title: Global rewiring of genome organisation during transition to gametogenesis in gonadal germ cells

city: London

first: Tien-Chi

last: Huang

address: Du Cane Road, Hammersmith Hospital Campus

department: Epigenetics

institute: MRC Laboratory of Medical Sciences

summary: Global epigenetic resetting in the gonadal primordial germ cells (PGCs) enables transition to gametogenesis and eventual restoring of totipotency after fertilisation. This reprogramming process involves global DNA demethylation, changes in nuclear morphology as well as remodeling of repressive histone modifications. Here, using combined cytological and Hi-C based methods, we reveal that following the epigenetic reprogramming and their commitment to gametogenesis, pre-meiotic gonadal germ cells are characterised by a novel principle of chromosome and genome architecture. This involves separation of individual chromosomes and anchoring of centromeres at the nuclear periphery, reduction of  inter-chromosome interactions and disentangling of chromosome ends. Furthermore, genome-wide mapping documents striking remodeling of 3D genome architecture across all observable levels including disruption of topological associated domains (TADs), loss of detectable loops and reduced active-active compartment interactions. We further show that the diminished TADs correlate with the reduced levels of CTCF thus providing a unique in vivo physiological model to understand genome folding principles. Last, but not least we show that primordial germ cell like cells (PGCLCs), derived from embryonic stem cells, do not exhibit the same chromatin organisation as embryonic germ cells suggesting that the 3D genome remodeling accompanies acquisition of meiotic competency. Collectively, our findings uncover the existence of a unique chromatin architecture in premeiotic male and female gonadal germ cells and document that alongside global DNA demethylation the germline epigenetic reprogramming involves erasure of memory at the genome architectural level through a complete re-organisation of 3D genome.

overall_design: Hi-C experiments on isolated PGC and somatic cells from female and male E13.5 mouse embryos

first: Maria

last: Rigau

first: Valeriya

last: Malysheva

first: Chad

last: Wildling

first: Stella

last: Siciliani

first: Irina

middle: B

last: Balsells

first: Camille

last: Dion

first: Mikhail

last: Spivakov

first: Juan

last: Vaquerizas

first: Petra

last: Hajkova


title: Fishing with Two Lines: A Hybrid Approach to Spatial Transcriptomic Discovery

status: Public on Jan 07 2026

city: Phoenix

first: Nicholas

last: Banovich

state: AZ

address: 445 North Fifth Street

department: Integrated Cancer Genomics

country: USA

institute: TGen - Translational Genomics Research Institute

summary: Spatial transcriptomics faces a trade-off between the number of genes assayed and depth of per-gene sensitivity. We developed a 'dual chemistry' method that combines the high sensitivity of a 10X Genomics Xenium V1 custom panel (up to 480 genes) with the broad coverage of the Prime 5K panel (5001 genes) on a single tissue section. This involved co-hybridizing Prime and V1 probes and sequentially running the V1 and Prime decoding chemistries. Applied to a human lung tissue microarray, we observed high concordance between the V1 and Prime chemistries when run independently (on serial sections) and the dual chemistry runs. Overlapping genes (profiled on both V1 and Prime chemistries) showed similar expression patterns in the dual run demonstrating the fidelity of the assay. By combining information from both the V1 and Prime chemistries within the same cell, we retain more cells, gain valuable additional information, and enable both high sensitivity profiling and discovery.

overall_design: 17 samples are included in this study from archived formalin fixed paraffin embedded (FFPE) tissue from human lung. A team with expertise in pediatric lung pathology selected a 3mm x 3mm target location for the region of interest for analysis. A FFPE tissue microarray (TMA) block was designed to fit all samples into the Xenium capture area (10.45mm x 22.45mm) in a 3 x 6 pattern of cores, with the top left core space remaining empty as an orientation marker. Three serial sections were placed onto three Xenium slides and prepped.

first: Arianna

middle: L

last: Williams-Katek

first: Saahithi

last: Mallapragada

first: Evan

middle: D

last: Mee

first: Brandon

middle: K

last: Fischer

first: Laurie

middle: C

last: Eldredge

first: Gail

middle: H

last: Deutsch

first: Jonathan

middle: A

last: Kropski

first: Jennifer

middle: M

last: Sucre

middle: E


title: Spatial characterization of the motor and non-motor somal and axonal transcriptome in adult healthy and mutant FUS mice

status: Public on Jan 08 2026

city: Leuven

first: Sandrine

last: Da Cruz

address: Herestraat 49 |

country: Belgium

institute: VIB-KUL Center for Brain & Disease Research

summary: Here we investigated the transcriptome of motor and non-motor axons and cell bodies in the context of mutant FUS-related amyotrophic lateral sclerosis (ALS). We applied Nanostring GeoMX Digital Spatial Profiler platform to profile the transcriptome of subcellular compartments in the lower motor circuitry of a mouse model ricapitulating ALS motor symptoms. This work sheds light for the first time on the transcriptomic alterations in axons and in somas which may contribute to axonal degeneration and neuromuscular junction denervation, early features of ALS.

overall_design: Four 5-um thick spinal cord and sciatic nerve sections derived from control and humanized FUS R521H mice were layered on normal glass microscope slides and sent to Nanostring Technologies facility in dry ice (Seattle, US). Slides were analyzed on the Nanostring GeoMx Digital Spatial Profiler platform using the Whole Mouse Transcriptome Atlas panel (Nanostring). Regions of interest were drawn on spinal cord ventral horns and full sciatic nerve sections, and further segmented into ChAT+ and ChAT- areas of interest.

first: Diana

last: Piol

first: Theo

last: Killian

first: Maria

last: Georgopoulou

first: Alejandro

last: Sifrim


title: Dps binds and protects DNA in starved Escherichia coli with minimal effect on chromosome accessibility, dynamics and organization

status: Public on Jan 06 2026

city: Bloomington

first: Xindan

last: Wang

state: IN

address: 1001 E 3rd St

department: Biology

institute: Indiana University at Bloomington

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Dps is the most abundant nucleoid-associated protein in starved Escherichia coli with ∼180000 copies per cell. Dps binds DNA and oxidizes iron, facilitating survival in harsh environments. Dps–DNA complexes can form crystalline structures, leading to the proposed model that Dps reorganizes the starved E. coli nucleoid into a compact liquid crystal, slowing chromosome dynamics, and limiting access of other proteins to DNA. In this work, we directly tested this model using live-cell super-resolution microscopy and Hi-C analysis. We found that after 96 h of starvation, Dps compacts the nucleoid, and increases short-range DNA–DNA interactions but does not affect chromosome accessibility to large protein nanocages or small restriction enzymes. We also report that chromosome dynamics and organization are primarily impacted by the bacterial growth phase; the effect of Dps is relatively minor. Our work clarifies the role of Dps in modulating nucleoid properties, and we propose an updated model for Dps–DNA interactions in which Dps binds, protects, and compacts DNA largely without influencing chromosome access, dynamics, and organization. Additionally, this work provides a general framework for assessing the impact of nucleoid-associated proteins on key aspects of chromosome function in live cells.

sample_organism: Escherichia coli str. K-12 substr. W3110

overall_design: Hi-C, ChIP-seq, and whole genome sequencing experiments were performed on wild-type and mutant Escherichia coli W3110 growing in High-Def Azure medium supplemented with 0.2% glucose.


title: Differential effects on tumor progression by APOBEC3A, APOBEC3B, and APOBEC3H Haplotype I in a breast cancer mouse xenograft model

city: Saskatoon

first: Franco

middle: J

last: Vizeacoumar

state: Saskatchewan

address: 4D40 Health Sciences Building, 107 Wiggins Road

department: Oncology

country: Canada

institute: University of Saskatchewan

type: Expression profiling by high throughput sequencing

summary: The APOBEC3 (A3) family of cytidine deaminases induce somatic mutations that are highly prevalent in cancers, but the functional consequences are largely unknown. To determine functional consequences we exposed MCF7 tumorigenic breast epithelial cells to APOBEC3A, APOBEC3B or APOBEC3H Haplotype I. Comparative analysis between cells pre and post -APOBEC3 exposure revealed fewer deamination-dependent γH2AX foci post-APOBEC3 exposure, despite maintaining A3 protein expression. In a mouse xenograft model, high expressing, but not low expressing APOBEC3A-exposed cells caused increased tumor progression. In contrast, high expressing, but not low expressing APOBEC3B-exposed cells decreased tumor size. APOBEC3H Haplotype I-exposed cells stochastically increased tumor progression independent of expression levels. Consistent with tumor data, RNA-seq showed upregulation of tumor enhancing pathways only in cells that enhanced tumor progressiongrowth. The results indicate that in a breast cancer xenograft model, APOBEC3A and APOBEC3H Haplotype I are more likely to contribute to enhanced tumor progression than APOBEC3B.

overall_design: MCF7 cells were engineered to express doxycycline inducible APOBEC3A, APOBEC3B, or APOBEC3H Haplotype I (APOBEC3H). Cells were (Induced, I) or were not exposed (Uninduced, U) to doxycycline for 3 weeks in soft agar. Cells were then isolated, RNA extracted and sequenced. Isogenic cells lines were compared in Induced (I) versus Uninduced (U) pairs as follows: APOBEC3A_I4 vs APOBEC3A_U1 (APOBEC3A low expression), APOBEC3A_I5 vs APOBEC3A_U6 (APOBEC3A high expression), APOBEC3B_I2 vs APOBEC3B_U1 (APOBEC3B high expression), APOBEC3B_I5 vs APOBEC3B_U2 (APOBEC3B low expression), APOBEC3H_I4 vs APOBEC3H_U1 (APOBEC3H High 1), APOBEC3H_I1 vs APOBEC3H_U2 (APOBEC3H High 2)

first: Milaid

middle: G

last: Rodríguez

first: Lai

last: Wong

first: Arzhang

last: Shayeganmehr

first: Diogo

last: Pellegrina

first: Frederick

middle: S

first: Mohamed

last: Helmy

first: Linda

last: Chelico


title: Tumor Extracellular Vesicles lncOSLMT Drives Lung Inflammatory Premetastatic Niche Formation in Osteosarcoma via m6A-Dependent hnRNPA2B1/COX-2 Axis

status: Public on Jan 04 2026

city: Guangzhou

first: Zehao

last: Guo

state: Guangdong

address: zhongshan 2 road

country: China

institute: The First Affiliated Hospital, Sun Yat-sen University

summary: Tumor-derived extracellular vesicles (EVs) play critical roles in premetastatic niche (PMN) formation. Here, we demonstrated that EVs from highly metastatic osteosarcoma cell lines preferentially localized to lung fibroblasts and induce inflammatory PMN formation. High-throughput profiling of EVs-derived long noncoding RNAs (lncRNAs) identified lncOSLMT as a candidate enriched in EVs and markedly upregulated in patient tumor and serum, with elevated levels correlating with poor prognosis. Mechanistically, in EVs, lncOSLMT directly bound the RNA-binding protein hnRNPA2B1. Following internalization by recipient lung fibroblasts, hnRNPA2B1 bound to N⁶-methyladenosine (m⁶A) -modified sites in the 3’UTR of PTGS2 mRNA, leading to transcript stabilization and increased COX-2 expression. For therapeutic intervention, we developed lactoferrin-resveratrol (LF-RES) nanoparticles, which loaded siRNA against lncOSLMT. Intravenous administration of LF-RES-siRNA in mice reduced EVs-induced lung inflammation and suppressed lung metastasis. Combination with EP2/EP4 antagonists produced enhanced anti-metastatic effects. These findings establish EVs-derived lncOSLMT as a key regulator of inflammatory PMN formation in the lung and highlight the potential of LF-RES-siRNA nanoparticles as a targeted anti-metastatic therapy in osteosarcoma.

overall_design: HFL-1 cells were treated with extracellular vesicles (EVs) derived from oelncOSLMT or vector control.

first: Xianbiao

last: Xie

first: Hongbo

last: Li


title: Ablation of VEGFA following a lumbar intervertebral disc injury attenuates intradiscal neurovascular features and prevents chronic low back pain symptoms

city: St. Louis

first: Simon

last: Tang

state: MO

address: 425 S. Euclid Ave, Campus Box 8233, Tang Lab, Washington University School of Medicine

department: Orthopaedic Surgery

institute: Washington University in St. Louis

summary: There are currently no therapies for the staggering disability and public health costs of chronic low back pain (LBP). Innervation of the degenerating intervertebral disc (IVD) is suspected to cause discogenic LBP, but the mechanisms that orchestrate the IVD’s neo-innervation and subsequent symptoms of LBP remain unknown. We hypothesize that Vascular Growth Endothelial Factor-A (VEGFA) critically mediates the neurite invasion in the IVD and contributes to prolonged LBP.  Initiating IVD degeneration through a mechanical injury, we evaluated the progression of neurovascular features into the IVD, as well as resultant LBP symptoms and locomotive performance at acute (3-weeks) and prolonged (12-weeks) time points following IVD injury. To determine the role of VEGFA, we used a mouse model with ubiquitous inducible recombination of the floxed VEGFA allele (UBC-CreERT2; VEGFAfl/fl).  The ablation of VEGFA attenuated the neurite and vessel infiltration into the degenerating IVD, and the VEGFA-null animals exhibited alleviated mechanical allodynia and improved locomotive performance. To determine the effects of IVD-derived VEGFA on endothelial cells and neurons, we cultured HMEC-1 endothelial cells and SH-SY5Y neurons using conditioned media from VEGFA-silenced (siRNA) human primary IVD cells stimulated by IL1b.  The endothelial cells and neurons exposed to the secretome of the VEGFA-silenced IVD cells exhibited reduced growth, suggesting that the inhibition of IVD-derived VEGFA may be sufficient to attenuate intradiscal neurovascular features. Together, we show that VEGFA orchestrates the growth of intradiscal vessels and neurites that cause low back pain and impaired function, and the inhibition of VEGFA can prevent prolonged low back pain.

overall_design: Human intervertebral disc (IVD) cells were isolated from the IVD tissue of eight patients removed during elective discectomy surgeries. IVD cells were plated and 1 ng/mL of IL-1β was added to the stimulate the cells for 24 hours. IL-1β was removed and cells were then transfected with Control, Scrambled siRNA (Scram) or VEGF siRNA (Vegfa)for 24 hours. Next, the IL-1β stimulated and siRNA transfected IVD cells were co-cultured with either SH-SY5Y neuronal cells (Nerves) for 48 hours or HMEC-1 endothelial cells (Endo) for 24 hours. The co-cultured nerve and endothelial csells were submitted for RNA sequencing.

first: Ryan

last: Potter

first: Remy

last: Walk

first: Hong

last: Moon

first: Addison

last: Liefer

first: Sade

middle: W

last: Clayton

first: Liufang

last: Jing

first: Lori

last: Setton

first: Munish

last: Gupta

middle: Y


title: Mating regulates growth, metabolism, and digestive efficiency in the female Drosophila midgut

status: Public on Jan 05 2026

city: Salt Lake City

first: Tahmineh

last: Kandelouei

state: Utah

address: 1950 Circle of Hope Dr.

institute: Huntsman Cancer Institute

summary: Adaptive changes in organ size and function occur in most animals, but how these changes are regulated is not well understood. Previous research found that mating in Drosophila females promotes intestinal stem cell proliferation and increases the overall size of the endodermal portion of the intestine (the “midgut”). Other studies reported mating-dependent changes in feeding behavior, midgut gene expression, and whole-body lipid storage, suggesting altered metabolism. Here, we show that mating dramatically alters female midgut metabolism and digestive function. Mating increased relative levels of TCA cycle intermediates, fatty acids, and ceramides in the gut, increased total midgut lipids and protein, and reduced relative carbohydrate levels. Mating also enhanced the efficiency of protein digestion relative to carbohydrate digestion. Corroborating a previous report, we found that the expression of genes that mediate protein and carbohydrate and metabolism was similarly altered. In addition, we noted a mating-dependent downregulation of oxidative stress response and autophagy genes. Mating-dependent increases in ecdysone receptor (EcR) signaling were important for increasing TCA cycle intermediates, protein, and ceramides in the female midgut, but had minimal effects on bulk lipid accumulation. Overall, this study contributes to our understanding of the physiological changes that occur during adaptive intestinal growth, and how they are regulated.

overall_design: We first compared the gene expression in mated and unmated flies whole gut (19464X1-8) and gut progenitor cells (19966X1-8) after 48 hours mating. Then, to investigate how ecdysone signaling pathway affects mating-induced changes, we compared mated and unmated flies, each expressing or not expressing EcR-RNAi. We aged the collected virgin flies for 5 days at 29°C to express EcR-RNAi under the control of ubiquitous (Actin-Gal4) (22551X1-16) or EC-specific (Myo1A-Gal4) (24047X1-2, X4-16) drivers. After 5 days of RNAi expression, we set the mating for 48 hours (25°C) by adding males. We then dissected the guts after 48 hours of mating for sample preparation. For mating experiment; mated female flies were cultured with equal number of males, whereas unmated were isolated apart from males from eclosion.  For this experiment, we used 4 replicates per condition/ 15 guts, exept for RNAseq of FACS-sorted progenitor cells that we used 100-150 guts/sample. Mated and unmated flies were age- and genotype-matched. We then performed gene expression profiling analysis using data obtained from RNAseq of mated and unmated flies gut after 48 hours mating.

first: Bruce

last: Edgar

first: Madeline

last: Houghton

first: Mitchell

middle: R

last: Lewis

first: Caroline

last: Keller

first: Marco

last: Marchetti

first: Xiaoyu

last: Kang


title: A therapeutic antisense oligonucleotide encompassing 2′-O-methoxyethyl modification triggers unique perturbation of the transcriptome

city: Ames

first: Ravindra

middle: N

last: Singh

state: IA

address: 2034 Veterinary Medicine

department: Biomedical Sciences

institute: Iowa State University

summary: Antisense oligonucleotides (ASOs) are short nucleic acids that act by annealing to complementary target RNA or DNA sequences. It is currently unknown how the transcriptome-wide off-target effects of different ASO chemistries targeting the same sequence differ. Nusinersen, the first FDA-approved treatment for spinal muscular atrophy (SMA), is an ASO that restores Survival motor neuron 2 (SMN2) exon 7 splicing by binding to the intronic splicing silencer N1 (ISS-N1) element in intron 7. We tested the transcriptome-wide off-target effects in SMA patient fibroblasts of three ASOs targeting ISS-N1: F18OMe, a 2'-O-methyl (OMe) ASO incorporating a phosphorothioate backbone, F18MOE, a 2'-O-methoxyethyl (MOE) ASO incorporating a phosphorothioate backbone, and F20PMO, a phosphorodiamidate morpholino (PMO) ASO. Using minigenes, we showed that skipping of POLR2H exon 2 and seven other exons is triggered by direct annealing of F18MOE to target exonic sequences, and the chemistry-specific effects of F18MOE on exon skipping are primarily due to enhanced mismatch tolerance of MOE. We confirmed that reduction of ASO length and mixed MOE/OMe chemistry are both effective strategies for mitigation of off-target effects. Our findings will be instructive for future design of ASO therapies for SMA as well as other diseases treatable by ASOs.

overall_design: GM03813 SMA patient cells were treated by nucleofection with ASOs targeting Intronic Splicing Silencer N1 incorporating three types of modifications: phosphorothioate backbone with 2'-O-Methyl modificaiton, phosphorothioate backbone with 2'-methoxyethyl modification, and phosphorodiamidate morpholino chemistry. RNA was isolated by TRIzol 24 hours after nucleofection and sequenced by Illumina sequencing

first: Eric

last: Ottesen

first: Wren

last: Murzyn

first: Robert

last: Kaas

first: Keaton

last: Bertrand

first: Jessica

last: Payne


title: 35 somites tail single cell RNAseq in control and homocysteine treated chicken embryo

city: Clermont-Ferrand

first: Felipe

last: Maurelia

address: 28, place Henri Dunant - BP 38

country: France

institute: iGRED

overall_design: LMO multiplexing of single cells prior to BD Rhapsody single cell encapsulation

first: Stephanie

last: Maupetit-Mehouas

first: Nicolas

last: Allègre

first: Yoan

last: Renaud

first: Pouria

last: Hosseinna

first: Jonas

last: Cruzel

first: Claire

last: Chazaud

first: Charlène

last: Guillot


title: Tumor Extracellular Vesicles lncOSLMT Drives Lung Inflammatory Premetastatic Niche Formation in Osteosarcoma via m6A-Dependent hnRNPA2B1/COX-2 Axis.

first: Zehao

last: Guo

overall_design: Nude mice were injected with 143B-derived EVs or MNNG/HOS-derived EVs via the tail vein, followed by RNA sequencing of lung tissues.

first: Xianbiao

last: Xie

first: Hongbo

last: Li


title: Tumor Extracellular Vesicles lncOSLMT Drives Lung Inflammatory Premetastatic Niche Formation in Osteosarcoma via m6A-Dependent hnRNPA2B1/COX-2 Axis [ncRNA-Seq]

type: Non-coding RNA profiling by high throughput sequencing

overall_design: Extracellular vesicles (EVs) isolated from different cell lines were subjected to lncRNA sequencing.


title: RUNX1 is Expressed in a Subpopulation of Dermal Fibroblasts and is Associated with Disease Severity of Systemic Sclerosis [scRNA-seq]

status: Public on Jan 01 2026

city: Lebanon

first: Rezvan

last: Parvizi

state: NH

address: 1 Medical Center Drive

department: Biomedical Data Science

institute: Dartmouth College

summary: The activation of Runt-related transcription factor 1 (RUNX1) in fibroblasts has been implicated in wound healing and fibrosis; however, the role of RUNX1 in the fibrotic progression of the autoimmune disease systemic sclerosis (SSc) is not known. Leveraging gene expression, genome-wide DNA methylation, and single-cell resolution data of SSc skin and fibroblast, we analyzed the impact of RUNX1 dysregulation in SSc dermal fibrosis. RUNX1 function was subsequently assessed using siRNA, pharmacologic inhibition, and CRISPR knockout in 2D and 3D fibroblasts cultures. Analysis of gene expression in multiple cohorts demonstrated an association between the severity of dermal fibrosis and the expression levels of RUNX1 in the skin of patients with SSc. Epigenomic analyses of methylation identified hypomethylated CpG sites proximal to the RUNX1 gene, implicating their potential role in the increased expression of RUNX1. Analysis of single-cell RNA-seq data from skin biopsies of individuals with SSc revealed that RUNX1 is higher in subpopulations of fibroblasts enriched in SSc, which are believed to contribute to fibrosis. RUNX1 CRISPR KO resulted in reduced alpha smooth muscle actin (α-SMA) expression. Inhibition of RUNX1 activity caused a reduction in fibroblast activation, contraction, extracellular matrix components, and proliferation rates including a reduction in SFRP4, LUM and COL1A1. This study is the first to demonstrate a potential role for RUNX1 in the pathogenesis of systemic sclerosis dermal fibrosis. RUNX1 is associated with more severe SSc fibrosis and is associated with a subpopulation of dermal fibroblasts implicated in fibrosis.

overall_design: Skin fibroblasts isolated from SSc patients (n=2) were treated for 72 hours with either RUNX1 siRNA (Dharmacon, catalog ID E-003926-00-0010) or non-targeting control pool siRNA (NC, Dharmacon, D-001910-10-05). Single cell suspensions were then processed for scRNA-seq.

first: Parvizi

last: Rezvan

first: Gudjonsson

last: Johann

first: Whitfield

last: Michael


title: Impact of copper on the physiology and transcriptome of Methylosinus trichosporium OB3b grown on either methane or methanol

status: Public on Jan 03 2026

city: Ann Arbor

first: Peng

last: Peng

state: MI

address: 1351 Beal Avenue

institute: University of Michigan

summary: This study investigates the combined effects of copper availability and carbon source (methane versus methanol) on the physiology and transcriptome of Methylosinus trichosporium OB3b, a model Type II methanotroph. Methanotrophs oxidize methane to carbon dioxide through intermediates such as methanol, formaldehyde, and formate, using two forms of methane monooxygenase (MMO): the copper-dependent particulate MMO (pMMO) and the soluble MMO (sMMO). Although Msn. trichosporium OB3b can utilize both methane and methanol as sole carbon sources, growth on methanol is significantly affected by copper. In the presence of copper, methanol-grown cells exhibited impaired growth, formate accumulation, and decreased pH, while buffering with MOPS restored growth. NADH/NAD ratios increased nearly tenfold in methanol-grown cultures with copper, indicating redox imbalance. Transmission electron microscopy revealed disrupted intracytoplasmic membranes under these conditions. Transcriptomic analysis showed that genes involved in methanol oxidation were differentially expressed in response to copper and carbon source, and two siderophore biosynthetic gene clusters were repressed during methanol growth with copper. Overall, the findings suggest that Msn. trichosporium OB3b modulates metallophore expression and carbon metabolism to manage oxidative and redox stress under methanol growth conditions. Understanding these regulatory mechanisms is critical for optimizing methanotroph-based biotechnological applications, including methanol-driven biosynthesis of valuable compounds such as methanobactin.

overall_design: RNA-seq profiling of Methylosinus trichosporium OB3b grown on methane with and without copper, and grown on methanol without copper and with copper plus MOPS buffer.

first: Jeremy

last: Semrau


title: Structural Basis of DNA-Dependent Coactivator Recruitment by the Tuft Cell Master Regulator POU2F3 [DMS_Screen]

city: Cold Spring Harbor

first: Damianos

last: Skopelitis

state: NY

address: One Bungtown Rd

department: Cancer Biology

institute: Cold Spring Harbor Laboratory

summary: The transcription factor POU2F3 defines the identity of tuft cells and underlies a distinct molecular subtype of small cell lung cancer (SCLC). Although POU2F3 is considered undruggable, its activity critically depends on the coactivators OCA-T1 and OCA-T2. Here, we demonstrate that acute suppression of either POU2F3 or OCA-T1 induces regression of tuft cell-like SCLC xenografts in vivo. To explore the structural basis and druggability of this dependency, we solved crystal structures of POU2F3 bound to OCA-T1 or OCA-T2 in complex with DNA, revealing a tripartite, DNA-dependent interface. We further employed deep mutational scanning to systematically assess the functional impact of 4,218 missense variants in POU2F3 and OCA-T1, uncovering both mutation-sensitive hotspots and structurally constrained regions critical for tumor cell fitness. These findings define a unique transcriptional complex that integrates DNA recognition with coactivator recruitment and nominate POU2F3–OCA-T as a structurally tractable vulnerability in tuft cell-like carcinomas.

overall_design: Deep Mutational Scanning (DMS) of CRISPR-resistant OCA-T1 and POU2F3 cDNA libraries  co-expressing sgRNAs targeting the endogenous OCA-T1(sgOCA-T1) or POU2F3(sgPOU2F3) genes respectively. NCI-H211 Cas9+ cells were transduced with lentiviral DMS libraries at low MOI and cultured for 10 population doublings.

first: Aktan

last: Alpsoy

first: Jonathan

last: Ipsaro

first: Sujay

last: Pal

first: Frank

last: Chung

first: Shannon

last: Carpenter

first: John

last: Desmarais

first: Xiaoli

last: Wu

first: Kenneth

last: Chang

first: Matthew

middle: T

last: DiMare

first: Erin

last: Harten

first: Staci

last: Bergman

first: Justin

last: Kinney

first: Jeffrey

last: Engelman

first: Hyo-Eun

last: Bhang

first: Leemor

last: Joshua-Tor

first: Christopher

last: Vakoc


title: Structural Basis of DNA-Dependent Coactivator Recruitment by the Tuft Cell Master Regulator POU2F3 [RNA-seq]

first: Damianos

last: Skopelitis

overall_design: RNA-seq of stably expressed CRISPR-resistant cDNAs for POU2F3 (WT or L191A mutant) and an empty control, 5 days after infection with an sgRNA targeting endogenous POU2F3 (sgPOU2F3) or a negative control (sgROSA), in NCI-H211 Cas9+ cells.

middle: B


title: Genetic rescue of mitochondrial complex I reverses metabolic defects in circadian mutant mice

city: Chicago

first: Joseph

last: Bass

state: IL

address: 303 E Superior St, Lurie 7-220

institute: Northwestern University

summary:
We used single nuclei RNA-seq to compare gene expression from adipocyte circadian mutant mice +/- expression of the yeast NADH dehydrogenase (NDI1).

We used RNA-sequencing of fractionated adipocytes from the visceral white adipose tissue of control mice, mice lacking the circadian clock activator Bmal1, and mice lacking the mitochondrial complex I subunit Ndufs2.

overall_design:
Visceral white adipose tissue (WAT) was isolated from 3-month old male mice and was homogenized, followed by filtering and centrifugation to isolate nuclei. Nuclei were then analyzed for single nuclei RNA-sequencing with 10X genomics.

Bulk RNA-seq: Visceral white adipose tissue (WAT) was isolated from 3-month old male mice and was digested with collagenase followed by differential centrifugation to float the adipocytes. The adipocyte fraction was then homogenized followed by RNA isolation, library preparation, and sequencing.

first: Chelsea

last: Hepler

first: Nathan

last: Waldeck

first: Joe


title: Persistent cortical excitatory neuron dysregulation in adult Chd8 haploinsufficient mice [snRNA-Seq]

city: Davis

first: Stephanie

last: Lozano

state: CA

address: 1544 Newton Ct

institute: University of California, Davis

summary: CHD8 mutations cause autism spectrum disorder, cognitive deficits, and macrocephaly. Chd8+/- mouse models exhibit macrocephaly and transcriptional pathology, with inconsistent findings regarding neurogenesis, neuron function, and behavior. Via stereology and single nuclei transcriptomics (snRNA-seq), we found increased Chd8+/- cortical volume was not explained by increase in neuron number. Differential expression (DE) was present across cortical cell types, with excitatory neurons exhibiting high DE burden and shared and subclass-specific DE signatures. Bulk RNA-seq DE of constitutive Chd8+/- and conditional Camk2a-Cre Chd8+/- mice identified shared transcriptional pathology. DE in synaptosomal versus nuclear mRNA identified overlapping DEGs, but also significant differences and exaggerated synaptosomal changes. Building on DE findings implicating glutamatergic neurons, we found Chd8+/- mice exhibited altered excitatory neuron spine density and dynamics, decreased GCaMP activity correlation, and sleep perturbation. Thus, Chd8 haploinsufficiency causes lasting excitatory neuron dysfunction, perturbs RNA regulation beyond transcription, and impacts neuronal properties, cortical microcircuits, and behavior.

overall_design: We profiled RNA expression of cortical dissections from adult wild-type and germline heterozygous Chd8 mutant mice. Single-nucleus RNA-sequencing (snRNA-seq) was performed on isolated cortical nuclei. Bulk RNA-sequencing was performed on whole cortical tissue from constitutive and conditional Chd8 mutant mice. Additional bulk RNA-sequencing was conducted on nuclear and synaptic fractions isolated from adult cortex to investigate compartment-specific expression changes.

first: Cesar

middle: P

last: Canales

first: Nicholas

last: Frost

first: Karol

last: Cichewicz

first: Wellington

last: Amaral

first: Nicolas

last: Seban

first: Ethan

last: Fenton

first: Ayanna

last: Wade

first: Nickolas

last: Chu

first: Emily

last: Smith

first: Cory

last: Ardekani

first: Samuel

last: Frank

last: Bennett

first: Pierre

last: Lavenex

first: Aspen

last: Kopley-Smith

first: Darlene

last: Rahbarian

first: Melissa

last: Corea

first: Daniela

last: Perla

first: Liam

last: Davis

first: Jiyuan

last: Zhu

first: Rebecca

last: Ortiz

first: Paris

last: Beauregard

first: Caitlin

last: Moyer

first: Jacob

last: Baker

first: Jingqi

last: Sun

first: Boxuan

last: Ma

first: Ju

last: Lu

first: Vikaas

last: Sohal

first: David

first: Yi

last: Zuo

first: Alex

last: Nord


title: Effect of I-125 Seed Implantation on Gene Expression in the Facial Nerve of Rabbits with Facial Nerve Injury

city: Kunming

first: Yu

last: Liu

address: No.295 Xichang Rd

institute: Affiliated Stomatology Hospital of Kunming Medical University

summary: Oral and maxillofacial tumors, particularly malignant ones, account for approximately 20% of head and neck malignancies. This anatomical region is characterized by complex structures and dense neurovascular networks. Tumor progression or surgical procedures can readily cause facial nerve injury, subsequently leading to impairments in patient communication, emotional expression, and social functioning. Brachytherapy using Iodine-125 (I-125) seeds has been widely employed in the treatment of various solid tumors due to its advantages, such as straightforward application and continuous low-dose radiation delivery to the tumor target area. However, recent studies have indicated that I-125 seed implantation may exert damaging effects on surrounding tissues, muscles, and nerves. Nevertheless, its specific mechanism of action in the context of facial nerve injury remains unclear. In this study, a rabbit model of facial nerve transection injury was established. I-125 seeds were implanted into the injury site, and facial nerve tissues from both the injury model and the I-125 implanted injury model were collected for transcriptome sequencing. The aim was to further untangle the molecular mechanism of I-125 radiation in facial nerve injury.

overall_design: To investigate the effect of I-125 seed implantation on facial nerve gene expression, a rabbit model of facial nerve injury was established via transection injury, and I-125 seeds were implanted into the injured area. On day 14 after modeling, injured facial nerve tissues were collected from the model group and the I-125 implantation group for RNA-seq analysis.

first: Jin

first: Xin

last: Ouyang

first: Lifu

last: Yu

first: YeMei

last: Qian

first: JinYi

last: Li

first: Xun

last: Sheng

first: FengFeng

last: Jia


title: Basal IFNλ2/3, but not IFNλ1, signaling is sufficient to control virus infection in intestinal epithelial cells

city: Gainesville

first: Yagmur

last: Keser

state: Florida

address: 1200 Newell Dr.

department: Molecular Genetics and Microbiology (MGM)

institute: University of Florida

summary: Interferon-lambdas (IFNλs) serve as critical mediators of antiviral defense at mucosal surfaces. Beyond their established role in regulating innate immune responses during infection, recent evidence demonstrates that IFNλs are constitutively expressed in pathogen-free environments, termed "basal" IFN expression. While intestinal epithelial cells constitutively express all basal IFNλ subtypes (IFNλ1, IFNλ2, and IFNλ3), their individual contributions to antiviral immunity remain poorly defined. Here, we systematically investigate the distinct roles of IFNλ1 and IFNλ2/3 in regulating intrinsic antiviral immunity using human intestinal epithelial T84 cells. Through genetic depletion of IFNλ1 or IFNλ2/3, we show that basal IFNλ2/3, but not IFNλ1, is essential for restricting replication and spread of diverse viruses, including vesicular stomatitis virus (VSV), mammalian orthoreovirus (MRV), rotavirus (RV), and vaccinia virus (VV). Transcriptomic profiling revealed that IFNλ2/3 selectively controls the basal expression of interferon-stimulated genes (ISGs), including key antiviral effectors and components of the IFN signaling machinery (e.g., STAT1, STAT2, IRF9). Loss of IFNλ2/3 reduced total STAT1 protein levels and blunted responsiveness to exogenous IFNλ, indicating compromised interferon signaling capacity. Furthermore, basal IFNλ2/3 was required for activating paracrine JAK/STAT signaling and ISG induction in neighboring bystander cells, thereby amplifying antiviral protection across the epithelial layer. These findings reveal a functional hierarchy among IFNλ subtypes and establish IFNλ2/3 as the dominant, non-redundant regulators of epithelial immune readiness. Our study provides the first comprehensive analysis of basal IFNλ subtype functions in the gut epithelium and underscores the central role of basal IFNλ2/3 in maintaining mucosal antiviral defense.

overall_design: To define the distinct roles of IFNλ subtypes in maintaining immune homeostasis and antiviral defense at basal levels in human intestinal epithelial cell, we generated T84 IFNλ1 KO, IFNλ2/3 KO and IFNLR KO cells. T84 WT and KO cells were seeded and harvested at two days post-seeding, and sent for RNA sequencing.

first: Sena

last: Bumin

first: Sorin O.

last: Jacobs

first: Steeve

last: Boulant

first: Megan

last: Stanifer

first: Amelia

last: Perez Valiente


title: Genomic profiling of active vitamin D colonic responses in African- and European-Americans identifies an ancestry-related regulatory variant of POLB

first: Sonia

last: Kupfer

department: Human Genetics

institute: University of Chicago

summary: We measured genomic responses to active vitamin D, 1α,25-dihydroxyvitamin D (1,25D), in colonic organoids from individuals of African and European ancestry. Given protective effects of 1,25D for gastrointestinal conditions such as colorectal cancer, organoid cultures enabled evaluation of condition-specific responses in relevant target tissue. We found significant alterations in transcriptional and chromatin accessibility responses to 1,25D treatment, including some with ancestry-associated differences, and also elucidated the role of cis-genetic variance on treatment responses. Integration of genomic profiling with genetic mapping found an indel that explains ancestry-associated differences in the regulation of POLB response to 1,25D which showed signals of positive natural selection.

overall_design: Human colonic organoids derived from indivdiuals of African ancestry (AA) and European ancestry (EA) were cultured, differentiated,  and treated with either 100nm/L 1α,25-dihydroxyvitamin D (1,25D) or vehicle control (0.1% ethanol). RNA and DNA was extracted for RNA-seq and ATAC-seq. Treatment time was  4 hours for ATAC-seq and 6 hours for RNA-seq. After applying QC filters, paired treatment and control samples were available for  53 individuals (26 AA/27 EA) for RNA-seq analysis and 25 individuals (10 AA/15 EA) for ATAC-seq analysis. Differentially responsive genes and differential chromatin accessibility were analyzed in the set of all samples as well as by population. eQTL and aQTL mapping was also performed to identify genetic variants associated with condition-specific responses and chromatin accessibility.

first: David

last: Witonsky

first: Bharathi

last: Laxman

first: Hina

last: Usman

first: Margaret

last: Bielski

first: Kristi

last: Lawrence


title: Persistent cortical excitatory neuron dysregulation in adult Chd8 haploinsufficient mice [RNA-Seq]

first: Stephanie

last: Lozano

first: Cesar

last: Canales

first: Nicholas

last: Frost

first: Karol

last: Cichewicz

first: Wellington

last: Amaral

first: Nicolas

last: Seban

first: Ethan

last: Fenton

first: Ayanna

last: Wade

first: Nickolas

last: Chu

first: Emily

last: Smith

first: Cory

last: Ardekani

first: Samuel

last: Frank

first: Jeffrey

last: Bennett

first: Pierre

last: Lavenex

first: Aspen

last: Kopley-Smith

first: Darlene

last: Rahbarian

first: Melissa

last: Corea

first: Daniela

last: Perla

first: Liam

last: Davis

first: Jiyuan

last: Zhu

first: Rebecca

last: Ortiz

first: Paris

last: Beauregard

first: Caitlin

last: Moyer

first: Jacob

last: Baker

first: Jingqi

last: Sun

first: Boxuan

last: Ma

first: Ju

last: Lu

first: Vikaas

last: Sohal

first: Yi

last: Zuo

first: Alex

last: Nord


title: Structural Basis of DNA-Dependent Coactivator Recruitment by the Tuft Cell Master Regulator POU2F3 [CUT&Run]

first: Damianos

last: Skopelitis

overall_design: CUT&RUN-seq of stably expressed FLAG-tagged POU2F3 (WT or L191A mutant) and IgG isotype control in the NCI-H211 cell line.

first: Aktan

last: Alpsoy

first: Jonathan

last: Ipsaro

first: Sujay

last: Pal

first: Frank

last: Chung

first: Shannon

last: Carpenter

first: John

last: Desmarais

first: Xiaoli

last: Wu

first: Kenneth

last: Chang

first: Matthew

last: DiMare

first: Erin

last: Harten

first: Staci

last: Bergman

first: Justin

last: Kinney

first: Jeffrey

last: Engelman

first: Hyo-Eun

last: Bhang

first: Leemor

last: Joshua-Tor

first: Christopher

last: Vakoc


title: Defining the vascular niche of human adipose tissue across metabolic conditions

status: Public on Dec 31 2025

city: Aarhus

first: Joanna

middle: Maria

last: Kalucka

address: Høegh-Guldbergs Gade, 10

department: Biomedicine

country: Denmark

institute: Aarhus University

summary: White adipose tissue requires a well-maintained vascular network to function properly. Although advances in single-cell transcriptomics have allowed the development of comprehensive human white adipose tissue atlases, there has been a little focus on deciphering the heterogeneity and the functional states of adipose vascular cells, including blood adipose endothelial cells (AdECs), adipose lymphatic endothelial cells (AdLECs), and mural cells (pericytes and vascular smooth muscle cells). Using single nucleus RNA sequencing (snRNA-seq), we mapped human subcutaneous adipose tissue cellular clusters, and focused on cells comprising the vascular niche. We further integrated our in-house generated cohort with seven publicly available datasets of human SAT single cell RNA-seq (scRNA-seq) and snRNA-seq. The generated atlas comprised nearly 70,000 vascular cells from 65 donors, which allowed us to explore the adipose vascular niche. By mining this rich resource, we identify eight endothelial populations, comprising seven canonical subtypes and one additional heterogeneous population of sub-endothelial AdECs. We also provide detailed analyses comparing the transcriptomes of vascular cells from individuals living with or without obesity and type 2 diabetes. These data provide an extensive atlas for the exploration of the adipose vascular niche and its modulation of adipose tissue biology in health and disease.

overall_design: Human deep subcutaneous adipose tissue samples were obtained from lean donors undergoing hemicolectomy, laparoscopic transabdominal preperitoneal approach, fundoplication with mesh hiatoplasty, or band-reinforced gastric bypass and obese donors undergoing elective cosmetic abdominoplasty, gastric sleeve resection, or gastric bypass surgeries at the Clinic for General, Visceral, and Pediatric Surgery of the University Medical Center Göttingen in Göttingen, Germany. Given the wide range of obesity and type 2 diabetes phenotypes, we used all the available clinical parameters to classify the donors. Obesity was defined based on body mass index (BMI) (kg/m2): Lean donors (BMI < 30) and donors with obesity (BMI > 30). Donors were classified as having diabetes based on the presence of a previous history of type 2 diabetes and antidiabetic medication. This yielded three groups in total matched for age and BMI; lean (2 females/ 2 males, age: 45.75±13.27, BMI: 23.27±0.72), obese (3 females/ 4 males, age: 38±5.78, BMI: 53.22±8.94), and obese diabetic (2 females/ 1 male, age: 42±6.16, BMI: 51.3±6.16). The human samples used in the present study were obtained based on the presence of a signed consent according to the University Medical Center Göttingen institutional review board ethical approval (38/4/21).

first: AlZaim

last: Ibrahim

first: Hassan

last: Mohamed N.

first: Kalucka

last: Joanna


title: METTL3-dependent m6A RNA Modifications Orchestrate the HNF1B-associated Redox and the Metabolic Vulnerability in Cancer [RNA-seq]

city: Seoul

first: Jae Seok

last: Roe

address: Yonsei-ro, 50

country: South Korea

institute: Yonsei University

summary: Internal RNA modifications, such as N6-methyladenosine (m6A), are widespread in mammalian cells but their importance in cancer metabolism remains poorly understood. Here, we demonstrate that the m6A methyltransferase complex, composed of METTL3 and METTL14, is a critical regulator of the metabolic dependencies in human cancers. Inhibiting METTL3-mediated m6A modifications, both genetically and chemically, significantly impairs the antioxidant capacity of pancreatic cancer cells, sensitizing them to the oxidative stress. We found that m6A modifications at the 3'-untranslated regions (3'-UTRs) of the HNF1B mRNA enhances its stability and expression levels. Furthermore, the loss of HNF1B triggers oxidative stress-induced cell death across multiple cancer types, recapitulating the metabolic dysfunction caused by m6A depletion and revealing HNF1B as a key mediator of the glutathione metabolic program. By establishing a link between m6A modifications and cellular antioxidant responses via HNF1B, our findings suggest that METTL3 is a metabolic vulnerability in cancer and highlight its potential as a therapeutic target for m6A-directed therapies in cancer.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: H3K4me3, H3K4me1, and H3K27ac ChIP-seq profilings of various pancreatic cancer cell lines with indicated perturbations.

first: Jae-Seok

first: Hwa-Ryeon

last: Kim

first: Minji

last: Park


title: Estrogen signaling in PDGFRα+ cells positively regulates cortical bone metabolism via IGFBP5 in female mice.

city: Toon

first: Aoi

last: Ikedo

state: Ehime

address: Shitsukawa

country: Japan

institute: Ehime University

summary: The prevalence of both osteoporosis and sarcopenia increases with age, and 60% of elderly sarcopenia patients also develop osteoporosis. However, the co-occurrence of osteoporosis and sarcopenia remains unclear. We performed single-cell 5’RNA-seq on human skeletal muscle tissues and investigated the enrichment of heritability for musculoskeletal traits in cell type specific cis-regulatory regions. We found the fibroblast-specific cis-regulatory regions are highly enriched in the heritability of bone mineral density (BMD). Using GWAS, we identified estrogen receptor α (ESR1) as a common transcription factor that correlated with both BMD and lean mass. We hypothesized that deficiency of estrogen signaling in fibroblast may attenuate musculoskeletal homeostasis. Therefore, we generated mice lacking Esr1 in PDGFRα (a fibroblast marker) + cells (Esr1ΔPα). Although muscle mass and grip strength were not different between groups, distal femoral BMD and cortical thickness were significantly lower in Esr1ΔPα compared to control. Bone histomorphometry showed that cortical bone in Esr1ΔPα exhibited a high turnover bone phenotype. Bulk RNA-seq using PDGFRα+ cells revealed that Igfbp5 expression was significantly higher in Esr1ΔPα compared to control. Furthermore, serum IGFBP5 level was significantly higher in Esr1ΔPα. IGFBP5 treatment in vitro significantly suppressed osteoblast differentiation and facilitated osteoclast differentiation. These results suggest that estrogen signaling in PDGFRα+ cells suppresses Igfbp5 expression, then maintains bone mass, indicating that estrogen signaling in PDGFRα+ cells plays a significant role in bone metabolism.

overall_design: To clarify the target gene (s) of Esr1 in PDGFRα+ cells from skeletal muscle that are involved in bone metabolism, we performed RNA-seq in PDGFRα+ cells from muscles of both control and Esr1ΔPα (cKO) mice.

first: Yuuki

last: Imai


title: Next-Generation Sequencing Facilitates Quantitative Analysis of Control and BET bromodomain Inhibitor-treated Uterine fibroids Cell Transcriptome

city: San Antonio

first: Azad

last: Khosh

state: TX

address: 7703 Floyd Curl Dr

institute: UTHSCSA

summary: We report that BET bromodomain inhibition alters multiple biological pathways in uterine fibroid cells

overall_design: Examine the transcriptome alteration in uterine fibroid cells with or without BET bromodomain inhibitors

first: Qiwei

last: Yang

first: Ali

last: Falahati

first: Ayman

last: Al-Hendy


title: Epigenetically modulating macrophage subpopulations to promote long-term allograft survival in a mouse heart transplant model

city: Houston

first: Ge

last: Deng

state: Texas

address: 6670 Bertner Avenue, R7-217

institute: Houston Methodist Hospital and Houston Methodist Research Institute

summary: Despite much-improved protocols that broadly suppress the adaptive immune cells, most allografts are still lost to chronic rejection, in which macrophages have been prominently featured in the graft. In both clinical and pre-clinical studies, the graft-infiltrating macrophages often acquire diverse effector activities, especially the M2-biased programs, to mediate graft damage. But the precise mechanisms that regulate such programs remain incompletely defined. In the present study, we took a genome-wide approach to profile the epigenomic changes of M2-biased macrophages and identified the bromodomain and extra-terminal domain family protein-4 (BRD4) as a critical epigenetic regulator of M2 cells. Further in vitro studies revealed that either blocking BRD4 using a chemical inhibitor or conditional deletion of Brd4 in myeloid cells profoundly inhibited the induction of M2 cells. Importantly, in a fully MHC-mismatched heart transplant model, in which treatment with low doses of CTLA-4Ig led to the development of chronic rejection, inhibition of BDR4 in transplant recipients resulted in long-term heart allograft survival, which was associated with diminished intra-graft M2 cells and absence of histological features of chronic rejection. Together, our data suggest that macrophages can be epigenetically modified in favor of transplant survival and that BRD4 seems a promising therapeutic target for blocking chronic allograft rejection.

overall_design: Bone marrow derived macrophages (BMDM) was stimulated with IL-4 to polarize into M2 with or without JQ1 treatment and  BRD4 or H3K27Ac ChIP seq was performed to explore the role of chromatin reader BRD4 in macrophage M2 polarization.

first: Xiaojun

last: Su

first: Si

last: Sun

first: Guangchuan

last: Wang

first: Samson

last: Hennessy-Strahs

first: Junhui

last: Li

first: Zhuyun

last: Mao

first: Rafik

last: Ghobrial

first: Xiang

last: Xiao

first: Wenhao

last: Chen

first: Xian


title: Inapparent maternal ZIKV infection impacts fetal brain development and postnatal behavior [BulkSeq]

status: Public on Dec 30 2025

city: Piscataway

first: Brian

last: Daniels

state: NJ

address: 604 Allison Road

department: Cell Biology and Neuroscience

institute: Rutgers, The State University of New Jersey

summary: Zika virus (ZIKV) has emerged as a significant public health concern due to its association with severe neurological outcomes in infants, including microcephaly and congenital Zika syndrome (CZS). However, while the majority of ZIKV infections during pregnancy do not result in CZS, the potential long-term neurological effects of mild or inapparent maternal infections remain poorly understood. In this study, we adapted a model of maternal ZIKV infection in human STAT2 knock-in (hSTAT2) mice to investigate the effects of ZIKV infection during mid-gestation, aiming to mirror typical asymptomatic infections as they occur in humans. We found that maternal ZIKV infection at mid-gestation leads to vertical transmission without causing overt developmental deficits or clinical signs in dams or offspring. Despite the absence of immediate clinical signs, transcriptomic analyses revealed significant changes in the developing fetal brain, particularly in genes related to synaptic function and neuronal development. These molecular alterations were associated with increased synaptic density in the hippocampus and heightened susceptibility to chemically induced seizures in offspring, suggesting subtle yet significant long-term neurological consequences. Using motion sequencing (MoSeq), an unsupervised machine learning approach that profiles naturalistic motor behavior, we also identified persistent, sex-biased alterations in the content and structure of spontaneous behavior in offspring exposed to maternal ZIKV infection. Our findings highlight that even mild maternal ZIKV infections can disrupt fetal neurodevelopment, underscoring the need for enhanced monitoring and public health measures for children exposed to ZIKV in utero but who do not experience severe developmental alterations at birth. Additionally, our study provides a valuable animal model and comprehensive, cell type-specific transcriptomic datasets that will facilitate new lines of investigation into the impact of inapparent maternal ZIKV infections on fetal and childhood brain development.

overall_design: We performed bulk RNA-seq on fetal brains and 3-week-old offspring brains derived from human STAT2 knock-in (hSTAT2-KI) dams that were injected with either PBS or Zika virus on indicated gestational days.

first: Tsui-Wen

last: Chou

first: Micheal

last: McCourt

first: Marissa

last: Lindman

first: Irving

last: Estevez

first: Benjamin

middle: D

last: Buckley

first: Joshua

middle: K

last: Thackray

first: Kailyn

last: Rodriguez

first: Marialaina

last: Nissenbaum

first: Charul

last: Mishra

first: Colm

last: Atkins

first: Alexander

last: Kusnecov

first: Max

last: Tischfield


title: Inapparent maternal ZIKV infection impacts fetal brain development and postnatal behavior [SingleNuclei]

overall_design: We performed single-nucleus RNA-seq on E18.5 fetal brains derived from human STAT2 knock-in (hSTAT2-KI) dams that were injected with either PBS or Zika virus at gestational day E12.5.

first: Cherul


title: Mapping the Cellular Landscape of Calvarial Bone Repair Accelerated by Sympathetic Nerve Inhibition

city: Shanghai

first: Lei

last: Zhao

state: Shanghai

address: 500 Zhennan Road

institute: Tongji University

summary: Understanding the dynamic changes of cells during calvarial bone repair is crucial for identifying novel therapeutic targets to enhance bone regeneration. However, the cellular changes and intercellular communication during calvarial defect repair remain poorly understood. To address this, we performed single-cell RNA sequencing on tissues collected at different time points post-defect. Our analysis revealed a significant enhancement in intercellular communication following defect, particularly among stem cells, endothelial cells, pericytes, and macrophages. Pathways related to neurogenesis were significantly enriched after defect. Furthermore, we found that inhibiting sympathetic nerves promoted calvarial bone repair. Mechanistically, sympathetic nerve inhibition enhanced angiogenesis and osteogenesis by promoting interactions between pericytes and endothelial cells, generating a novel senescenced  Arg1+ macrophages, which contributed to bone repair by secreting osteogenesis-related cytokines. Besides, inhibition of sympathetic nerves promotes the generation of Shisa3+ suture cell subpopulation and enhances osteogenic differentiation capacity. Importantly, senolytics abrogated the repair benefits brought about by sympathetic nerve inhibition, underscoring the critical role of senescent macrophages in the repair process.

overall_design: To further investigate how sympathetic nerve inhibition promotes calvarial bone defect repair, single-cell RNA sequencing was performed on calvarial bone samples collected 7 and 14 days after frontal bone defect induction with or without sympathetic nerve inhibition.

first: Zhaoning

last: Xu

first: Yiyun

last: Wang


title: RUNX1 is Expressed in a Subpopulation of Dermal Fibroblasts and is Associated with Disease Severity of Systemic Sclerosis

first: Rezvan

last: Parvizi

type: Methylation profiling by genome tiling array

overall_design: A total of 16 samples [eight samples from 2D monolayer cultures of fibroblasts isolated from two patients with Systemic Sclerosis (SSc) or one healthy control donor, and eight samples from 3D cultures (2 replicates from each biological sample)] were selected for DNA extraction. Genomic DNA was extracted using the Qiagen QIAcube by QIAamp DNA Mini Kit. To ensure that all samples met DNA quality control criterion, we used Agilent 4200 TapeStation (Genomic DNA ScreenTape, Agilent technologies, Santa Clara, CA). Between 500 ng and 1 µg of DNA from these 2D and 3D samples were bisulfite converted and processed according to the Illumina Infinium MethylationEPIC array protocols at the University of Southern California’s Molecular Genomics Core Laboratory (Los Angeles, CA).

first: Toledo

last: Diana

first: Michael

middle: L

last: Whitfield


title: Mrc1 facilitates epigenetic inheritance through proper parental histone segregation

city: New York

first: zhiguo

last: zhang

address: 1130 St. Nicholas Avenue

department: Pediatric and Genetics and Development

institute: Columbia University

summary: Chromatin-based epigenetic memory relies on the equal distribution of parental histone tetramers, which serve as templates for duplicating parental chromatin, to newly synthesized daughter DNA strands. Histone chaperones within the replisome, such as the histone binding domains (HBDs) of Mcm2 and Pol alpha, are critical for transferring parental histones to the lagging strand. However, the mechanisms and impact of parental histone transfer on epigenetic inheritance remain debated. Using fission yeast heterochromatin assembly as a model, we discovered that replisome component Mrc1 is crucial for both epigenetic inheritance and transfer of parental histones to the lagging strand, akin to  a Mcm2-HBD mutation. Isolation of separation-of-function mutations revealed that Mrc1’s role in epigenetic inheritance is distinct form its DNA replication checkpoint and replisome speed control functions. Instead, Mrc1 prevents undesirable replisome interactions to facilitate interactions between Mcm2 and Pol alpha for the proper passage of parental histones. These findings unveil a novel function of Mrc1 and underscore the critical role of parental histone segregation in epigenetic inheritance.

overall_design: H3K4me3 eSPAN performed in S.pombe followed by Next Generation Sequencing

first: Yimeng

last: Fang

first: Xu

last: Hua

first: Zhiguo

last: Zhang

first: Songtao

last: Jia


title: Defining the role of RNase E in the mycobacterial degradosome-like network

city: Worcester

first: Scarlet

last: Shell

state: MA

address: 100 Institute Rd

department: Biology and Biotechnology

institute: Worcester Polytechnic Institute

summary: mRNA degradation is a fundamentally important process that is regulated in response to stress in the globally important pathogen Mycobacterium tuberculosis.  Several mycobacterial ribonucleases (RNases) are hypothesized to function together to coordinate mRNA degradation, but the interactions among them are mostly undefined.  One of these enzymes, RNase E, contains intrinsically disordered regions (IDRs) and initiates mRNA degradation.  Here, we aimed to define the interactions between major mycobacterial mRNA degradation enzymes and identify the function(s) of the two IDRs of RNase E in the nonpathogenic model Mycolicibacterium smegmatis.  We found that the two IDRs differentially impact mRNA degradation rates in vivo but are largely functionally redundant in their impacts on steady-steady transcript abundance.  In vitro, the IDRs are uninvolved in catalysis but play major roles in RNA binding and interactions with other mRNA degradation enzymes, namely PNPase, RNase J, and RhlE1.  In vivo, these enzymes localize with RNase E, but its IDRs play only a minor role, suggesting substantial redundancy in subcellular localization mechanisms.  Collectively, we propose a degradosome-like network model in mycobacteria, held together by dynamic, transient interactions among RNA degradation enzymes and RNA that can be disrupted during physiologically relevant stress to allow for adaptability.

overall_design: M. smegmatis strains were constructed in which the native copy of rne (encoding RNase E) was deleted and a copy of rne with its native promoter and 5' UTR was inserted into the L5 phage integration site. All rne versions had N-terminal 6xhis-3xFLAG tags. The N-terminal deletion lacked codons 2-329, the C-terminal deletion lacked codons 824-1037, and the N- and C-terminal double deletion lacked both.

first: Abigail

last: Rapiejko

first: Ying

last: Zhou

first: Junpei

last: Xiao

first: Vidhyadhar

last: Nandana

first: Jared

last: Schrader


title: Transcriptome analysis of circulating microRNAs associated with Chagas disease susceptibility and chronic Chagas cardiomyopathy severity

city: Rio de Janeiro

first: Eric

middle: Henrique

last: Roma

state: Rio de Janeiro

address: Av. Brasil, 4365

department: Instituto Nacional de Infectologia

country: Brazil

institute: Fundação Oswaldo Cruz

summary: Chagas disease (CD), caused by infection with the protozoan parasite Trypanosoma cruzi, is a major public health concern in Latin America. Understanding the molecular mechanisms driving disease progression and identifying biomarkers are crucial. We investigated the association of circulating microRNAs (miRNAs) with CD susceptibility and heart disease progression. A multicentric prospective observational study was conducted with 150 CD patients (46 indeterminate, 104 CCC [chronic chagasic cardiomyopathy] staged A-D) and 42 healthy controls from CD endemic areas. Sequencing of circulating miRNAs was performed, and differential expression analyses were conducted. We identified 40 differentially expressed miRNAs between CD patients and healthy controls, highlighting miR-199b-5p, miR-153-3p, miR-143-3p, and miR-223-3p upregulated, and miR-150-3p, miR-4508, miR-486-5p, and miR-3960, downregulated in CD patients. Moreover, functional analysis using Ingenuity Pathway Analysis software revealed that these miRNAs were involved in immune response and cardiovascular signaling pathways. Several miRNAs (miR-6734-5p, miR-1285-5p, miR-10527-5p, miR-31-5p, miR-5187-5p, miR-6515-5p) tended to present a higher expression in patients with severe compared to those with mild CCC, while miR-30c-2-3p presented lower expression in these groups. This study provides evidence for the dysregulation of specific miRNAs in CD, highlighting their potential role in disease pathophysiology and possible use as biomarkers for CD susceptibility and CCC severity.

overall_design: miRNA-seq profiling total RNA extracted from human serum of samples from patients of Chagas Disease in indeterminate and chronic Chagas cardiomyopathy

middle: H

first: Fabielle

last: Marques-Santos

first: Alinne

last: Rezentti

first: Luciana

middle: F

last: Portela

first: Filipe

last: da Costa

first: Alejandro

last: Hasslocher-Moreno

first: Marcelo

last: de Holanda

first: Luiz

last: Sangenis

first: Andréa

first: Joseli

last: Lannes-Vieira

first: Tania

middle: C

last: Araujo-Jorge

first: Roberto

last: Ferreira

last: Saraiva

first: Maria

last: Bonecini-Almeida


title: METTL3-dependent m6A RNA Modifications Orchestrate the HNF1B-associated Redox and the Metabolic Vulnerability in Cancer [MeRIP-seq]

first: Jae Seok

last: Roe

overall_design: m6A MeRIP-seq profilings of various pancreatic cancer cell lines with indicated perturbations.

first: Jae-Seok

first: Hwa-Ryeon

last: Kim

first: Minji

last: Park


title: Indolent primary cutaneous B cell lymphomas resemble persistent antigen reactions without signs of dedifferentiation

city: Vienna

first: Johannes

last: Griss

address: Währinger Gürtel 18-20

department: Department of Dermatology

country: Austria

institute: Medical University of Vienna

summary:
Primary cutaneous B-cell lymphoma encompass clinically heterogeneous entities. While primary cutaneous diffuse large B-cell lymphoma, leg type (pcDLBCL-LT) is aggressive, primary cutaneous follicle centre lymphoma (pcFCL) and primary cutaneous marginal zone lymphoma (pcMZL) typically follow an indolent course. To clarify their pathophysiological basis, we perform single-cell RNA sequencing on pcFCL, pcMZL, and pcDLBCL-LT, alongside reactive B-cell rich lymphoid proliferations (rB-LP), gastric mucosa-associated lymphoid tissue (MALT) lymphoma, and systemic counterparts.
Here we show that the indolent pcMZL, pcFCL, and rB-LP exhibit a persistent germinal centre reaction, not observed in pcDLBCL-LT or gastric MALT lymphoma. Further, pcMZL top expanded clones develop within lesions from naïve and not post-germinal centre B cells as currently presumed. Our data thus indicate that pcMZL and pcFCL, similar to rB-LP may be driven by (a yet unknown) antigen. While our data indicates that pcFCL exhibits some features of true lymphomas, it clearly supports the classification of pcMZL as a lymphoproliferative disease.

overall_design:
Samples from primary cutaneous marginal zone (pcMZL), follicle center (pcFCL), and diffuse large B cell lymphoma leg type (pcDLBCL-LT) where compared to reactive B cell rich lymphoid hyperplasia (rB-LP) and gastric malt lymphoma (MALT).

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Submitter states that: due to restrictions from the ethics review board, we are not allowed to release the respective RAW data
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first: J

first: S

last: Gansberger

first: I

last: Oyarzun

first: M

last: Drach

first: V

last: Nguyen

first: L

middle: E

last: Shaw

first: U

last: Mann

last: Porkert

first: W

last: Weninger

last: Dolak

first: B

last: Aschenbrenner

middle: M

last: Lichtenberger

last: Farlik

last: Ziegler-Santos

first: C

last: Wagner

last: Simonitsch-Klupp

last: Jonak

first: P

last: Brunner


title: The role of the circadian transcriptional network in the aging Drosophila eye

city: West Lafayette

first: Sarah

last: McGovern

state: IN

address: Department of Biochemistry

department: Biochemistry

institute: Purdue University

summary: The circadian rhythm controls 24-hour periodic behaviors and physiology, and is observed across animal kingdoms including animals, plants, and fungi. The circadian clock is synchronized with the solar day, maintaining a robust 24-hour periodicity in consistent environmental conditions. Despite this robustness, behaviors that desynchronize the circadian clock with the solar day (e.g., shift working, sleep deprivation) have been widely implicated as being detrimental to human health. Additionally, the circadian rhythm in humans shows both an altered phase and a decrease in amplitude with aging. The circadian clock is synchronized by light at the highest level via direct innervation from the eyes to the suprachiasmatic nucleus in the hypothalamus. During aging, visual function decreases, which can result in decreased circadian photoreception, linking loss in visual function with decreased circadian rhythmicity. Despite these links between aging, alterations in circadian rhythm, and age-related decline in visual function, much remains unknown about the complex interplay between these processes. To profile transcriptome-wide rhythmic changes in photoreceptors during aging, photoreceptor nuclei were collected from young (D10) and old (D50) flies every four hours and used for nuclear RNA-seq.

overall_design: Drosophila were maintained in population cages in a 25°C incubator with a 12:12 hour light:dark cycle. 400 male flies in triplicate were collected at the indicated days post-eclosion (D10 and D50) and at the indicated Zeitgeber times (ZT0, ZT4, ZT8, ZT12, ZT16, ZT20). GFP-positive photoreceptor nuclei were immunoprecipitated using the nuclei immunoenrichment protocol (dx.doi.org/10.17504/protocols.io.buiqnudw), followed by RNA isolation and purification.

first: Gaoya

last: Meng

first: Makayla

last: Marlin

first: Sophia

middle: A

last: Pruitt

first: Vikki

last: Weake


title: Brainstem metabolic changes in a mouse model of Dravet Syndrome

city: Salt Lake City

first: Philip

middle: J

last: Moos

state: UT

department: Pharmacology & Toxicology

institute: University of Utah

summary: Dravet Syndrome (DS) is a severe genetic epileptic encephalopathy caused by mutations in the SCN1A gene that encodes the voltage-gated sodium channel (NaV1.1) subunit alpha. DS is characterized by intractable seizures, progressive developmental delay, cognitive impairment, and high mortality due to sudden unexpected death in epilepsy (SUDEP). Post-ictal apnea that precedes asystole has been observed to lead to SUDEP; however, the exact molecular underpinnings are unclear. Seizure-induced hippocampal metabolic alterations have been reported in DS mice. Whether such alterations occur in the brainstem, a master regulator of autonomic functions, thereby influencing morbidity, mortality/SUDEP, and seizure outcomes is unknown. We used Scn1aA1783V/WT DS mice and showed that there are temporal alterations in the brainstem metabolome which are distinct in comparison to the forebrain metabolome. Glycolytic, and pentose phosphate pathway intermediates were significantly elevated in the brainstem of DS mice during the period of enhanced susceptibility to mortality (post-natal day P20-30). Post P20-30, mitochondrial aconitate, and the antioxidant glutathione were significantly elevated. Single nuclei RNA sequencing (snRNA seq), and proteomic analyses revealed alterations in genes associated with neurotransmission, cellular respiration, protein translation, as well as systematic rewiring of protein kinase-mediated pathways that were specific to the brainstem. These findings suggest that there are widespread metabolic changes in the brainstem of DS mice that are associated with alterations in druggable molecular pathways.

overall_design: The goal of this study was to evaluate baseline differences in the brainstem transcriptomes of a mouse with Dravet Syndrome (Scn1aA1783V/WT, carries a knock-in missense mutation in the gene SCN1A that encodes for a voltage-gated sodium channel subunit alpha) compared to a wildtype (WT) C57Bl6 mouse. Brainstem tissue was collected from mice during post-natal days P40-50. This is the developmental time period where Dravet mice have survived past the critical period of enhanced susceptibility to mortality (P20-30). This study will help us understand what the brainstem (critical region for regulation of autonomic functions) transcriptome looks like and whether transcriptomic alterations could play a role in influencing seizures, morbidity, and mortality outcomes in Dravet Syndrome mice.

first: Cameron

middle: S

last: Metcalf

first: Ashwini

last: Sri Hari


title: Connectome-seq: High-throughput Mapping of Neuronal Connectivity at Single-Synapse Resolution via Barcode Sequencing

city: Urbana

first: Boxuan

last: Zhao

address: 505 S Goodwin Ave

institute: UIUC

summary: Understanding neuronal connectivity at single-cell resolution remains a fundamental challenge in neuroscience, with current methods constrained by an inherent trade-off between throughput and synaptic precision. Here we present Connectome-seq, a high-throughput method that combines engineered synaptic proteins, RNA barcoding, and single-compartment sequencing to map neuronal connectivity at single-synapse resolution. We validate this approach in the mouse pontocerebellar circuit, successfully identifying thousands of connections including the predominant excitatory projections from pontine neurons to cerebellar granule cells, while also revealing potentially novel synaptic partnerships. By enabling systematic mapping of neuronal connectivity across brain regions with single-cell precision, Connectome-seq provides a scalable platform for comprehensive circuit analysis across different experimental conditions and biological states. This advance in connectivity mapping methodology opens new possibilities for understanding circuit organization in complex mammalian brains.

overall_design: Pons and cerebellum tissue was obtained from Sun1-sfGFP-Myc mice, and nuclei and synaptosomes were subsequently isolated via fluorescence-activated cell sorting, selecting based on GFP, HA, or V5 signals, before undergoing single-nucleus and single-synaptosome RNA sequencing (snRNA-seq, ssRNA-seq) analysis.


title: Rhythmic Transcription and Aging: Insights from the Drosophila Photoreceptor Transcriptome and Epigenome

summary: Rhythmic changes in the transcriptome are widespread during aging in Drosophila photoreceptors. To better understand the epigenetic factors underlying these changes, we profiled RNA PolII occupancy and levels of H3K4me1, H3K4me2, and H3K4me3 using CUT&RUN. To profile changes in chromatin accessibility, we also performed ATAC-seq. To obtain robust rhythmic data across age, we collected both young (D10 post-eclosion) and old (D50 post-eclosion) flies every four hours throughout the day in a 12-hour light:12-hour dark cycle in triplicate.

overall_design: Drosophila were maintained in population cages in a 25°C incubator with a 12:12 hour light:dark cycle. 400 male flies in triplicate were collected at the indicated days post-eclosion (D10 and D50) and at the indicated Zeitgeber times (ZT0, ZT4, ZT8, ZT12, ZT16, ZT20). GFP-positive photoreceptor nuclei were immunoprecipitated using the nuclei immunoenrichment protocol (dx.doi.org/10.17504/protocols.io.buiqnudw), followed by CUT&RUN (dx.doi.org/10.17504/protocols.io.zcpf2vn) or ATAC-seq.

middle: N


title: An absolute quantification atlas of small non-coding RNAs across mammalian tissues and cell lines

first: Wen

last: Xiao

address: 320 Yueyang Road

department: Institute of Biochemistry and Cell Biology

institute: Shanghai Institutes for Biological Sciences, CAS

summary: The low quantitative accuracy of conventional small noncoding RNA sequencing (sncRNA-seq) methods due to extensive ligation bias commonly limits functional investigation of microRNAs (miRNAs) and PIWI-interacting RNAs (piRNAs). Here, we developed 4NBoost, a single-tube sncRNA-seq protocol designed to minimize bias in the estimated absolute quantification of miRNA and piRNA transcripts through the incorporation of quantitative exogenous RNA spike-ins. With 4NBoost, we profiled sncRNA expression across 20 murine tissues, 18 macaque tissues, and 24 widely used cell lines, as well as 4 Arabidopsis tissues, to establish a comprehensive quantitative reference atlas. Compared with existing small RNA databases, our data revealed substantial biases in miRNA abundance, strand selection, and tissue-specific expression at both individual and family levels. To further extend its utility, we employed machine learning to model and correct biases in conventional datasets, effectively recovering ground truth transcript abundances. All 4NBoost data and the accompanying bias-correction model are freely available via SmRNAQuant (http://wulg-lab.sibcb.ac.cn/SmRNAQuant/), a web-based repository for exploring sncRNA expression. Together, the 4NBoost, bias-correction model, and SmRNAQuant provide powerful resources to advance sncRNA research.

sample_organism:
Arabidopsis thaliana
Macaca fascicularis
Homo sapiens
Mus musculus

overall_design:
Absolute quantification of miRNA and piRNA expression profiles in common tissues and cell lines using 4NBoost.
Pleaes note that total 242 samples are used for formal analysis, and their processed expression profiles are provided in the 'absolute quantification of miRNA expression for each sample.xlsx'.

first: Yuli

last: Zheng

first: Hongdao

last: Zhang

first: Beiying

last: Xu

first: Ruiwen

first: Ligang

last: Wu


title: Fezf2 promotes differentiation of Aire-expressing and mimetic epithelial populations regulating thymic homeostasis

city: San Francisco

first: James

last: Gardner

address: 505 Parnassus Ave

institute: UCSF

summary: Fezf2 has been implicated in shaping tissue-restricted antigen (TRA) expression and as an “Aire-like” factor in the thymus. Here we demonstrate loss of Fezf2 results primarily in a developmental block in mTEC development with pronounced expansion of Ccl21a-expressing mTECs at the expense of thymic tuft cells and most Aire-high and recently described post-Aire “mimetic” populations. While loss of either Aire or Fezf2 leads to a loss of post-Aire mimetic subtypes, their transcriptional programs are distinct; whereas Aire positively regulates the expression of thousands of genome-wide targets, Fezf2 orchestrates a restricted transcriptional program balanced between induction and repression that largely impacts TEC development. Strikingly, most Fezf2-repressed genes map to Ccl21a-expressing mTECs, suggesting Fezf2 maintains a cellular state conducive to the development of Aire-expressing mTECs and downstream access to terminally differentiated mimetic programs. At least some mimetic cell programs appear to have functions beyond simply serving as antigen reservoirs; thymic microfold cells (M cells) organize the medullary B cell niche in a Ccr6-dependent manner and promote IgA class-switching, analogous to Peyer’s Patches. In Aire and Fezf2 KO mice, where development of thymic M cells is impaired, B cell class-switching is similarly disrupted. Therefore, our data reveal Fezf2 as a gatekeeper of mTEC terminal development which cooperates with Aire to allow the full program of medullary epithelial diversity, supporting unexpected layers of mimetic cell function that impact thymic homeostasis beyond antigen diversity.

overall_design: WT control (3 replicates), Fezf2 KO, and Aire KO CD45-, EpCAM+ TECs were sorted from C57BL/6 mice for scRNA-seq analysis of major TEC subpopulations

first: Xian

last: Liu

first: Joe

last: Germino

first: Yi

last: Wang

first: Jared

last: Balolong

first: Hong

last: Sun

first: Irina

last: Proekt

first: Vasilis

last: Ntranos

first: Mark

last: Anderson

first: Corey

last: Miller


title: Chemotherapy triggers immune evasion by fostering LEPR+ Kupffer cell differentiation in liver metastases [CUT&Tag, ATAC-seq]

status: Public on Dec 29 2025

first: Xuege

institute: Shanghai Institute of Nutrition and Health

summary: Conventional chemotherapy achieves clinical efficacy beyond its cytotoxic effects by reactivating immune surveillance. However, whether chemotherapy promotes immune evasion by remodeling the tumor microenvironment (TME) remains largely unexplored. Here, we integrate cross-species single-cell and spatial transcriptomics to explore how chemotherapy reprograms immune cell dynamics and plasticity. Our findings reveal a central role for chemotherapy-educated, liver-resident Kupffer cells (KCs) in promoting immune tolerance and chemoresistance in liver metastases. These reprogrammed KCs, characterized by leptin receptor expression (LEPR+), originate from preexisting KCs and are differentiated via STING-ID1 signaling triggered by cGAMP released from chemotherapy-treated tumor cells. Unlike conventional KCs, LEPR+ KCs infiltrate tumors and engage in MerTK-dependent efferocytosis, which diminishes chemotherapy-induced immunogenic cell death (ICD) and suppresses antitumor immunity. Notably, targeting LEPR+ KCs enhances tumor immunogenicity and strengthens antitumor T-cell responses. Our study demonstrates that therapy-induced KC differentiation fosters immune evasion and suggests combining efferocytosis inhibitors with immunotherapy to overcome chemoresistance.

overall_design: This series is under a superseries and composed of cut&tag seq profiles and atac seq profiles.

first: Jun

last: Qin

first: Qiang

last: Pan

first: Yaqi

last: Li


title: METTL3-dependent m6A RNA Modifications Orchestrate the HNF1B-associated Redox and the Metabolic Vulnerability in Cancer [ChIP-seq]

first: Jae Seok

last: Roe

summary: Internal RNA modifications, such as N6-methyladenosine (m6A), are widespread in mammalian cells but their importance in cancer metabolism remains poorly understood. Here, we demonstrate that the m6A methyltransferase complex, composed of METTL3 and METTL14, is a critical regulator of the metabolic dependencies in human cancers. Inhibiting METTL3-mediated m6A modifications, both genetically and chemically, significantly impairs the antioxidant capacity of pancreatic cancer cells, sensitizing them to the oxidative stress. We found that m6A modifications at the 3'-untranslated regions (3'-UTRs) of the HNF1B mRNA enhances its stability and expression levels. Furthermore, the loss of HNF1B triggers oxidative stress-induced cell death across multiple cancer types, recapitulating the metabolic dysfunction caused by m6A depletion and revealing HNF1B as a key mediator of the glutathione metabolic program. By establishing a link between m6A modifications and cellular antioxidant responses via HNF1B, our findings suggest that METTL3 is a metabolic vulnerability in cancer and highlight its potential as a therapeutic target for m6A-directed therapies in cancer.

overall_design: H3K4me3, H3K4me1, and H3K27ac ChIP-seq profilings of various pancreatic cancer cell lines with indicated perturbations.

first: Jae-Seok

first: Hwa-Ryeon

last: Kim

first: Minji

last: Park


title: Identification of the Role of Vitamin D and VDR in Human Endometrial Stromal Cells

city: RTP

first: Franco

last: Demayo

state: NC

address: 111 TW Alexander Drive

institute: NIEHS

summary: In women undergoing in vitro fertilization, higher vitamin D status has been associated with improved live birth rates. Among women with polycystic ovarian syndrome (PCOS), vitamin D has been associated with improvements in spontaneous ovulation. Vitamin D receptor (VDR) is a nuclear receptor activated by 1,25 dihydroxyvitamin D which is the most active metabolite of vitamin D. Mice that lack the vitamin D receptor exhibit arrested follicular development, uterine hypoplasia, prolonged estrous cycles, and subfertility. Also, one study of mice reported that the vitamin D receptor is expressed in gonadotropin-releasing hormone (GnRH) neurons, which might suggest a role for vitamin D in hypothalamic signaling. Since the vitamin D receptor knockout mouse is sub fertile with uterine hyperplasia, the most likely cause of vitamin D deficiency may be due to estrogen production by the ovary or estrogen responsiveness of the uterus. So, in this study, we want to identify the effect of vitamin D on human endometrial stromal cells associated with female reproduction.

overall_design: Experimental Design: There are 4 groups, and 12 samples in total. All RNAs will be extracted from the human endometrium stromal cell line (T-HESC). 1) Non-targeting siRNA transfection (control) - treated with vehicle (n=3), treated with 1,25-dihydroxyvitamin D3 (n=3) 2) VDR siRNA transfection (VDR knockdown) -  treated with vehicle (n=3), treated with 1,25-dihydroxyvitamin D3 (n=3)  Data Analysis Strategy: Dr. Tianyuan Wang from the informatics group will help us with the analysis.  1) Remove adaptor 2) Require unique mapping and allow 1 mismatch 3) Remove duplicated reads 4) Down-sampling to the appropriate sequencing depth for each 5) Compare between different groups (siNT vs siVDR, Vehicle vs ligand (1,25-dihydroxyvitamin D3))

first: MyeongJin

last: Yi

first: Tianyuan

first: Francesco

last: DeMayo


title: Epigenetic Signatures of Brain Aging by Single Nucleus Methylation Sequencing [FC-9mo-m-020]

city: La Jolla

first: Joseph

middle: R

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

type: Methylation profiling by high throughput sequencing

summary: Illustrating aging effects on the epigenomic features of brain is critical to understand brain functional decline and neurodegeneration. Single nucleus methylation sequencing was applied to brain regions of both male and female mouse at the age of 2, 9 and 18 months. We use these data to identify the epigenomic changes with aging in mouse brains.

overall_design:
Apply snmC-seq3 to mouse brain regions to identify aging effects on epigenomics

Processed data for these samples are available at:

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE313770

first: Wei

last: Tian

first: Anna

last: Bartlett

first: Jordan

last: Altshul

first: Rosa

last: Gomez Castanon

last: Nery

first: Jacinta

last: Lucero

first: Julia

last: Osteen

first: Huaming

last: Chen

first: M

last: Behrens


title: Chemotherapy triggers immune evasion by fostering LEPR+ Kupffer cell differentiation in liver metastases [RNA-seq]

first: Xuege

last: Wang

overall_design:
This series is under a superseries and composed of mRNA seq profiles, scRNA seq profiles and stereo seq profiles.

***************************************************************
Raw files for human/patient samples were not submitted to GEO due to concerns about submitting personally identifiable sequence data for open access.
***************************************************************

first: Jun

last: Qin

first: Qiang

last: Pan

first: Yaqi

last: Li


title: CLK and CYC CUT&RUN in aging Drosophila photoreceptors

first: Sarah

last: McGovern

summary: Rhythmic changes in the transcriptome are widespread during aging in Drosophila photoreceptors. To investigate the mechanisms underyling these rhythmic changes, we performed CUT&RUN in photoreceptors of the core transcriptional activators that control the circadian rhythm, CLK and CYC, in both young and old flies across the circadian day.

overall_design: Drosophila were maintained in population cages in a 25°C incubator with a 12:12 hour light:dark cycle. 200 male flies in triplicate were collected at the indicated days post-eclosion (D10 and D50) and at the indicated Zeitgeber times (ZT4, ZT12, ZT16). GFP-positive photoreceptor nuclei were immunoprecipitated using the nuclei immunoenrichment protocol (dx.doi.org/10.17504/protocols.io.buiqnudw), followed by CUT&RUN (dx.doi.org/10.17504/protocols.io.zcpf2vn). For CUT&RUN, 1 ug of either anti-GFP antibody, or IgG was used.  MNase digestion was performed for 5 min using 1 ug of antibody.

first: Gaoya

last: Meng

first: Makayla

last: Marlin

first: Sophia

last: Pruitt

first: Vikki

last: Weake


title: Deep targeted sequencing reveals genomic differences between primary and recurrent high-grade serous ovarian cancer

status: Public on Dec 23 2025

city: Incheon

first: Mi-Ryung

last: Han

address: 265, Harmony-ro, Yeonsu-gu, Incheon, Republic of Korea

institute: Incheon National University

summary: High-grade ovarian cancer (HGSOC) is a highly fatal disease with frequent recurrence and high mortality rates, despite ongoing treatment advancements. Next-generation sequencing (NGS) is an experimental technique that can identify extensive genetic information, making it a key component of precision medicine. We conducted a study based on a sample of 108 patients retrospectively selected from Severance Hospital and Gangnam Severance Hospital. We aimed to identify genetic factors associated with HGSOC recurrence and survival using deep targeted sequencing. This study identified key genetic alterations associated with recurrence and survival in HGSOC and confirmed that somatic mutations are linked to disease prognosis. We expect that these findings will contribute to more precise prognosis prediction and the development of personalized therapeutic strategies for patients with recurrent ovarian cancer.

overall_design: Gene fusion profiling of primary and recurrent HGSOC patients by TSO500 targeted-sequencing. All sample was derived from tumor tissue.

first: Jae-Hoon

last: Kim

first: Seong-Woo

last: Park

first: Young-Hoon

first: Jee-Whan

first: Yoo-Kyung

last: Lee

first: Han-Byoul

last: Cho

first: In-Ho


title: β-sitosterol-mediated cardioprotection: a transcriptomic perspective

status: Public on Dec 27 2025

city: Xiamen

first: Zhonggui

last: Shan

state: Fujian

address: No. 55, Zhenhai Road

department: School of Medicine

institute: Xiamen University

summary: β-sitosterol has been implicated in mitigating cardiovascular diseases, yet its role in MI remains underexplored. This study investigates the therapeutic potential and underlying mechanisms of β-sitosterol  in MI using both in vivo and in vitro models.Transcriptome sequencing combined with molecular docking and protein validation assays revealed that β-SITO exerts its beneficial effects primarily through the regulation of inflammatory and necroptotic signaling pathways, particularly via modulation of NF-κB, NLRP3 inflammasome, and RIPK3/MLKL-mediated necroptosis.

overall_design: RNA-seq analysis of HO-induced NMCMs treated with either vehicle or β-SITO.


title: RNA-seq of ISL1 overexpression during islet differentiation.

city: New York City

last: Hu

address: 430 East 67th Street

department: Developmental biology

institute: Sloan Kettering Institute

summary: This study aims to investigate the impact of ISL1 overexpression on hPSC-derived islet differentiation. hPSCs from four genotypes (WT, ISL1-/-, PDX1-/-, and PAX6-/-) were differentiated to pancreatic progenitors (day 11), transduced with ISL1-IRES2-BFP or BFP control lentivirus, and further differentiated to SC-islet (day 18). The BFP+ cells were isolated by flow cytometry sorting and subjected to RNA-seq to assess transcriptional responses to ISL1 overexpression across different genetic backgrounds.

overall_design: This study generated RNA-seq on 21 samples.  Cells were transduced with either ISL1-IRES2-BFP or BFP control on day 11 of islet differentiation and harvested on day 18. Most conditions were represented by three biological replicates. Three conditions, ISL1 overexpression in WT, BFP control overexpression in WT, and ISL1 overexpression in PDX1-/-, were represented by two biological replicates.

first: Danwei

last: Huangfu

first: Dingyu

last: Liu

first: Jiahui

last: Zhao


title: Bronchial epithelial cell-derived extracellular vesicles drive inflammasome activation and NTHi infection in COPD

status: Public on Dec 22 2025

city: Belfast

first: Clifford

last: Taggart

address: 97 Lisburn Road

country: United Kingdom

institute: Queen's University Belfast

summary: Extracellular vesicles (EVs) are lipid-membrane bound vesicles that can be beneficial or detrimental depending on the content they carry. As epithelial cells are the first line of defense against harmful particles, this work explored the role of COPD bronchial epithelial cell-derived EVs (CepEVs) in the pathogenesis and progression of chronic obstructive pulmonary disease (COPD). RNA sequencing of macrophages stimulated with CepEVs revealed the upregulation of various inflammasome-related genes, alongside significant IL-1b and IL-18 release, which could be attenuated with caspase-1 or NLRP3 inhibition. The proteome of CepEVs was also assessed, which highlighted a significant reduction in antibacterial proteins compared to healthy EVs (HepEVs). When functionally assessed in NTHi infection of THP-1 cells, pre-incubation with HepEVs stimulated NTHi clearance and reduced pro-inflammatory cytokine release by macrophages, which was reduced in CepEV-stimulated cells. This study shows for the first time that CepEVs are able to both prime and activate the inflammasome in healthy macrophages, and highlights EV-induced inflammasome inhibition as a potential therapeutic target for the dysregulated inflammation seen in COPD. Alongside the inflammasome, we were also able to show that CepEVs are deficient for multiple antibacterial proteins, and that one or more of these proteins are essential in mounting an immune response against NTHi in macrophages. This finding contributes to a potential therapeutic pipeline through the supplementation of the depleted antibacterial proteins in CepEVs, allowing for efficient bacterial clearance and reduced consequential inflammatory burden. CepEV co-incubation resulted in a persistent state of inflammation and infection. Both sets of findings contribute to the overall knowledge of COPD pathogenesis, and highlight epithelial EVs as key players in the propagation of inflammation and susceptibility to infection.

overall_design: RNA-seq analysis of THP-1 cells stimulated with COPD bronchial epithelial cell-derived EVs or healthy bronchial epithelial cell-derived EVs for 48hrs


title: Epigenetic Signatures of Brain Aging by Single Nucleus Methylation Sequencing [FC-9mo-m]

first: Joseph

last: Ecker

first: Wei

last: Tian

first: Anna

last: Bartlett

first: Jordan

last: Altshul

first: Rosa

last: Gomez Castanon

last: Nery

first: Jacinta

last: Lucero

first: Julia

last: Osteen

first: Huaming

last: Chen

first: M

last: Behrens


title: RNA-seq of A375 cells treated with I-BET726 alone and sequential combination of I-BET726 and Oxaliplatin

first: Xiaohan

address: Tongji University

institute: Tongji University/ major in Bioinformatics

summary: Sequential therapy is a promising approach to enhance antitumor efficacy; however, rational design of sequential drug treatments remains challenging. Here, we applied an AI framework, AlphaTherapy, to identify a specific sequential drug combination of I-BET726 and Oxaliplatin that exhibits antitumor effects in melanoma (A375 cells). To investigate the molecular mechanisms underlying the antitumor activity of this combination, gene expression was profiled by RNA sequencing (RNA-seq) after treatment.

overall_design: RNA-seq was performed on A375 cells under the following conditions: untreated control (DMSO), 2 µM I-BET726 for 72 h, withdrawal treatment (2 µM I-BET726 for 72 h followed by 72 h without drug), and sequential treatment (2 µM I-BET726 for 72 h followed by 10 µM Oxaliplatin for 72 h).

first: Yue

last: Deng

first: Shuxian

last: Li

first: Xun

last: Huang


title: Tractable mouse TNBC models capture the heterogeneous tumor immune microenvironment and adaptation to PD-L1 blockade

city: Merelbeke

first: Robbe

last: Salembier

state: East-Flanders

address: Salisburylaan 133

department: Department of Veterinary and Biosciences

institute: Ugent

summary: Triple-negative breast cancer (TNBC) patients exhibit variable responses to programmed death (PD)-ligand (L)1 blockade, largely determined by the ‘hot’ versus ‘cold’ state of the tumor immune microenvironment (TIME). We here characterized 9 mouse TNBC models, relying on intraductal mammary gland inoculation of established mouse TNBC cell lines, with a heterogeneous TIME to study anti-PD-L1 resistance mechanisms. Complementary in vitro and in vivo screening classified the 4T1-hot-based model, a highly inflamed control through its immunogenic luciferase tag expression compared to the untagged 4T1-cold-based model, as displaying the ‘hottest’ TIME. However, both 4T1-based counterparts did not respond to anti-PD-L1, which was attributed to their immunosuppressive myeloid cell content as well as upregulation of cancer-associated fibroblasts in the 4T1-hot and high PD-L1-expressing CXCL10+ tumor-associated macrophages in 4T1-cold primary tumors. These anti-PD-L1 adaptation mechanisms across TIME states as captured by mouse TNBC models highlight specific cellular targets for future studies.

overall_design: RNA was isolated from 4T1-hot and 4T1-cold primary tumors at 3 w p.i. using Rneasy Mini Kit (QiAgen, Valencia, CA, USA). All analyses were done on 4 samples  or 3 samples per treatment group (IgG control- or anti-PD-L1-treated) for 4T1-cold and 4T1-hot TNBC models respectively. Bulk RNA sequencing was done in collaboration with Azenta Life Sciences and performed on Illumina Novaseq system (paired end, length of 150 bp), aiming for 10 million reads per sample.

first: Caro

last: De Haes

first: Kristel

last: Demeyere

first: Steven

last: Van Laere

first: Lucie

last: Cervenkova

first: Nicolaas

last: Van Renne

first: Christos

last: Sotiriou

first: Evelyne

last: Meyer

first: Jonas

last: Steenbrugge


overall_design: RNA was isolated from primary tumors of all TNBC mouse models (D2A1, EMT6, 4T1-cold, AT3, 4T1-hot, 66CL4, PY230, MET1 and MVT1) at 2 w p.i and healthy mammary glands from Matrigel-inoculated BALB/C, C57BL/6 and FVB/N mice using Rneasy Mini Kit (QiAgen, Valencia, CA, USA). All analyses were done on 3 samples for all primary tumors and healthy mammary glands, except n=4 for PY230 and AT3 primary tumors. Bulk RNA sequencing was done in collaboration with Azenta Life Sciences and performed on Illumina Novaseq system (paired end, length of 150 bp), aiming for 10 million reads per sample. Differential expression of 2 w primary tumors was obtained for each model comparing to their respective healthy control mammary gland (BALB/c vs 4T1-hot, 4T1-cold, EMT6, D2A1 and 66CL4 tumors, C57BL/6 vs Py230 and AT3 tumors, FVB/N vs MVT1 and MET1 tumors). Identifying hallmarks of cancer for each model and comparing these models to eachother based on log2-fold changes in expressed genes using selection of different gene sets.