title: The impact of rearing environment on C. elegans: Phenotypic, transcriptomic and intergenerational responses to 3D enriched habitats

city: Montreal

first: Michael

last: Hendricks

state: QC

address: 1205 Avenue Docteur Penfield

institute: McGill University

summary: Environmental context profoundly influences organismal biology, yet laboratory studies often rely on simplified conditions that may not fully capture natural phenotypic repertoire. This exploratory study investigated how rearing environment affects various aspects of Caenorhabditis elegans biology by comparing worms cultured in three-dimensional decellularized fruit tissue scaffolds with those raised on standard two-dimensional agar plates. While fat content and feeding rate remained stable across conditions, other life history traits demonstrated varying degrees of plasticity in response to environmental context. We observed that scaffold-grown worms exhibited reduced body size, altered reproductive strategies, and mild enhancements in stress resistance, burrowing ability, swimming kinematics and exploratory behavior. RNA sequencing revealed distinct transcriptional profiles between scaffold-grown and agar-grown worms, with most changes arising within one generation. Some traits showed evidence of intergenerational inheritance. Our findings highlight the sensitivity of C. elegans biology to rearing conditions and underscore the importance of considering environmental context in interpreting laboratory results. This work sets the foundation for future research into the mechanisms underlying environmental adaptation and phenotypic plasticity in model organisms.

overall_design: RNA-seq profiling of WT yound adult C. elegans grown under 2 different rearing habitats (traditional agar habitat or 3D decellularized fruit tissue scaffold) with ancestors (>10 prior generations) also grown on either of these 2 habitats (2x2 factorial design): (1) worms with an agar ancestry and raised on agar (agar:agar); (2) worms with an agar ancestry, but raised on scaffold (agar:scaffold); (3) worms with a scaffold ancestry, but raised on agar (scaffold:agar); and (4) worms with a scaffold ancestry and raised on scaffold (scaffold:scaffold). 3 sequencing replicates per condition. Each sample was pooled from worms collected from at least 3 different plates, on at least 3 different days.

first: Aurélie

last: Guisnet

first: Maxime

last: Rivest


title: Haplotype-Resolved Analysis of the Filaggrin Gene Elucidates its Complex Role in Human Adaptation and Disease

status: Public on Feb 01 2026

city: Philadelphia

first: Yuanqing

last: Feng

state: Pennsylvania

address: 430 Clinical Research Building, 415 Curie Boulevard

department: Genetics

country: USA

institute: University of Pennsylvania

type: Expression profiling by high throughput sequencing

summary: The filaggrin gene (FLG) encodes a key epidermal barrier protein, and both copy number variations (CNVs) and loss-of-function (LoF) mutations are major contributors to atopic dermatitis (AD) and allergic diseases. However, the highly repetitive structure of FLG has impeded a complete understanding of its functional landscape. Analyzing 697 haplotype-resolved assemblies from ethnically diverse populations, we provide a comprehensive, nucleotide-level atlas of FLG variation. We resolved the sequences of major FLG alleles—defined by both internal repeat number and nucleotide variation—uncovering sequences with 9–20 repeats (expanding beyond the canonical R10, R11, and R12 allele groups) and delineating eight recurrent alleles (e.g., R11.1, R12.1) with ancestry-specific distributions. We identified tag variants for specific FLG alleles and refined population-specific AD burden estimates by correcting misannotated LoF variants. We detected strong signatures of local adaptation in European and southern African Khoisan-speaking populations. We further identified rs1933064 as a causal regulatory variant within an FLG enhancer and demonstrated that the ancestral A allele reduces enhancer activity and FLG expression. This allele is associated with increased AD and asthma risk but higher serum vitamin D levels, and ancient DNA analysis reveals it has risen in frequency over the past ~10,000 years—consistent with positive selection. Collectively, we present an unprecedented sequence-resolved atlas of FLG variation, revealing the contributions of distinct alleles to AD risk, vitamin D biology, and environmental adaptation.

overall_design: HaCaT cells were subjected to lentiviral CRISPR perturbation to generate FLG enhancer knockout cells and compared to control HaCaT cells. Cells were infected with lentiviruses carrying Cas9 (lentiCRISPR v2; Addgene 52961) and sgRNA (pLKO5 backbone), selected with puromycin, expanded, and harvested for RNA extraction. RNA-seq was performed on biological replicates of each condition.

first: Ning

last: Xie


title: Integrative transcriptomic analysis uncovers the miRNA-centric regulation of Japanese encephalitis virus infection in porcine trophoblast cells.

city: Yangzhou

first: Juan

last: Yang

address: 大学南路88号

department: College of Veterinary Medicine

country: China

institute: Yangzhou University

type: Non-coding RNA profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Lycorine suppresses cell growth and attenuates stemness through PI3K/AKT pathway in ovarian cancer

city: jiangsu Huai an

first: Yao yao

last: Tang

address: No. 9 Keji Avenue, Qingjiangpu District,

institute: Jiangsu College of Nursing

summary: Ovarian cancer remains the most lethal gynecological malignancy worldwide, with poor prognosis due to chemotherapy resistance and cancer stem cell-driven recurrence. This study comprehensively investigates the antitumor effects of lycorine, a natural alkaloid derived from Lycoris radiata, on human ovarian cancer models. Our results demonstrate that lycorine significantly inhibits ovarian cancer cell proliferation, induces apoptosis, and suppresses cancer stemness properties through modulation of the PI3K/AKT signaling pathway. In vitro, lycorine treatment reduced the expression of stemness markers (CD133, CD44, NANOG, SOX2, OCT4, and LIN28) and impaired tumor sphere formation. RNA sequencing and pathway enrichment analysis confirmed significant inhibition of PI3K/AKT signaling, accompanied by decreased phosphorylation of AKT and mTOR. In vivo, lycorine (5 mg/kg) effectively suppressed tumor growth in A2780-luc xenograft models, reduced stem cell subpopulations, and exhibited minimal toxicity. Furthermore, lycorine sensitized ovarian cancer cells to cisplatin and counteracted cisplatin-induced enrichment of cancer stem cells. These findings highlight lycorine as a promising multi-target therapeutic agent against ovarian cancer, particularly for addressing stemness-driven chemoresistance and recurrence.

overall_design: A2780 cells after 24-hour treatment with 10 µM lycorine, as determined by transcriptome sequencing

first: Yaoyao


title: Transcriptomic impacts of TFIIB D207G editing in Jurkats during 2 h TRAIL treatment

city: Berkeley

first: Britt

last: Glaunsinger

state: California

address: RM 565, 1951 Oxford St

department: PMB

institute: University of California, Berkeley

summary: Cellular stressors often cause widespread repression of RNA polymerase II (RNAP II) activity, which is thought to facilitate a focused transcriptional output towards stress resolution. In many cases, however, the underlying regulatory mechanisms remain unknown. Here, we demonstrate that stress-induced downregulation of the general transcription factor TFIIB tempers expression of specific stimulus response genes. Following a variety of stressors, TFIIB is proteolytically cleaved between its cyclin folds at conserved aspartic acid residue D207 by caspases- 3 and 7. Cleavage in this portion of the protein significantly reduces the ability of TFIIB to form a TBP-TFIIB-DNA promoter complex in vitro. Using both overexpression and endogenous base-editing, we find that B and T cells that are unable to cleave TFIIB upregulate expression of a select gene set during apoptosis. These TFIIB-sensitive genes are primarily short, stimulus-responsive and proto-oncogenic loci, and cleavage of TFIIB temporally restricts their expression. Failure to cleave TFIIB during stress leads to aberrant lymphocyte proliferation during chemical perturbation. Hence, caspase targeting of TFIIB destabilizes transcription to tune gene expression, allowing for proper stress resolution.

overall_design: Using Jurkat T cells, which are sensitive to apoptotic stimuli, two different sgRNAs targeting the TFIIB D207 locus were validated (D207G-#1 and D207G-#2; also referred to as sgRNA1 and sgRNA2 in the sequencing below). A control dinucleotide base edit was made in the AAVS1 locus (Control/sgRNA3). Pooled populations with ≥ 85% editing at each target locus were validated by amplicon sequencing. Pooled populations were expanded for ≥ 10 days after delivery of A•G base editor RNA and the sgRNA, and then submitted to SLAM-sequencing (edit stability was monitored for all experiments and protein-level impacts were confirmed in parallel by western blotting). Cells were treated with SUPERKILLER TRAIL (Enzo) and 4sU (to label nascent RNA) for 2 h prior to harvesting . This was followed by RNA extraction, alkylation, library preparation, RNA-sequencing, and differential gene expression analysis.

first: Leah

last: Gulyas

middle: A


title: Bulk RNA-seq of adult pig and rat central canal–associated spinal cord cells

city: Ottawa

first: Sasi Kumar

last: Jagadeesan

state: ON

address: 1053 Carling Avenue,

department: Neuroscience

country: Canada

institute: Ottawa Hospital Research Institute

summary: Bulk RNA sequencing was performed on central canal–associated spinal cord cells isolated from adult pig (Sus scrofa) and rat (Rattus norvegicus) spinal cords and expanded under ex vivo culture conditions. Libraries were sequenced on the Illumina NovaSeq 6000 platform using 150 bp single-end reads. Transcript abundances were quantified using Salmon (v1.x) against species-specific reference transcriptomes (pig: ss11; rat: rn6). This dataset enables cross-species analysis of transcriptional programs associated with proliferative activation and progenitor-associated states in the mammalian spinal cord.

sample_organism:
Sus scrofa
Rattus norvegicus

platform_organism:
Sus scrofa
Rattus norvegicus

overall_design: Central canal–associated regions were microdissected from adult pig and rat spinal cords. Cells were expanded as adherent cultures under defined serum-free conditions. Total RNA was extracted and strand-specific poly(A)+ libraries were prepared using the Illumina TruSeq Stranded mRNA workflow. Libraries were sequenced on an Illumina NovaSeq 6000 (150 bp, single-end). Transcript quantification was performed with Salmon (v1.x) using ENSEMBL/ENCODE v104 transcript annotations. Raw FASTQ files and per-sample transcript-level quantifications (quant.sf) are provided.

first: Eve C

last: Tsai

first: Ryan Vimukthie

last: Sandarage

first: Ahmad

last: Galuta


title: Integrated multi-platform metabolomics reveals fatty acid-mediated inflammatory signatures in pretibial myxedema

city: Shanghai

first: Jiayi

last: Cai

address: Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Ruijin 2nd Road

summary: Context: Pretibial myxedema (PTM) is a refractory autoimmune dermopathy associated with Graves’ disease. Although metabolic dysregulation has been recognized in thyroid-associated disorders, the metabolic profile and its functional role in PTM remain unclear. Objective: To characterize the metabolic landscape of PTM lesions and explore the contribution of fatty acids to fibroblast dysfunction and inflammation. Methods: We performed untargeted metabolomic profiling of PTM skin lesions and healthy controls using LC-MS and GC-MS, integrated with spatial metabolomics to localize metabolic changes. Functional assays were conducted by stimulating human foreskin fibroblasts (HFFs) with palmitic acid (PA) and oleic acid (OA), followed by RNA sequencing, cytokine assays, and immunohistochemistry. Results: PTM lesions exhibited substantial metabolic reprogramming, including accumulation of fatty acids and elevated tricarboxylic acid cycle intermediates. Spatial metabolomics confirmed pronounced lipid deposition in the dermis, the primary site of PTM pathology. RNA-seq of fibroblasts stimulated with PA and OA revealed enrichment of inflammatory pathways, including IL-17 and NF-κB signaling, and marked upregulation of IL-8 (CXCL8). Fatty acid stimulation induced robust IL-8 secretion, consistent with increased IL-8 expression in PTM lesions. Moreover, PA promoted α-SMA expression in fibroblasts, suggesting induction of myofibroblast differentiation. Conclusions: Our findings demonstrate that dermal fatty acid accumulation in PTM may contribute to fibroblast-mediated inflammation and fibrosis. This study provides novel insights into the metabolic-immunologic interface underlying PTM pathogenesis.

overall_design: Human foreskin fibroblasts (HFFs) were treated with Vehicle, Palmitic Acid (PA), or Oleic Acid (OA) to investigate the effect of fatty acids on fibroblast inflammation. Total RNA was extracted and sequenced to identify differentially expressed genes and enriched pathways.

first: Li

last: Zhang

first: Jie

last: Zheng

first: Meng

last: Pan

first: Xia

last: Li

first: Xiaoqing

last: Zhao

first: Shuoting

last: Wang

first: Zirou

last: Shang

first: Han

last: Cao

first: Xiaoying

last: Chen


title: Clonal memory of colitis accumulates and promotes tumor growth [ATAC-Seq]

city: Cambridge

first: Surya

last: Nagaraja

state: MA

address: 7 Divinity Ave, Bauer 2nd Floor 208

department: HSCRB

institute: Harvard University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Chronic inflammation is a well-established risk factor for cancer, but the underlying molecular mechanisms remain unclear. Using a mouse model of colitis, we demonstrate that colonic stem cells retain an epigenetic memory of inflammation following disease resolution that persists for over 100 days. We find memory of colitis to be characterized by a cumulative gain of activator protein 1 (AP-1) transcription factor activity, with more durable changes to chromatin as well. Further, we develop SHARE-TRACE, a method that enables simultaneous profiling of gene expression, chromatin accessibility and clonal history in single cells, enabling high resolution tracking of epigenomic memory. This reveals that inflammatory memory is propagated cell-intrinsically and inherited through stem cell lineages, with certain clones demonstrating dramatically stronger memory than others. Finally, we show that colitis primes stem cells for amplified expression of regenerative gene programs following oncogenic mutation that accelerates tumor growth and this phenotype is dependent on AP-1 activity. Together, our findings provide a mechanistic link between chronic inflammation and malignancy, revealing how long-lived epigenetic alterations in regenerative tissues may contribute to disease susceptibility and suggesting potential therapeutic strategies to mitigate cancer risk in patients with chronic inflammatory conditions.

overall_design: To idenitfy whether transcription factor motif accessbility varied by region within the colon, bulk ATAC-seq was performed on six sigments between the rectum and cecum.

first: Lety

last: Ojeda-Miron

first: Ruochi

first: Ena

last: Oreskovic

first: Conrad

last: Hock

first: Yan

last: Hu

first: Daniel

last: Zeve

first: Karina

last: Sharma

first: Roni

middle: R

last: Hyman

first: Qiming

first: Andrew

last: Castillo

first: David

middle: T

last: Breault

first: Öme

middle: H

last: Yilmaz

first: Jason

middle: D

last: Buenrostro


title: Clonal memory of colitis accumulates and promotes tumor growth [IVFP]

overall_design: To examine binding relationships between AP-1 factors and FOX transcrption factors, in vitro binding assays were performed. Purified transcription factor proteins were incubated with cloned naked DNA sequences and binding was assessed using Tn5 transposition.

last: Zhang


title: Clonal memory of colitis accumulates and promotes tumor growth [tissue EM-seq]

type: Methylation profiling by high throughput sequencing

overall_design: Enzymatic methyl seq (EM-seq) was performed to examine methylation changes following recovery from colitis and the impact of AP-1 inhibiton with T-5224 on these marks.


title: Clonal memory of colitis accumulates and promotes tumor growth [organoid EM-seq]

overall_design: Enzymatic methyl seq (EM-seq) was performed to examine cell-intrinsic methylation changes following recovery from colitis in organoids.


title: Deep mutational scanning of CHD2 for variant interpretation in neurodevelopmental disorders [RNA-seq]

city: Chicago

first: Gemma

last: Carvill

state: IL

address: 303 E Chicago, Ward 9-183

department: Neurology

institute: Northwestern University

summary: De novo pathogenic variants in CHD2 are one of the most common causes of the neurodevelopmental disorders (NDDs) that include refractory epilepsy, intellectual disability and autism spectrum disorders. In addition, somatic CHD2 variants, acquired later in life, are highly recurrent in certain types of leukemias. For both types of conditions, loss-of-CHD2 function is the likely pathogenic mechanism, and most variants are truncations. However, there is also evidence that missense variants can disrupt or abrogate CHD2 function, leading to loss-of-function, though they are harder to interpret, and many are classified as variants of uncertain significance (VUS). VUS are one of the biggest challenges for human geneticists, and represent the biggest class of variants returned on clinical genetic test reports, in part because we have a poor understanding of how missense variants impact protein function. Our research addresses these challenges by developing a multiplex assay of variant effect (MAVE) to discriminate between pathogenic and benign missense variants. We leveraged the fact that CHD2 is a chromatin remodeler and thus affects gene expression, protein abundance and the DNA methylation landscape to attempt to develop high-throughput assays.  We aimed to establish a CHD2 transcriptomic signature using mRNA sequencing from multiple pathogenic and benign variant HAP1 cell lines. While CHD2 is a well-known chromatin remodeler and is expressed at appreciable levels in these cells, we were unable to establish a CHD2-related transcriptomic signature in HAP1s, possibly due to the cell line choice as most manifestations in patients are neurological.

overall_design: We aimed to establish a CHD2 transcriptomic signature using short read mRNAseq in clonal HAP1 cell lines, including five benign, 9 pathogenic CHD2 variants using prime-editing and assessed alongside two clonal wildtype lines. mRNA libraries were prepared and sequenced using a paired-end 150bp protocol on an Illumina instrument. Reads we mapped to the genome (hg38) using STAR and quantified using RSEM using default parameters using the nf-core/rnaseq v3.18.0 pipeline. Differentially expressed genes were called with DESeq2, with an adjusted p-value cutoff of 0.05 and an absolute log2FC cutoff of 1.

middle: L

first: Nicholas

last: Bodkin

first: Jeffrey

last: Calhoun


title: Clonal memory of colitis accumulates and promotes tumor growth [Visium]

first: Surya

overall_design: Visium spatial transcriptomics was performed to compare gene expression of adenomas formed following resolution of colitis and under normal conditions.


title: Transcriptomic profiling of MCF-7 breast cancer cells post HOXB2 knockdown

city: Guwahati

first: Anil

middle: Mukund

last: Limaye

state: Assam

address: IIT Guwahati

department: Department of Biosciences and Bioengineering

country: India

institute: Indian Institute of Technology Guwahati

summary: Application of Next-generation sequencing technology to identify genes modulated by HOXB2 depletion in MCF-7 cells

overall_design: MCF-7 cells were transfected with HOXB2-specific siRNA or scrambled (control) siRNA for 24 h.

first: Ajay

last: Kumar

first: Sonia

last: Ningthoujam


title: Deep mutational scanning of CHD2 for variant interpretation in neurodevelopmental disorders

type: Methylation profiling by genome tiling array

summary: De novo pathogenic variants in CHD2 are one of the most common causes of the neurodevelopmental disorders (NDDs) that include refractory epilepsy, intellectual disability and autism spectrum disorders. In addition, somatic CHD2 variants, acquired later in life, are highly recurrent in certain types of leukemias. For both types of conditions, loss-of-CHD2 function is the likely pathogenic mechanism, and most variants are truncations. However, there is also evidence that missense variants can disrupt or abrogate CHD2 function, leading to loss-of-function, though they are harder to interpret, and many are classified as variants of uncertain significance (VUS). VUS are one of the biggest challenges for human geneticists, and represent the biggest class of variants returned on clinical genetic test reports, in part because we have a poor understanding of how missense variants impact protein function. Our research addresses these challenges by developing a multiplex assay of variant effect (MAVE) to discriminate between pathogenic and benign missense variants. We leveraged the fact that CHD2 is a chromatin remodeler and thus affects gene expression, protein abundance and the DNA methylation landscape to attempt to develop high-throughput assays.    We aimed to establish a CHD2 episignature using DNA methylation arrays from multiple pathogenic and benign variant HAP1 cell lines. While episignatures have been well-established in blood samples from individuals with CHD2 pathogenic variants, we were unable to establish a CHD2-related DNA methylation signature in HAP1s, either due to the cell line, or because episignatures are established during embryogenesis (or both).

overall_design: To test for a CHD2 DNA methylation signature we generated 14 clonal HAP1 cell lines, including five benign, 9 pathogenic CHD2 variants using prime-editing and assessed alongside two clonal wildtype lines. DNA methylation was assessed using Illumina Infinium MethylationEPIC version 2 and processed with the Sesame R package (version 1.24.0) using default parameters. Resulting beta values and p-values were analyzed using the “differentially methylated position” functions in the Methylize Python package (version 1.1.1).


title: Clonal memory of colitis accumulates and promotes tumor growth [ATAC-seq]

last: Nagaraja

overall_design: To deternine the efffects of AP-1 inhibition on transcription factor binding, colonic organoids were derived from mice with chronic colitis or healthy controls and subsequently treated with AP-1 inhbitor T-5224.

first: Lety

last: Ojeda-Miron

first: Ruochi

first: Ena

last: Oreskovic

first: Conrad


title: Interleukin-4:STAT6 signaling delays protective CD8 T cell bystander activation by antagonizing IL-18 sensing

city: Eugene

first: John

last: Postlethwait

state: OR

address: 1210 University Of Oregon

department: Biology

institute: University of Oregon

summary: Memory CD8 T cells (Tmem) are activated into innate-like killers by cytokines such as IL-12, IL-15 and IL-18; but mechanisms regulating this phenomenon (termed bystander activation) are unclear. We show that basal IL-4 signals antagonize IL-18 sensing and blunt IFNg production following bystander activation of Tmem in mice.  Furthermore, IL-4 treatment can act directly on Tmem in a STAT6-dependent manner, to limit their control of a bystander bacterial infection. Nevertheless, we find that IL-4 does not simply block bystander activation but rather alters Tmem gene expression to tune effector molecule expression. Defective bystander activation of homeostatic Tmem in some strains relates, in part, to IL-4 exposure, but we show that these differences are erased in Tmem produced by TCR activation leading to uniform IL-18 receptor expression and capacity for bystander activation/cytotoxicity. Our data demonstrate that bystander activation by inflammatory cytokines is subject to regulation by both IL-4 and by prior antigen experience. These findings underscore the importance of the cytokine milieu in dictating the ability of bystander CD8 Tmem to mediate pathogen control.

overall_design: We isolated CD8 T cells from OT-I memory mice (mice with adoptively-transferred OT-I memory T cells that were expanded by VSV-OVA at least 30d prior). Cells were pooled from secondary lymphoid organs across 2 animals per sample. We divided cells for in vitro culture with media, IL-12/15, IL-12/15/18, or SIINFEKL peptide (TCR agonist) ± IL-4 (all cytokines at 100ng/mL, SIINFEKL at 1µM). We used these samples to test how IL-4 alters gene transcription during steady state (mock), bystander activation (IL-12/15, IL-12/15/18), and TCR activation (SIINFEKL). We used FACS to isolate live OT-I T cells, which we sorted into RLT buffer + beta-mercaptoethanol. We isolated RNAs, which were prepared into libraries by the University of Minnesota Genomics Core (UMGC) using Watchmaker Stranded mRNA prep kits. The UMGC pooled libraries, which were sequenced on an Aviti Freestyle Medium 2x150bp run. Runs generated  ≥500 million pass filter reads for the pool, with all expected barcode combinations detected and mean quality scores ≥Q35.

middle: J

last: Maurice

first: Juan

middle: E

last: Abrahante Lloréns

first: Braedan

middle: M

last: McCluskey

first: Todd

last: Knutson

first: Stephen

middle: C

last: Jameson


title: Zrsr1 Protects Against Obesity-Associated Hepatic Lipogenesis Independent of Minor Intron Splicing by Inhibiting the LXR-SREBP1c Axis [HFD_RNA-seq]

first: Yinkun

last: Fu

address: chongqing Rd

department: school of medicine

institute: shanghai jiaotong university

summary: Minor intron retention resulting from dysregulation of minor intron splicing factors is an emerging risk factor for the metabolic-associated steatotic liver disease (MASLD). However, whether impaired expression of these splicing factors exerts critical roles in MASLD progression independent of their minor intron splicing activity remains largely undefined. Here, we show that hepatic expression of the minor intron splicing factor Zrsr1 is significantly downregulated in mice fed a high-fat diet (HFD), while canonical minor intron splicing remains unperturbed. Hepatic Zrsr1 overexpression effectively mitigates HFD-induced obesity and insulin resistance, demonstrating that Zrsr1 expression protects MASLD progression via a minor intron splicing-independent mechanism. Notably, Zrsr1 cell-autonomously suppresses liver X receptor (LXR) activation-induced de novo lipogenesis in both hepatocyte models and mouse models. Mechanistically, we demonstrate that Zrsr1 directly interacts with LXRα, and this physical interaction suppresses the transactivation of the LXRα/retinoid X receptor α (RXRα) complex, thereby inhibiting the subsequent transcription of sterol regulatory element-binding protein 1c (Srebp1c). Collectively, these findings define a novel, splicing-independent function of the minor intron splicing factor Zrsr1 in mediating hepatic de novo lipogenesis via constraining the LXR-SREBP1c axis, which in turn mitigates MASLD progression. This work expands the functional repertoire of minor intron splicing factors beyond their classical splicing role, providing new insights into the molecular mechanisms underlying hepatic fatty acid metabolism and MASLD pathogenesis.

overall_design: To investigate the gene expression in livers of  hepatic overexpression Zrsr1 mice fed HFD , we established  hepatic overexpression Zrsr1 and vec mice fed with HFD for13 weeks.We performed gene expression profile using data obtained from RNA-seq of liver from the indicated mice.

first: Xin

last: Peng

first: Hongyong

last: Song

first: Xunyun

last: Zhao


title: Simultaneous measurements of translation rate and transcriptome uncovers linked regulation within an active bacterial cell population.

city: Chapel Hill

first: Adam

last: Rosenthal

state: North Carolina

address: 1521 East Franklin Street, Apartment C213

department: Microbiology and Immunology

institute: UNC

summary: Cell-to-cell variation within clonal bacterial populations provides bacterial communities important advantages including opportunities for bet-hedging and metabolic division of labor. In recent years the extent of bacterial heterogeneity has been documented both at the transcriptome level and with physiological measurements of cell growth rate and translation rate. However, methods that link physiological parameters to a single cell’s full transcriptomic state are lacking, making it difficult to identify the regulatory mechanisms that couple physiology and transcriptional output. Here we introduce a method that combines click-chemistry enabled labeling of nascent polypeptides to measure translation rates in single cells alongside microfluidic encapsulation and single cell transcriptomic measurements, providing a tandem measurement of translation rate and transcriptome in thousands of single Bacillus subtilis cells. In a culture experiencing nutrient limitation, we identified a subpopulation of cells with a higher rate of protein translation that uniquely overexpresses genes for several metabolic processes including acetoin production and arginine synthesis. Using a genetic approach informed by the gene expression in this subpopulation, we identified a regulatory mechanism that couples the increase in protein abundance of a transcriptional regulator AlsR with expression of alsR regulated genes in this subpopulation.

overall_design: Before microfluidic encapsulation, bacteria were either treated or not treated with OPP as per instructions in the click-it OPP kit (thermofisher scientific) and fixed in 1% paraformaldehyde after OPP incubation in order to preserve transcripts and permeabilized by mild lysozyme treatment. OPP positive samples were processed with click-ligation of a probe using copper click reagents in the Click-it OPP kit. Permeabilized bacteria were then incubated with the corresponding DNA probe library. Non-hybridized probes were removed with repeated washes . Next, the bacteria were run through a 10X Chromium Controller, where the DNA probes were captured and barcoded in a manner analogous to the barcoding of the transcriptome of eukaryotic cells

first: Christopher

last: Baumann

first: Molly

last: Hydorn

first: Samuel

last: Cooke

first: Jonathan

last: Dworkin


title: Clonal memory of colitis accumulates and promotes tumor growth [CUT&Tag]

first: Surya

last: Nagaraja

overall_design: CUT&Tag was performed for the Fos protein to map binding sites in healthy and colitis recovered tissue and banchmark computational predictions.

first: Lety

last: Ojeda-Miron

first: Ruochi

last: Zhang

last: Hock

first: Yan

last: Hu

first: Daniel

last: Zeve

first: Karina

last: Sharma

first: Roni

last: Hyman

first: Qiming

first: Andrew

last: Castillo

first: David

last: Breault

first: Öme

last: Yilmaz

first: Jason

last: Buenrostro


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

city: Ann Arbor

first: Stephen

last: Weiss

state: MI

address: 210 Washtenaw Ave

institute: University of Michigan

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

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

first: Adam

middle: W

last: Olson


title: Intrinsic and non-cell autonomous roles for a neurodevelopmental syndrome-linked transcription factor

city: Nashville

last: Miller III

state: Tennessee

address: 465 21st Avenue South

department: Cell and Developmental Biology

institute: Vanderbilt University

summary: Transcription factors (TFs) are essential for neuronal identity, yet their potential non–cell-autonomous functions remain largely unexplored. Here, we uncover both cell- and non–cell-autonomous roles for the conserved terminal selector UNC-3 in C. elegans motor neurons (MNs). UNC-3 is an ortholog of human EBF3, mutations in which cause a severe neurodevelopmental syndrome. Single-cell RNA sequencing of cholinergic MNs, which express unc-3, and downstream GABA MNs, which do not, revealed that unc-3 loss disrupts neuronal identity in distinct ways across MN classes. Four cholinergic MN classes lose their molecular identity entirely, whereas the AS class retains it partially, illuminating terminal selector–driven neuronal diversification processes. Integrated transcriptomic and genomic analyses uncovered a dual cell-autonomous role for UNC-3 as both a direct activator and repressor of neuron-type–specific genes in cholinergic MNs, including repression of alternate neurotransmitter programs. Unexpectedly, unc-3 loss also caused widespread transcriptional, morphological, and connectivity defects in downstream GABA MNs. Mechanistically, these non-cell-autonomous effects are mediated by cholinergic neurotransmission and include activation of the pro-regenerative bZIP TF CEBP-1 (C/EBP) and dysregulation of UNC-6/Netrin signaling. These findings redefine terminal selectors as both intrinsic and extrinsic regulators of neuronal identity and circuit assembly, offering a mechanistic framework for understanding EBF3 syndrome pathogenesis.

overall_design:
Ventral nerve cord MNs were isolated from two strains of worms. Two samples were collected from lin-39p::RFP worms (GSM7486859 and  GSM7486860 re-used from GSE234962), and three samples were collected from lin-39p::RFP; unc-3(n3435) worms. MNs were isolated by FACS and analyzed by 10X Genomics 3' single-cell RNA sequencing.

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

first: Jayson

last: Smith

first: Seth

last: Taylor

first: Honorine

last: Destain

first: Grace

last: Kim

last: Hall

first: John

middle: G

last: White

first: Paschalis

last: Kratsios


title: Zrsr1 Protects Against Obesity-Associated Hepatic Lipogenesis Independent of Minor Intron Splicing by Inhibiting the LXR-SREBP1c Axis [zrsr1 HFD]

first: Yinkun

last: Fu

first: Xin

last: Peng

first: Hongyong

last: Song

first: Xunyun

last: Zhao


title: Ly6C+Sca-1+ virtual memory CD8+ T cells responding to IL-15/Rα complex promote chronic liver inflammation

city: Seoul

first: Jaeil

last: Lee

address: 103 Daehak-ro, Jongno-gu

country: South Korea

institute: Seoul National University

summary: Virtual memory (VM) CD8+ T cells are cytokine-driven, memory-phenotype lymphocytes maintained independently of antigen exposure. However, their role in chronic hepatic inflammation remains poorly defined. Here, we examined whether signaling through the IL-15/Rα complex (IL-15C) modulates VM CD8+ T cell responses during chronic liver injury. Mice were pretreated with IL-15C prior to induction of chronic liver injury using thioacetamide (TAA). VM CD8+ phenotypes, transcriptional profiles, and hepatic accumulation were analyzed by flow cytometry and mRNA sequencing. Type I interferon-deficient and CD8-depleted mouse model were used to assess the contribution of cytokine signaling and CD8+ T cells to the observed responses. IL-15C induced robust expansion of VM CD8+ T cells in both the spleen and liver, with preferential enrichment of a Ly6C+Sca-1+ subsets. IL-15C reprogrammed VM CD8+ T cells toward an effector and migratory phenotype, characterized by increased expression of EOMES, T-bet, NKG2D, and inflammatory chemokine receptors, along with reduced tissue-residency signatures. During chronic TAA-induced liver inflammation, VM CD8+ T cells, particularly the Ly6C+Sca-1+ subsets, accumulated in the liver, and IL-15C pretreatment further enhanced hepatic immune cell infiltration and was associated with sustained liver injury and fibrotic responses. Notably, IL-15-induced VM T cells exhibited reduced PD-1 expression and sustained NKG2D expression, especially within CD62L+ and CD69+ VM T cell populations.  These findings demonstrate that IL-15C drives the expansion and phenotypic reprogramming of VM CD8+ T cells toward an effector-like, migratory state and is associated with enhanced hepatic immune cell infiltration during chronic liver injury.

overall_design: Comparison of gene expression patterns of wild-type (WT) naïve T cells, WT VM T cell, IL-15C-induced naïve T cells, IL-15C-induced VM T cells by mRNA sequencing analysis

first: Sung Min

last: Choi

first: Hyun Ji

last: Boo

first: Kyeong Cheon

last: Jung

first: Jae Il


title: Bulk RNA-seq analysis of mouse bone under microgravity (0G) and normal gravity (1G)

city: Shimotsuke

first: Makoto

last: Kuro-o

state: Tochigi

address: 3311-1 Yakushiji

country: Japan

institute: Jichi Medical University

summary: This study presents bulk RNA-seq data generated from mouse bone samples to investigate transcriptomic changes induced by microgravity. Total RNA was extracted from bone tissues, and RNA-seq libraries were prepared using a poly(A)-selection protocol and sequenced on an Illumina platform. The resulting data were used to compare gene expression profiles between ground control (1G) and microgravity (0G) groups.

overall_design: Bulk RNA-seq was performed on bone tissues collected from mice under control and microgravity conditions. For each condition, total RNA extracted from bone tissues of six mice was pooled in equal amounts and subjected to bulk RNA-seq analysis.Differential gene expression analysis was conducted to identify transcriptional changes associated with exposure to microgravity.

first: Hirosaka

last: Hayashi

first: Yutaka

last: Miura

first: Yoshitaka

last: Iwazu

first: Hideyuki

last: Mukai

first: Yoshiyuki

last: Mori

first: Takahiro

last: Kuchimaru

first: Nobuhiko

last: Ohno

first: Tatsuya

last: Aiba

first: Risa

last: Okada

first: Daisuke

last: Kamimura

first: Dai

last: Shiba

first: Hiroshi

last: Kurosu


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

first: Stephen

last: Weiss

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

first: Adam

last: Olson


title: NSD2 Drives Podocyte Injury in Diabetic Kidney Disease via Epigenetic Regulation of Hippo Signaling [RNA-Seq]

city: Beijing

first: Peng

last: Qu

address: China-Japan Friendship Hospital No. 2 Yinghuayuan East Street, Chaoyang District, Beijing 100029, P.R. China

institute: Institute of Clinical Medical Sciences, China-Japan Friendship Hospital

summary: Podocyte lipid accumulation has emerged as an important driver during the progression of diabetic kidney disease (DKD), yet the underlying mechanisms remain not fully clarified. Here, we identified the histone methyltransferase NSD2 as a key epigenetic regulator of podocyte lipid accumulation and injury in DKD. NSD2 expression is markedly increased in podocytes from both DKD patients and mouse models, and its levels shows a positive correlation with disease severity. Genetic deletion of Nsd2 in podocytes, as well as pharmacological inhibition of its methyltransferase activity, substantially reduced podocyte injury and proteinuria in mouse models. In contrast, transgenic Nsd2 overexpression in podocytes aggravated these pathological alterations. Mechanistically, elevated NSD2 in DKD enhances H3K36me2 deposition at the Ajuba promoter, resulting in its transcriptional upregulation and subsequent suppression of Hippo signaling. This epigenetic change promotes lipid accumulation in podocytes, leading to cytoskeletal disturbances and increased apoptosis. Collectively, our findings reinforce lipid accumulation as a central contributor to DKD progression and indicate that NSD2, as a pivotal epigenetic regulator in this process, could represent a reasonable therapeutic target for DKD.

overall_design: Primary podocytes were isolated from podocyte-specific Nsd2 knockout mice and floxed control mice after HFD/STZ-induced diabetic injury. RNA-seq was performed on podocytes collected at 20 and 28 weeks of age to characterize NSD2-dependent transcriptional changes during early and advanced stages of DKD(n = 3).


title: ROS-related genes as potential diagnostic biomarkers in tuberculosis

first: xuetian

last: shang

address: No.9 Beiguan Street, Tongzhou District

institute: Beijing Chest Hospital, Capital Medical University

summary: Microarray profiling of 10 active-TB versus 10 healthy donors (validated in GEO cohorts) revealed 1 300 differential transcripts, 709 ROS-related; within the monocyte module TNFSF13B scored highest, giving AUC > 0.8 for TB versus health or other lung disease, 6-fold induction in Mtb-infected THP-1 macrophages, and post-treatment decline, establishing TNFSF13B as a macrophage oxidative-stress biomarker for active tuberculosis.

overall_design: Genome-wide mRNA profiling of peripheral blood mononuclear cells (PBMCs) from tuberculosis patients (TB), and healthy controls (HCs) was conducted using the Agilent microarray technique. TB:10 samples; HC:10 samples.

first: Xuetian

last: Shang

first: Dong

last: Jing

first: Siyv

last: Yao

first: Xinyue

last: Zhang

first: Yuehan

last: Zhao

first: Yadong

last: Wu

first: Lanyue

first: Liping

last: Pan


title: microRNA-25 drives initial resistance to immune checkpoint therapy by repressing innate and humoral immunity via Syndecan3 [In_vitro_RNA_seq_B16]

city: La Jolla

first: Zhouting

last: Zhu

address: 9500 Gilman Drive MC 0762

institute: UC San Diego

summary: Immune Checkpoint Therapy (ICT) has demonstrated durable responses and long-lasting immunologic memory in cancer treatment. However, overcoming primary and acquired resistance remains a major challenge. Here, we show that CRISPR-Cas9-mediated deletion of miRNA-25 (miR-25) sensitizes tumors to ICT across three syngeneic mouse tumor models. Single-cell RNA sequencing (scRNA-seq) of the tumor microenvironment (TME) revealed that miR-25 deficiency induces innate immunity by upregulating major histocompatibility complex class II (MHC II) in antigen-presenting M1-like macrophages and enhances the classical complement cascade in cancer-associated fibroblasts (CAFs) to drive a humoral immune response. The complement activation polarizes CAFs from myofibroblastic CAFs (myCAFs) toward inflammatory CAFs (iCAFs) while simultaneously reduces immune-suppressive interactions between CAFs and tumor associated macrophages (TAMs). This shift results in a reduced macrophage population and fosters a pro-inflammatory, anti-tumor TME. Syndecan-3 (Sdc3), a membrane proteoglycan expressed in tumors, is repressed by miR-25 through miRISC (microRNA induced silencing complex) upon IFN-γ exposure. Using an adenine base editor (ABE8e) to mutate the miR-25 binding site in the 3’ untranslated region (3’ UTR) of Sdc3 effectively overcomes the resistance. The repression of SDC3 by miR-25 is further validated in five human cancer cell lines upon IFN-γ exposure but remains unaffected in non-cancerous cells. These findings identify miR-25 as a key driver of initial resistance through the repression of SDC3 and demonstrate that miR-25 deletion or stabilization of SDC3 could transform immune resistant "cold" tumors into immune responsive "hot" tumors, offering therapeutic avenues to enhance cancer immunotherapy.

overall_design: We sought to identify miR-25 targets using RNA-seq on B16 cells treated with IFN-γ in vitro.

first: Zhaoyang

last: Jia

first: Tariq

last: Rana


title: microRNA-25 drives initial resistance to immune checkpoint therapy by repressing innate and humoral immunity via Syndecan3

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

overall_design: Refer to individual Series


title: Xenium spatial transcriptomics of stage 28 embryos and regenerating 3 cm axolotl tails (3, 7, 10, 14 dpa) including mature unamputated tails

city: BAR HARBOR

first: CGDS

last: Data

state: ME

address: 159 OLD BAR HARBOR RD

institute: MDI Biological Laboratory

summary: 100 genes were selected, including cell-specific markers, transcription factors and signalling molecules, to understand tail patterning and gene oscillations in the embryo and in comparison to the tail.

overall_design: Stage 28 embryos were staged according to external morphology, fixed in 4% paraformaldehyde (PFA) in PBS at 4 °C overnight, washed thoroughly in PBS, and then infiltrated with 2% gelatin in PBS at 37 °C for 30 min under vacuum to improve tissue integrity and section adherence before embedding. For tail regeneration samples, 3 cm axolotls were amputated at five myotomes posterior to the cloaca, and regenerating tail stumps were collected at 3, 7, 10 and 14 days post-amputation, together with mature unamputated tails from size-matched animals. At each time point, tails were dissected, carefully oriented, and embedded in OCT compound in separate molds, then snap-frozen and stored at −80 °C until processing; subsequently, all samples were cryosectioned at 20 µm thickness using a cryostat microtome for Xenium spatial transcriptomics.

first: Vijayishwer

middle: S

last: Jamwal

first: Riley

last: Grindle

first: Ryan

middle: P

last: Seam

first: Fred

last: Kolling

first: Prayag

last: Murawala

first: Joel

last: Graber


title: Phenotypic changes in cortical astrocytes translatome across the estrous cycle

city: New Haven

first: Gianfilippo

last: Coppola

state: CT

address: 333 Cedar st

department: Pathology

institute: Yale University

summary: Astroglia have recently been implicated in various functions in the brain including modulating neuronal network functions, forming components of the blood brain barrier, and responding to neuroinflammation. Indeed, the neocortex contains neuronal circuits responsible for mediating complex higher-order behaviours and astroglia have recently been implicated in modulating neocortical behaviours. Neocortical astroglia express gonadal hormone receptors and respond to alterations in circulating gonadal hormones, which readily access the brain, with changes in function as well as protein and gene expression. In female rodents, circulating levels of estrogen and progesterone fluctuate across the estrous cycle and these cyclic changes might be expected to alter astroglia function. While some work has characterized astroglial protein expression changes during the estrous cycle in the cortex, no one has examined changes in active gene translation in astroglia across the estrous cycle. We use translating ribosome affinity purification with RNA sequencing (TRAPseq) to characterize the astroglial translatome in adult female mice during metestrus, proestrus, and estrus and compared it with that of male mice. We find the largest differences in the translatome between proestrus and estrus, and that males and females on metestrus cluster closely together, suggesting the neocortical astroglial translatome is responsive to circulating gonadal hormones. Additionally, neuroplastic processes are amongst the top gene ontologies called when examining differentially expressed genes between the different days of the cycle and between the days of the cycle. This suggests that cortical astrocyte phenotypes are rapidly modified across the estrous cycle, which may influence neocortical neuronal network function.

overall_design: RNA sequencing on astrocytes mRNA prepared using translating ribosome affinity purification (TRAP) from male and female B6;FVB-Tg(Aldh1l1-EGFP/Rpl10a)JD130Htz/J mice. Female mice were collected at 09:00 during different days of the estrous cycle (metestrus, proestrus, estrus).

first: Gareth

last: Rurak

first: Chase

last: Groulx

first: Ashley

last: McFee

first: Argel

last: Aguilar-Valles

first: François

last: Charih

first: James

last: Green

first: Barbara

last: Woodside

first: Natalina

last: Salmaso


title: microRNA-25 drives initial resistance to immune checkpoint therapy by repressing innate and humoral immunity via Syndecan3 [Bulk_tumor_RNA_seq_B16]

first: Zhouting

last: Zhu

overall_design: Since we initiated our studies using B16 melanoma model and observed similar anti-PD-1 immunotherapy enhancement effects in MC38 (GSE31304), we sought to validate the innate and humoral immune responses in B16 miR-25 KO tumors. We validated immune activation through transcriptomic analysis of the B16 melanoma TME. miR-25 KO B16 tumors under combination therapy were compared to control tumors with the same treatment.

first: Zhaoyang

last: Jia

first: Lingling

last: Wang

first: Hui

last: Hui

first: Tariq

last: Rana


title: Transcription elongation can be sufficient, but is not necessary, to advance replication timing [b-del_RNA-seq]

city: San Diego

first: David

last: Gilbert

state: CA

address: 3525 John Hopkins Ct., Ste. 200

institute: San Diego BioMEd

summary: DNA replication timing (RT) is correlated with transcription during cell fate changes but there are many exceptions, underscoring a need for reductionist approaches. Here, we manipulated length and strength of transcription at a single site upstream of the silent, late-replicating, Pleiotrophin (Ptn) gene in mouse embryonic stem cells (mESCs). Reporter genes driven by two of four promoters elicited an RT advance while all four promoters advanced RT when driving the endogenous Ptn gene. Inducible transcription of the Ptn gene, but not the reporter gene, elicited a rapid and reversible RT advance. Deletion of the Ptn promoter and enhancer, followed by differentiation to neural precursors, eliminated transcription without attenuating the natural Ptn domain RT advance. Together with new genome-wide analyses, our results provide a solid empirical base with which to re-evaluate many decades of seemingly contradictory literature. We also identify vectors that do not disturb RT and provide a robust system to induce RT changes, permitting mechanistic studies of transcription’s role in RT and the consequences of RT changes to epigenomic remodeling.

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

first: Athanasios

last: Vouzas

first: Takayo

last: Sasaki

first: Juan Carlos

last: Rivera-Mulia

first: Jesse

last: Turner

first: Amber

middle: N

last: Brown

first: Karen

last: Alexander

first: Laura

last: Brueckner

first: Bas

last: van Steensel


title: Transcriptomic analysis of Platycodin D (PD)-improved idiopathic pulmonary fibrosis (IPF) mice

first: Jiahua

address: No. 16 South Xiaojie, Dongzhimennei, Dongcheng District,

department: Experimental Research Center

institute: China Academy of Chinese Medical Sciences

summary: This study focuses on the role of PD, a natural compound derived from traditional Chinese medicine, in the prevention and treatment of IPF, a disease in which pulmonary fibroblast-to-myofibroblast transdifferentiation is a key pathogenic driver. By employing both in vivo and in vitro IPF models, combined with techniques including transcriptome analysis, Lip-SMap, molecular docking, molecular dynamics simulations, Cellular Thermal Shift Assay (CETSA), and Surface Plasmon Resonance (SPR), the research demonstrates that PD alleviates lung injury, mitigates systemic and pulmonary inflammation, reduces oxidative stress, and notably suppresses myofibroblast transdifferentiation in IPF models. Further mechanistic investigations identify PPP2R1A as a direct target of PD; PD stabilizes and activates protein phosphatase 2A (PP2A) by binding to PPP2R1A, thereby inhibiting the PI3K/Akt signaling pathway. Collectively, these findings indicate that PD exerts anti-IPF effects at least partially through the PPP2R1A/PP2A/PI3K/Akt axis, highlighting its potential value as a therapeutic agent targeting myofibroblast transdifferentiation in IPF management.

overall_design: IPF models were used to assess the effects of PD on inflammation, oxidative stress, and fibroblast‑to‑myofibroblast transdifferentiation. Core targets and mechanisms were identified using a comprehensive assay, which comprised transcriptome analysis and the Lip‑SMap technology.   Molecular docking, molecular dynamics simulations, CETSA, SPR, and functional recovery experiments were performed to validate the direct targets of PD and elucidate its anti‑IPF molecular actions.


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

city: Edinburgh

first: Grzegorz

last: Kudla

address: Crewe Road

department: MRC HGU

country: United Kingdom

institute: University of Edinburgh

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

sample_organism:
Saccharomyces cerevisiae
synthetic construct

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

first: Hasan

last: Çubuk

first: Marcin

last: Plech

first: Vahid

last: Aslanzadeh

first: Marie

last: Zikanova

first: Vaclava

last: Skopova

first: Stanislav

last: Kmoch

first: Yuxin

last: Shen

first: Joseph

last: Marsh


title: microRNA-25 drives initial resistance to immune checkpoint therapy by repressing innate and humoral immunity via Syndecan3 [single_cell_RNA_seq_MC38]

first: Zhouting

last: Zhu

overall_design: To investigate changed microRNAs in responding B16 melanoma, we applied GM-CSF secrecting irradiated B16 cells and anti-PD-1 to treat B16 tumors inoculated on immune competent mice. To vailidate the TME change, we did scRNA-seq to explore immune/tumor/stroma component change in MC38 tumors treated with anti-PD-1.

first: Zhaoyang

last: Jia

first: Tariq

last: Rana


title: Co-translational targeting defect caused by Srp68 knockout leads tomeiotic arrest during spermatogenesis in mice

city: Jinan

first: Hanzhen

last: Li

state: Shandong

address: 44 Wenhua West Road

institute: Shandong University

summary: Co-translational targeting by the signal recognition particle delivers nascent secretory and membrane proteins into the endoplasmic reticulum, yet its role in mammalian germ cells remains unclear. Here, we found that SRP68 is indispensable for spermatogenesis in mice. Conditional Srp68 deletion in germ cells results in defective synapsis and double-strand break repair, leading to meiotic prophase I arrest and male infertility. Proteomic profiling revealed that SRP68-deficient spermatocytes exhibit significant reduced endoplasmic reticulum (ER)-associated signal peptide-containing proteins, accompanied by structural disorganization. Additionally, multiple factors involved in ER–mitochondrial contact are decreased in SRP68-deficient spermatocytes, leading to mitochondrial calcium ion depletion, depolarized membrane potential, and insufficient ATP production. These findings demonstrate that SRP68-dependent co-translational targeting is essential for meiotic progression, providing a basis for interpreting ER-related causes of male infertility.

overall_design: We performed Smart-seq2 on FACS-isolated leptotene/zygotene spermatocytes from control and SKO mice at postnatal day 12 .For Smart-seq2, cell lysis, mRNA reverse transcription, and cDNA amplification were performed using the Discover-sc WTA Kit V2 (Vazyme, N711). Following this, cDNA fragmentation and adapter ligation were carried out with the TruePrep Flexible DNA Library Prep Kit for Illumina (Vazyme, TD504). All procedures were conducted in strict accordance with the manufacturer's protocols. The Smart-seq2 library sequencing was performed by Novogene on Illumina platforms, generating 150 bp paired-end reads.


title: Transcription elongation can be sufficient, but is not necessary, to advance replication timing [Repli-seq]

first: David

last: Gilbert

overall_design:
To investigate the relationship between RT regulation and transcription, we focused on mouse Pleiotrophin (Ptn) gene locus the replication timing and transcription of which are developmentally regulatged; switching from late RT and transcription "OFF" in embryonic stem cell to early RT and transcription "ON" in NPC. We inserted various promoters in one allele on the same locus in F121-9 hybrid embryonic stem cell expressing the tetracycline transactivator from the Rosa26 locus to see how transcription induction and replication timing differ between the WT allele and manipulated allele. In addition, to investigate position effect, we inserted hPGK promoter-eGFP casette to multiple loci using PiggyBac as described in PMC7073462. We also deleted Ptn gene transcription start site in another mESC line 46C and induced the differentiation to NPC to observed how the depletion of Ptn gene transcription affects RT in NPC. The processed data files for samples F121_WT_4DN_E_Rep1, F121_WT_4DN_E_Rep2, F121_WT_4DN_L_Rep1, F121_WT_4DN_L_Rep2 were genrated from 4DN public data. Their raw data files are available at 4DN data portal, specifically, https://data.4dnucleome.org/experiment-set-replicates/4DNESWPIPVZT/#raw-files and https://data.4dnucleome.org/experiment-set-replicates/4DNES1PHNYOP/#raw-files

NIH Common Fund "4D Nucleome" Program grant U54DK107965 (BvS and DMG).

first: Athanasios

last: Vouzas

first: Takayo

last: Sasaki

first: Juan Carlos

last: Rivera-Mulia

first: Jesse

last: Turner

first: Amber

last: Brown

first: Karen


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

last: Alexander

first: Laura

last: Brueckner

first: Bas

last: van Steensel


title: Contribution of Gli1+ stem cells to smooth muscle cells in atherosclerosis and vascular injury

city: Shanghai

first: Jialing

last: Mou

address: NO.320 Yueyang Road

institute: CEMCS

summary: Adventitial stem cells (ASCs), identified by Gli1 expression, have been proposed as key contributors to the vascular smooth muscle cell (SMC) population during atherosclerosis development. However, their precise role remains a subject of debate. To clarify this, we initially used a Gli1-CreER lineage tracing tool to track these cells in an atherosclerosis model. Our fate-mapping studies revealed that Gli1+ cells contribute to a small subset of SMCs. To definitively differentiate between the true lineage transformation and potential ectopic labeling by Gli1-CreER in SMCs, we developed a dual recombinase-mediated genetic strategy to label Gli1+ ASCs while eliminating ectopic labeling in SMCs. The results from this dual lineage tracing approach demonstrated that Gli1+ ASCs do not contribute to the SMC population in atherosclerotic plaques. Instead, Gli1+ ASCs differentiate into a significant portion of SMCs vascular anastomosis injury, suggesting their role is context-dependent. These findings challenge current paradigms and highlight the need to reconsider cellular targets for therapeutic interventions in atherosclerosis.

overall_design: Two groups of whole cells sorted from the femoral artery Gli1-CreER;R26-tdT mouse(homeostatic, injury) respectively, and subjected to scRNA-seq.


title: Tuning siRNA Specificity through Seed Region Incorporation of Deoxyribonucleotide Stereoisomers

city: Carlsbad

first: Sagar

last: Damle

address: 2855 Gazelle Ct

institute: Ionis Pharmaceuticals

summary: Precise chemical design continues to drive advances in RNA-based therapeutics. Here, we report the synthesis and site-specific incorporation of four canonical phosphoramidites (U, C, A, and G), each bearing non-natural nucleoside configurations: β-D-2′-deoxyxylonucleosides and α-L-2′-deoxyribonucleosides. These stereochemically distinct nucleoside analogs were introduced at positions 6 and 7 within siRNA seed regions. When applied to siRNAs targeting Ttr, ACTN1, and Marc1, these modifications reduced off-target gene repression in functional assays and, in several cases, in transcriptome-wide differential expression analyses, while preserving robust on-target activity. In vivo, Marc1-targeting siRNAs containing these modified nucleosides showed decreased hepatotoxicity, as evidenced by reduced serum ALT and AST levels. Collectively, these findings establish β-D-2′-deoxyxylonucleoside and α-L-2′-deoxyribonucleoside analogs as promising chemical tools for enhancing the specificity and safety of siRNA therapeutics. This work underscores the power of integrating rational nucleoside design with comprehensive functional and in vivo evaluation to advance drug development based on RNA interference (RNAi).

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
To validate the target specificity of siRNAs with a single β-D-2′-deoxyxylonucleoside or α-L-2′-deoxyribonucleoside modification in the seed region, we employed differential gene expression (DGE) analysis. This approach was applied to data from both cultured cells and in vivo models, offering a detailed assessment of the modification's impact on gene expression.

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

first: Mehran

last: Nikan

first: Thazha

last: Prakash

first: Guillermo

last: Vasquez

first: Graeme

last: Freestone

first: Marie

last: Annoual

first: Michael

last: Tanowitz

first: Hongda

first: Rodrigo

last: Galindo-Murillo

first: Stephanie

last: Klein

first: Audrey

last: Low

first: Clare

last: Quirk

first: Andrew

last: Watt

last: Migawa

first: Eric

last: Swayze


title: microRNA-25 drives initial resistance to immune checkpoint therapy by repressing innate and humoral immunity via Syndecan3 [single_clone_RNA_seq_B16]

first: Zhouting

last: Zhu

overall_design: We selected independent single-clone B16 cells harboring homozygous miR-25 knockout and compared their transcriptomic profiles with wild-type B16 cells and pooled miR-25 knockout cells.

first: Zhaoyang

last: Jia

first: Tariq

last: Rana


title: microRNA-25 drives initial resistance to immune checkpoint therapy by repressing innate and humoral immunity via Syndecan3 [small_RNA_seq_B16]

overall_design: B16 cells were injected subcutaneously into the right flank of immunocompetent C57BL/6J mice on day 0. To stimulate an immune response, mice were vaccinated on the opposite flank with GVAX cells (irradiated B16 cells engineered to secrete granulocyte-macrophage colony-stimulating factor, GM-CSF). on days 1 and 4. Anti-PD-1 monoclonal antibodies were administered systemically on days 6, 9, and 12. We analyzed four treatment groups: no treatment (Control), monotherapy with GVAX (GVAX), monotherapy with PD-1 antibody (αPD-1), and combination therapy with both GVAX and αPD-1 (Comb). To investigate changes in miRNA expression during immunotherapy, we isolated tumor RNAs from the treatment groups on day 13 for small RNA sequencing.

first: Gulshanbir

last: Baidwan

first: Hui

last: Hui


title: The type I and III interferon responses restrict infection with tick-borne orthoflaviviruses through IFI6

city: Paris

first: Felix

last: Streicher

address: Rue du Dr. Roux 25-28

country: France

institute: Institut Pasteur

summary: Tick-borne orthoflaviviruses (TBOVs) are a growing global health concern. Several representatives of this viral family cause fatal disease in humans with increasing case numbers throughout the last decades. The innate immune response, especially interferon (IFN)-dependent signaling, is an essential part of the human defense system that counteracts infection with TBOVs and other viruses. Even though they activate the same signaling cascade, IFNs belonging to the type I and III families trigger differing gene expression patterns. Which genes the two IFN families induce to restrict infection with TBOVs remains poorly characterized. Here we show that type I and III IFNs are both capable of restricting TBOV infection of human cell lines in a cell type-specific manner. Infection of C57BL/6J mice with knockouts for either IFN type I or III receptors further underscored the critical role of IFN signaling in controlling TBOV replication in vivo. To assess the contribution of single genes to controlling TBOV infection in human cells, we used a CRISPR/Cas9-KO-based screening approach. This strategy identified IFI6 as a central player for IFN type I- and III-driven responses against TBOVs. We further defined IFI6 as an ER-resident protein that restricts TBOV replication at a post-entry step. Our work thus opens new perspectives for targeting weak points in the life cycle of TBOVs and other orthoflaviviruses, potentially paving the way for the development of new antiviral therapeutics.

overall_design: Two parallel CRISPR screens targeting Interferon-Stimulated Genes in which enrichment of sgRNA sequences in infected cells was monitored in two independent cell lines (Caco2-TC7 and DAOY). Cells were infected with TBEV-Hypr for 24h following 16h treatment with IFN (IFNλ1 for Caco2-TC7 and IFNα2 for DAOY).

first: Devin

last: Kenney

first: Vincent

last: Caval

first: Maxime

last: Chazal

first: Sophie-Marie

last: Aicher

first: Ségolène

last: Gracias

first: Ferdinand

last: Roesch

first: Florian

last: Douam

first: Nolwenn

last: Jouvenet


title: ΔNp73 isoform defines a TP53mutant-like poor risk subgroup of acute myeloid leukemia

city: Groningen

first: Diego A

last: Pereira-Martins

state: Groningen

address: Hanzeplein 1

department: Hematology

country: Netherlands

institute: University Medical Center Groningen

summary: Among acute myeloid leukemia (AML) patients, a subgroup remains notoriously refractory to current treatment options, with underlying mechanisms poorly understood. Here, using a multi-omics approach, we reveal that this resistant patient subgroup is characterized by high expression of the oncogenic TP73 isoform ΔNp73, exhibiting similarly poor outcomes as TP53-mutant AML. ΔNp73, which lacks a transcriptional activation domain but retains chromatin binding properties, competes with TP53 for specific gene targets, thereby downregulating TP53 signaling. We demonstrate that the transcription factor CEBPA controls ΔNp73 expression in AML cells by binding to an intragenic enhancer region. Genetic or pharmacological inhibition of the transcriptional activity of CEBPA with guanfacine reduces ΔNp73 levels and restores drug sensitivity involving ferroptosis-mediated cell death, acting synergistically with venetoclax. Our study sheds light on a previously undercharacterized poor risk subgroup of AML, which may support patient stratification and inform treatment considerations.

overall_design: RNA-seq profiling of MOLM13 cell models containing 1) cDNA-DNp73 to overexpress the DNp73 isoform, 2) CRISPR-Cas9 knockout of the intragenic region +24Kb TSS of the TP73 gene and 3) the empty vector/scrambled control.

first: Diego

first: Jan Jacob

last: Schuringa


title: Efect of L-Ergothioneine treatment in kidneys of Slc7-/- cystinuria mouse model

city: Hospitalet de Llobregrat

first: Clara

last: Mayayo

state: Barcelona

address: Gran Via Hospitalet, 199

country: Spain

institute: IDIBELL

summary: Cystinuria (OMIM #220100) is the most common inherited aminoaciduria and it is caused by mutations in the SLC3A1 and SLC7A9 genes, which encode the heavy and light subunits of the b0,+ amino acid transport system. Defects in renal reabsorption lead to the hyperexcretion of cystine, lysine, arginine and ornithine. The low solubility of cystine at physiological urine pH induces its precipitation and calculi formation. New therapeutic alternatives are currently being under investigation and the antioxidant L-Ergothioneine appears to be a good candidate, as it prevents cystine lithiasis formation when administered in the mouse model of cystinuria. As it has been described that L-Ergothioneine needs to be internalized in the kidney to be effective, this data provide the changes in kidney gene expression after L-Ergothioneine treatment (16 mg/kg/day) to try to understand the mechanisms modeleld by this molecule modelate.

overall_design: RNA-seq profile of kidneys from Slc7a9-/- cystinuric mice treated with L-Ergothioneine or untreated.

first: Manuel

last: Palacín

first: Virginia

last: Nunes


title: Antidepressant sertraline biases resistance emergence via stress-driven rewiring of the pentose phosphate pathway: tktA enables metabolic rollback

city: beijing

first: yueting

last: cui

address: xinjiekou street

institute: beijing normal university

summary: Selective serotonin reuptake inhibitors (SSRIs) may accelerate antibiotic resistance, but the metabolic changes behind this process—and how to restore susceptibility—are still not well understood. We demonstrated that sertraline led to a biased resistance profile in Escherichia coli, characterized by early accumulation of mutations targeting rifampicin and ciprofloxacin. These genetic alterations were linked to a compensatory respiratory mechanism dependent on Complex I, leading to reduced nicotinamide adenine dinucleotide and superoxide/hydrogen peroxide buildup. They also caused a rapid shift of glucose from glycolysis to the pentose-phosphate pathway (PPP) to produce reduced nicotinamide adenine dinucleotide phosphate during oxidative stress, similar to paraquat-like redox stress. Inhibiting the non-oxidative PPP, especially transketolase A (tktA), eliminated the sertraline-primed advantage and brought back antibiotic susceptibility, decreasing survival by approximately 10,000 times during antibiotic challenge, even with rpoBC and gyrAB mutations fixed. These findings uncover an electron transfer chain/PPP–coupled redox module as the hidden driver behind sertraline-induced resistance, highlighting mutation-agnostic ways to restore bacterial sensitivity. By reframing SSRI-induced resistance as a modifiable metabolic trait, we provide a basis for using metabolic adjuvants to shield the millions of SSRI users from the unintended risk of antibiotic resistance—transforming a pharmacological challenge into a manageable, reversible target

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: RNA-seq profiling of Escherichia coli MG1655 after 40 days of adaptive evolution under 40 mg/L sertraline to compare differential gene expression.

first: Yueting

last: Cui

first: Shiyuan

last: Xue

first: Jianhua

last: Guo

first: Chengdong

last: Zhang


title: The TCR-SUB1-DOCK2 Signaling Axis Governs Autoimmunity by Regulating CD4+ T Cell Migratory Capacity

city: shanghai

first: xiaoxue

last: li

institute: Shanghai Jiao Tong University

summary: Aberrant activated T cell infiltration is a key driver of autoimmune pathogenesis, highlighting the therapeutic potential of inhibiting T cell migration. However, the regulatory mechanisms governing tissue ingress of antigen-specific T cells remain elusive. Here, we report that SUB1, a transcription factor upregulated in CD4+ T cells from patients with autoimmune disorders, is regulated by the TCR–IRF4 axis. SUB1 deficiency diminished DOCK2 expression by 50%, impairing Rac-dependent actin polymerization and T cell migration, and consequently suppressed the onset of experimental autoimmune encephalomyelitis (EAE). Mechanistically, SUB1 promotes chromatin accessibility at the Junb and Dock2 loci via liquid–liquid phase separation (LLPS), facilitating biomolecular condensate formation. Furthermore, SUB1 directly activates Junb transcription and cooperates with JUNB to enhance Dock2 expression. Our results identify SUB1 as a critical regulator of antigen-specific CD4+ T cell migration and propose it as a promising therapeutic target for autoimmune diseases.

overall_design:
Histone H3K27ac and H3K4me CHIP-seq analysis using  CD4+ T cells isolated from WT and Sub1-KO mice
Flag ChIP-seq in OT-II cells overexpressing Flag-SUB1
Flag ChIP-seq following the overexpression of Flag-JUNB in in both WT and Sub1-KO CD4+ T cells


title: The TCR-SUB1-DOCK2 Signaling Axis Governs Autoimmunity by Regulating CD4+ T Cell Migratory Capacity [RNA-Seq]

overall_design: RNA sequencing (RNA-seq) analysis using splenic CD4+ T cells isolated from WT and Sub1-KO mice on day 7 of EAE modeling.


title: The TCR-SUB1-DOCK2 Signaling Axis Governs Autoimmunity by Regulating CD4+ T Cell Migratory Capacity [ATAC-Seq]

overall_design: ATAC sequencing (ATACA-seq) analysis using splenic CD4+ T cells isolated from WT and Sub1-KO mice on day 7 of EAE modeling.


title: NSD2 Drives Podocyte Injury in Diabetic Kidney Disease via Epigenetic Regulation of Hippo Signaling

first: Peng

last: Qu

summary: Podocyte lipid accumulation has emerged as an important driver during the progression of diabetic kidney disease (DKD), yet the underlying mechanisms remain not fully clarified. Here, we identified the histone methyltransferase NSD2 as a key epigenetic regulator of podocyte lipid accumulation and injury in DKD. NSD2 expression is markedly increased in podocytes from both DKD patients and mouse models, and its levels shows a positive correlation with disease severity. Genetic deletion of Nsd2 in podocytes, as well as pharmacological inhibition of its methyltransferase activity, substantially reduced podocyte injury and proteinuria in mouse models. In contrast, transgenic Nsd2 overexpression in podocytes aggravated these pathological alterations. Mechanistically, elevated NSD2 in DKD enhances H3K36me2 deposition at the Ajuba promoter, resulting in its transcriptional upregulation and subsequent suppression of Hippo signaling. This epigenetic change promotes lipid accumulation in podocytes, leading to cytoskeletal disturbances and increased apoptosis. Collectively, our findings reinforce lipid accumulation as a central contributor to DKD progression and indicate that NSD2, as a pivotal epigenetic regulator in this process, could represent a reasonable therapeutic target for DKD.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from kidneys and isolated glomeruli  of 24-week HFD/STZ-induced diabetic mice and control mice.


title: Myelo-Erythroid Lineage Commitment Regulation [HPC7_ChIP]

city: Oxford

first: Claus

last: Nerlov

address: John Radcliffe Hospital, University of Oxford

department: MRC Molecular Haematology Unit

institute: Weatheral Institute of Molecular Medicine

summary: LMO4 is an IL-33–inducible master regulator of type 2 myelopoiesis that instructs myeloid fate via GATA factor chromatin re-allocation.

overall_design: ChIP-seq performed in transfected HEK-293T cell line

first: Alexandre

last: Fagnan

first: Christina

last: Di Genua

first: Roy

last: Drissen

first: Zishan

first: Yiran

last: Meng

first: Fränze

last: Progatzky


title: Intraspecific variation in the duration of epigenetic inheritance

first: Germano

last: Cecere

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

department: Development and stem cell biology

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

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

first: François

last: Frejacques

first: Marie

last: Saglio

first: Mohammed

last: Aljohani

first: Christian

last: Froekjaer-Jensen

first: Almira

last: Chervova

first: Loan

last: Bourdon

first: Lise

last: Frézal

first: Marie-Anne

last: Félix


title: NSD2 Drives Podocyte Injury in Diabetic Kidney Disease via Epigenetic Regulation of Hippo Signaling [Cut & Run]

first: Peng

address: China-Japan Friendship Hospital No. 2 Yinghuayuan East Street, Chaoyang District, Beijing 100029, P.R. China

institute: Institute of Clinical Medical Sciences, China-Japan Friendship Hospital

overall_design: Primary podocytes were isolated from podocyte-specific Nsd2 knockout mice and floxed control mice after HFD/STZ-induced diabetic injury. RNA-seq was performed on podocytes collected at 20 and 28 weeks of age to characterize NSD2-dependent transcriptional changes during early and advanced stages of DKD(n = 3).


title: Myelo-Erythroid Lineage Commitment Regulation [HEK_ChIP]

first: Claus

last: Zhang


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

city: Bethesda

first: Keita

last: Saeki

state: Maryland

address: 6 Center Drive

institute: NIH/NICHD

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

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

first: Keiko

last: Ozato


title: snRNA-sequencing of two human dorsal root ganglia

city: DURHAM

first: Jing

last: Xu

state: NC

address: 816 Louise Circle

institute: Duke university

summary: The dorsal root ganglion (DRG) integrates peripheral sensory signals and plays a central role in pain and neuropathy. Using single-nucleus RNA sequencing (snRNA-seq) of human DRG. We spearted 17 clusters and identified 6 major cell types, including sensory neurons and satellite glial cells (SGCs).

overall_design: We performed single-nucleus RNA sequencing (snRNA-seq) on 2 human DRG tissue

first: Charles

last: Novak

first: Zihan

last: Yan

first: Dmitry

last: Velmeshev

first: Richard

last: Cheney

first: Ru-Rong

last: Ji


title: Unique B and plasma cell signature differentiates hidradenitis suppurativa from psoriasis and atopic dermatitis.

city: Dublin

first: Walter

last: Kolch

address: School of Medicine, University College Dublin, Belfield, Dublin 4.

country: Ireland

institute: Systems Biology Ireland

summary: Background Hidradenitis suppurativa (HS), psoriasis (PsO) and atopic dermatitis (AD) are inflammatory skin diseases which, despite sharing some immunological pathways, have unique disease pathogenesis and distinct pathology. For example, Th17 cells are central to PsO pathogenesis and have also been implicated in HS inflammation. AD, on the other hand, is classically referred to as a Th2-mediated disease, however incidence of AD is twice as likely in HS patients compared with healthy individuals, demonstrating an association between HS and AD. Objective To date the transcriptomics of HS, PsO and AD have not been directly compared. Therefore this study aimed to evaluate the transcriptomic differences between HS, PsO and AD lesions to identify a biological signature that defines HS inflammation. Methods Bulk RNA sequencing was performed on 19 healthy controls, 15 HS, 21 PsO and 15 AD lesional skin samples. Results Principal component analysis (PCA) identified a distinct transcriptome in HS lesions compared with healthy control skin, with increased expression of inflammatory mediators and more active inflammatory pathways including TNF, IL-17 and B cell signalling pathways. PsO lesions were defined by a strong IL-17 signature and while an IL-17 signature existed in HS lesions, HS was distinguished from PsO lesions by a unique B cell signature. When compared to AD lesions, HS lesions had a more complex inflammatory profile involving TNF, B cell and NLR signalling while AD lesions had high expression of Th2-associated genes. Weighted gene co-expression analysis suggested T cell signalling and epidermal development are important characteristics of PsO lesions while HS lesions can be defined by complement activation, B cell signalling and fibroblast-associated pathways indicating the potential for scarring in HS. Cell type deconvolution identified an enrichment of keratinocytes and T cells in PsO, Th2 cells in AD and B cells and plasma cells in HS. Finally, gene expression analysis identified increased expression of B cell, plasma cell and immunoglobulin-associated genes in HS lesions relative to healthy control skin, PsO and AD lesions. Conclusion These data suggest that HS pathogenesis is more complex than AD or PsO and highlights an important role of B and plasma cells in HS inflammation.

overall_design: Bulk RNA sequencing was performed on  21 PsO and 15 AD lesional skin samples.

first: Conor

last: Smith

first: Roisin

last: Hambly

first: Solene

last: Gatault

first: Luis

middle: F

last: Iglesias-Martinez

first: Sean

last: Kearns

first: Helen

last: Rea

first: Vivien

last: Marasigan

first: Kate

last: Lynam-Loane

first: Shivashini

last: Kirthi

first: Roselind

last: Hughes

first: Jean

last: Fletcher

first: Brian

last: Kirby


title: Study on the mechanism of action of NUDT21 in acute T-lymphocytic leukemia [CUT&Tag]

city: suzhou

first: yang

last: yang

address: zhongnan road

institute: soochow university

summary: Alternative polyadenylation (APA) is a widespread post-transcriptional mechanism that regulates transcript stability, localization, and translation. While dysregulated APA has been implicated in multiple cancers, its role in T-cell acute lymphoblastic leukemia (T-ALL) remains poorly understood. Here, we identify NUDT21, a core subunit of the APA machinery, as an essential oncogenic regulator in T-ALL. NUDT21 is significantly upregulated in T-ALL patient samples and associated with poor prognosis. Functional assays demonstrate that NUDT21 knockdown inhibits T-ALL cell proliferation, induces apoptosis, and suppresses leukemia progression in vivo. Integrative PAS-seq and RNA-seq analysis reveals that NUDT21 maintains distal polyadenylation site usage of oncogenic transcripts, including UBE2D3, whose 3′UTR shortening upon NUDT21 loss leads to decreased expression and impaired leukemic cell growth. In addition to its APA role, NUDT21 occupies gene regulatory regions and directly activates transcriptional programs enriched for MYC and E2F targets, promoting cell cycle progression and ribosome biogenesis. Pharmacological suppression of NUDT21 using ouabain, a cardiac glycoside, downregulates UBE2D3 and E2F/MYC effectors, resulting in robust anti-leukemic effects.Our findings reveal a dual regulatory role of NUDT21 in T-ALL, functioning through both APA-dependent and APA-independent mechanisms to sustain leukemic proliferation. Targeting NUDT21 or its downstream programs represents a promising therapeutic strategy for T-ALL.

overall_design: CUT&Tag profiles of J.gamma1 cells NUDT21 were generated by CUT&Tag sequencing, in double, using Illumina NovaSeq X plus.

first: Yang

last: Yang

first: Shuiyan

last: Wu


title: Study on the mechanism of action of NUDT21 in acute T-lymphocytic leukemia [eCLIP-seq]

overall_design: eCLIP profiles of J-Gamma1 cells NUDT21 were generated by eCLIP sequencing, using DNBSEQ-T7.


title: Study on the mechanism of action of NUDT21 in acute T-lymphocytic leukemia [RNA-Seq]

overall_design: mRNA profiles of J-Gammal cells treated with short hairpin RNAs (shRNAs) targeting NUDT21 or negative control (shNC) were generated by RNA sequencing, in double, using Illumina NovaSeq X plus.


title: Full transcriptome analysis reveals key regulatory networks and potential therapeutic targets of dorsal root ganglion in rats with painful diabetic peripheral neuropathy

city: Beijing

first: Zhenxuan

last: Gao

state: Chaoyang

address: No.2 yinghua east street

institute: Chinese Academy of  Medical Sciences & Peking Union Medical College

summary: Painful diabetic peripheral neuropathy (PDPN) is a common and highly disabling complication of diabetes, the mechanism of which remains incompletely elucidated and lacks effective treatment methods. The dorsal root ganglion (DRG) plays a central role in the occurrence and development of PDPN. This study systematically delineates the mRNA–lncRNA–miRNA interaction network of the DRG in a rat model of PDPN for the first time, reveals the important roles of inflammatory signaling, neurotrophic factor deficiency, metabolic reprogramming, and ion channel abnormalities in the pathogenesis of PDPN, and proposes multiple potential molecular targets, providing theoretical basis and experimental support for the early diagnosis and precision treatment of PDPN.

overall_design: Diabetes was induced by a single intraperitoneal injection of streptozotocin at 45 mg/kg dissolved in 0.1 M citrate buffer (pH 4.5). Seventy-two hours after injection, fasting blood glucose was measured; rats with a glucose level ≥ 16.7 mmol/L were considered diabetic. After an 8-week observation period, the PDPN model was confirmed by combining these data with behavioral test results.

first: ZhenXuan

first: Li

last: Zhang


title: Intrinsic higher potency of basal urothelial cells to intermediate and umbrella cells as the cell of origin for bladder cancer

city: Santa Cruz

first: Nicholas

last: Chu

state: California

address: 1156 High Street

department: MCD Biology

institute: University of California, Santa Cruz

summary: Transcriptome profiling of bladder cancer has revealed distinct basal-like and luminal-like molecular subtypes, which may be correlated with pathological subtypes of different patient outcomes. However, whether these molecular subtypes originate from the corresponding cell types in the normal urothelium and whether different cells of origin influence bladder cancer progression remain unclear. Here, we conducted cell-type-specific lineage tracing in CRISPR/Cas9-induced mouse bladder cancer models of Pten and Trp53 targeting. We show that although basal, intermediate, and superficial umbrella cells can all serve as the cell of origin for bladder cancer, transformed umbrella cells were gradually displaced by tumor cells from inner layers, particularly transformed basal cells, which had highest stemness. Histological and single cell RNA-sequencing data comparing basal- and intermediate-cell-induced bladder tumors revealed that basal-induced tumors displayed higher heterogeneity, and contained unique cell clusters including Krt14+Ki67+ highly proliferative basal cells, squamous cell carcinoma, and transitioning cells towards the Gata3+ luminal subtype. Trajectory analysis confirmed the cell lineage differentiation hierarchy uncovered in lineage tracing. Moreover, human bladder cancer molecular subtype signatures were highly enriched in mouse tumor cell clusters of the corresponding cell of origin, and a gene signature derived from the unique basal-induced clusters is predictive of worse patient outcome. Overall, our results support that the basal and luminal molecular subtypes of bladder cancer have the corresponding cells of origin as their basis, and that urothelial basal cells are intrinsically more competitive than intermediate and umbrella cells in generating aggressive bladder cancer subtypes.

overall_design: Singe cell mRNA profiles from tumors derived from mouse bladder urothelial basal cells or intermediate/luminal cells, induced by CRISPR targeting Pten and Trp53 in a cell-type-specific manner. Libraries were prepared using 10x Genomics Chromium Single Cell 3' Solution with v3.1 chemistry and sequenced using Illumina NovaSeq X.

first: Chuan

last: Yu

first: Alexandra

last: Aguirre

first: Jonathan

last: Green

first: Qing

last: Xie

first: Beatrice

last: Knudsen

first: Zhu

middle: A

last: Wang


title: Study on the mechanism of action of NUDT21 in acute T-lymphocytic leukemia [PAS-seq]

overall_design: PAS-seq profiles of J-Gammal cells treated with short hairpin RNAs (shRNAs) targeting NUDT21 or negative control (shNC) were generated by PAS-seq, in double, using Illumina NovaSeq X plus.


title: Blocking Host Factors IAP and DDX3 Reverse HIV-1 Latency and Restore Apoptosis Vulnerability of the HIV-1 reservoir

city: Amsterdam

first: Neeltje

last: Kootstra

address: Meibergdreef 9

institute: AmsterdamUMC

summary: Antiretroviral therapy (ART) effectively suppresses HIV-1 replication but does not purge the latent HIV-1 reservoir. Strategies aimed at HIV-1 latency reversal and subsquent elimination of infected cells are being explored. Targeting the inhibitor of apoptosis proteins (IAP) and DEAD-box polypeptide 3 (DDX3) RNA helicase reduce the HIV-1 reservoir ex vivo. However, mechanisms driving elimination of HIV-1 infected cells remain unclear. Here we uncovered the mechanism regarding latency reversal and induction of cell death specific for HIV-1 infected cells. Inhibition of IAP by second mitochondrial-derived activator of caspases mimetic (SMACm; AZD5582) resulted in activation of non-canonical NF-κB that induced HIV-1 transcription also in combination with a DDX3 inhibitor (DDX3i; FH1321). Transcriptome analysis revealed that HIV-1 actively suppressed apoptosis-related genes. SMACm treatment resulted in a broad induction of these genes irrespective of infection. Notably, DDX3 inhibition specifically restored the expression of the majority of HIV-1 suppressed genes, and when combined with SMACm restored almost all HIV-1 downregulated genes, thereby rendering HIV-1 infected cells vulnerable to apoptosis. Thus, our data strongly suggest that inhibition of host factors IAP and DDX3 not only induces latency reversal but also restores HIV-1 induced suppression of apoptotic processes in infected cells leading to reservoir elimination.

overall_design: The combination of SMACm and DDX3i induces cell death specifically of HIV-1 infected but not uninfected PBMCs from PWH. To explore the underlying mechanism, we analyzed the gene expression during HIV-1 infection and assessed the effect of the different compounds using a survival/apoptosis pathway qPCR array. After 48 hours of infection of SUPT1-CCR5 cells with HIV-1 NL4-3BaL, cells were treated with DDX3i, SMACm, or their combination and after 6 hours, transcription of survival and apoptosis genes was analyzed by qPCR array.

first: Jade

last: Jansen

first: Shirley

last: Man

first: Fenna

first: Ad

last: van Nuenen

first: Karel

last: van Dort

first: Claudi

last: Zamperini

first: Conraed

last: Houck

first: Teunis

middle: B

last: Geijtenbeek