis (PSC) is a progressive cholestatic disease with up to 80% of patients also suffering from ulcerative colitis (PSC-UC). The difficulty in the diagnosis along with the increased risk for developing cancer represent a clinical challenge. Furthermore, the precise molecular factors regulating the phenotype of this disease subtype remain unknown. Methods: We applied methyl-capture sequencing and mRNA sequencing to colonic mucosal biopsies from 3 groups of treatment-naïve children at diagnosis from the DOCHAS study - UC (n=10), PSC-UC (n=10) and healthy controls(n=10). Results: Differential gene expression between UC and PSC-UC identified disease-associated genes that were either up- or down-regulated in UC or PSC relative to controls. Specifically, expression of these genes was regulated by master transcriptional regulators (pro-caspases, IL7RA) and transcription factors (AR, p53, JUND, CEBPA). Importantly, gene expression comparison between UC vs PSC-UC revealed 4 up- and 4 down-regulated genes in PSC-UC patients. Notably, RAB31 and TENM3 identified as upregulated in the PSC-UC patients, are also significantly up-regulated in gastrointestinal (GI) cancers. Differential methylation analysis between controls biopsies vs PSC-UC and UC demonstrated >1000 differentially methylated regions (DMRs) with a large proportion of these DMRs enriched in enhancer regions. Conclusion: Our study, for the first time, identifies distinct gene expression and DNA methylation alterations that differentiate UC from PSC-UC at diagnosis in treatment-naïve paediatric patients, some of which are associated with GI cancers. These findings suggest the potential utility of these molecular markers as predictive biomarkers for PSC development in UC or for assessing dysplasia risk in PSC-UC. Further validation in larger patient cohorts is warranted.

overall_design: The study analyzed colonic mucosal biopsies from 30 treatment-naïve pediatric patients, grouped into primary sclerosing cholangitis with ulcerative colitis (PSC-UC), ulcerative colitis (UC-only), and healthy controls, with 10 patients in each group. Samples included both disease and control groups, enabling comparative analyses. Experimental conditions included treatment-naïve status and matched clinical parameters such as age and sex, minimizing confounding factors. Variables investigated were gene expression and DNA methylation alterations to uncover molecular differences between PSC-UC and UC, and the regulatory pathways driving these differences. The inclusion of healthy controls provided a baseline reference for identifying disease-specific changes.

first: Ololade

last: Lawal

first: Ciaran

last: McDonnell

first: Luke

last: Grant

first: John

last: O’Brien

first: Ian

last: Stephens

first: Grainne

last: Kirwan

first: Flavia

last: Genua

first: Alexander

last: Kel

first: Anna

last: Dominik

first: Roisin

last: Stack

first: Gregory

last: Yochum

first: Michael

last: McDermot

first: Glen

last: Doherty

first: Seamus

last: Hussey

first: Sudipto

last: Das


title: The 3D genomics of lampbrush chromosomes highlights the role of active transcription in chromatin organization [scHi-C]

city: Novosibirsk

first: Timofey

last: Lagunov

address: Prospekt Lavrentyeva 10

country: Russia

institute: Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences

summary: Lampbrush chromosomes are giant meiotic bivalents in growing oocyte nuclei that have served as a classic model system for studying chromatin organization and RNA synthesis for over a century. Despite their importance, the molecular mechanisms underlying lampbrush chromosomes formation and their distinctive chromomere-loop architecture have remained poorly understood. Here, we provide the first comprehensive genomic, cytological, and biophysical analysis of lampbrush chromosome organization by integrating single-cell Hi-C, RNA-seq, NOMe-seq, FISH mapping, and chromatin simulations. Single-nucleus Hi-C analysis revealed CTCF-independent contact domains with stable boundaries defined by transcription units in a convergent orientation. Сontact domains identified through Hi-C analysis correspond to insulated chromomeres in lampbrush chromosomes. Small transcriptionally inactive contact domains surrounded by transcription units in the diverged orientation form ‘chromatin knots’, which are often detached from the chromosome axis. Transcription loops frequently manifest as a 'cross' pattern with reduced contacts within chromatin domains. Integrative analysis of the whole-genome data uncovers the mechanisms underlying lampbrush chromosome structure, revealing how hypertranscription modulates chromatin stiffness and repositions SMC complexes to establish the distinctive chromomere-loop organisation. Biophysical modeling through polymer simulation reproduces key features of lampbrush chromosomes, including transcription loop formation, chromomere compaction, and insulation patterns. These findings offer a unifying framework for understanding the remarkable chromatin architecture of lampbrush chromosomes and their transcription-dependent organization.

overall_design: Single cell Hi-C of the WT chicken oocyte nucleus on lumpbrush chromosome and post-lumpbrush chromosome stages in some biological replicates.

first: Maria

last: Gridina

first: Artem

last: Nurislamov

first: Tatiana

last: Kulikova

first: Antonina

last: Maslova

first: Viktor

last: Konstantinov

first: Andrey

last: Popov

first: Alla

last: Krasikova

first: Veniamin

last: Fishman


title: Müller glia-microglia cross talk reprograms the Müller glia transcriptome for cell division-related processes during retina regeneration

first: Daniel

last: Goldman

summary: In the injured zebrafish retina, Müller glia (MG) reprogram their transcriptome and undergo an asymmetric division that produces a multipotent progenitor for retinal repair.  Although MG cell division is regulated by microglia, its underlying mechanism remains unknown.  Here we report that microglia contribute to MG reprogramming by preferentially stimulating the expression of genes associated with cell division-related processes like chromosome segregation, DNA replication, and mitotic cell cycle.  Furthermore, we report that depleting microglia systemically from early development leads to a compensatory immune cell response in the retina. Our studies illustrate the profound effects microglia can have on neighboring cells and support a two-step model of MG reprogramming, where dying neurons initiate and microglia complete this reprogramming process.

overall_design: There are two sets/batches of experiments (RS14 and RS19). In the first, all fish are wild-type, and there are four groups with 3 samples each :  (1) uninjured-untreated control, (2) needle poke-induced retinal injury treated with PLX3397 (pexidartinib), (3) needle poke-induced retinal injury treated with Z-VAD-FMK (carbobenzoxy-valyl-alanyl-aspartyl-[O-methyl]-fluoromethylketone), and (4) needle poke-induced retinal injury treated with DMSO (Dimethyl sulfoxide). In the second, wild-type and mutant fish are used, with 3 samples per group: (1) uninjured  WT control, (2) NMDA-induced retinal injury in WT,  (3) NMDA-induced retinal injury in csf1ra-mutants,  (4) NMDA-induced retinal injury in csf1rb-mutants,  (5) uninjured csf1ra-mutants,  (6) uninjured csf1rb-mutants.

first: Soumitra

last: Mitra

first: Sulochana

last: Devi

first: Mi-Sun

last: Lee

first: Aresh

last: Sahu

first: Jon

last: Jui


title: The vaccine platform used for COVID-19 primary immunization shapes the quality of the human B cell response to a vaccine boost

first: Chaim

last: Schramm

address: 40 Convent Dr

department: Vaccine Research Center

institute: NIAID, NIH

summary: Different COVID-19 vaccine modalities expressing the same SARS-CoV-2 spike antigen present a unique opportunity to contrast the immunologic outcomes associated with each vaccine platform. Here we characterized the memory B cell response elicited by 12 different combinations of primary series and boost vaccines spanning adenovirus vector, mRNA and subunit protein technologies. Cross-reactive B cells for ancestral virus and Omicron BA.1 expanded in similar proportions across all vaccine regimens. However, mRNA boost following adenovirus vector prime resulted in the greatest increase in antigen-specific B cell frequencies, predominantly of a highly activated ‘atypical’ B cell subset, identified by flow cytometry and single-cell sequencing. Using lineage tracking by single-cell IG sequencing we characterized B cell lineages exhibiting different phenotypes at subsequent time-points. Furthermore, the same mRNA boost induced markedly different memory B cell phenotypes depending on the modality of the prime, suggesting that the type of response elicited by boosting is dependent on the nature of pre-existing memory B cells imprinted by the vaccine priming.

overall_design: SARS-CoV-2-specific B cells were sorted from PBMC samples from people vaccinated with either Janssen Ad26.COV2.S, Moderna mRNA-1273, or Pfizer/BioNTech BNT162b2 and boosted with either these vaccines or Novavax NVX-CoV2373 at pre-boost, 2 weeks post-boost and 6 months post-boost.These cells were processed using the 10x Chromium for single cell sequencing.

first: Noemia

last: Lima

first: Lauren

last: McCormick

first: Samuel

last: Li

first: Christian

last: Wake

first: Abby

last: Spangler

first: Yoav

last: Pinto

first: William

last: Catalano

first: Amy

middle: R

last: Henry

first: Farida

last: Laboune

first: I-Ting

last: Teng

first: Kirsten

last: Lyke

first: Robert

middle: L

last: Atmar

first: Meagan

last: Deming

first: Lisa

last: Jackson

first: Angela

last: Branche

first: Christina

last: Rostad

first: Judith

last: Martin

first: Christine

last: Johnston

first: Richard

last: Rupp

first: Angelica

last: Kottkamp

first: Rebecca

last: Brady

first: Martin

last: Backer

first: Srilatha

last: Edupuganti

last: Posavad

first: Paul

last: Roberts

first: Peter

last: Kwong

first: Sarah

last: Andrews

last: Douek


title: Identification and characterization of a non-biological small molecular mimic of a Zika virus conformational neutralizing epitope

city: Pittsburgh

first: Donald

last: Burke

state: Pennsylvania

address: 130 Desoto St

institute: University of Pittsburgh

summary: Antigenic similarities between Zika virus (ZIKV) and other flaviviruses pose challenges to the development of virus-specific diagnostic tools and effective vaccines. Starting with a DNA-encoded one-bead-one-compound combinatorial library of 508,032 synthetic, non-natural oligomers, we selected and characterized small molecules that mimic ZIKV epitopes. High-throughput FACS_x0002_based bead screening was used to select molecules that bound IgG from ZIKV-immune but not from dengue-immune sera. Deep sequencing of the DNA from the “Zika-only” beads identified 40 candidate molecular structures. A lead candidate small molecule “CZV1-1” was selected that correctly identifies serum specimens from Zika-experienced patients with good sensitivity and specificity (85.3% and 98.4%, respectively). Binding competition studies of purified anti-CZV1-1 IgG against known ZIKV-specific monoclonal antibodies showed that CZV1-1 mimics a nonlinear, neutralizing conformational epitope in the domain III of the ZIKV envelope. Purified anti-CZV1-1 IgG neutralized infection of ZIKV in cell cultures with potencies comparable to highly specific ZIKV_x0002_neutralizing monoclonal antibodies. This study demonstrates an innovative approach for discovery of synthetic non-natural molecular mimics of conformational virus epitopes. Such molecular mimics may have value in the development of novel diagnostic assays and vaccines for Zika, as well as for other viruses.

overall_design:
Sera were collected from persons who had experienced prior dengue infections only, prior Zika infection only, or neither infection. Sera of individuals without previous serological markers of Zika and dengue infections are used as negative controls to identify PICCOs binding to Zika or dengue infected sera.”
A DNA encoded library of One Bead One Compound beads was synthesized that expressed a combinatorial library of 500,000 + "random" PICCOs Peptoid Inspired Conformationally Constrained Oligomers. The DNA encoded the ordering of the oligomers in the PICCO, as well as a bead specific barcode
PICCO-Beads were mixed with pools of human sera with known zika or dengue infection history, and binding was assessed by flow cytometry sorting to select beads with bound antibody
The DNA on beads with a high number of flow cytometry Zika hits, high dengue hits, or both, were subjected to NGS
Based on the DNA sequences, the chemical structures of PICCOs were identified
Based on their chemical structures, high hit PICCOs were clustered into groups with similar chemical structures
High interest PICCOs that bound exclusively Zika, or dengue, or both, were resynthesized on beads
High ingterest PICCO-beads were evaluated for their sensitivty and specificity in diagnosing Zika

first: Yongseok

last: Park

first: Priscila

last: Castanha


title: The Arp2/3 complex controls the development of homeostatic microglia

city: Freiburg

first: Maximilian

last: Frosch

address: Breisacher Str. 64

department: Institute of Neuropathology

country: Germany

institute: University Medical Center Freiburg

summary: Microglia are the major brain-resident immune cell subsetthat areessential during pathology and physiology in the central nervous system. The regulation of functional elementsrequired for microglialhomeostasis needsto be precisely orchestrated.To date, the underlying mechanismshave not been fully investigated. Here,we show that actin network dynamics mediated by the Arp2/3 complex play a crucial role in microglial cell function. Upon interruption of Arp2/3 complex integrity in the conditional knockoutmouse model, we found significant alterations in microglial cell morphology, motility, and chemotaxisfunction.Transcriptomics analysis revealedthat Arp2/3-deficient microglia downregulatehomeostatic signature and upregulatecell activationthat isassociated with APOE induction, Ms4a7upregulation,and TGFsignaling impairment. In vitrostudies confirm that the Arp2/3 downstream actin-related molecules are required for mediating the TGFsignaling pathway in microglia. Our resultsshow that the Arp2/3complexis required for microglia cell dynamics and plays a key role in maintaining microglial cell homeostasis by regulating the TGF-β signaling.

overall_design: scRNA-seq of CD45+ cells from control and Arpc4dCx3cr1 mice

first: Shima

last: Safaiyan

first: Gianni

last: Monaco


title: The effect of Terc deficiency on differentiation and maturation of OCs during aging [culture dishes]

city: Shanghai

first: Junjie

last: Gao

address: 600 Yishan Road

institute: Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

summary: Aging alters the bone function and elevates osteoporosis disability in diseases such as fractures. Understanding how aging alters bone marrow cellular differentiation could help us identify potential anti-aging targets to restore cellular homeostasis.

overall_design: Unbiased RNA-sequencing was performed to test whether the osteoclasts (OCs) from different ages of wild typt (WT) mice or Terc-/- mice have difference in gene expression.

first: Hao

last: Li


title: Transcription elongation can be sufficient, but is not necessary, to advance replication timing

city: San Diego

first: David

last: Gilbert

state: CA

address: 3525 John Hopkins Ct., Ste. 200

institute: San Diego BioMEd

summary: DNA replication timing (RT) often correlates with transcription during cell fate transitions, yet notable exceptions indicate a complex relationship. Using a reductionist system in mouse embryonic stem cells, we manipulate transcriptional length and strength at a single locus upstream of the silent, late-replicating Pleiotrophin (Ptn) gene. Small reporter genes driven by two of four promoters advance RT, whereas all promoters advance RT when driving the 96-kb endogenous Ptn gene. Inducible transcription of Ptn, but not the reporter, triggers a rapid and reversible RT advance, providing a system to manipulate RT independent of differentiation. Strikingly, deletion of the Ptn promoter and enhancers abolishes transcription yet does not prevent the developmental RT switch to early replication during neural differentiation. These findings, supported by parallel genome-wide analyses during differentiation, demonstrate that transcriptional elongation can causally advance RT in a rate-dependent and context-specific manner, but that transcription is neither necessary nor sufficient for RT advancement. Our results provide a solid empirical base with which to re-evaluate decades of seemingly contradictory literature.

overall_design: To investigate the relationship between RT regulation and transcription, we focused on mouse Pleiotrophin (Ptn) gene locus the replication timing and transcription of which are developmentally regulatged; switching from late RT and transcription "OFF" in embryonic stem cell to early RT and transcription "ON" in NPC. We inserted various promoters in one allele on the same locus in F121-9 hybrid embryonic stem cell expressing the tetracycline transactivator from the Rosa26 locus to see how transcription induction and replication timing differ between the WT allele and manipulated allele. In addition, to investigate position effect, we inserted hPGK promoter-eGFP casette to multiple loci using PiggyBac as described in PMC7073462. We also deleted Ptn gene transcription start site in another mESC line 46C and induced the differentiation to NPC to observed how the depletion of Ptn gene transcription affects RT in NPC.

first: Athanasios

last: Vouzas

first: Takayo

last: Sasaki

first: Juan Carlos

last: Rivera-Mulia

first: Jesse

last: Turner

first: Amber

middle: N

last: Brown

first: Karen

last: Alexander

first: Laura

last: Brueckner

first: Bas

last: van Steensel


title: Comprehensive analysis of tonsillar gene expression and the tonsillar microbiota in patients with palmoplantar pustulosis and pustulotic arthro-osteitis

status: Public on Jan 30 2026

city: Shinjuku

first: Satomi

last: Kobayashi

state: Tokyo

address: 2-5-1 Nakaochiai

country: Japan

institute: Seibo International Catholic Hospital

summary: Background: Tonsillectomy improves or cures symptoms in patients with palmoplantar pustulosis (PPP) and suppresses disease progression in patients with pustulotic arthro-osteitis (PAO), highlighting the important role of tonsils in the pathogenesis of PPP/PAO.  Objective: To identify active inflammatory pathways in the tonsil tissue of patients with PPP/PAO, and to clarify the characteristics of tonsillar microbiota.  Methods: We assessed gene expression in tonsil tissue removed from Japanese adults with PPP/PAO or recurrent tonsillitis (RT)/sleep apnea syndrome (SAS) using microarray and quantitative reverse transcription polymerase chain reaction analysis. We also performed a comprehensive analysis of the tonsillar microbiota (tonsillar crypts) using next-generation sequencing. Potential associations between tonsillar gene expression and bacterial composition were evaluated.  Results: Twenty-five tonsils from patients with PPP/PAO and 15 tonsils from patients with RT/SAS were included. The gene expression of inflammatory cytokines and molecules involved in the Th17, Th2, and Treg pathways was significantly higher in the tonsillar tissue of patients with PPP/PAO than in patients with RT/SAS. There were no significant differences in genus-level tonsillar microbiota between the two groups. Correlation analysis revealed a significant positive correlation between Streptococcus spp. and the expression of Th17 and Th2 pathway genes. Correlation patterns were similar between the PPP/PAO and RT/SAS groups for Streptococcus spp. but differed for the other genera.  Conclusion: The tonsils of patients with PPP/PAO are in a complex inflammatory state, with enhanced Th17, Th2, and Treg responses. Members of the Streptococcus genus may be involved in the induction of inflammatory characteristics in PPP/PAO.

overall_design: This observational study was conducted from July 2020 to November 2022. Tonsil tissue removed at Seibo International Catholic Hospital from Japanese adult patients as part of their PPP/PAO, recurrent tonsillitis (RT), or sleep apnea　syndrome (SAS) treatment was used. Gene expression analysis was performed to identify molecular variations in inflammatory pathways in the tonsillar crypt tissue of patients with PPP/PAO using patients with RT/SAS as a comparator. A comprehensive analysis of the tonsillar microbiota was conducted to elucidate the tonsillar bacterial composition of patients with PPP/PAO. A correlation analysis was conducted to evaluate potential associations between tonsillar gene expression and bacterial composition.

first: Masato

last: Komai


title: CPSF73 activation and 3’ Pol II pausing are lost during read-through transcription after heat shock

city: Boulder

first: Kaitlyn

last: Walsh

state: CO

address: 3415 Colorado Ave

institute: CU Boulder

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Multiomics identifies unique modulators of calf muscle pathophysiology in peripheral artery disease and chronic kidney disease

city: Gainesville

first: Terence

last: Ryan

address: 1864 Stadium Rd

institute: University of Florida

summary: This project aimed to map transcriptome changes in the skeletal muscle of patients with and without PAD (peripheral artery disease) and CKD (chronic kidney disease)

overall_design: bulk RNA sequencing was performed on gastrocnemius muscle specimens obtained from control, PAD, CKD, and PAD+CKD patients.


title: Distinct networks of expressed genes are associated with neophobia in the hippocampus of male and female Eurasian tree sparrows (Passer montanus)

city: Durham

first: Sara

last: Lipshutz

state: NC

address: 124 Science Drive

department: Biology

institute: Duke University

summary: Neophobia, avoidance of novel stimuli, is an ecologically and evolutionarily relevant behavioral trait that varies among individuals and across species. Especially among wild animals, the neuromolecular mechanisms underlying individual variation in neophobia have not been well characterized. We examined three neophobic behaviors in captive female and male Eurasian tree sparrows (Passer montanus) from a wild population introduced to the USA in 1870: responses towards novel objects, novel foods, and repeated presentations of the same initially novel object. We compared transcriptomic patterns associated with neophobia in three brain regions, the striatum, dorsal hippocampus, and rostral hippocampus, using differential expression and co-expression network analyses. We found that the striatum and hippocampus had distinct transcriptomic profiles, as did the rostral and caudal subregions of the hippocampus, supporting recent hypotheses that these subregions are functionally specialized. Despite the absence of sex differences in neophobic behaviors, neophobia-associated gene modules revealed sex-specific patterns within brain regions. For females, neophobic behaviors more strongly correlated with gene modules in the caudal hippocampus, a region involved in stress and anxiety, whereas for males, neophobic behaviors correlated with gene modules in the rostral hippocampus, a region that may play a larger role in spatial cognition. These modules exhibited significant overlap, suggesting that neophobic behaviors in both females and males are driven by shared neurobiological mechanisms, though they exhibit sex-specific patterns of brain region localization. Further, this work highlights the importance of examining both male and female animals in neurobiological research.

overall_design: RNA-seq profiling of striatum, dorsal hippocampus, and rostral hippocampus of captive, wild-caught, female and male Eurasian tree sparrows (Passer montanus)

first: Alexandra

last: Bentz

first: Ella

last: Cochran

first: Kevin

last: Krajcir

first: Melanie

last: Kimball

first: Christine

last: Lattin


title: The gene expression profiles of SOX9+ basal cells (BCs) compared to basal cells during the ALT injury/regeneration process in the surface airway epithelium (SAE).

city: Boston

first: Nora

last: Barrett

state: Massachusetts

address: 60 Fenwood Rd

department: Allergy and Clinical Immunology

institute: Brigham and Women's Hospital

summary: Tissue-resident stem cells are crucial for repairing barrier tissues that experience frequent damage. However, the local signals that regulate this repair process remain largely unidentified. Here, we show that tuft cell-dependent CysLT activate the LTE4 receptor OXGR1 on SOX9+ accessory stem cells in submucosal glands (SMGs). Activated SMG progenitors regenerate the stem compartment of the SAE, but they also introduce a pro-inflammatory and mesenchymal program, leading to reduced differentiation of ciliated cells. This results in ineffective epithelial repair, causing epithelial injury and inflammation. These findings highlight a significant connection between tuft cell sensing of tissue damage and the onset of abnormal wound healing processes observed in the human airway.

overall_design: To understand the distinctions between basal cells (BCs) derived from SOX9+ SMG progenitors and conventional SOX9- BCs in the SAE, we treated lineage-traced Sox9-tdT reporter mice with four doses of Alternaria (ALT) and then sorted these populations from the single suspensions of tracheal tissues.

first: Minkyu

last: Lee

first: Michael

last: Mandanas


title: A functional overlap between actively transcribed genes and insulator elements [ChIP-seq]

city: Oxford

first: Lucy

last: Cornell

address: John Radcliffe Hospital/Headley Way

department: Weatherall Institute Molecular Medicine

institute: The University of Oxford

summary: Mammalian genomes are subdivided into large (50-2000 kb) regions of chromatin referred to as Topologically Associating Domains (TADs or sub-TADs). Chromatin within an individual TAD contacts itself more frequently than with regions in surrounding TADs thereby directing enhancer-promoter interactions. In many cases, the borders of TADs are defined by convergently orientated boundary elements associated with CCCTC-binding factor (CTCF), which stabilises the cohesin complex on chromatin and prevents its translocation. This delimits chromatin loop extrusion which is thought to underlie the formation of TADs. However, not all CTCF-bound sites act as boundaries and, importantly, not all TADs are flanked by convergent CTCF sites. Here, we examined the CTCF binding sites within a ~70 kb sub-TAD containing the duplicated mouse α-like globin genes and their five enhancers (5’-R1-R2-R3-Rm-R4-α1-α2-3’). The 5’ border of this sub-TAD is defined by a pair of CTCF sites. Surprisingly, we show that deletion of the CTCF binding sites within and downstream of the α-globin locus leaves the sub-TAD largely intact. The predominant 3’ border of the sub-TAD is defined by a steep reduction in contacts: this corresponds to the transcribed α2-globin gene rather than the CTCF sites at the 3’-end of the sub-TAD. Insertion of actively transcribed fragments of the α-globin gene between the enhancers and native genes leads to a reduction in native α-globin expression and accumilation of cohesin at the insertion site. Together, these observations provide direct evidence that actively transcribed genes can behave as insulator elements.

overall_design: To determine the function of the CTCF bound sites at the predominant 3’ border of the alpha globin sub-TAD, the sites were deleted using CRISPR:Cas9 and mice with desired mutations were bred to homozygosity. Primary definitive erythrocytes (Ter119+) were collected for characterisation by CTCF ChIP-seq. In addition, fragments of the alpha globin gene were introduced in a region between the super enhancer and the native alpha globin genes in mESCs with a Hba-a1:mVenus fusion. These mESCs also carried a large deletion spanning the locus alpha globin on the other allele, hence these cells are hemizygous. CD71+ erythroid cells were generated from edited mESC using an in vitro embryoid body differentiation protocol, and collected for characterisation by Rad21 ChIP-seq.

first: Susannah

last: Holliman

first: Mira

last: Kassouf


title: A functional overlap between actively transcribed genes and insulator elements [RNA-seq]

overall_design: Fragments of the alpha globin gene were introduced in a region between the super enhancer and the native alpha globin genes in mESCs with a Hba-a1:mVenus fusion. These mESCs also carried a large deletion spanning the locus alpha globin on the other allele, hence these cells are hemizygous. CD71+ erythroid cells were generated from edited mESC using an in vitro embryoid body differentiation protocol. To determine the transcriptional output from the inserts, PolyA(+) and PolyA(-) RNA was collected from CD71+ and prepared for sequencing.


title: A functional overlap between actively transcribed genes and insulator elements [CaptureC]

overall_design: To determine the function of the CTCF bound sites at the predominant 3’ border of the alpha globin sub-TAD, the sites were deleted using CRISPR:Cas9 and mice with desired mutations were bred to homozygosity. Primary definitive erythrocytes (Ter119+) were collected for characterisation by CaptureC. In addition, fragments of the alpha globin gene were introduced in a region between the super enhancer and the native alpha globin genes in mESCs with a Hba-a1:mVenus fusion. These mESCs also carried a large deletion spanning the locus alpha globin on the other allele, hence these cells are hemizygous. CD71+ erythroid cells were generated from edited mESC using an in vitro embryoid body differentiation protocol, and collected for characterisation by CaptureC.


title: A functional overlap between actively transcribed genes and insulator elements [ATAC-seq]

overall_design: To determine the function of the CTCF bound sites at the predominant 3’ border of the alpha globin sub-TAD, the sites were deleted using CRISPR:Cas9 and mice with desired mutations were bred to homozygosity. Primary definitive erythrocytes (Ter119+) were collected for characterisation by ATAC-seq. In addition, fragments of the alpha globin gene were introduced in a region between the super enhancer and the native alpha globin genes in mESCs with a Hba-a1:mVenus fusion. These mESCs also carried a large deletion spanning the locus alpha globin on the other allele, hence these cells are hemizygous. CD71+ erythroid cells were generated from edited mESC using an in vitro embryoid body differentiation protocol, and collected for characterisation by ATAC-seq.


title: The 3D genomics of lampbrush chromosomes highlights the role of active transcription in chromatin organization [scNOME-seq]

first: Timofey

last: Lagunov

overall_design: Single cell CpG and GpC methylation profiling of the WT chicken lumpbrush chromosomes in 11 biological replicates.

first: Maria

last: Gridina

first: Artem

last: Nurislamov

first: Tatiana

last: Kulikova

first: Antonina

last: Maslova

first: Viktor

last: Konstantinov

first: Andrey

last: Popov

first: Alla

last: Krasikova

first: Veniamin

last: Fishman


title: Transcriptomic profiling of wild-type and TigarKO mouse hearts [RNA-Seq]

city: Bronx

first: Jeffrey

last: Pessin

state: NY

address: 1301 Morris Park Avenue

department: Medicine and Molecular Pharmacology

institute: Albert Einstein College of Medicine

summary: Myocardial infarction induces profound transcriptional remodeling in the heart, particularly affecting mitochondrial pathways. To characterize zone-specific transcriptomic responses, we performed RNA sequencing of infarct, border, and remote regions from wild-type (WT) and TKO mouse hearts following infarction. Analysis of infarct territories revealed extensive preservation of mitochondrial gene expression in TKO hearts compared with WT controls. In contrast, mitochondrial DNA–encoded gene expression showed no significant differences between WT and TKO hearts in either the border or remote zones. Similarly, expression of nuclear-encoded genes in the border and remote zones was largely unchanged between genotypes. Together, these data indicate that transcriptional differences between WT and TKO hearts are predominantly localized to the infarct region, while border and remote zones exhibit minimal genotype-dependent changes.

overall_design: Wild-type (WT) and TKO mice were subjected to myocardial infarction, and each heart was separated into infarct, border, and remote regions using consistent anatomical criteria. Total RNA was isolated from each region and used for bulk RNA sequencing. Gene expression profiles were compared between WT and TKO hearts within each region, with a focus on mitochondrial DNA-encoded and nuclear-encoded genes.

first: Yan

last: Tang

first: Li

last: Liu

first: Daorong

last: Feng


title: DNA methylation analysis of the Parkin gene in wild-type and TIGAR-deficient mouse tissues [EM-seq]

summary: Parkin expression is persistently increased in TIGAR-deficient (TKO) mouse hearts, even after restoration of TIGAR expression in adulthood, suggesting a developmental epigenetic mechanism. To investigate whether DNA methylation contributes to this regulation, we performed whole-genome bisulfite sequencing (WGBS) on cardiac tissues from wild-type and TKO mice. RNA sequencing confirmed increased Parkin transcript levels across all exons in TKO hearts. WGBS analysis identified multiple differentially methylated regions (DMRs) across the Parkin gene body, with consistently lower methylation levels in TKO hearts. A prominent hypomethylated region was detected within intron 10, while no significant methylation changes were observed in the Parkin promoter CpG island. These data suggest that TIGAR deficiency is associated with stable, gene body–specific DNA methylation changes that correlate with increased Parkin expression.

overall_design: Cardiac tissues were collected from wild-type and TIGAR-deficient (TKO) mice. Genomic DNA was isolated and analyzed by whole-genome bisulfite sequencing to assess DNA methylation patterns.


title: DNA methylation analysis of the Parkin gene in wild-type and TIGAR-deficient mouse tissues [Bisulfite-seq]


title: The 3D genomics of lampbrush chromosomes highlights the role of active transcription in chromatin organization


title: Pervasive and programmed nucleosome distortion patterns on single mammalian chromatin fibers

status: Public on Jan 29 2026

city: Los Angeles

first: Marty

last: Yang

address: 615 Charles E Young Dr S

department: Biological Chemistry

institute: University of California, Los Angeles

summary: We present a genome-scale method to map the single-molecule co-occupancy of structurally distinct nucleosomes, subnucleosomes, and other protein-DNA interactions via long-read high-resolution adenine methyltransferase footprinting. Iteratively Defined Lengths of Inaccessibility (IDLI) classifies nucleosomes on the basis of shared patterns of intranucleosomal accessibility, into: i.) minimally-accessible chromatosomes; ii.) octasomes with stereotyped DNA accessibility from superhelical locations (SHLs) +/-1 through +/-7; iii.) highly-accessible unwrapped nucleosomes; and iv.) subnucleosomal species, such as hexasomes, tetrasomes, and other short DNA protections. Applying IDLI to mouse embryonic stem cell (mESC) chromatin, we discover widespread nucleosomal distortion on individual mammalian chromatin fibers, with >85% of nucleosomes surveyed displaying degrees of intranucleosomally accessible DNA. We observe epigenomic-domain-specific patterns of distorted nucleosome co-occupancy and positioning, including at enhancers, promoters, and mouse satellite repeat sequences. Nucleosome distortion is programmed by the presence of bound transcription factors (TFs) at cognate motifs; occupied TF binding sites are differentially decorated by distorted nucleosomes compared to unbound sites, and degradation experiments establish direct roles for TFs in structuring binding-site proximal nucleosomes. Finally, we apply IDLI in the context of primary mouse hepatocytes, observing evidence for pervasive nucleosomal distortion in vivo. Further genetic experiments reveal a role for the hepatocyte master regulator FOXA2 in directly impacting nucleosome distortion at hepatocyte-specific regulatory elements in vivo. Our work suggests extreme—but regulated—plasticity in nucleosomal DNA accessibility at the single-molecule level. Further, our study offers an essential new framework to model transcription factor binding, nucleosome remodeling, and cell-type specific gene regulation across biological contexts.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Single-molecule long-read adenine methyltransferase footprinting of protein-DNA contacts in vivo with PacBio sequencing. Datasets include E14 (wild-type), CTCF-AID, and SOX2-FKBP mouse embryonic stem cell (mESC) lines, as well as primary hepatocytes isolated from C57BL/6J (wild-type) and heterozygous FOXA2-dHx knock-in mice.

first: Vijay

last: Ramani

first: Hannah

last: Richter


title: scRNA-Seq of Retinal microglia from 6 months old Balb/c mice infected with MCMV at birth

city: Philadelphia

first: Jessica

last: McCord

institute: Thomas Jefferson University

summary: We used a single cell sequencing approach using 10x Genomics scRNAseq to understand the transcriptional differences between microglia from MCMV infected animals vs controls. MCMV infection at birth resulted in increased retinal degeneration with age. Microglia from mice infected with MCMV appeared to have an alternative activation state compared to age matched uninfected controls. We utilized a depletion and repopulation strategy to reset the population of microlgia using PLX5622, a CSFR1 inhibitor. This study allowed analysis of the transcriptional changes caused by MCMV infection early in life potentially contributing to neurodegeneration.

overall_design: Balb/c mice were infected with MCMV or injected with PBS (controls) less than 24hrs after birth. PLX5622 (a CSF1R inhibitor) was adminstered 2 months after infection for 7 days to deplete microglia. Microglia repopulated 21 days (3 months of age) and were aged to 6 months. Whole eyes were collected at 6 months from 5 Control (uninfected untreated), Infeted (MCMV infected untreated) and PLX (MCMV infected treated). Retina and RPE/choroid were isolated and Microglia were seperated by FACs. Pooled microglia from 5 Retina and RPE/Choroid from 5 mice per group were analyized by sc- RNA seq.

first: Christopher

last: Snyder


title: VRK1 is a Novel Therapeutic Target for Small Cell Neuroendocrine Carcinoma of the Cervix

city: Kyoto

first: Masahiro

last: Inoue

state: Kyoto

address: Med-Pharm Collaboration Bldg 503, Shimoadachi-cho 46, Sakyou-ku, Kyoto, 606-8304, Japan

department: Clinical Bio-resource Research and Development

institute: Kyoto Univ Graduate School of Medicine

summary: Small cell neuroendocrine carcinoma of the cervix (SCNEC) is classified as a high-grade neuroendocrine carcinoma of the cervix and has a worse prognosis than other major histological types of cervical cancer, such as squamous cell carcinoma and adenocarcinoma, due to the lack of effective treatments. Developing novel therapeutic targets based on its molecular characteristics is highly desirable; however, it has been limited due to the rarity of SCNEC and the resulting lack of research resources. Herein, we identified vaccinia-related kinase 1 (VRK1) as a potential therapeutic target for SCNEC. VRK1 was focused via our previous reported proteomic analysis of patient-derived organoids. Immunohistochemistry of patient samples revealed that VRK1 expression is consistently high in SCNEC, whereas its expression is variable in other cervical carcinomas. VRK1 knockdown significantly suppressed cell proliferation in three-dimensional cultures and xenograft tumor growth in vivo. Gene Set Enrichment Analysis of RNA-seq data obtained from mouse xenograft models indicated that VRK1 is associated with mitochondrial function. Subsequent in vitro experiments demonstrated that VRK1 knockdown suppressed SCNEC cell proliferation and simultaneously impaired mitochondrial function under the unique condition with oxidative stress. Finally, low VRK2 expression, proposed as a biomarker for the effectiveness of VRK1 knockdown, was consistently observed in SCNEC. These findings suggest that SCNEC is an optimal tumor group for targeting VRK1. VRK1 knockdown induced significant anti-tumor effects, highlighting its potential as a therapeutic target for SCNEC. Mechanistically, these effects appear to be mediated through mitochondrial dysfunction.

overall_design: One sample for each condition.


title: Rational design of immune gene therapy combinations via in vivo CRISPR activation screening of tumor microenvironment modulators [scRNA-seq]

status: Public on Jan 26 2026

city: New Haven

first: Chuanpeng

last: Dong

state: CT

address: 850 West Campus Dr

department: Genetics

institute: Yale University School of Medicine

summary: The hostile tumor microenvironment (TME) is major challenge for cancer immunotherapies. Here, we design and perform TME-targeted in vivo CRISPR activation (CRISPRa) screens to uncover factors that promote anti-tumor immunity, culminating in rationally designed immune gene therapy combinations. Through adeno-associated virus (AAV) delivery, we find that multiplexed activation of pooled immunoregulatory genes encoding antigen presentation, cytokine, and co-stimulation molecules (APCM) leads to enhanced anti-tumor immunity. A CRISPRa screen targeting APCM genes in metastatic tumors identifies CD80, TNFSF14, CXCL10, TNFSF18, TNFSF9, and IFNG as the top immunostimulatory candidates. Further optimization pinpoints 4-1BBL(TNFSF9) + IFNG + IL12B (4II) as a potent streamlined therapeutic combination. AAV delivered 4II has potent in vivo anti-tumor efficacy in multiple tumor models, by enhancing tumor antigen presentation while simultaneously promoting the infiltration, activation, and expansion of anti-tumor T cells. We further demonstrate that APCM therapy synergizes with CAR-T therapy against human solid tumors in vivo. CRISPRa screens and gene activation systems targeting APCM factors thus represent a powerful approach for rapid development of off-the-shelf immune gene therapies against solid tumors.

overall_design: Seven days post CAR-T cell infusion, CD3+ T cells were isolated from the lung following treatment with either AAV-vector or 4II.

first: Feifei

last: Zhang

first: Ryan

middle: D

last: Chow

first: Emily

last: He

first: Lvyun

last: Zhu

first: Shan

last: Xin

first: Daniyal

last: Mirza

first: Yanzhi

first: Xinyu

last: Ling

first: Qin

last: Han

first: Sidi

last: Chen

first: Guangchuan

last: Wang


title: Rational design of immune gene therapy combinations via in vivo CRISPR activation screening of tumor microenvironment modulators [CRISPR]

overall_design: To generate metastatic lung tumors and perform in vivo screening under immune pressure, E0771-APCM library cells were injected into 8-12 weeks old female C57BL/6J mice intravenously.

last: Feng


title: A functional overlap between actively transcribed genes and insulator elements

first: Lucy

last: Cornell


title: Rational design of immune gene therapy combinations via in vivo CRISPR activation screening of tumor microenvironment modulators [Bulk RNA-seq]

overall_design: E0771 cells were transduced with AAV-Vector, AAV-IFNG, IL12B, 41BBL and AAV-4II for 5 days.


title: Transcriptional pathways of localized early prostate cancer

city: Ribeirão Preto

first: William

last: Lautert Dutra

address: Av. Bandeirantes, 3900

institute: Universidade de São Paulo

overall_design: Refer to individual Series


title: CARM1-mediated hypoxanthine-enriched exosome biogenesis rewires inosine metabolism of CD8+ T cells and impairs their antitumor ability

status: Public on Jan 23 2026

city: Jinan

first: Fabao

last: Liu

state: Shandong

address: #44 wenhua xi road

institute: Shandong university

summary: Cancer cells engage in complex interactions with tumor infiltrating immune cells to overcome barriers to tumor progression. Targeting biogenesis of tumor-derived exosomes is a promising strategy for disrupting intracellular communication. Herein, we identify co-activator-associated arginine methyltransferase 1 (CARM1) as a key regulator of tumor-derived exosome biogenesis and metabolite sorting, thereby inhibiting CD8+ T cell-mediated antitumor immunity. Genetic ablation of CARM1 in breast cancer cells impairs the secretion of immunosuppressive exosomes, leading to enhanced CD8+ T cell infiltration, proliferation, and effector function in tumors. Mechanistically, CARM1 methylates apoptosis-linked gene-2 interacting protein X (ALIX) at Arg757, facilitating its interaction with endosomal sorting complex required transport (ESCRT) components, and promoting the biogenesis of tetraspanin-enriched exosomes. CARM1-dependent ALIX methylation enables selective packaging hypoxanthine into exosomes through direct binding to ALIX at the F676 pocket. Excess hypoxanthine disrupts inosine metabolism in the activated CD8+ T cells, inhibiting glycolysis, nucleotide synthesis, and effector cytokine production. Co-administration of CARM1 inhibitor with inosine significantly increases tumor infiltrating CD8+ T cell cytotoxicity, reduces exhaustion markers programmed cell death 1 and T cell immunoglobulin mucin 3 (PD-1+TIM-3+) expression and suppresses tumor growth. Collectively, the CARM1-ALIX-hypoxanthine axis functions as immunosuppressive mechanism in tumor growth, and targeting CARM1 combined with inosine supplement may represent a novel therapeutic regimen for breast cancer therapy.

overall_design: RNA-seg profling of wildtype CD8+ T cells treated with Glucose, Inosine and Inosine combined with hypoxanthine

first: Jilong

last: Yin

first: Xi

last: Hu


title: Identification of a dihydroartemisinin-related prognostic signature and its contribution to the tumor microenvironment of pancreatic cancer

city: Shenzhen

first: Jinglin

last: Lai

address: No. 1120 Lianhua Road

department: Central Laboratory

institute: Peking University Shenzhen Hospital

summary: Background: Pancreatic ductal adenocarcinoma (PDAC) is characterized by high metastatic potential and a stroma-rich tumor microenvironment (TME). Dihydroartemisinin (DHA) has shown antitumor potential in various cancers, but its therapeutic effects on the TME of PDAC are not yet understood. Methods: DHA-related differentially expressed genes (DEGs) were identified by high-throughput RNA sequencing in PDAC cells and utilized to explore the biological functions of DHA. The clinical value of DHA was examined by constructing a prognostic risk model using the TCGA dataset. We identified SERPINB5 as a downstream target of DHA involved in TME remodeling through cancer-associated fibroblast (CAF) regulation. The clinical value of SERPINB5 was validated through prognostic risk modeling and immunohistochemistry staining. Results: Our findings indicate that DHA may affect CAF-mediated TME remodeling. Prognostic risk modeling indicates that DHA was associated with PDAC prognosis, implying its clinical potential. DHA may improve the prognosis of PDAC patients by downregulating the expression of SERPINB5, which may participate in regulating CAFs. Conclusions: This study suggests that DHA might improve the prognosis of PDAC patients, and it may influence the PDAC TME by downregulating SERPINB5, offering new insights into DHA's antitumor mechanisms and its potential clinical applications in PDAC treatment.

overall_design: Following the manufacturer's instructions, total RNA was extracted from DHA-treated and untreated HM-SUIT-2 cells. The RNA samples were then sent to Bioinformatics Institute  for transcriptome profiling via RNA-seq.

first: Jianhua

last: Qu

first: Zilong

last: Yan

first: Tongning

last: Zhong


title: Hippocampal estrogen levels, receptor types and epigenetics contribute to sex-specific memory-vulnerabilities to concurrent acute stresses [RNA-Seq]

status: Public on Jan 27 2026

first: Shuo

last: Zhang

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

summary: It is increasingly recognized that acute traumatic events (e.g., mass shootings, natural disasters) can provoke enduring episodic memory deficits and generalization of trauma cues, and these are more common in women. We investigated mechanisms and sex differences of memory vulnerability to multiple acute concurrent stresses (MACS) in mice, focusing on the sex hormone 17β-estradiol and its receptors in hippocampus. Surprisingly, high physiological hippocampal estradiol levels, observed in proestrus females and males, were required for MACS-induced episodic memory disruption and sensitization and generalization of stress cues. High estradiol levels  were associated with permissive chromatin states in stress-vulnerable mice, while chromatin permissiveness and hippocampal estradiol were low in stress-resilient estrus females. Estrogen receptor (ER)β activation in resilient estrus females increased chromatin permissiveness and  enduring vulnerability to MACS, while ERα mediated milder stress-induced memory disruptions in males. Thus, hippocampal estradiol levels and sex modify chromatin states to enable long-lasting memory vulnerabilities to MACS.

overall_design: RNA-seq profiling of the mouse whole hippocampus of males, females in estrus or females in proestrus.

first: Rachael

last: Hokenson

first: Kiara

last: Rodríguez-Acevedo

first: Yuncai

first: Annabel

middle: K

last: Short

first: Sarah

last: Samrari

first: Brinda

last: Devireddy

first: Brittany

middle: J

last: Jensen

first: Julia

last: Winter

first: Christine

last: Gall

first: Kiran

last: Soma

first: Elizabeth

last: Heller

first: Tallie

middle: Z

last: Baram


title: Spatial Transcriptomics Analysis of Macrophage-to-Myofibroblast Transition in Bronchiolitis Obliterans Following Hematopoietic Stem Cell Transplantation

status: Public on Jan 22 2026

city: Houston

first: Akira

last: Yamamoto

state: Texas

address: One Baylor Plaza

institute: Baylor College of Medicine

summary: Bronchiolitis obliterans (BO) is a severe, fibrotic manifestation of chronic graft-versus-host disease (GVHD) after hematopoietic stem cell transplantation (HSCT). Macrophage-derived TGF-β is linked to GVHD-related fibrosis; however, its role in BO remains unclear. Given emerging evidence of macrophage-to-myofibroblast transition (MMT) in fibrosis, this study aimed to investigate whether MMT contributes to BO development. We analyzed lung samples from three HSCT recipients with BO who underwent lung transplantation, with tissues from two patients with lung cancer as controls. Spatial transcriptomics was performed to profile gene expression in foamy macrophages across anatomical regions and histological stages, compared to control peribronchiolar regions.

overall_design: Spatial transcriptomic profiling of bronchioles using GeoMx DSP

first: Nobuharu

last: Fujii


title: Identification of β-catenin dependent and independent genes in an orthotopic model of pancreatic cancer

city: Cardiff

first: NATHAN

last: HARMSTON

address: Museum Avenue

institute: Cardiff University

summary: Wnt signaling regulates metazoan development and homeostasis, in part by β-catenin dependent activation and repression of a large number of genes. However, Wnt signaling also regulates genes independent of β-catenin, genes that are less well characterized. In this study, using a pan-Wnt inhibitor we performed a comprehensive transcriptome analysis in a Wnt-addicted orthotopic cancer model to delineate the β-catenin-dependent and independent arms of Wnt signaling. We find that while a large percentage of Wnt-regulated genes are regulated by β-catenin, ten percent of these genes are regulated independent of β-catenin. Interestingly, a large proportion of these β-catenin independent genes are Wnt-repressed.

overall_design: Timecourse RNA-seq in HPAF-II cells treated with ETC-159 with or without mutation in β-catenin

first: Nathan

last: Harmston

first: David

last: Virshup

first: Babita

last: Madan


title: ACSS2 upregulation enhances neuronal resilience to aging and neurodegeneration [Cut&Run]

status: Public on Dec 09 2025

first: Shuo

last: Zhang

state: PA

summary: Epigenetic mechanisms, including histone acetylation, play a key role in learning and memory, with recent evidence of a role in neuronal function in Alzheimer’s disease and Related Dementia (ADRD). Acetyl-CoA synthetase 2 (ACSS2), an enzyme that generates acetyl-CoA, is central to histone acetylation and gene regulation, particularly in neurons, due to their unique metabolic demands and their postmitotic state. ACSS2 can be recruited to the nucleus and to chromatin, locally supplying acetyl-CoA to directly fuel histone acetyltransferase enzymes and key neuronal gene expression. This regulatory mechanism may be a promising target for therapeutic intervention in neurodegenerative diseases because systemic ACSS2 deletion in mice, although largely normal in physiology, is greatly impaired in memory. Here we investigated whether increasing levels of ACSS2 could protect neurons against disease and age-associated cognitive decline. Given the role of tau in ADRD, we used primary hippocampal neurons that mimic the sporadic development of tau pathology, and used the P301S transgenic mouse model for tau-induced memory decline. Our results show in these in vitro and in vivo models of tauopathy, that ACSS2 upregulation mitigates tau-induced transcriptional alterations, enhances neuronal resilience against tau pathology, improves long-term potentiation, and ameliorates memory deficits. Expanding upon these findings, we investigated deficits in aged mice, and reveal that increasing histone acetylation through ACSS2 upregulation improves age-associated memory decline. These findings indicate that increasing ACSS2 is highly effective in countering age- and tau-induced transcriptome changes, preserving elevated levels of synaptic genes, and safeguarding synaptic integrity.  We thus highlight ACSS2 as a key player in the epigenetic regulation of cognitive aging and ADRD, providing a foundation for targeted therapeutics to enhance brain resilience and function.

overall_design: Cut&Run-seq for mouse primary hippocampal neurons treated with hAD-tau or PBS.

first: Naemeh

last: Pourshafie

first: Shelley

last: Berger

first: Nancy

last: Bonini

first: Desi

last: Alexander


title: Hypertension has stage-dependent signatures in the hypertensive rat frontal brain

status: Public on Jan 01 2026

city: Würzburg

first: Silke

last: Appenzeller

address: Schweinfurter Str. 28

institute: University Wuerzburg

summary: Long-term arterial hypertension causes cerebral microvascular dysfunction and doubles dementia risk in aging. However, cognitive health preservation by therapeutical blood pressure lowering alone might be limited by disease duration, the degree of irreversible tissue damage and whether microvascular function can be restored. This study aimed to understand cellular and molecular temporo-spatial pathomechanisms in the course of arterial hypertension. We investigated initial, early chronic and late chronic hypertension effects in the frontal brain of hypertensive rats by applying behavioral tests, histology, immunofluorescence, FACS and microvascular/neural tissue RNA sequencing as well as 18F-FDG PET imaging. Chronic hypertension caused frontal brain-specific behavioral deficits. From a mechanistic perspective our results suggest continuous microvascular stress and wounding due to hypertension, which in turn leads to an early recruitment of activated microglia and peripheral immune cells, blood-brain-barrier breakdown and an energy-demanding hypermetabolic state. Vascular adaptation mechanisms e.g., vessel wall strengthening by production of cellular adhesion molecules and extracellular matrix (ECM), and angiogenesis were first observed first in late chronic stages. Additionally, we identified late-chronic vascular accumulation of Igfbp-5 in the brains of rats and humans with hypertensive cerebral small vessel disease, possibly attenuating protective Igf-1 signaling in the cerebral microvasculature. Thus, we characterized cellular and molecular temporo-spatial pathomechanisms in the course of arterial hypertension, that might represent critical points for clinical decision-making and could therefore be used to prevent irreversible tissue damage.

overall_design: Total number of samples is 38

first: Philipp

last: Ulbrich

first: Lorena

last: Morton

first: Michael

last: Briese

first: Naomi

last: Lämmlin

first: Hendrik

last: Mattern

first: Mohammed

last: Hasanuzzaman

first: Melina

last: Westhues

first: Mahsima

last: Khoshneviszadeh

first: Daniel

last: Gündel

first: Magali

last: Toussaint

first: Peter

last: Brust

first: Torsten

last: Kniess

first: Anja

last: Oelschlegel

first: Jürgen

last: Goldschmidt

first: Sven

last: Meuth

first: Hans-Jochen

last: Heinze

first: Grazyna

last: Debska-Vielhaber

first: Stefan

last: Vielhaber

first: Axel

last: Becker

first: Alexander

last: Dityatev

first: Deniz

last: Yilmazer-Hanke

first: Solveig

last: Jandke

last: Sendtner

first: Ildiko

last: Dunay

first: Stefanie

last: Schreiber


title: ACSS2 upregulation enhances neuronal resilience to aging and neurodegeneration [RNA-seq]

first: Shuo

last: Zhang

summary: Epigenetic mechanisms, including histone acetylation, play a key role in learning and memory, with recent evidence of a role in neuronal function in Alzheimer?s disease and Related Dementia (ADRD). Acetyl-CoA synthetase 2 (ACSS2), an enzyme that generates acetyl-CoA, is central to histone acetylation and gene regulation, particularly in neurons, due to their unique metabolic demands and their postmitotic state. ACSS2 can be recruited to the nucleus and to chromatin, locally supplying acetyl-CoA to directly fuel histone acetyltransferase enzymes and key neuronal gene expression. This regulatory mechanism may be a promising target for therapeutic intervention in neurodegenerative diseases because systemic ACSS2 deletion in mice, although largely normal in physiology, is greatly impaired in memory. Here we investigated whether increasing levels of ACSS2 could protect neurons against disease and age-associated cognitive decline. Given the role of tau in ADRD, we used primary hippocampal neurons that mimic the sporadic development of tau pathology, and used the P301S transgenic mouse model for tau-induced memory decline. Our results show in these in vitro and in vivo models of tauopathy, that ACSS2 upregulation mitigates tau-induced transcriptional alterations, enhances neuronal resilience against tau pathology, improves long-term potentiation, and ameliorates memory deficits. Expanding upon these findings, we investigated deficits in aged mice, and reveal that increasing histone acetylation through ACSS2 upregulation improves age-associated memory decline. These findings indicate that increasing ACSS2 is highly effective in countering age- and tau-induced transcriptome changes, preserving elevated levels of synaptic genes, and safeguarding synaptic integrity. We thus highlight ACSS2 as a key player in the epigenetic regulation of cognitive aging and ADRD, providing a foundation for targeted therapeutics to enhance brain resilience and function.

overall_design: To investigate the transcriptomic changes induced by ACSS2 upregulation in mouse primary hippocampal neurons

first: Naemeh

last: Pourshafie

first: Shelley

last: Berger

first: Nancy

last: Bonini

first: Desi

last: Alexander