title: Comprehensive mass spectrometry screening-derived atlas of HDAC inhibitors revelas histone specific acetylation chnages [RNA-seq]

city: St. Louis

first: Rashmi

last: Karki

address: 660 S. Euclid Ave

institute: Washington University in St. Louis

summary: Histone deacetylases inhibitors (HDACi) have emerged as valuable therapeutics in cancer and other diseases, yet their effect on histone post-translational modification remains incompletely characterized. Here, we applied quantitative mass spectrometry and high throughput sequencing to systematically profile site-specific histone modification changes in response to a panel of HDAC inhibitors. This platform enabled mapping of histone modification changes across hundreds of sites including low abundant histone marks. Furthermore, integrative analysis of ChIP-seq and RNA-seq identified genome wide binding site for a low-abundant histone mark H2A.Z acetylation in HeLa cells and MDA-MB-231 breast cancer cells, highlighting the role of H2A.Z acetylation in regulating gene expression through various biological pathways and specific genes involved in tumor suppressor pathways. Our findings provide a functional resource for identification and quantification of epigenetic changes and transcriptional regulation of histone H2A.Z acetylation upon pharmacological perturbation

overall_design: RNA-seq profiling for HeLa and MDA-MB-231 cells treated with Entinostat (1uM) for 24h. Controls were treated with DMSO. Two replicates were included for  each conditions.

first: Francisca

last: Vitorino

first: Richard

middle: M

last: Searfoss

first: Joanna

last: Lempiäinen

first: Benjamin

last: Garcia

first: Cheryl

middle: H

last: Arrowsmith


title: Ftsj1 deficiency influences diverse ncRNA networks in murine organs (miRNAs)

status: Public on Mar 17 2026

city: Greifswald

first: Stefan

last: Simm

address: Walter-Rathenau-Straße 48

department: Bioinformatics

country: Germany

institute: University Medicine Greifswald

type: Non-coding RNA profiling by high throughput sequencing

summary: Beyond the regulation of mRNAs by individual ncRNA types, such as miRNAs or lncRNAs, their interplay as so-called competitive endogenous RNAs (ceRNAs) appears to play a pivotal role in diseases. In our study we aimed to get a holistic understanding of the tRNA 2’O-methyltransferase FTSJ1 and its regulatory role in the context of cognitive disability. Here, we investigated the impact of Ftsj1 deficiency on ceRNA networks across different mouse organs. Our study underscores the critical role of organ-specific ceRNA networks, particularly in metabolic regulation, and emphasizes the need for cross-organ analyses to unravel the complexity of ceRNA-mediated gene regulation. Our findings reveal a prominent ceRNA network in the liver, mediated by four hub miRNAs (miR-378d, miR-3076-5p, miR-3474, and miR-296-3p) and enriched with acetyl CoA-related genes, including Acly, Acss2, and Mvk. These genes are integral to fatty acid metabolism, which is heavily disrupted in both liver and kidney. In contrast, brain tissues exhibited minimal changes, suggesting only a limited impact directly related to Ftsj1 in this organ. These results suggest that the cognitive disability associated with Ftsj1 is driven by metabolic and ceRNA crosstalk along the liver-brain and kidney-brain axes. This dataset comprises the miRNA-seq data used in our study.

overall_design: RNA-seq profiling of 3 Ftsj1-deficient and 3 wildtype mice with degradome seq in 5 different organs, brain, heart, kidney, liver, spleen.

first: Heiko

last: Dunkel

first: Andreas

middle: W

last: Kuß

first: Lars

middle: R

last: Jensen

first: Oliver

last: von Bohlen und Halbach


title: Ftsj1 deficiency influences diverse ncRNA networks in murine organs (degradome) [RNA-Seq]

summary: Beyond the regulation of mRNAs by individual ncRNA types, such as miRNAs or lncRNAs, their interplay as so-called competitive endogenous RNAs (ceRNAs) appears to play a pivotal role in diseases. In our study we aimed to get a holistic understanding of the tRNA 2’O-methyltransferase FTSJ1 and its regulatory role in the context of cognitive disability. Here, we investigated the impact of Ftsj1 deficiency on ceRNA networks across different mouse organs. Our study underscores the critical role of organ-specific ceRNA networks, particularly in metabolic regulation, and emphasizes the need for cross-organ analyses to unravel the complexity of ceRNA-mediated gene regulation. Our findings reveal a prominent ceRNA network in the liver, mediated by four hub miRNAs (miR-378d, miR-3076-5p, miR-3474, and miR-296-3p) and enriched with acetyl CoA-related genes, including Acly, Acss2, and Mvk. These genes are integral to fatty acid metabolism, which is heavily disrupted in both liver and kidney. In contrast, brain tissues exhibited minimal changes, suggesting only a limited impact directly related to Ftsj1 in this organ. These results suggest that the cognitive disability associated with Ftsj1 is driven by metabolic and ceRNA crosstalk along the liver-brain and kidney-brain axes. This dataset comprises the degradome sequencing data used in our study. Degradome expression levels were used to validate miRNA – mRNA interaction pairs.

overall_design: RNA-seq profiling of 3 Ftsj1-deficient and 3 wildtype mice with degradome seq in 5 different organs, brain, heart, kidney, liver, spleen.  (4 samples per genotype for Spleen)


title: Ftsj1 deficiency influences diverse ncRNA networks in murine organs (poly-A-seq and rRNA-depletion-seq)

type: Expression profiling by high throughput sequencing

summary: Beyond the regulation of mRNAs by individual ncRNA types, such as miRNAs or lncRNAs, their interplay as so-called competitive endogenous RNAs (ceRNAs) appears to play a pivotal role in diseases. In our study we aimed to get a holistic understanding of the tRNA 2’O-methyltransferase FTSJ1 and its regulatory role in the context of cognitive disability. Here, we investigated the impact of Ftsj1 deficiency on ceRNA networks across different mouse organs. Our study underscores the critical role of organ-specific ceRNA networks, particularly in metabolic regulation, and emphasizes the need for cross-organ analyses to unravel the complexity of ceRNA-mediated gene regulation. Our findings reveal a prominent ceRNA network in the liver, mediated by four hub miRNAs (miR-378d, miR-3076-5p, miR-3474, and miR-296-3p) and enriched with acetyl CoA-related genes, including Acly, Acss2, and Mvk. These genes are integral to fatty acid metabolism, which is heavily disrupted in both liver and kidney. In contrast, brain tissues exhibited minimal changes, suggesting only a limited impact directly related to Ftsj1 in this organ. These results suggest that the cognitive disability associated with Ftsj1 is driven by metabolic and ceRNA crosstalk along the liver-brain and kidney-brain axes. This dataset comprises the poly-A and rRNA-depletion total RNA sequencing data used in our study for mRNAs and lncRNAs.

overall_design: RNA-seq profiling of 3 Ftsj1-deficient and 3 wildtype mice with poly-A-seq and rRNA-depletion-seq in 5 different organs, brain, heart, kidney, liver, spleen.


title: Epigenetic control of telomeric RNA maintains heterochromatin in telomerase-driven cancers [nanopore]

status: Public on Mar 18 2026

city: Saskatoon

first: Franco

middle: J

last: Vizeacoumar

state: Saskatchewan

address: 4D40 Health Sciences Building, 107 Wiggins Road

department: Oncology

country: Canada

institute: University of Saskatchewan

summary: Tumor heterogeneity presents a major clinical challenge. Reactivation of telomerase (hTERT) is a near-universal hallmark of cancer, yet direct inhibition of hTERT has shown limited therapeutic benefit. To uncover tractable telomerase-related vulnerabilities, we applied a synthetic dosage lethality (SDL) strategy to identify genes required only when hTERT is overexpressed. We performed genome-wide CRISPR/Cas9 and shRNA screens across multiple isogenic cell line pairs differing in hTERT expression. From these datasets, 100 high-confidence candidates were prioritized and validated using an arrayed in vitro CRISPR screen and a pooled in vivo CRISPR screen across diverse cancer models, non-malignant cells, and patient-derived organoids. Through this pipeline, we identified FTSJ3, an RNA 2′-O-methyltransferase, as a top SDL target of hTERT. Depletion of FTSJ3 selectively impaired the viability of hTERT-positive cancer cells while sparing normal cells. Mechanistically, FTSJ3 installs 2′-O-methylation on the telomeric RNA TERRA, a modification essential for TERRA stability and function. Loss of FTSJ3 destabilizes TERRA, disrupts recruitment of the histone methyltransferase SUV39H1, and diminishes H3K9 trimethylation and HP1 assembly at sub-telomeric regions. This breakdown of repressive telomeric chromatin leads to genome instability and apoptosis specifically in hTERT-positive cells. These findings highlight SDL as a powerful strategy for uncovering telomerase-dependent liabilities and establish FTSJ3 as a central regulator of telomere stability in telomerase-active cancers. Targeting FTSJ3 enzymatic activity offers a promising therapeutic entry point, acting upstream of TERRA to eliminate telomerase-driven malignancies selectively.

overall_design: Nanopore sequencing for the TERRA Seq was performed on 2 models with and without FTSJ3 knockdown. Total of 4 samples

first: Jared

middle: D

last: Price

first: Frederick

middle: S

first: Judy

last: Wong

first: Andrew

last: Freywald


title: Ftsj1 deficiency influences diverse ncRNA networks in murine organs (circRNAs)

summary: Beyond the regulation of mRNAs by individual ncRNA types, such as miRNAs or lncRNAs, their interplay as so-called competitive endogenous RNAs (ceRNAs) appears to play a pivotal role in diseases. In our study we aimed to get a holistic understanding of the tRNA 2’O-methyltransferase FTSJ1 and its regulatory role in the context of cognitive disability. Here, we investigated the impact of Ftsj1 deficiency on ceRNA networks across different mouse organs. Our study underscores the critical role of organ-specific ceRNA networks, particularly in metabolic regulation, and emphasizes the need for cross-organ analyses to unravel the complexity of ceRNA-mediated gene regulation. Our findings reveal a prominent ceRNA network in the liver, mediated by four hub miRNAs (miR-378d, miR-3076-5p, miR-3474, and miR-296-3p) and enriched with acetyl CoA-related genes, including Acly, Acss2, and Mvk. These genes are integral to fatty acid metabolism, which is heavily disrupted in both liver and kidney. In contrast, brain tissues exhibited minimal changes, suggesting only a limited impact directly related to Ftsj1 in this organ. These results suggest that the cognitive disability associated with Ftsj1 is driven by metabolic and ceRNA crosstalk along the liver-brain and kidney-brain axes. This dataset comprises the circRNA sequencing data used in our study.

overall_design: RNA-seq profiling of 3 Ftsj1-deficient and 3 wildtype mice with circRNA-seq in 5 different organs, brain, heart, kidney, liver, spleen.

first: Jonah

last: Schreier

first: Franziska

last: Sperling


title: Xist RNA Dependent and Independent Mechanisms Regulate Dynamic X Chromosome Inactivation in B Lymphocytes [CUTandRUN_PRC2]

city: Philadelphia

first: Montserrat

last: Anguera

state: PA

address: 3800 Spruce Street, Rosenthal Room 390EB

department: Biomedical Sciences

country: USA

institute: University of Pennsylvania School of Veterinary Medicine

type: Genome binding/occupancy profiling by high throughput sequencing

summary: X-chromosome inactivation (XCI) maintenance in female B cells is dynamic (dXCI), where naïve cells lack cytological enrichment of Xist RNA and heterochromatic marks on the inactive X-chromosome (Xi), and these marks re-localize after stimulation. Here, we report the epigenetic profiling of silencing (H3K27me3, H2AK119Ub, H3K9me3, DNA methylation (DNAm)) and activating (H3K27ac) marks on the Xi during dXCI and investigate the requirement for Xist RNA in maintaining the Xi epigenetic landscape. We find that the Xi in naïve B cells is depleted for H2AK119Ub and H3K9me3 but enriched for DNAm and H3K27me3 which maintain an epigenetic memory of transcriptional silencing dependent on Xist RNA. Upon stimulation, Xist-independent H3K27me3 and Xist-dependent H2AK119Ub modifications accumulate across the Xi. Thus, naïve B cells maintain an epigenetic memory of silencing in the absence of Xist RNA localization via retention of DNAm and H3K27me3, and both H3K27me3 and H2AK119Ub accumulate on the Xi post-stimulation in an Xist-dependent and -independent manner. These data have critical implications for understanding molecular mechanisms underlying female-biased immune responses.

overall_design: CUT&RUN analysis for the histone modification H3K27me3 in unstimulated CD23+ B cells. B cells originated from mice with an Ezh2 conditional deletion using CD19-cre (n=2 WT control and 2 cKO) or from female F1 mus x cast mice treated with the Ezh2 inhibitor EPZ6438 (n=1 DMSO control, 1 6-day EPZ treatment, 1 7-day EPZ treatment).

first: Natalie

middle: E

last: Toothacre

middle: C


title: Xist RNA Dependent and Independent Mechanisms Regulate Dynamic X Chromosome Inactivation in B Lymphocytes [WGBS]

type: Methylation profiling by high throughput sequencing

overall_design: Whole genome bisulfite sequencing analysis in F1 mus x cast CD23+ B cells that were unstimulated or stimulated for 24 hours with CpG (n = 3 per condition). F1 mus x cast is a hybrid mouse model of skewed XCI generated through mating female C57BL/6 mice harboring a heterozygous Xist deletion to male M. m. castaneous mice.


title: A Respiratory Syncytial Virus trailer sequence modulates viral replication and copy-back defective viral genome generation and propagation kinetics

city: Rochester

first: Justin

last: Brennan

state: NY

address: 601 Elmwood Ave.

department: Microbiology & Immunology

institute: University of Rochester Medical Center

summary: Copy-back defective viral genomes (cbDVGs) are key inducers of antiviral responses during negative-sense RNA virus infection. Once considered byproducts of in vitro viral replication, cbDVGs have since been detected in clinical specimens and implicated in affecting infection outcomes. The molecular mechanism of cbDVG generation remains unclear, thereby hindering our ability to manipulate cbDVG production during infection for therapeutic gain. Previous work showed that respiratory syncytial virus (RSV) cbDVG re-initiation sites cluster in trailer-end hotspots R1, R2, and R3, and that a poly-U mutation in R1 selectively reduced cbDVG formation at the mutated region. Here, we reported that a 10U mutation in R2 drastically reduced cbDVGs in this region in both minigenome and recombinant virus systems. Furthermore, during high-MOI passaging of the R2-10U virus, we observed delayed detection of cbDVGs with re-initiation sites in R1-R3 (trailer cbDVGs) compared to WT, while no differences in virus titers were observed. Interestingly, we observed the rapid emergence and accumulation of a viral variant bearing a 2-ribonucleotide deletion (R2-8U) within the R2-10U mutation sequence as early as P0. Compared to R2-10U, the R2-8U virus was stable, displayed faster generation and accumulation of trailer cbDVGs, restored cbDVGs with R2 re-initiation sites, and exhibited enhanced genomic replication. Overall, our data identify a sequence in the RSV trailer whose mutation critically modulates both viral replication and the generation/propagation of trailer cbDVGs. Our data also suggest that cbDVG generation, particularly near the trailer, may be an evolutionary tradeoff for more rapid virus genomic replication.

overall_design:
To investigate the impact of mutations in the RSV trailer sequence on the generation and accumulation of copy-back defective viral genomes we serially passaged WT, R2-10U, and R2-8U viruses at  MOI 5 to generate viral stocks enriched with cbDVGs (HD). Figure 3: total RNA was extracted from the supernatants of infected passage 10 (P10) cells for the WT and R2-10U viruses. Total RNA was extracted from the HD supernatants of passage 6 (P6) cells for R2-8U. To generate viral stocks with low cbDVG content (LD) WT and R2-10U passage 3 viruses were passaged at MOI 0.001 until passage 5 (P5) and total RNA was extracted from the supernatants of infected cells. For HD and LD viruses, 2 WT lineages (L1-L2) and 3 R2-10U lineages (L1-L3) were made by passaging in independent HEp2 cell infections. 1 R2-8U HD lineage was sequenced. Figure 6: passaging and RNA extraction were performed as described. Here, lineages refer to 2 independent instances of the RSV reverse genetic system. Note that HD virus passaging proceeded to P5 while LD passaging proceeded to P4. Additionally, note that HD and LD passaging began at P3, respectively. To confirm that the R2-8U mutation was not an artifact arising during transcription or RNA sequencing, an RSV mini genome construct bearing the R2-10U mutation was in vitro transcribed, DNase digested and lithium chloride purified prior to RNA-sequencing. Note that these files are named 10U_R1 and 10U_R2.
RNA-seq data was analyzed using the ViReMa algorithm to identify the break/rejoin junction sequences that are unique to cbDVGs and do not fully align to the viral reference genome.

first: Yan

last: Sun


title: Defective ventral neurogenesis due to midfetal Chd8 mutation drives autistic-like behavior in mice

city: Kanazawa

first: Kenta

last: Nitahara

state: Ishikawa

address: 13-1, Takaramachi

department: Department of Histology and Cellular Biology

country: Japan

institute: Kanazawa Univeristy

summary: Autism spectrum disorder (ASD) is a common neurodevelopmental condition characterized by behavioral abnormalities. Although mouse models have been widely adopted to recapitulate the pathology of ASD, the identification of specific neural abnormalities responsible for autistic-like behavior has remained challenging. Here we provide insight into this causal relation by identifying the critical period and cell type responsible for the development of such behavior in ASD model mice with a Chd8 mutation. We found that Chd8 mutation induced at embryonic day 14.5 gave rise to ASD-like behavioral phenotypes, including abnormal social interaction and increased anxiety-like behavior, as well as to accelerated cell-cycle exit and differentiation in ventral progenitor cells. Restoration of Chd8 expression in ventral progenitor cells ameliorated both the behavioral phenotypes and aberrant ventral differentiation in Chd8 mutant mice. Our findings indicate that Chd8 mutation during the midfetal period—in particular, in ventral progenitor cells—contributes to the development of autistic-like behavior.

overall_design: scRNA-seq analysis was performed using tdTomato-positive cells from the forebrains of mice at P5 (Chd8 control vs mutant). The target cells were isolated by fluorescence-activated cell sorting according to the presence or absence of tdTomato signal.

first: Atsuki

last: Kawamura

first: Masaaki

last: Nishiyama


title: Xist RNA Dependent and Independent Mechanisms Regulate Dynamic X Chromosome Inactivation in B Lymphocytes [CUTandRUN_F1]

overall_design: CUT&RUN analysis for the histone modifications H3K27me3, H2AK119Ub, H3K27ac, and H3K9me3 and the Polycomb subunits Ring1B and Suz12 in F1 mus x cast CD23+ B cells that were unstimulated or stimulated for 12 or 24 hours with CpG (n = 3-5 per condition). F1 mus x cast is a hybrid mouse model of skewed XCI generated through mating female C57BL/6 mice harboring a heterozygous Xist deletion to male M. m. castaneous mice.


title: Xist RNA Dependent and Independent Mechanisms Regulate Dynamic X Chromosome Inactivation in B Lymphocytes [CUTandRUN_Xist]

overall_design: CUT&RUN analysis for the histone modifications H3K27me3, H2AK119Ub, and H3K27me3 in CD23+ B cells with an in vivo or ex vivo deletion of Xist RNA. in vivo experiments use B cells from female mice with an mb1-cre Xist conditional deletion that were unstimulated or stimulated for 24 hours with CpG (n=3-4 WT control and 3-5 cKO). ex vivo experiments use B cells from female Xist flox/flox mice that were unsitmulated or treated ex vivo with TAT-Cre recombinant protein then stimulated with CpG for 24 hours (n=3 WT and 3 KO).


title: RNA-seq analysis of subcutaneous white adipose tissues from pancreatic tumor-bearing mice and non-tumor controls

city: New York

first: Christine

last: Chio

address: 1130 St. Nicholas Ave

institute: Columbia University Medical Center

summary: At 4-5 weeks post-surgery, a time when adipose depletion is robust by tumor progression, the transcriptome of sWAT from tumour-bearing mice is strongly enriched for oxidative phosphorylation as well as markers of adipose browning such as Elovl3, Ucp1, and Dio2.

overall_design: Pancreas ductal adenocarcinoma (PDAC) cells are orthotopically tranplanted to MSRA WT and MSRA full-body KO host, and subcutaneous adipose tissues are collected at 4-5 weeks post-surgery. Total RNA (RIN value > 7) was extracted from adipose tissues, and poly-A pull-down was performed to enrich mRNAs. Library construction was performed using Illumina TruSeq chemistry, with the final PCR step being modified using the KAPA HiFi HotStart Ready Mix. Libraries were sequenced using Element AVITI at Columbia Genome Center.


address: 13-1 Takaramachi

department: Department of Histology and Cell Biology

institute: Graduate School of Medical Sciences, Kanazawa University

summary: Autism spectrum disorder (ASD) is characterized by its distinctive behavioral abnormality. Often mouse models were adopted to recapitulate the ASD pathology, however, difficulties reside in distinguishing neural abnormalities primarily responsible for the autistic behavior. Chromatin remodeler, CHD8, is encoded by the most frequently mutated gene in individuals with ASD. Here we investigated the etiology of the ASD due to CHD8 mutation by identifying the critical period to develop behavioral symptoms. By applying inducible Cre/loxP system and behavioral examinations, we discovered that neural stem cell-specific mutation of Chd8 at E14.5, but not at E17.5, manifested behavioral phenotypes. Single cell transcriptome analysis revealed that Chd8 mutation was associated with premature cell-cycle exit and differentiation at ventral progenitor cells. Furthermore, we generated a knock-in mouse to restore CHD8 expression in a Cre-dependent manner. CHD8 restoration in neural stem cells at E14.5 or ventral progenitor cells ameliorated behavioral phenotypes whereas the restoration in neural stem cells at E17.5 did not. These findings suggested that Chd8 mutation at 14.5 especially in ventral progenitor cells was associated with behavioral abnormality. The combination of behavioral examinations and transcriptome analysis allowed us to find the association between neural changes and behavioral symptoms.

overall_design: Nanostring CosMx Mouse Neuroscience Panel was applied to WT and Chd8 mutant brain at adulthood.


title: Alternative splicing-triggered mRNA decay informs splice-switching targets for neurodevelopmental disorders

status: Public on Mar 16 2026

city: Chicago

first: Xiaochang

last: Zhang

state: IL

department: Department of Human Genetics

institute: University of Chicago

summary: Alternative splicing-triggered nonsense-mediated mRNA decay (AS-NMD) critically regulates gene expression, but the extent to which neuronal genes are regulated by AS-NMD remains understudied. Here, we identified more than 3,000 developmentally regulated AS-NMD exons in mouse and human brains, and validated them in cultured neurons. AS-NMD suppresses synaptic genes during brain development and differentially regulates more than 200 causal genes for neurodevelopmental disorders (NDDs). We detected an AS-NMD exon in GRIA2 and identified splice-switching antisense oligonucleotides that suppressed GRIA2 NMD and increased its functional isoforms. In summary, this study uncovers genes repressed by AS-NMD in the brain and nominates amenable splice-switching targets for treating dominant NDDs such as autism spectrum disorders and developmental epileptic encephalopathy.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: (1) Neuroa2 Upf1 siRNA and control. (2) Primary neurons from E16.5 CD1 mouse, CHX and DMSO. (3). Human iPSCs induced neurons (day 4), CHX and DMSO treatments


title: Epigenetic control of telomeric RNA maintains heterochromatin in telomerase-driven cancers [array]

overall_design: Samples were collected at different time points after infection with the 90k shRNA libraries and probes were prepared to hybridize to microarray chips to identify SDL partners of TERT gene.

first: Omar

last: Abuhussein


title: Preconception exposures of female mice to a panel of metabolic disruptors induce sexually dimorphic metabolic perturbations in their offspring

city: Santa Cruz

first: Carlos

last: Diaz-Castillo

state: California

address: 448 Physical Sciences Building

institute: University of California Santa Cruz

summary: In recent years, there has been a growing emphasis on research investigating the transmission across generations of the effects of exposure to environmental factors, which may predispose to chronic diseases. It has been hypothesized that the propagation of such effects is mediated by alterations in gene regulatory elements, such as DNA methylation, histone modifications, and non-coding RNAs. Studies in Drosophila and mice have demonstrated that the compartmentalization of eukaryotic genomes into heterochromatin and euchromatin can mediate multigenerational metabolism-disrupting effects elicited by exposure to various metabolism disruptors. These findings suggest that eukaryotic nuclear genomes may possess the capacity to integrate the impact of environmental cues in a metastable manner that is phenotypically relevant. Here, we present the results of a murine model to assess whether preconception exposure to three metabolism disruptors of distinct nature, including dietary factors and environmental toxicants, intended to emulate the complexity of human exposures, results in metabolic alterations in the offspring of exposed individuals. Our findings align with our central hypothesis but also open an unexpected avenue to explore whether preconception exposure to metabolism disruptors predisposes the offspring of exposed individuals to not only typical metabolic diseases such as obesity but also to complex metabolic-psychiatric conditions such as anorexia.

overall_design: We generated RNA-seq data from gonadal white adipose tissue (GWAT) and liver samples from 11-week-old female and male mice, first-generation (F1) descendants of five groups of female mice exposed for 3.5 weeks to the following combinations of treated water and diets: 0.1% dimethylsulfoxide (DMSO) in water and a control diet (CD; Envigo Teklad Diets TD.140148) [DMSO group], 5 nM tributyltin (TBT) and 0.1% DMSO in water and CD [5TBT group], 50 nM tributyltin and 0.1% DMSO in water and CD [50TBT group], 10 µg/L sodium meta(arsenite) (inorganic arsenic, iAs) and 0.1% DMSO in water and CD [IAS group], and 0.1% DMSO in water and Total Western Diet (TWD; Envigo Teklad Diets TD.110919) [TWD group]. A total of 100 samples were collected: 5 exposure groups x 2 F1 sexes x 2 tissues (GWAT and liver) x 5 biological replicates.

first: Stephanie

last: Aguiar

first: Raquel

last: Chamorro-Garcia


title: SLC1A5 prevents aortic aneurysm and dissection by glutaminolytic-epigenetic orchestration of vascular smooth muscle cell homeostasis [CUT&Tag]

city: Guangzhou

first: Zhiping

last: Liu

state: Guangdong

address: No. 855, East Xingye Avenue

country: China

institute: Jinan University

summary: In this study, we found that H3K9ac level were reduced both in vitro (Slc1a5 knockdown VSMCs) and in vivo (Slc1a5 knockout mice). To further investigate the potential functional significance that SLC1A5-mediated H3K9ac contributed to the pathogenesis of aortic aneurysm and dissection (AAD), we performed genome-wide cleavage under targets and tagmentation (CUT&Tag) analysis to identify candidate genes regulated by H3K9ac (CST, 9649S) in Slc1a5 knockdown mouse VSMCs. Following CUT&Tag, H3K9ac associated DNAs were amplified using non-biased conditions, labeled, and sequenced with Illumina novaseq Xplus.

overall_design: The CUT&Tag assay was performed on Slc1a5 knockdown mouse vascular smooth muscle cells to specifically capture and sequence the DNA fragments associated with H3K9ac binding sites regulated by SLC1A5.

first: Pinglian

last: Yang

first: Zhechang

last: Gao

first: Weile

last: Ye

first: Ke

last: He

first: Suowen

last: Xu

first: Jiaojiao

last: Wang


title: Single-cell RNA analysis of allele-specific MHC expression in peripheral blood mononuclear cells of Mauritian-origin cynomologus and Indian-origin rhesus macaques

city: Madison

first: David

last: O'Connor

state: WI

address: 585 Science Drive

department: Pathology and Laboratory Medicine

institute: University of Wisconsin-Madison

summary: We have employed a single-cell sequencing approach using 10X Genomics 5'scRNAseq to study expression of the Major Histocompatibility Complex (MHC) in peripheral blood mononuclear cells (PBMC) from Mauritian-origin cynomolgus and Indian-origin rhesus macaques. The MHC region has undergone a complex series of duplications in macaques relative to humans. Steady-state RNA levels of macaque MHC class I and class II transcripts vary over several orders of magnitude in whole blood and bulk PBMC. This study represents the first 5'scRNAseq analysis to quantify allele-specific levels of MHC transcripts in various PMBC subsets of macaques and provides insights into how they may shape immune responses.

sample_organism:
Macaca fascicularis
Macaca mulatta

platform_organism:
Macaca fascicularis
Macaca mulatta

overall_design: Peripheral blood mononuclear cells (PBMC) from Mauritian-origin cynomolgus and Indian-origin rhesus macaques were isolated from fresh whole blood by Ficoll-Plaque centrifugation and analyzed using 5' scRNA-seq

first: Max

last: Ertl

first: Roger

last: Wiseman

first: Anthony

last: Veltri

first: Julie

middle: A

last: Karl

first: Miranda

last: Stauss

first: William

middle: K

last: Gardner

first: Nicholas

last: Minor


title: Bioinspired, Mitochondria-targeted Single-atom Nanozyme Enhances Bone Regeneration by Reprogramming Stem Cell Energy Metabolism

city: hongkong

first: yuwen

last: wang

address: G10A, G/F, Run Run Shaw Science Building,

department: Biomedical Engineering

country: Hong Kong

institute: The Chinese University of Hong Kong

summary: A bioinspired nanozyme—TPP-DMSN-Fe/Cu—mimics mitochondrial complex IV and targets mitochondria to regulate cellular energy metabolism. This approach markedly boosts bone regeneration in vivo, as demonstrated by enhanced bone volume and mineral density in critical-sized bone defects rat models. The study opens new avenues for mitochondria-targeted therapies in bone repair.

overall_design: Control group; DMSN group; DMSN-Fe/Cu group; TPP-DMSN-Fe/Cu group (all 10ug/ml) treat with C3H/10T1/2 after 7 days osteogenic differentiation.

first: Yuwen

first: Zhong

last: Li


title: Microbiota-derived polyphosphates govern mucosal immunity through multilevel suppression of STAT/IL-27 signaling  (multiome)

city: Boston

first: Markus

last: Bosmann

state: MA

address: 72 E Concord Street

department: Pulmonary Centre, Department of Medicine

institute: Boston University

summary: The interplay between gut bacteria and mucosal immune cells is crucial for maintaining intestinal homeostasis. Dysregulation of this immune-microbiome axis has been implicated in the pathogenesis of inflammatory bowel diseases, but the mechanisms driving the health-to-disease transition remain unclear. Here, we demonstrate that polyphosphates, a bacterial metabolite, influence mucosal immunity during both homeostasis and inflammation. Germ-free mice were monocolonized with polyphosphate competent Escherichia coli or a ∆ppk E. coli mutant strain deficient in polyphosphate production, affecting subsets of T cells and mononuclear phagocytes. Transfer of lamina propria immune cells into RAG1-/- mice indicated that polyphosphate-experienced T cells induced more severe colitis. Mechanistically, polyphosphate exposure suppressed chromatin accessibility of the Stat1, Stat3 and Il10 genes in CD4+ T cells. Ultra-pure polyphosphates corresponding to the molecular sizes produced by microbes decreased gene expression of STATs as observed by snRNA-seq, antagonized IL-27 production in mononuclear phagocytes through suppression of STAT1, and disrupted IL-27-induced STAT1/STAT3 phosphorylation in naïve CD4+ and CD8+ T cells. IL-27Rα-/- lamina propria immune cells were more aggressive in promoting colitis, suggesting that the paralyzing effects of polyphosphates on IL-27/IL-27Rα signaling are functionally significant. In conclusion, the intestinal microbiota utilizes polyphosphates to disrupt the protective balance of innate and adaptive immune cell networks.

overall_design: 4 individual sets of peritoneal cells were stimulated with long-chain polyphoshates for 18 hours or remained untreated. 7-AAD-CD45+ cells were flow sorted and single-nuclei ATAC and RNA-seq was performed.

first: Kevin

last: Brueck

first: Archana

last: Jayaraman


title: RNA sequencing analysis of A498 renal cancer cells following knockdown of ELOVL2 and ELOVL5

city: Tsukuba

first: Shotaro

last: Sakka

state: Ibaraki

address: 1-1-1 Tennodai

institute: University of Tsukuba

summary: Long-chain fatty acid elongases ELOVL2 and ELOVL5 are key regulators of polyunsaturated fatty acid metabolism. To investigate transcriptomic changes induced by depletion of these enzymes, RNA sequencing was performed in A498 renal cancer cells following siRNA-mediated knockdown of ELOVL2 and/or ELOVL5. Transcriptomic profiles were compared among control cells, ELOVL2 knockdown cells, ELOVL5 knockdown cells, and double knockdown cells.

overall_design: A498 renal cancer cells were transfected with control siRNA or siRNAs targeting ELOVL2, ELOVL5, or both genes. Three biological replicates were analyzed for each condition, yielding 12 samples in total. Libraries were sequenced on an Illumina NextSeq 500 platform using paired-end 36-base reads.


title: An atlas of genetic effects on the monocyte methylome across European and African populations

city: New Orleans

first: Hong-Wen

last: Deng

state: LA

institute: Tulane University

summary: This study investigates the genetic regulation of DNA methylation in purified human monocytes across African American and European American populations. Whole-genome bisulfite sequencing (WGBS) and whole-genome sequencing (WGS) were performed on participants from the Louisiana Osteoporosis Study cohort to characterize methylation quantitative trait loci (meQTLs), heritability patterns, and methylome-wide associations with complex traits. The study provides a comprehensive multi-ancestry monocyte methylome atlas.

overall_design:
Peripheral blood samples were collected from African American and European American adult males. Monocytes were purified using negative selection. DNA methylation was profiled using whole-genome bisulfite sequencing, and genetic variation was assessed using whole-genome sequencing. Cis- and trans-meQTL analyses, methylation heritability estimation, methylation imputation modeling, and methylome-wide association studies were conducted. Processed methylation matrices are provided as chromosome-specific files.

***************************************************************
Based on guidance from the NIH Program Office, arrangements are currently underway to deposit the raw WGBS data (for human/patient samples) in the NIH Aging Research Biobank, an authorized NIH-designated controlled-access repository.
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first: Wanheng

last: Zhang

first: Chuan

last: Qiu

first: Xiao

first: Zichen

first: Kuan-Jui

last: Su

first: Zhe

last: Luo

first: Minghui

last: Liu

first: Bingxin

last: Zhao

first: Lang

last: Wu

first: Qing

last: Tian

first: Hui

last: Shen

first: Chong


title: Müllerian duct maintenance at the cranial region is promoted by Gata2

first: Fei

address: 2015 Linden Drive, Room 4206/4210

department: CBS

institute: School of Veterinary Medicine, University of Wisconsin Madison

summary: The paradigm of sexual differentiation holds that female embryos retain Müllerian ducts (the precursor of female reproductive tract organs) by default in the absence of anti-Müllerian hormone (AMH). Whether Müllerian duct maintenance requires active signaling has remained unclear. Here, we show that deletion of mesenchymal Gata2 induces selective regression of the cranial Müllerian duct (future oviduct). This regression did not result from ectopic AMH signaling but from loss of region-specific NRG1 signaling. In contrast, the caudal Müllerian duct (future uterus) was retained but displayed disrupted epithelial differentiation when Gata2 was deleted in either mesenchymal or epithelial compartments. Our findings reveal a region-specific, GATA2-dependent program that actively maintains the cranial Müllerian duct, reshaping our understanding of female reproductive tract development.

overall_design: Cranial and caudal Mesonephros were collected from control and Gata2 cKO embryos at E16.5 and snap-frozen on dry ice. RNA was extracted using the PicoPure RNA Isolation Kit (Life Technologies, KIT0204) according to the manufacturer’s protocol. Three samples per region per group were sent to Novogene for bulk RNA sequencing.

first: Shuai

last: Jia


title: Dissecting the cellular architecture of breast cancer brain metastases reveals prognostically distinct immune landscapes

city: Heidelberg

first: Christel

last: Herold-Mende

department: Department of Neurosurgery

institute: University Hospital Heidelberg

summary: Breast cancer brain metastases (BCBM) are a severe condition with high demand for improved personalized treatment, but a comprehensive understanding of BCBM immune-microenvironment heterogeneity and susceptibility to immunotherapy is lacking. Here, we multimodally profile the immune niche in a clinically well-annotated cohort of 156 BCBM applying tissue cytometry, bulk and single nuclei RNA-sequencing, flow cytometry, and spatial transcriptomics, complemented by functional studies in patient-derived models. Integrative analyses reveal two immune landscapes predicting prolonged patient survival and that are not deducible from paired primary tumors: 1) BCBM with a high proportion of CD8+ tissue-resident-like memory T cells as major players of tumor immune control. 2) BCBM containing tertiary lymphoid structures. Surrogate signatures of these landscapes are prognostic in independent BCBM and primary breast cancer cohorts, are associated with fewer metastases, and predict immunotherapy response. Our work provides critical insights into anti-tumor immunity in BCBM and identifies novel biomarkers with translational relevance.

overall_design: Refer to individual Series

first: Lena

last: Jassowicz

first: Rolf

last: Warta


title: Targeting RANKL-Independent Osteoclastogenesis Overcomes Denosumab Resistance in ER+ Breast Cancer Bone Metastasis [circRNA-seq]

first: Chang

last: Gong

address: No. 107, Yanjiang West Road, Yuexiu Dist

institute: Sun Yat-sen Memorial Hospital, Sun Yat-sen University

summary: Bone metastasis remains a major cause of morbidity in ER+ breast cancer, with RANKL inhibitor resistance emerging as a critical clinical challenge. Nearly 40% of patients develop progressive skeletal lesions despite denosumab therapy, highlighting an urgent need to identify resistance mechanisms and alternative therapeutic strategies. We identified a RANKL-independent osteoclast activation pathway mediated by the CRKL/circCCDC50/NFATc1 axis. Mechanistically, CRKL promotes EIF4A3-dependent circCCDC50 biogenesis, which is packaged into large oncosomes and transferred to osteoclast precursors. Nuclear circCCDC50 recruits CARM1 to epigenetically activate NFATc1 transcription, establishing a self-reinforcing loop that sustains osteolysis despite RANKL blockade. Pharmacological inhibition of CARM1 (TP-064) effectively suppresses osteoclastogenesis and bone metastasis in denosumab-resistant models. These findings reveal a targetable resistance mechanism and provide a clinically actionable strategy to overcome microenvironment-driven metastasis through dual targeting of tumor and bone niches.

overall_design: circRNA-seq profiling of large oncosomes from primary breast cancer cells derived from a Denosumab-responsive patient (#3) and a non-responsive patient (#5).

first: Qun

last: Lin

first: Jinpeng

first: Zhuxi

last: Duan


title: EBV INFECTION OUTCOMES DETERMINED BY MONOCYTE AND TREG-DRIVEN IMMUNE DYNAMICS IN AN EX VIVO PBMC MODEL

first: Priyankara

last: Wickramasinghe

address: 3601 Spruce Street

institute: The Wistar Institute

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


title: Targeting RANKL-Independent Osteoclastogenesis Overcomes Denosumab Resistance in ER+ Breast Cancer Bone Metastasis [RNA-seq]

overall_design: RNA-seq profiling of primary breast cancer cells derived from Denosumab-responsive patients (#1, #2, #3) and Denosumab-non-responsive patients (#4, #5, #6).


title: Foxl2 preserves chromatin accessibility at a distal super-enhancer which regulates the Fshb-Kcna4 locus

city: London

first: Probir

last: Chakravarty

address: 1Midland Road

country: United Kingdom

institute: Francis Crick

summary: A large “gene desert” located far upstream from Fshb and Kcna4 contains several gonadotrope-specific accessible chromatin sites which were seen in chromatin conformation capture (3C) to make distinct contacts with both genes. Expression of Fshb and Kcna4 was strongly inhibited by JQ-1, which represses super-enhancer activity, and the region displays super-enhancer characteristics. The sites of open chromatin were seen, in chromatin immunoprecipitation (ChIP), to bind Brd4 and Med1, most notably at a site -67 kb from the Fshb gene, as well as binding Ctcf further upstream (-123 kbp), all of which were increased following activin exposure. The locus is transcribed to chromatin-associated lncRNAs whose levels correlate with Fshb and Kcna4 mRNA levels in vivo and in cultured gonadotrope cells, indicating coordinated regulation. CRISPR interference (CRISPRi) confirmed distinct functions for each element and, together with the 3C data, indicate that the -67 kb locus mediates basal and activin-stimulated Fshb expression, while the site at -59 kb contributes to activin-stimulation of both genes. Single-cell multiomics revealed that the -67 kb locus is accessible in pituitary stem cells and throughout gonadotrope differentiation, preceding opening of the Fshb promoter, although it is closed in other differentiated cell types, suggesting a gonadotrope-specific factor that keeps it open at this stage. Foxl2 was found to bind this element, contributes to maintaining its chromatin accessibility, and recruits Supt16h, a component of the Facilitates Active Chromatin Transcription (FACT) histone chaperone complex. These findings define a distal, Foxl2-bound super-enhancer that regulates Fshb transcription and shapes the gonadotrope regulatory landscape.

overall_design: Multiomic analysis of single nuclei from sorted Sox9iresGFP positive pituitary cells from P3 males and females

first: Tal

last: Refael

first: Gil

last: Golan

first: Daniella

last: Darsa

first: Lilach

last: Pnueli

first: Karine

last: Rizzoti

first: Philippa

last: Melamed


title: Catestatin impedes melanoma progression and drug resistance by reprogramming oncogenic signaling pathways

city: San Diego

first: Satadeepa

last: Kal

address: 9500 GILMAN Dr

institute: UCSD

summary: Melanoma remains one of the most aggressive and treatment-resistant cancers, emphasizing the need for novel therapeutics. In our current study we report a peptide-based approach as potential therapeutic. The expression and role of Catestatin(CST), a Chromogranin A(CgA)-derived peptide with immunomodulatory and reparative properties in skin injury led us to examine its connection to melanoma. Advancing melanoma stages showed decreased CST expression. CST administration to patient derived cells and melanoma cell lines A375, B16F10, SKMEL28 revealed increased apoptosis, decreased proliferation and metastatic ability of the melanoma cells without affecting cell viability for normal skin fibroblasts. CST reduced growth kinetics and tumor weight in B16F10 derived in vivo melanoma tumors. Transcriptomic analyses of catestatin treated human cell line and mouse tumor revealed downregulation of hypoxia, collagen remodeling, epithelial to mesenchymal transition pathways (EMT), stress adaptive responses that are accountable for melanoma progression. In Vemurafenib-resistant A375 cells, CST increased apoptosis and repressed multiple resistance associated genes. These results highlight CST as a promising therapeutic candidate capable of opposing melanoma progression and overcoming resistance to current targeted treatments.

overall_design: RNA-seq was performed on mouse tumor tissue (C and S groups) and human A375 melanoma cell lines (B, SS, RC, RS groups) with CST-treated and control conditions. Libraries were sequenced on Illumina NovaSeq 6000 (paired-end), and differential expression analyses compared CST-treated versus control within each group.

first: Suborno

last: Jati

first: Sushil

last: Mahata


title: Clec3b⁺ fibroblasts are the primary effectors of portal fibrosis following activation via a KLF4/periostin axis

city: Changchun

first: Lin

last: Lei

address: 5333 Xi’an Road, Changchun, Jilin, China

department: State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, College of Veterinary Medicine

institute: Jilin University

summary: Portal fibrosis, a determinant of progression in virtually all chronic liver diseases, prototypically develops in biliary diseases. Using single-cell RNA sequencing and genetic cell fate tracing in mouse models, we identified Clec3b⁺ fibroblasts as a distinct subset of portal fibroblasts, which rapidly expand after biliary injury and give rise to the bulk portal myofibroblasts. Mechanistic analyses revealed that Clec3b⁺ portal fibroblasts activation is governed by a Krüppel-like factor 4 (KLF4)/periostin (POSTN) axis, i.e., KLF4 directly binds the Postn promoter and represses its transcription in quiescent fibroblasts, whereas after injury, KLF4 is downregulated, which allows POSTN, acting via αvβ5 integrin, to drive portal fibroblast activation and portal fibrosis. Our findings identify Clec3b+ portal fibroblasts as the primary effectors of portal fibrosis and demonstrate that the KLF4/POSTN signaling axis regulates their activation, offering potential therapeutic targets for inhibiting fibrosis in biliary diseases.

overall_design:
We conducted a comprehensive scRNA-seq analysis of the bilio-vascular trees from the mice  subjected to bile duct ligation (BDL)-induced cholestasis, and compared the profiles with those of control mice. We identified 15 major hepatic cell clusters comprising myeloid cells, lymphoid cells, endothelial cells, epithelial cells, and mesenchymal cells, and explored the extent of cell diversity within fibrotic mesenchymal cell populations.

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The table below lists GEO accessions reused/reanalyzed for this study.
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last: LEI

first: Chenchen

last: ZHAO

first: Wenwen

last: GAO

first: Guowen

last: LIU

first: Xinwei

last: LI


title: Programmable RNA-triggered counterselection in eukaryotic cells using CRISPR-Cas12a2

city: Salt Lake City

first: Emily

middle: Rose

last: Wilson

state: UT

address: 2000 Circle of Hope

department: Oncological Sciences

institute: Huntsman Cancer Institute

summary: To identify upregulated gene sets and pathways enriched by GeCas12a2 activation.

overall_design: RNA-seq in HeLa cervical cancer cells expressing GFP, treated with GeCas12a2 in complex with either a GFP targeting gRNA (gGFP), a non-targeting gRNA (gNT), or treated with Nigericin as a positive control or phosphate buffered saline (PBS) as a vehicle control.

first: Jared

last: Thompson

first: Xiaoyang

last: Zhang

first: Yang

last: Liu


last: Zhao

state: Jilin Province

address: 5333 Xi’an Road

department: College of Veterinary Medicine

overall_design: To investigate the potential mechanisms by which KLF4 influences the transition of Clec3b-tdT⁺ portal fibroblasts into myofibroblasts, Clec3b-tdT⁺ cells were isolated from the livers of normal Clec3bCreERT2;R26tdT mice via fluorescence-activated cell sorting (FACS). These cells were then transduced with either a Klf4-overexpressing lentivirus (Lenti-Klf4) or a control lentivirus (Lenti-Ctrl). Following transduction, total RNA was extracted from the cells under both conditions, and RNA-seq was performed to analyze the gene expression profiles of Clec3b-tdT⁺ cells in response to Klf4 overexpression compared to the control.

last: Gao

first: Menglin

first: Guoyue

last: Lv

first: Zhongqi

last: Fan

first: Chantal

last: Housset

first: Fouad

last: Lafdil

first: Axelle

last: Cadoret

first: Sara

last: Lemoinne

first: Yongkang

last: Cheng

first: Jinxia

last: Li

first: Fanrong

last: Kong

first: Xiliang

last: Du

first: Yuxiang

last: Song


title: Fis suppresses late-stage virulence gene expression in Yersinia pseudotuberculosis at environmental temperatures

city: Bochum

first: Franz

last: Narberhaus

address: Universitätsstraße 150

department: Microbial biology

institute: Ruhr University Bochum

summary: The nucleoid-associated protein Fis is a key transcriptional regulator in Gram-negative bacteria that supports rapid adaptation to environmental changes. In Yersinia pseudotuberculosis, Fis plays a critical, yet poorly understood role in virulence. Here, we present a comparative transcriptomic analysis of Y. pseudotuberculosis wild type and fis deletion mutant at environmental (25°C) and host-relevant (37°C) temperatures. Our data show that Fis modulates the expression of more than 600 genes across 16 functional categories. Notably, Fis exerts reciprocal, temperature-dependent control over virulence genes, including those encoding the type III secretion system (T3SS) and Yersinia effector proteins (Yops), flagella biosynthesis, and cell adherence/invasion factors. Functional assays revealed that fis deletion disrupts this regulatory balance, producing a host-defense-like state at 25°C characterized by complete loss of motility, upregulation of the virulence master regulator LcrF, aberrant Yop secretion, impaired phagocytosis by host cells, and increased pathogenicity in the Galleria mellonella infection model. These findings establish Fis as a central regulator that coordinates motility and early host-cell engagement while preventing premature activation of antiphagocytic defenses, thereby optimizing the initial stages of infection.

overall_design: Illumina RNA sequencing of the transcriptomes of Yersinia pseudotuberculosis wild type and fis deletion mutant (dfis) at different growth phases (OD600 0.5 & 1.5) and different temperatures (25°C & 37°C)

first: Soheila

last: Javadi

first: Stephan

last: Pienkoß

first: Dominik

last: Meggers

first: Andrea

last: Wimbert

first: Vivian B.

last: Brandenburg

first: Pascal

last: Dietze

first: Sina

last: Schäkermann

first: Lilo

last: Greune

first: Petra

last: Dersch


title: UV irradiation alters TFAM binding specificity and compaction of DNA

city: Worcester

first: Raluca

last: Gordan

address: 368 Plantation St, AS5-1059

department: Genomics and Computational Biology

institute: University of Massachusetts Chan Medical School

summary: Mitochondria lack nucleotide excision repair; however, mitochondrial DNA (mtDNA) is resistant to mutation accumulation following DNA damage. These observations suggest additional damage sensing or protection mechanisms. Transcription Factor A, Mitochondrial (TFAM) compacts mtDNA into nucleoids and binds differentially to certain forms of DNA damage. As such, TFAM has emerged as a candidate for protecting mtDNA or sensing damage. To examine the possibilities that TFAM might protect DNA from damage or act as a damage sensing protein for irreparable forms of mtDNA damage, we used live-cell imaging and HeLa cell-based assays, atomic force microscopy (AFM), and high-throughput protein-DNA binding assays to characterize the binding properties of human TFAM to ultraviolet-C (UVC) irradiated DNA and the cellular consequences of UVC irradiation. Our cell data show increased TFAM mRNA after exposure and suggest an increase in mtDNA degradation without a loss in mitochondrial membrane potential that might trigger mitophagy. Our protein-DNA binding assays indicate a reduction in sequence specificity of TFAM following UVC irradiation and a redistribution of TFAM binding throughout the mitochondrial genome. Our AFM data show increased compaction of DNA by TFAM in the presence of damage. Despite the TFAM-mediated compaction of mtDNA in vitro, we do not observe any protective effect of increased TFAM protein on DNA damage formation in cells or in vitro. Increased TFAM protein did not alter levels of mtDNA damage over time after UVC exposure in vivo, but knockdown of TFAM did alter mtDNA damage levels in HeLa cells both at baseline and after UVC exposure. Taken together, these studies indicate that UVC-induced DNA damage alters TFAM binding and promotes compaction by TFAM in vitro. We hypothesize that that TFAM may act as a damage sensing protein in vivo, sequestering damaged genomes to prevent mutagenesis by facilitating removal or suppression of replication.

overall_design: We designed a custom library to cover the entirety of the human mitochondrial genome using a sliding 33-nucleotide window width with a 2-nucleotide shift for each consecutive probe. A subset of the chambers were irradiated with UVC to induce photolesions on the DNAs. We then incubated the chambers with either 30 nM or 300 nM TFAM. The concentrations of TFAM were selected based on preliminary experiments to ensure fluorescence intensity values were well within the range of detection. We were able to identify locations in the mitochondrial genome at which TFAM exhibits high occupancy and observed changes in sequence specificity of TFAM binding in the context of UVC-irritated DNA.


title: Expression of cFLIP is necessary for diffuse large B cell lymphoma pathogenesis

status: Public on Mar 15 2026

city: Cologne

first: Alessandro

last: Annibaldi

state: North-Rhine-Westphalia

address: Robert-Koch-Strasse 21

institute: Center for Molecular Medicine Cologne

summary: Diffuse large B cell lymphoma (DLBCL) is a highly heterogenous malignant disease that remains a major clinical challenge as relapsed and refractory disease is difficult to treat. Apoptosis evasion is a major feature of DLBCL. However, while the suppression of intrinsic apoptosis has long been recognized as a lymphoma-promoting event, the role of extrinsic apoptosis has remained poorly defined. Here, we demonstrated at the genetic level that expression of cFLIP, the most crucial, non-redundant inhibitor of extrinsic apoptosis, in B cells is necessary for the development of diffuse large B cell lymphoma (DLBCL) in an autochthonous murine model. Indeed, B cell-specific deletion of Cflar, the gene encoding for cFLIP, prevented lymphomagenesis mediated by oncogenic Myd88 and overexpression of BCL2. In human lymphoma cells, we showed that the absence of cFLIP sensitizes ABC- but not GCB DLBCL subtype cells to TRAIL- or LPS-induced, Caspase-8-mediated apoptosis. Furthermore, we unveiled a cell death-independent role of cFLIP in the suppression of pro-inflammatory cytokines at the transcriptional level, selectively in the ABC subtype. These results indicate that the suppression of intrinsic apoptosis can support lymphomagenesis only if extrinsic apoptosis is properly controlled. Moreover, licensing extrinsic apoptosis via cFLIP deletion can efficiently promote the death of DLBCL cells despite the suppression of the intrinsic pathway. Overall, these data provide the rationale for the development of cFLIP inhibitors for the treatment of ABC DLBCL and possibly other haematological cancers.

overall_design: RNA-Seq profiling of untreated CFLAR wildtype and CFLAR knockout TMD8 and SU-DHL-4 human DLBCL cell lines.

first: Kristie

last: Bariboloka

first: Justinas

last: Valiulis

first: Martin

last: Peifer


title: Modeling human enterovirus A71 infection using an intestinal microphysiological system

city: Bunkyo-ku

first: Kazuo

last: Takayama

state: Tokyo

address: Yushima 1-5-45

institute: Institute of Science Tokyo

summary: Enterovirus A71 (EV-A71), a causative virus of hand, foot, and mouth diseases, primarily infects and replicates in the intestine and, in severe cases, spreads to the central nervous system (CNS), leading to neurological complications. Therefore, suppressing viral replication in the intestine is important to prevent severe complications. However, the intestinal pathophysiological changes in EV-A71-infected patients remain poorly understood. In this study, we aimed to examine the intestinal response to EV-A71 infection using the intestinal microphysiological system (MPS) we previously developed using human pluripotent stem cells and microfluidic devices. The viral RNA was detectable in the cell culture supernatant of the intestinal MPS for 14 days after the viral infection. Despite this, EV-A71 infection did not induce significant morphological changes in the intestinal MPS and alter the expression of epithelial cell markers, suggesting that the virus can infect the intestinal MPS without causing intestinal epithelial damage. In addition, we found that the secretion of interferons (IFNs) in the cell culture supernatant was not increased by viral infection. Interestingly, the treatment with recombinant IFNs increased the expression of innate immune response-related genes and reduced viral mRNA levels. A strong association was observed between EV-A71 infection and IFN signaling in the intestinal MPS. We believe that the intestinal MPS would be a valuable platform for studying EV-A71 infection and evaluating antiviral strategies.

overall_design: Total RNA was collected from the EV-A71-infected intestinal MPS, and then RNA-seq was performed.


title: Age-related gene expression alteration responding to mechanical force and TGFβ signaling

city: Villigen

last: Shivashankar

state: Aargau

address: Forschungsstrasse 111

department: LNB

country: Switzerland

institute: Paul Scherrer Institute

summary: The aging process significantly alters the biomechanical properties of fibroblasts, impacting their cytoskeletal and chromatin organization. These changes are pivotal in modulating cellular responses to mechanical and biochemical stimuli. This study investigates the hypothesis that aging leads to fibroblasts’ divergent adaptation mechanisms to external stimuli. Herein, fibroblasts from young and old cohorts were embedded in 3D collagen gels and subjected to tension force alone (tension stimulus) or tension +/- Transforming Growth Factor beta (TGFb) (tension/TGFb stimuli). The study revealed that mechanical forces and aging exert profound effects on chromatin architecture. Young cells adapted more rapidly to mechanical stress and showed a heightened responsiveness to TGFβ compared to older cells. The identification of key transcription factors implicated in age-dependent responses was further examined, assessing their potential in cellular rejuvenation.

overall_design: RNA-seq profiling of primary dermal fibroblasts from two age groups (old: 75 years old; young: 10 years old) seeded in 3D collagen gel exposed to tension force and TGFβ stimulation

first: Yawen

last: Liao

first: Luezhen

last: Yuan

first: Trinadha

last: Sornapudi

first: G

middle: V


title: The m5C orchestrator NSUN7 drives SPARC/HMGB1 axis–mediated inflammation to exacerbate kidney injury [RNA-Seq]

city: Hefei

first: Yuhang

last: Dong

address: Meishan Road NO.81

institute: Anhui Medical University

summary: Growing evidence indicates that kidney inflammation is a major contributor to the pathogenesis of various renal diseases, including acute kidney injury (AKI). Although RNA modifications have been implicated in regulating kidney inflammation, their precise roles remain largely unknown. Here, we show that kidney inflammation and injury were associated with elevated RNA 5-methylcytosine (m5C) modifications, primarily driven by the m5C “writer” NOP2/Sun RNA methyltransferase family member 7 (NSUN7). Both global and kidney-specific deletion of Nsun7 in mice reduced m5C abundance, attenuated inflammatory responses, and decreased macrophage infiltration, underscoring its proinflammatory role in the kidney. Mechanistically, we identified secreted protein acidic and cysteine-rich (SPARC) as a major downstream effector of NSUN7. SPARC upregulation amplified inflammatory responses in renal tubular epithelial cells by interacting with high mobility group box 1 and further promoted proinflammatory macrophage infiltration via tubular-macrophage crosstalk. Notably, therapeutic silencing of Nsun7 using a kidney-specific DNA tetrahedral molecular carrier developed for this study effectively alleviated inflammation and improved renal outcomes in AKI models. Collectively, our findings identify NSUN7 as a key driver of renal inflammation via SPARC regulation and underscore its potential as a therapeutic target in inflammatory kidney diseases.

overall_design: To identify specific targets of NSUN7 in renal inflammation, we conducted RNA-seq and m5C MeRIP-seq analyses in cisplatin-stimulated HK2 cells with or without silencing of NSUN7

first: Xiaoming

last: Meng


title: Regulation of STK38 by autophagy governs YAP1 activity during paligenosis

city: Houston

first: Jason

last: Mills

state: TX

address: 1 Baylor Plaza

department: Gastroenterology

institute: Baylor College of Medicine

summary: Paligenosis is a conserved process that enables mature cells to reenter the cell cycle in response to tissue injury, progressing through stages of autodegradation, gene expression changes, and proliferation. The Hippo signaling pathway, particularly YAP1, plays a key role in regulating this process, with Serine/Threonine Kinase 38 (STK38) identified as a key regulator that inhibits YAP1 in uninjured cells but is degraded via autophagy during injury. This degradation of STK38 leads to YAP1 activation, which drives cellular plasticity and proliferation.  Additionally, the secretory maturation factor MIST1 helps preserve STK38 function, suggesting a broader, evolutionarily conserved role for autophagy in tissue regeneration.

overall_design: This study involves four groups of mice: 1.HDTAM-treated Atp4b-DTR mice – Transgenic Atp4b-DTR mice received high-dose tamoxifen (HDTAM) for 2 days to induce chief cell paligenosis. The gastric corpus was harvested 24 hours after the final injection. 2.DT-treated Atp4b-DTR mice – Atp4b-DTR mice were treated with diphtheria toxin (DT) for 2 days to induce reversible parietal cell ablation. The gastric corpus was harvested 24 hours post-treatment.3.Control Atp4b-DTR mice – Atp4b-DTR mice without DT treatment.4.Wild-type controls – Wild-type B6 mice without HDTAM treatment. The gastric corpus was dissociated into single cells using a combination of mechanical and chemical techniques. Three mice were used per group/condition.

first: Yongji

last: Zeng

first: Steven

last: Bark


title: FOXM1 drives metabolic adaptations in colorectal cancer brain metastases and represents a potential therapeutic target

city: Tel Aviv

first: Guy

last: Shapira

address: Chaim Levanon 30

country: Israel

institute: Tel Aviv University

summary: Colorectal cancer (CRC) is a leading cause of cancer-related mortality in the Western world. While brain metastasis (BMs) are relatively uncommon in CRC, they represent the fourth most frequent cause of BMs overall and their occurrence is increasingly recognized as a complication in advanced CRC, associated with poor prognosis and limited treatment options. The brain microenvironment presents unique metabolic challenges, including low oxygen levels and restricted lipid availability. In order to survive in this hostile environment, CRC cells must acquire metabolic adaptations allowing them to survive and proliferate. To identify key drivers that enable CRC cells to metastasize to and survive within the brain, we conducted a transcriptomic screen of CRC BMs. Among the upregulated genes, FOXM1 was identified, a transcription factor critical for tumor progression. This was further validated by immunohistochemistry in human samples. To study the role of brain microenvironment in mediating FOXM1 upregulation, CRC cells were cultured in either astrocyte-conditioned media (A-CM) or compared to hepatocyte-conditioned media (H-CM). CRC cells exposed to A-CM exhibited markedly higher FOXM1 expression. Moreover, using an in vivo model of intracranial CRC BM mouse model demonstrated significant FOXM1 overexpression in CRC cells following brain injection. And notably, our study revealed a significant correlation between FOXM1 and fatty acid synthase (FASN) in the brain microenvironment. These findings suggest that FOXM1 plays a key role in CRC brain metastasis and may serve as a promising therapeutic target. Targeting FOXM1 could provide novel treatment strategies for CRC patients with BMs, potentially improving outcomes in this challenging disease setting.

overall_design: RNAseq of FFPE samples from KRAS-mutated colorectal cancer brain metastasis n=7 and liver metastasis n=10

first: Fayhaa

last: Khair-Dabour

first: Inbal

last: Greenberg

first: Sivan

last: Fuchs

first: Asia

last: Zubkov

first: Ido

last: Wolf

first: Tami

last: Rubinek


title: An infectious murine model for hepacivirus-associated fibrosis and hepatocellular carcinoma

city: New York

first: Brad

last: Rosenberg

state: New York

address: 1 Gustave L Levy Pl

department: Microbiology

institute: Icahn School of Medicine at Mount Sinai

summary: The NrHV-HCC model represents the first immunocompetent infectious system that faithfully recapitulates the multistage progression from chronic viral hepatitis to spontaneous hepatocellular carcinoma, bridging a long-standing translational gap between mechanistic mouse studies and human liver cancer. By mirroring the immunopathological, molecular, and sex-associated features of chronic HCV infection, this model provides an unparalleled platform to investigate virus-host interactions underlying fibrosis and oncogenesis. High HCC penetrance and the genetically tractable C57BL/6 background further enhance experimental utility, enabling precise mechanistic dissection and genetic manipulation in a physiologically relevant setting. The capacity to study spontaneous tumor development in the context of natural infection allows for rigorous testing of antifibrotic and anti-cancer strategies, while the persistence of oncogenic potential after viral clearance raises important questions about irreversible disease reprogramming and elevated cancer risk following viral cure - issues of direct relevance to patients cured of HCV.

overall_design: To investigate the transcriptional and mutational landscape of NrHV infected mice and resultant tumors, mock or NrHV infection was established in C57BL/6 mice depleted for CD4 T cells at days -4 and 14 post infection. "Bulk" RNA sequencing (RNA-Seq) was performed on liver/tumor tissue gathered at from both experimental cohorts to assess transcriptional changes over time. To study the mutational landscape, we performed Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets (MSK-IMPACT), a custom hybridization capture–based assay encompassing all genes that are druggable by approved therapies or are targets of experimental therapies being investigated in clinical trials at Memorial Sloan Kettering Cancer Center (MSKCC), as well as frequently mutated genes in human cancer (somatic and germline mutations).

first: Mariana

last: Noguiera Batista

first: Juliano

last: Bordignon

first: Ana

last: Luiza Pamplona Mosimann

first: Charles

last: Rice


title: Single-cell multiomic integration identifies widespread, cell-type resolved fetal reactivation in the diseased human heart

city: Philadelphia

first: William

last: Gao

state: PA

address: 415 Curie Blvd

department: Genetics

institute: UNIVERSITY OF PENNSYLVANIA

summary:
Background:
As the first organ to develop in utero, the human heart undergoes extensive molecular, structural and metabolic remodeling during development and must sustain its function throughout life.

Results:
We generate an integrated multiomic atlas of human cardiac cells, combining newly generated and publicly available single-nucleus RNA sequencing datasets from 299 donors and single nucleus ATAC-seq datasets from 106 donors. Developmental and disease-associated processes drive far more extensive molecular remodeling than sex-associated or aging-dependent effects. Across nearly all cardiac cell types, developmental and disease-driven changes exhibit strong overlap at both the transcriptomic and epigenomic levels, revealing widespread reactivation of fetal-associated gene programs beyond cardiomyocytes. Both cardiac development and disease show convergent shifts in intercellular communication, including increased TGFβ signaling. Integration of gene expression and chromatin accessibility data reveals putative cell-type–specific transcriptional factors driving fetal reactivation in major cardiac diseases. Spatial transcriptomics data orthogonally identifies localization of this fetal reactivation signature within spatially distinct niches in ischemic and fibrotic zones of acute myocardial infarction. Finally, we construct a cell-type–resolved enhancer-to-gene linkage map that refines the association of dilated and hypertrophic cardiomyopathy genetic risk loci to downstream target genes.

Conclusions:
This study presents a comprehensive multimodal, cell-type–resolved atlas of the human heart, providing a foundation for understanding human cardiac gene regulation across the human lifespan and in cardiac diseases.

overall_design:
New datasets were generated for this study. snRNA-seq (Drop-seq platform) was generated for 17 donors. snATAC-seq using 10X Genomics ATAC.

As part of this study, we also integrated additional datasets across previously published studies. The table below lists reanalyzed samples, and the link to the raw data sources (fragment files or BAM files, depending on the study).

The final processed ATAC dataset is GSE290367_integrated_ATAC_adata.h5ad.gz, which includes log normalized counts in adata.X and raw counts in adata.layers['counts']. The final processed RNA dataset is GSE290367_integrated_RNA_adata.h5ad.gz, with the raw counts in adata.layers['counts'] and the log normalized counts in adata.X.

first: Peng

last: Hu

first: Qi

last: Qiu

first: Kenneth

last: Bedi

first: Kotaro

last: Sasaki

last: Margulies

first: Hao

last: Wu


title: AURKA inhibitor VIC-1911 induces mitotic defects and functional BRACness, sensitizing prostate cancer to PARP inhibition

status: Public on Mar 14 2026

city: Atlanta

first: Jindan

last: Yu

state: GA

address: E330, 1760 Haygood Dr NE

department: Urology

institute: Emory University

summary: VIC-1911, formerly known as TAS-119, is a next-generation, ATP-competitive AURKA inhibitor with high selectivity over AURKB and AURKC. In this study, we demonstrate that VIC-1911 potently and selectively inhibits AURKA signaling in diverse prostate cancer (PC) cell models, including both androgen receptor (AR)-positive and AR-negative cell lines. VIC-1911 treatment suppressed AURKA phosphorylation and downstream effectors at nanomolar concentrations without affecting AURKB/C activity, resulting in mitotic defects, DNA double-strand breaks (DSBs), and apoptosis. Transcriptomic profiling and immunofluorescence analysis revealed robust activation of DNA damage response pathways and the p53 pathway, consistent with mitotic catastrophe-induced genotoxic stress. Functionally, VIC-1911 significantly inhibited PC cell proliferation and tumor growth in xenograft models, including castration-resistant and AR-negative tumors. Given its ability to induce DNA damage, we evaluated the combinatorial effect of VIC-1911 with PARP inhibitors (PARPi). The combination exhibited synergistic anti-tumor effects in vitro and in vivo, leading to enhanced mitotic abnormalities, γH2AX accumulation, and cleaved PARP expression, even in homologous recombination (HR)-proficient settings. Importantly, VIC-1911 monotherapy and its combination with PARPi were well tolerated in vivo. These findings position VIC-1911 as a promising therapeutic agent for advanced prostate cancer, either as monotherapy or in combination with PARPi to broaden clinical efficacy beyond HR-deficient tumors

overall_design: To investigate thethe gene expression profiles induced by treatmetn with AURKA inhibitor, PARP inhibitor, or their combination in prostate cancer cells we performed RNA-seq analysis of cells treated with either vehicle (VEH), VIC-1911 (AURKAi), OLA (PARPi), or their combination (COMBO).

first: Galina

last: Gritsina

last: Chu

first: Jonathan C

last: Zhao


title: Senataxin promotes recombination fidelity during antigen receptor gene diversification

city: Paris

first: Ludovic

last: Deriano

address: 25-28 Rue du Docteur Roux

department: Immunology

country: France

institute: Institut Pasteur

summary: Immunoglobulin (Ig) and T cell receptor (TCR) V(D)J gene recombination relies on non-homologous end-joining (NHEJ), which repairs DNA double-strand breaks (DSBs) introduced by the RAG1/2 nuclease complex. Functional redundancies exist between NHEJ and the ATM kinase-dependent chromatin DSB response, likely masking the activity of additional factors. Here, we performed targeted CRISPR/Cas9 knockout screens (+/- ATM kinase inhibition) in pro-B cells and identified Senataxin (SETX) as a novel player in V(D)J recombination. We show that SETX supports V(D)J recombination, particularly when the ATM kinase is inhibited or in an XLF-deficient background. Furthermore, we show that SETX suppresses the formation of aberrant coding end-to-signal end hybrid joints during V(D)J recombination, both in vitro and in vivo. Finally, SETX prevents the aberrant joining of AID-induced DNA ends during class switch recombination (CSR). Overall, our work reveals an important role for SETX in promoting recombination fidelity and suppressing genome instability during antigen receptor gene diversification.

overall_design: RNA-seq profiling of WT and Setx-/- v-Abl pro-B cell clones after 45h ABLki treatment. N = 3 biological replicates for each cell line.

first: Alice

last: Libri

first: Jinglong

last: Wang

first: Timea

last: Marton

first: Wei

first: François

last: Dossin

first: Gabriel

last: Balmus

first: Bernardo

last: Reina-San-Martin

first: Richard

last: Frock

first: Chloé

last: Lescale


title: Effects of RRAGD p.(Ser76Leu) variant in human induced pluripotent stem cell-derived cardiomyocytes gene expression

status: Public on Mar 13 2026

city: Nijmegen

first: Sara

last: van Katwijk

address: Geert Grooteplein Zuid 28

department: Medical BioSciences

country: Netherlands

institute: Radboudumc

summary: RRAGD p.(Ser76Leu) has been associated with dilated cardiomyopathy. To study the effects of this variant on cardiomyocyte gene expression profile, we generated a human induced pluripotent stem cell-derived cardiomyocyte (hiPSC-CM) model carrying heterozygous mutation of the variant. After bulk-RNA seq, we showed that 124 genes were upregulated and 48 genes were downregulated in RRAGD p.(Ser76Leu) hiPSC-CMs compared to RRAGD WT hiPSC-CMs. Further analyses revealed that pathways related to muscle development were downregulated, while pathways associated with actin cytoskeleton regulation were upregulated.

overall_design: First, heterozygous RRAGD p.(Ser76Leu) variant was introduced into the hiPSCs using CRISPR-Cas9. Then, these hiPSCs were differentiated into cardiomyocytes. After 80 days in culture, total RNA was extracted from RRAGD p.(Ser76Leu) and RRAGD WT hiPSC-CMs. These RNA's were then subjected to bulk RNA-seq. RNA samples from four differentiation rounds were sequenced per cell line.

first: Anastasia

last: Adella

middle: B

first: Pieter

last: Leermakers

first: Willem

last: van Ham

first: Hesther

last: de Ruiter

first: Judita

last: Ilgutyte

first: Suzanne

last: Hendrickx

first: Levi

last: Nijland

first: Teun

last: de Boer

first: Eva

last: van Rooij

first: Joost

middle: G

last: Hoenderop

first: Jeroen

last: de Baaij


title: Role of HIV-1 in IL-8 response of human stellate cells to gram-positive microbial products

city: Bethesda

first: Laurence

last: Zhang

address: 9000 Rockville pike

institute: NIH/Kelly

summary: Patients living with Human Immunodeficiency Virus (PLWH) develop accelerated liver fibrosis, but the exact mechanism remains unknown. Unlike gram-negative bacterial products, the impact of gram-positive microbial products in Human Immunodeficiency Virus 1 (HIV-1) associated liver inflammation and fibrosis remains poorly understood. In this study, we investigated the effect of lipoteichoic acid (LTA), a major gram-positive bacterial component, on HSCs in the context of HIV-1 infection. Our data revealed that HIV-1 infection sensitizes HSCs to LTA stimulation, leading to an amplified IL-8 response mediated through histone acetylation that may accelerate liver fibrosis progression in PLWH. As microbial translocation persists despite effective antiretroviral therapy, these findings underscore the need for targeted strategies to mitigate liver fibrosis in HIV-1 infected patients.

overall_design: Total RNA from Lx2 cells treated with medium, HIV-1BaL (MOI = 0.1), and/or LTA (1 μg/mL) was sequenced (n = 3 per group). RNA quality was assessed by a Nano Drop 2000 Bioanalyzer, and RNA-Seq was performed by Mount Sinai NGS Core. Reads were aligned with STAR, quantified with HTSeq, and analyzed with DESeq2 using hg19 annotation.CHIP-seq was analyzed using a pipeline of bowtie2, macs callpeak2, samtools, bedtools, and deeptools

first: Lumin

first: Rabab

middle: O

last: Ali

first: Naichaya

last: Chamroonkul

first: Parissa

last: Tabrizia

first: Myron

last: Schwart

first: Ganesh

last: Gunasekaran

first: Maria

last: Isabel Fiel

first: Thomas

last: Schiano

first: Steven

last: Ward

first: Meena

last: Bansal


title: EBV INFECTION OUTCOMES DETERMINED BY MONOCYTE AND TREG-DRIVEN IMMUNE DYNAMICS IN AN EX VIVO PBMC MODEL [RNA-Seq EBV enrich]

first: Priyankara

last: Wickramasinghe

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

summary: Epstein-Barr virus (EBV) infects >95% of the adult population with diverse outcomes ranging from benign latency to cancers and autoimmune diseases. Immunological control of EBV infection is known to be an important determinant of EBV infection outcomes. However, species-specific viral tropism and limited infection models have impeded mechanistic insights into early host–immune control of EBV infection. Here, we use ex vivo infection of peripheral blood mononuclear cells (PBMCs), rather than routinely used B cell enriched culture systems, to study immune and viral dynamics during primary EBV infection. We combined bulk RNA sequencing, EBV transcript enrichment, and flow cytometry to characterize cellular responses across Days 1, 7–8, and 14 post-infection. Early infection triggered a monocyte-specific antiviral response marked by changes in the expression of genes associated with lipid metabolism (LIPA, lysosomal acid lipase) and chemotaxis (CCR1 and CCR2). Inhibitors of LIPA increased EBV titers during primary infection, indicating that LIPA is part of an early monocyte-driven antiviral response. At later timepoints post-infection, donor-dependent variability in lymphoblastoid cell line (LCL) outgrowth was associated with divergent immune states. Donors that failed to generate LCLs demonstrated increased frequencies of CD8+ T cells and reduced numbers of regulatory T cells (CD4⁺CD25⁺FOXP3⁺). EBV transcriptomics revealed that LCL-failed donors exhibited elevated early lytic gene expression but did not establish a type III latency program.  Our findings suggest that individual variations in immune cell composition and gene expression may account for differences in the immune response to EBV.  These findings define temporal immune and viral signatures that predict transformation outcome and highlight intact PBMCs as a tractable model to study EBV pathogenesis in a genetically diverse, human-specific context.

overall_design: RNA-seq of human PBMCs infected with EBV (control, non-enriched) and EBV-captured (EBVc, probe-enriched) conditions. Two biological replicates were collected for each condition, each with two technical replicates. Sequencing performed as paired-end polyA RNA-seq on Illumina NovaSeq X.

first: Leena

last: Yoon

first: Lauren

middle: N

last: MacMullen

first: Leonardo

last: Muñoz

first: Alina

last: Gu

first: Jamie

last: Bregman

first: Mary

last: Campion

first: Avi

last: Srivastava

first: Rena

last: Xian

first: Richard

middle: F

last: Ambinder

first: Andrew

last: Kossenkov

first: Samantha

last: Soldan

first: Paul

last: Lieberman


title: Sensitive monitoring of enhancer and noncoding RNA transcription via ribozyme-assisted RNA editing

city: Beijing

first: Yangming

last: Wang

address: No.5 Yiheyuan Road, Haidian District

department: College of Future Technology

institute: Peking University

summary: The primary goal of this study is to provide tools for understanding transcriptional regulation of native genomic elements that combine high sensitivity, quantitative output, and broad applicability. Existing methods often have limited dynamic range, disrupt host RNAs, or fail to detect short-lived transcripts. Here, we present ribozyme-processed ADAR-engaging RNA-directed editing (REDDIT), a technology that converts transcriptional events into reporter protein translation via precise A-to-I RNA editing. REDDIT sensitively detects transcription from protein-coding genes, long noncoding RNAs (lncRNAs), primary microRNAs (pri-miRNAs), and enhancer RNAs (eRNAs), including low abundance and short-lived species, while minimally perturbing host gene expression, RNA processing, and the global editome. We apply REDDIT to monitor the naïve-to-primed transition in human embryonic stem cells (hESCs) and convert it into a transcription recorder that permanently logs transient and combinatorial transcriptional inputs when paired with Cre recombinase. Finally, by adapting REDDIT for high-throughput screening, we uncover multiple signaling pathways that regulate lncRNA and eRNA biogenesis. REDDIT therefore provides a scalable platform for quantitative monitoring and retrospective analysis of endogenous transcriptional dynamics across diverse genomic contexts.

overall_design:
RNA-seq profiling of a cell lines that stably express the mCherry-TAG-GFP reporter (REDDIT_hESC_ctrl) and corresponding knock-in cell lines (REDDIT_NANOG, REDDIT_MIR302, REDDIT_ACTB_intron1, REDDIT_ACTB_polyA, REDDIT_SOX2_polyA); RNA-seq profiling of a cell lines that stably express the mCherry-TAG-GFP reporter (REDDIT_mESC_ctrl) and corresponding knock-in cell lines (REDDIT_lncenc1); RNA-seq profiling of REDDIT_MIR302 cells at Day 0, Day 5, Day 12, Day 14-high, Day 14-low, Day 20 of cardiomyocyte differentiation; RNA-seq profiling of wildtype mESC treated with DMSO (WT_mESC_DMSO_48h or WT_mESC_DMSO_7 days) and UNC0638 (WT_mESC_UNC0638_48h or WT_mESC_UNC0638_7 days); RNA-seq profiling of wildtype hESC treated with DMSO (WT_hESC_DMSO) and RepSox (WT_hESC_RepSox); GRO-seq profiling of wildtype hESC treated with DMSO (GRO_WT_hESC_DMSO) and RepSox (GRO_WT_hESC_RepSox).
The editing efficiency of the premature stop codon in the mCherry-TAG-GFP reporter was assessed through RNA sequencing and amplicon analysis. RNA libraries were constructed from NANOG-REDDIT hESCs during the process of neural induction, and mRNA sequences flanking the premature stop codon were amplified and analyzed following transfection with different ART RNA designs.

first: Jing

first: Jia-Zhen

first: Lu-Feng

last: Hu


title: EBV INFECTION OUTCOMES DETERMINED BY MONOCYTE AND TREG-DRIVEN IMMUNE DYNAMICS IN AN EX VIVO PBMC MODEL [RNA-Seq Mock]

first: Priyankara

overall_design: Cryopreserved peripheral blood mononuclear cells (PBMCs) from healthy donors (n = 5) were thawed into RPMI 1640 medium (Cat# 11875085, Gibco) supplemented with 10% fetal bovine serum (FBS), 1% GlutaMAX (Cat# 35050061, Gibco), and antibiotics (100 U/mL penicillin and 100 µg/mL streptomycin; Cat# 15140122, Gibco). Following thawing, cells were rested overnight at 37 °C with 5% CO₂ before infection. Cells were plated at a density of 1 × 10⁶ cells/mL in 12-well plates. Infection was performed using the Mutu I strain of Epstein–Barr virus (EBV) at a multiplicity of infection (MOI) = 1. Parallel mock-infected controls were prepared using the same medium without virus. Samples were collected from both conditions (mock and EBV-infected) at multiple timepoints post-infection to capture dynamic transcriptional and immunological responses. Each biological replicate (donor) was processed independently to control for donor variability.

middle: M


title: DNMT3L crosstalk with piRNA biogenesis in postnatal spermatogonial progenitor cells

city: Taipei City

first: Shau-Ping

last: Lin

state: select a state

address: 4F, No. 81, Chang-Xing St.,

department: Institute of Biotechnology

country: Taiwan

institute: National Taiwan University

summary: We analyzed small RNAs expression profiles of different developmental stages (0 dpp and 8 dpp) to investigate the potential role of DNMT3L in spermatogonial stem cells. We observed that the relative proportion of microRNA and piRNA were similar between wild-type and Dnmt3l knockout mice. However, piRNA origin and composition significantly differed in 8 dpp Dnmt3l-deficiency samples, and the genomic location of predicted precursors remarkably shifted as well.

overall_design: This study provides small RNA-seq profiling derived from the same RNA samples previously used for long RNA-seq analysis in GSE54411. One pair of samples were enriched neonatal germ cells (P0) and 2 pair of samples were from THY1+ spermatogonia stem/progenitor cells (SSCs/SPCs) derived from testes of Dnmt3l knockout (KO) and wild type (WT) mice at postnatal day 0 and day 8, respectively.

first: Hung-Fu

last: Liao

first: Johnson Sheng-Jia

last: Zhou

first: Hsien-Hen

first: Kai-Wei

last: Chang

first: Gabrielle

last: Chungunco

first: Pauline

last: Yen


title: Gene expression profiling of vomeronasal organ in Cnpy1 knockout and wildtype mice.

city: Hyderabad

first: Adish

last: Dani

state: Telangana

address: 36/P, Gopanpally

country: India

institute: Tata Institute of Fundamental Research, Hyderabad

summary: Distinct families of V1R or V2R type GPCRs G-protein coupled receptors (GPCRs) are expressed in the mouse vomeronasal organ within spatially segregated vomeronasal sensory neurons (VSNs) that are also identified by the expression of cognate G-protein subunits, Gαi2 or Gαo. How vomeronasal GPCRs detect chemo-signals important for innate social and reproductive behaviors, requires understanding the molecular and cellular diversification accompanying VSN differentiation from a stem cell population. Here, we identify mouse Cnpy1 as a novel VNO specific ER chaperone, with expression restricted to Gαo VSNs. Absence of Cnpy1 leads to reduced neuronal activation, behavioral defects and a substantial loss of neurons by apoptosis during postnatal development. Co-immunoprecipitation followed by mass spectrometry, identified specific interactions of Cnpy1 with V2R GPCRs along with other ER chaperones.  Together with our earlier findings of hypertrophic and gyroid ER in Gαo neurons, these results highlight a critical role for ER chaperones and ER architecture, necessary for the proper function of Gαo sensory neurons.

overall_design: Poly-A mRNA sequencing was performed on vomeronasal organs from wildtype (Cnpy1+/+) and Cnpy1 knockout (Cnpy1-/-) littermate mice at 60 days postnatal age.

first: GVS

last: Devakinandan


title: Performance differences in spatial transcriptomics platforms identify Treg biology in human inflammatory bowel disease [CosMx]

city: Chicago

first: Parambir

last: Dulai

state: IL

address: 259 E Erie St Ste 1600

institute: Northwestern University

summary: Spatial transcriptomics is a rapidly growing field with the potential to enhance our ability to uncover novel biology, support drug development, and guide biomarker discovery. However, a biologically validated comparison of leading single-cell-level spatial transcriptomics platforms to guide scientists is lacking in the field. Using intestinal biopsies (n = 40) from patients with inflammatory bowel disease (IBD) of varying disease states and disease locations and non-diseased controls, we systematically compared two imaging based spatial transcriptomics platforms (CosMx and Xenium) to guide translational work for two NIDDK supported IBD consortiums and the Crohn’s and Colitis Foundation Plexus Biorepository.  In vitro experiments were conducted to validate key biologic findings. We present a comprehensive data resource of over 1.5 million spatially profiled intestinal cells from healthy and IBD samples. We observed CosMx to have overall better data quality than Xenium in both ulcerative colitis and Crohn’s disease across the full spectrum of commercially available panels. The performance of Xenium, but not CosMx, was significantly influenced by block quality and panel size, with a decline in data quality as the panel size increased. We demonstrate operational feasibility for CosMx in multi-center studies, and CosMx uniquely identified Treg-associated biology in both ulcerative colitis and Crohn’s disease which was validated by in vitro experiments. This study highlights the performance differences between CosMx and Xenium, demonstrating the strengths of CosMx for biology discovery in IBD research. Further studies are needed to explore the broader applicability of CosMx in other gastrointestinal conditions.

overall_design: 24 CosMx multi-tissue 1K panel (Ileum_CD_Inflamed: 5, Ileum_CD_NonInflamed: 5, Ileum_UC_NonInflamed: 2, Rectum_CD_Noninflamed: 2, Rectum_CD_inflamed: 2, Rectum_UC_inflamed: 6, Rectum_UC_Noninflamed: 2); 16 Xenium multi-tissue 337 panel (Ileum_CD_Inflamed: 2, Ileum_CD_NonInflamed: 2, Ileum_UC_NonInflamed: 2, Rectum_CD_Noninflamed: 2, Rectum_CD_inflamed: 2, Rectum_UC_inflamed: 4, Rectum_UC_Noninflamed: 2); 4 CosMx multi-tissue 6K panel (Rectum_HC:1, Rectum_UC_nonInflamed: 1, Rectum_UC_inflamed: 2); 4 Xenium multi-tissue 337 panel with segmentation (Rectum_HC:1, Rectum_UC_nonInflamed: 1, Rectum_UC_inflamed: 2); 4 Xenium multi-tissue 377 panel without segmentation (Rectum_HC:1, Rectum_UC_nonInflamed: 1, Rectum_UC_inflamed: 2); 4 Xenium colon-specific panel (Rectum_HC:1, Rectum_UC_nonInflamed: 1, Rectum_UC_inflamed: 2); 4 Xenium 5K panel (Rectum_HC:1, Rectum_UC_nonInflamed: 1, Rectum_UC_inflamed: 2); 38 CosMx multi-tissue 1k panel for different slide processing conditions (thickness_um: 4,5,6,7; fixation_time_hr: 6,24,48,72; delayed_cut_week:0,2,4,6; storage_vacuum: NA, FALSE, TRUE); 2 CosMx 2.0 multi-tissue 1k panel for comparison between different AtoMx platform version

first: Yiming

last: Li

first: Wenjing

last: Yang

first: Hai

first: Alan

last: Robinson

first: Tianming

last: Yu

first: Jenny

middle: Y

last: Ding

first: Cenfu

last: Wei

first: Stephen

last: Hanauer

first: Emanuelle

last: Bellaguarda

first: Laura

last: Yun

first: Ronen

last: Sumagin

first: Guang-Yu

first: James

last: Lewis

first: Deyu

last: Fang

first: Yingzi

last: Cong

first: Yuan

last: Luo


title: TET3-mediated DNA demethylation contributes to the formation of stable epialleles in tomato [low coverage WGBS]

city: Coventry

first: Javier

last: Antunez Sanchez

address: Gibbet Hill Campus

department: Life Sciences

institute: University of Warwick

summary: DNA methylation is a critical epigenetic modification in plants that regulates gene expression, silences transposable elements (TEs), and supports proper development. Traditionally, heritable epimutations in plants have been generated using genetic mutants or chemical inhibitors, but these approaches often lack precision or stability. In this study, we investigated the effects of globally altering DNA methylation in tomato, a species with a large, TE-rich genome, through the ectopic expression of the catalytic domain of the human DNA demethylase TEN-ELEVEN TRANSLOCATION3 (hTET3cd). We found that TET3-mediated demethylation induced stable hypomethylation at CG and CHG sites and that these changes were inherited across multiple generations, including in non-transgenic siblings. Interestingly, demethylation in heterochromatic pericentromeric regions was often accompanied by gains in CHH methylation, suggesting the compensatory activation of the RNA-directed DNA methylation (RdDM) pathway. Differentially methylated region (DMR) analysis revealed that CG and CHG methylation loss was widespread, while CHH DMRs showed complex patterns of gain and loss, particularly near gene-rich regions and transposable elements enriched for 24-nt small RNAs. Transcriptomic analyses showed distinct gene expression profiles in both TET3 and non-transgenic progeny, with altered expression of TEs and associated genes. These findings demonstrate that enzymatic manipulation of the methylome via hTET3cd can generate stable, heritable epigenetic variation, and highlight the dynamic interplay between targeted DNA demethylation and endogenous mechanisms that act to restore epigenetic homeostasis.

overall_design: To determine the efect of TET3 mediated demethylation, we performed a low coverage Whole Genome Bisulfite Sequencing (WGBS) on yong leavels of an array of plants from different transgenic lines. After selecting 2 plants for further analysis, we performed deep coverage WGBS using expanded leaves from wild-type, hTET3cd transgenic plants, and a Non-Transgenic Sibling (WT, TET3, NTS).

last: Antunez-Sanchez


title: CHI3L1 contributes to an immune suppressed tumour microenvironment in highly invasive brain metastases

city: Montreal

first: Peter

last: Siegel

state: Quebec

address: 1160 Pine Ave. West

department: Rosalind and Morris Goodman Cancer Research Centre

institute: McGill University

summary: Brain metastases (BrM) occur in up to 40% of cancer patients, causing nearly one-fifth of cancer deaths. While immune checkpoint inhibitors (ICIs) benefit some BrM patients, responses remain highly variable. This variability partly reflects distinct histopathological growth patterns that include minimally invasive (MI) and highly invasive (HI) brain BrM. Here we show that MI BrM exhibit robust immune infiltration, whereas HI lesions are immunosuppressed. However, histological differentiation between MI and HI can be challenging due to subjective margin assessment. Here, using highly multiplexed spatial proteomics on 119 tumour sections from 46 patients with BrM, we identify CHI3L1 as a key mediator of the immunosuppressive microenvironment in HI BrM. In preclinical models, genetic deletion of CHI3L1 converts immune-cold metastases into lymphocyte-rich, ICI-responsive lesions infiltrated by granzyme-B+ CD8+ T cells. In BrM patients treated with ICI, immunohistochemical quantification of CHI3L1 expression was a stronger predictor of ICI response than traditional MI/HI classification. Thus, CHI3L1 represents a promising biomarker and therapeutic target for BrM.

overall_design: Nanostring Digital Spatial profiling using the Cancer Transcriptome Atlas to characterize transcriptional differences between cancer cells of highly invasive and minimally invasive Brain metastases.

first: Sarah

last: Maritan

first: Elham

last: Karimi

first: Matthew

last: Dankner

first: Aldo

last: Hernandez-Corchado

first: Miranda

middle: W

last: Annis

first: Yashar

last: Aghazadeh-Habashi

first: Morteza

last: Rezanejad

first: Bridget

last: Liu

first: Nebras

last: Koudieh

first: Emilie

last: Pichette

first: Benoit

last: Fiset

first: Yuhong

first: Ali

last: Nehme

first: Chun

last: Lee

first: Jack

last: Elias

first: Morag

last: Park

first: Yasser

last: Riazalhosseini

first: Hamed

last: Najafabadi

first: Kevin

last: Petrecca

first: Marie-Christine

last: Guiot

first: Daniela

last: Quail

first: Logan

last: Walsh

first: Parvaneh

last: Fallah


title: TET3-mediated DNA demethylation contributes to the formation of stable epialleles in tomato [RNA-seq]

first: Javier

last: Antunez Sanchez

overall_design: To determine the effect of TET3 mediated demethylation, we performed a transcriptome RNA-seq analysis using expanded leaves from wild-type, hTET3cd transgenic plants, and a Non-Transgenic Sibling (WT, TET3, NTS).

last: Antunez-Sanchez