title: Microglia replacement by ER-Hoxb8 conditionally immortalized macrophages provides insight into Aicardi-Goutières Syndrome neuropathology

city: Philadelphia

first: Frederick

middle: Chris

last: Bennett

state: PA

address: 3501 Civic Center Blvd

department: Neurology

institute: University of Pennsylvania

summary: Microglia, the brain’s resident macrophages, can be reconstituted by surrogate cells - a process termed “microglia replacement.” To expand the microglia replacement toolkit, we here introduce estrogen-regulated (ER) homeobox B8 (Hoxb8) conditionally immortalized macrophages, a cell model for generation of immune cells from murine bone marrow, as a versatile model for microglia replacement. We find that ER-Hoxb8 macrophages are highly comparable to primary bone marrow-derived (BMD) macrophages in vitro, and, when transplanted into a microglia-free brain, engraft the parenchyma and differentiate into microglia-like cells. Furthermore, ER-Hoxb8 progenitors are readily transducible by virus and easily stored as stable, genetically manipulated cell lines. As a demonstration of this system’s power for studying the effects of disease mutations on microglia in vivo, we created stable, Adar1-mutated ER-Hoxb8 lines using CRISPR-Cas9 to study the intrinsic contribution of macrophages to Aicardi-Goutières Syndrome (AGS), an inherited interferonopathy that primarily affects the brain and immune system. We find that Adar1 knockout elicited interferon secretion and impaired macrophage production in vitro, while preventing brain macrophage engraftment in vivo - phenotypes that can be rescued with concurrent mutation of Ifih1 (MDA5) in vitro, but not in vivo. Lastly, we extended these findings by generating ER-Hoxb8 progenitors from mice harboring a patient-specific Adar1 mutation (D1113H). We demonstrated the ability of microglia-specific D1113H mutation to drive interferon production in vivo, suggesting microglia drive AGS neuropathology. In sum, we introduce the ER-Hoxb8 approach to model microglia replacement and use it to clarify macrophage contributions to AGS.

overall_design: Myeloid cells (progenitors, monocytes, or macrophages) sequenced in vitro or in vivo (brain-engrafted), with or without CRISPR-editting. A minimum of 3 replicates per sample.

first: Nemec

last: Kelsey M

first: Uy

last: Genevieve

first: Chaluvadi

last: V Sai

first: Purnell

last: Freddy S

first: Elfayoumi

last: Bilal

first: Byerly

last: Leila

first: O'Reilly

last: Micaela L

first: O'Brien

last: Carleigh A

first: Aisenberg

last: William H

first: Lombroso

last: Sonia I

first: Guo

last: Xinfeng

first: Blank

last: Niklas

first: Oon

last: Chet Huan

first: Yaqoob

last: Fazeela

first: Temsamrit

last: Brian

first: Rawat

last: Priyanka

first: Thaiss

last: Christoph A

first: Bailis

last: Will

first: Williamson

last: Adam P

first: Wang

last: Qingde

first: Bennett

last: Mariko L

last: F Chris


title: Pathogenic Role of MIF Receptor (CD74) Expressing T cells in Inflammatory Arthritis

status: Public on Dec 18 2025

city: New Haven

first: Edward

last: Doherty

state: CT

address: 300 Cedar street

department: Internal Medicine

country: USA

institute: Yale School of Medicine

type: Expression profiling by high throughput sequencing

summary: High expression alleles of the innate cytokine, macrophage migration inhibitory factor (MIF), are associated with the development or the severity of autoimmune inflammatory diseases, including rheumatoid arthritis. Numerous studies support MIF’s role in activating inflammatory pathways and MIF inhibition reduces joint pathology in different experimental models of arthritis.  We examined the impact of gene deletion of MIF or its cognate receptor CD74 in the T cell-dependent model of collagen-induced arthritis (CIA) and observed the complete absence of arthritis development, suggesting an unforeseen role for MIF/CD74 signaling in the development of arthritogenic T cells.  While MIF has been shown in model systems to contribute to T cell activation by augmenting innate responses, fewer than 1% of T lineage cells express CD74 in naïve spleens and lymph nodes, and its functional consequences in pathogenic T cell subpopulations have not been studied.  We found CD74+ T cells to expand during CIA and to increase in number within joint synovium, where they express an effector memory phenotype and recapitulate CIA development upon transfer into naïve mice. We further found evidence for the presence of CD74+ T cells in the circulation and joint synovium of patients with rheumatoid arthritis.  MIF-dependent, CD74+ T cells may contribute to the chronicity of rheumatoid synovitis and to disease relapse in previously inflamed joints.

overall_design: Single cell suspensions were prepared from the 3 spleens of mice either naïve or 28 days after injection with CFA + Chicken Type II collagen.  Samples were then barcoded using TotalSeq Ahashtags (BioLegend, San Diego, CA). The samples were processed at Yale’s W.M. Keck Biotechnology Resource Laboratory with 10x Genomics (Pleasanton, CA) microfluidics for single cell isolation with RNA sequencing performed on the resulting plates.

first: Lais

last: Osmani

first: Joshua

last: Bilsborrow

first: Jennefer

last: Par-Young

first: Susanna

last: Choi

first: Pathricia

last: Tilstam

first: Min

last: Shin

first: Marta

last: Piecychna

first: Helen

last: Cai

first: Lin

last: Leng

first: Wan-Uk

last: Kim

first: Insoo

last: Kang

first: Richard

last: Bucala


title: Agouti integrates environmental cues to regulate paternal behaviour

city: Princeton

first: Forrest

middle: Dylan

last: Rogers

state: NJ

address: 40 Woodlands Way

department: Princeton Neuroscience Institute

institute: Princeton University

summary: Paternal care is rare among mammals and the neural mechanisms governing its emergence are poorly understood. We leveraged the natural paternal behaviour of African striped mice (Rhabdomys pumilio), and natural variation therein, to explore the neurobiological mechanisms that subserve male parental care. To support this aim, we performed single-nucleus RNA-sequencing (snRNA-seq) using the 10X Genomics platform in MPOA samples from sexually naïve alloparental (n=3), infanticidal (n=3), or control males (n=3), as well as sires (n=4), and dams (n = 4).

overall_design: We performed single-nucleus RNA-sequencing using the 10X Genomics platform in MPOA samples from sexually naïve alloparental (n=3), infanticidal (n=3), or control males (n=3), as well as sires (n=4), and dams (n = 4). Following euthanasia via rapid decapitation, we isolated brain tissue from the medial preoptic area of each animal. This tissue was flash frozen. Frozen samples were processed to isolate nuclei prior to sequencing. One sample corresponds to one animal. We did not pool samples.

middle: D

first: Sehee

first: Sarah

middle: A

last: Mereby

first: Anna

middle: M

last: Kasper

first: Anastasios

middle: B

last: Callanan

first: Ricardo

last: Mallarino

first: Catherine

middle: J

last: Pena


title: Role of Slit3 in mouse organoids

status: Public on Dec 19 2025

city: South San Fracisco

first: David

last: Castillo-Azofeifa

state: CA

address: 1 DNA Way

institute: Genentech

summary: To elucidate the transcriptional response upon Slit3 treatment in mouse organoids

overall_design: Comparitive gene expression of treated vs. control organoids


title: Transcriptional Profiling of Synovial Macrophages using Minimally Invasive Ultrasound-Guided Synovial Biopsies in Rheumatoid Arthritis [dataset2]

city: Chicago

first: Deborah

middle: R

last: Winter

state: IL

address: 240 E. Huron Street, M300

institute: Northwestern University

summary: Pilot study of the feasibility and clinical significance of whole tissue and cell-type-specific transcriptional profiling of cells from synovial biopsy in Rheumatoid Arthritis (RA)

overall_design:
RNA-seq of sorted CD206+ macrophages obtained from synovial biopsy of wrists in adults with RA.  Osteoarthritis (OA) tissue from whole joint replacement is processed analalagously for comparison.

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

first: Harris

last: Perlman


title: RNA-sequencing of lineage-traced memory Th2 cells after Heligmosomoidese polygyrus bakeri infection: IL-5 vs. IL-13

city: Seattle

first: Jakob

middle: Helmuth

last: von Moltke

state: Washington

address: 750 Republican Street

department: Immunology

institute: University of Washington

summary: Despite being intestine-restricted, the helminth Heligmosomoidese polygyrus bakeri (Hpb) induces systemic accumulation of Th2 cells, providing the opportunity to sequence Th2 cells in multiple tissue of the same mouse. Here we first compared IL-5-Cre and IL-13-Cre for permanent fluorescent labeling of Th2 effector cells after Hpb infection Next, we compared IL-5-Cre traced memory Th2 cells from multiple tissues: mesenteric lymph nodes (MLN), small intestine lamina propria (SILP) and mesenteric fat (MFAT). As a control, we also sorted naive CD4+ T cells from the MLN.

overall_design: We bred Red5 (RFP and Cre expressed from the Il5 locus) and YetCRE13 (YFP and Cre expressed from the Il13 locus) mice with Ai6 (Rosa26::STOPfl/fl::ZsGreen) or Ai9 (Rosa26::STOPfl/fl::TdTomato) mice, respectively, to generate lineage traced Il5-Ai6 and Il13-Ai9 mice.These mice were infected with Hpb and drug cleared with pyrantel pamoate after 14 days. Cells were sorted by flow cytometry 4 weeks after drug clearance.

first: Alison

middle: G

last: Stanbery


title: Single cell and isoform-specific translational profiling of the mouse brain

city: La Jolla

first: Brian

last: Yee

address: 9500 Gilman Dr

department: Health

institute: UCSD

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

overall_design: Refer to individual Series


title: 16S rRNA gene sequencing of human fecal microbiota before and after exercise intervention

city: Nanjing

first: xinyuan

last: ge

state: Jiangsu

address: Longmian Road 818

country: China

institute: Nanjing Medical University School of Public Health

summary: Lean nonalcoholic fatty liver disease (NAFLD) is increasingly recognized as a distinct clinical phenotype with limited evidence for effective non-pharmacological interventions and unclear mechanistic pathways. Aerobic exercise is recommended for NAFLD management, yet its effects and underlying gut microbiota–mediated mechanisms in lean NAFLD remain insufficiently characterized. This study is based on a randomized controlled trial (ClinicalTrials.gov identifier: NCT04882644) in which 100 adults with lean NAFLD were randomly assigned to a 3-month aerobic exercise intervention or usual care. 63 paired fecal samples were collected at baseline and after intervention. Gut microbiota profiles were generated using 16S rRNA gene sequencing. The dataset includes processed taxonomic abundance tables derived from fecal samples collected before and after the intervention. These data were used to characterize exercise-induced alterations in gut microbial diversity, composition, and functional potential, and to explore interindividual heterogeneity in microbiota responses to aerobic exercise in lean NAFLD. The microbiome data deposited in this series support integrative analyses with clinical phenotypes and circulating metabolomic profiles, aiming to elucidate gut microbiota–associated mechanisms underlying the metabolic benefits of aerobic exercise in lean NAFLD.

overall_design:
Fecal samples were collected at baseline and after exercise intervention. Relative abundance of bacterial taxa was calculated from 16S rRNA gene sequencing data.

***************************************************************
Raw sequencing data are not included in this submission due to ethical restrictions related to human subject privacy.
***************************************************************

first: Ci

last: Song

first: Chengxiao

last: Yu

first: Xin

last: Xu

first: Zhibin

last: Hu


title: Ectopic expression of cytosolic DHODH uncouples de novo pyrimidine biosynthesis from mitochondrial electron transport

city: San Francisco

first: Andrea

last: Curtabbi

address: 140 Dolores Street APT 208

institute: UCSF

summary: Dihydroorotate dehydrogenase (DHODH) is a rate-limiting enzyme of de novo pyrimidine synthesis. In most eukaryotes, this enzyme is bound to the inner mitochondrial membrane, where it couples orotate synthesis to ubiquinone reduction. As ubiquinone must be regenerated by respiratory complex III, pyrimidine biosynthesis and cellular respiration are tightly coupled. Consequently, inhibition of respiration suppresses DNA synthesis and cell proliferation. Here, we show that expression of Saccharomyces cerevisiae URA1 gene (ScURA) in mammalian cells uncouples pyrimidine biosynthesis from mitochondrial electron transport. ScURA forms a homodimer in the cytosol that uses fumarate as electron acceptor instead of ubiquinone, enabling respiration-independent pyrimidine biosynthesis. Cells expressing ScURA are resistant to drugs that inhibit complex III and the mitochondrial ribosome. Additionally, ScURA enables the growth of mtDNA-lacking ρ0 cells in uridine-deficient medium and ameliorates the phenotype of cellular models of mitochondrial diseases. Overall, this genetic tool uncovers the contribution of pyrimidine biosynthesis to the phenotypes arising from electron transport chain defects.

overall_design: RNAseq analysis of 143B WT cells (CONTROL) or expressing ScURA (ScURA) treated with antimycin/myxothiazol (INHIBITOR for WT and SCURINH for ScURA) or veichle

first: Sara Natalia

last: Jaroszewic

first: Rocío

last: Sanz Cortés

first: Rebeca

last: Acín-Pérez

first: Dimitrios

last: Prymidis

first: Maksym

last: Cherevatenko

first: Raquel

last: Martínez-de-Mena

first: María Jesús

last: Esteban-Amo

first: Miguel

last: de la Fuente

first: Christian

last: Frezza

first: José Antonio

last: Enríquez


title: Transcriptional control of hepatocellular carcinoma cells aggressiveness by AAV2/8-mediated delivery of human centenarian-associated SIRT6 N308K/A313S

city: Rome

first: Niccolò

last: Liorni

address: Via Enea 57

department: Computational Biology and Bioinformatics

country: Italy

institute: Policlinico Universitario Agostino Gemelli

summary: Hepatocellular carcinoma (HCC) is the 6th most prevalent cancer and a chief cause of cancer-related mortality throughout the world. SIRT6 is a fundamental sirtuin that governs several disease processes encompassing inflammation and cancer, including HCC. Longevity in centenarian Ashkenazi Jews was recently associated to novel allelic variants of SIRT6 (N308K/A313S), which ameliorate genome maintenance and DNA repair, and suppress cancer cells. It is currently unknown whether the above-mentioned SIRT6 variants display divergent or similar roles in HCC pathogenesis, compared to the wild type (WT) counterpart. In this work, our goal was to elucidate how these new centenarian-associated SIRT6 genetic variants may modulate HCC cell lines (HepG2 and Huh-7) aggressiveness and behavior, using functional and transcriptomic approaches. We demonstrate that adeno-associated virus (AAV2/8)-mediated overexpression of centenarian-associated SIRT6 variants hampered HCC cells proliferation, with transcriptomic data showing modulation of hallmark genes involved in the turnover of collagen/extracellular matrix (ECM). Also, we found that AAV2/8-mediated overexpression of SIRT6 N308K/A313S decreased invasion and also increased stiffness in HCC cells, as measured by nanoindentation, in a more pronounced fashion compared to SIRT6 WT. Intracellular stiffness is a property of the cancer cells themselves, which, along with ECM invasiveness, plays a significant role in the progression of HCC. In conclusion, these data suggest that increased intracellular stiffening mirror increased cell motility and invasive behavior, and it can be indicative of suppressed cancer development and progression by centenarian-associated SIRT6 N308K/A313S mutant.

overall_design: RNA-seq profiling of HepG2 and Huh-7 liver cancer cells transduced with AAV2/8-Luc (carrying Luciferase only), AAV2/8-SIRT6-WT (carrying the wild type sequence of human SIRT6) and AAV2/8-SIRT6-N308K/A313S for 72 hours.

first: Maanya

last: Vittal

first: Ahmed

last: Kazail

first: Jonathan

last: C. Jarvi

first: Eric

last: Leire

first: Riaz

last: Akhtar

first: Tommaso

last: Mazza

first: Manlio

last: Vinciguerra


title: LncRNA and mRNA expression characteristics and bioinformatics analysis of exosomes from sheep ovaries with different reproductive capacities

city: nanjing

first: chenbo

last: yan

address: Weigang No.1

institute: Nanjing Agricultural University

summary: Hu sheep (HS) is known for its year-round estrus and multiple births, and is an ideal model for studying the mechanisms of high reproductive capacity in livestock. We established an RNA sequencing dataset to compare the expression profiles of long non coding RNA (lncRNA) and messenger RNA (mRNA) in the ovarian tissue exosomes of Hu sheep and low reproductive sheep breeds (Mongolian sheep) during estrus period.

overall_design: RNA-seq expression profiles of ovaries during estrus in Hu sheep and Mongolian sheep


title: Joint single-cell profiling of Cas9 edits and transcriptomes reveals on- and off-target effects on gene expression

first: Graham

last: McVicker

address: 10010 N Torrey Pines Rd

institute: Salk Institute for Biological Studies


title: Effect of chronic mechanical compression on co-cultures of human induced neurons and murine glia

city: Notre Dame

first: Christopher

last: Patzke

state: IN

address: 109A Galvin Life Sciences Building

department: Department of Biological Sciences

institute: University of Notre Dame

summary: Human induced neurons and primary murine glia were subjected to a controlled in vitro model of mechanical compression to determine how solid stress—similar to forces present in glioblastoma—directly alters neuronal and glial transcriptional programs. RNA sequencing was performed after 24 hours of compression, with species-specific alignment enabling independent analysis of neuronal and glial responses. Compressed human neurons showed strong activation of hypoxia-responsive metabolic genes, pro-inflammatory signaling pathways, and intrinsic apoptotic programs. Murine glia exhibited parallel induction of hypoxia and apoptotic pathways, accompanied by robust NF-κB/AP-1-driven inflammatory cytokine expression characteristic of astrocytic and microglial activation. These data define the conserved transcriptional responses by which neurons and glia detect and respond to solid stress, providing a resource for understanding mechanotransduction and neuroinflammatory signaling in diseases characterized by mass effect, including glioblastoma.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: RNA-seq profiling of human induced neurons and murine glia co-cultures maintained under control conditions or subjected to 24 hours of controlled mechanical compression (0.14 kPa) to model solid stress-induced transcriptional responses in each cell type.

last: Zarodniuk

first: Anna

last: Wenninger

first: Julian

last: Najera

first: Jihaeng

last: Lee

first: Jack

last: Markillie

first: Cameron

last: MacKenzie

first: Jenny

last: Bergqvist-Patzke

first: Bianca

last: Batista

first: Megna

last: Panchbhavi

first: R’nld

last: Rumbach

first: Alice

last: Burchett

first: Charles

last: Sander

first: Meenal

last: Datta


title: Single-cell multi-omic and multi-region atlas of the Aging Male Mouse Brain

first: Joseph

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

type: Methylation profiling by high throughput sequencing

summary: Aging is the primary risk factor for many neurodegenerative diseases, primarily attributed to progressive changes in cellular epigenomes. Despite this known association, the complexity of the mammalian brain complicates the identification of brain regions and cell types that are most susceptible to aging effects. While alterations in gene expression have been observed in aging neural cells, comprehension of the epigenetic regulatory mechanisms underlying the transcriptomic changes remains largely elusive.  To unveil these complexities in a comprehensive manner, we utilized single-nucleus methylome sequencing (snmC-seq3) and multi-omic sequencing (snm3C-seq) to produce extensive datasets comprising 132,551 methylomes and 72,666 chromatin conformation-methylome joint profiles from eight distinct brain regions of C57BL/6J mice aged 2, 9, and 18 months. These regions include the anterior hippocampus (AHC), posterior hippocampus (PHC), frontal cortex (FC), amygdala (AMY), nucleus accumbens (NACB), PAG/PCG, entorhinal cortex (ENT), and caudate putamen (CP). We utilized this dataset to investigate age-related changes in DNA methylomes and transcription factor motifs potentially affected by methylation alterations. We also examined methylation changes in transposable elements, observing locus-specific retrotransposon activation. At the chromatin conformation level, we analyzed aging-related changes in compartmentalization, topologically associating domains (TADs), and chromatin loops. Furthermore, we explored regional heterogeneity during aging within identical cell types and validated our findings using the MERFISH dataset.

overall_design: C57BL/6J (males and females) mice of different ages were purchased from Jackson Laboratories and maintained in the Salk animal barrier facility on 12-hour dark-light cycles with food ad-libitum for up to 4 weeks (Housing condition: Temperature: 21-23 °C, relative humidity: 61-63%). Brains were extracted, sliced, and dissected in an ice-cold dissection buffer as previously described (Liu et. al. 2021). Females were synchronized for their estrous cycle by exposing them to male bedding for three days, and collected during diestrus. For snmC-seq3 and snm3C-seq samples, brains were sliced coronally at 600 μm intervals from the frontal pole across the whole brain, yielding 18 slices, and dissected brain regions were obtained according to the Allen Brain Reference Atlas Common Coordinate Framework version 3 (CCFv3) as previously described (Liu et. al. 2023). For nuclei isolation, each region was dissected from 2-7 animals and pooled to make 2-3 biological replicates. No statistical methods were used to predetermine sample size. We empirically determined to use two to three biological experiments for all single-cell epigenomic experiments to achieve minimum reproducibility for this large-scale project. Blinding and randomization is not performed during handling the tissue samples. Additionally, all dissected regions were digitally registered into CCFv3 using ITK-SNAP60 (v4.0.0) at a 25 μm resolution.

first: Qiurui

last: Zeng

first: Wei

last: Tian

last: Bartlett

last: Nery

first: Rosa

last: Gomez Castanon

first: Julia

last: Osteen

first: Jordan

last: Altshul

first: Nicholas

last: Johnson

first: Mia

last: Kenworthy

first: Cynthia

last: Valadon


title: Precision nanotherapy remodels the tumor-associated macrophage to reverse immunnosuppressive in pancreatic cancer [scRNA-seq]

city: Hsinchu

first: Hsin mei

last: Lee

address: Guangfu Rd.

country: Taiwan

institute: National Tsing Hua University

summary: Pancreatic ductal adenocarcinoma (PDAC) is characterized by an immunosuppressive stroma rich in tumor-associated macrophages (TAMs) that limit the therapeutic efficacy. We introduce a TAM-targeted nanotherapy platform that selectively delivers either a CSF1R inhibitor or the STING agonist cGAMP to immunosuppressive TAMs. While CSF1R inhibitor–loaded nanoparticles efficiently depleted TAMs and produced moderate antitumor effects, TAM-targeted cGAMP nanoparticles reprogrammed TAMs into immune-stimulating effectors. This reprogramming normalized aberrant vasculature, alleviated desmoplasia, and enhanced infiltration and activation of cytotoxic immune cells. In combination with gemcitabine, PD-1 checkpoint blockade, or CAR-NK cell therapy, TAM-targeted STING activation provided an in situ immunostimulatory signal that markedly improved antitumor efficacy in preclinical PDAC models. Ex vivo efficacy in human PDAC tissues and a favorable safety profile show the translational potential of this TAM-targeted nanotherapy to overcome the immune desert of PDAC.

overall_design: Murine PDAC tumors with or without TAM-cGAMPnp treartment was harvested for single-cell seq analysis

first: Yunching

last: Chen

first: Hsin-Mei


title: Translational Downregulation of 5’ TOP mRNAs During T Cell Exhaustion [Ribo-Seq]

city: Berkeley

first: Jamie

last: Cate

address: 2151 Berkeley Way

institute: UC Berkeley

summary: T cell exhaustion is a dysfunctional state that arises during chronic infections and cancer, characterized by impaired effector functions and sustained expression of inhibitory receptors. While transcriptional, epigenetic, and metabolic rewiring have been well documented in exhausted T cells, a comprehensive understanding of how translation is regulated in this state remains incomplete. To address this gap, we performed ribosome profiling and RNA sequencing on exhausted human CD8⁺ T cells to globally assess translational control. Our analyses reveal a marked repression of 5’ terminal oligopyrimidine (TOP) mRNAs during exhaustion. Unexpectedly, we demonstrate that this translational repression occurs despite evidence of elevated mTOR activity in exhausted T cells. These findings uncover a previously unknown layer of translational control in exhausted T cells.

overall_design: Ribosome profiling on human CD8+ T cells (Tchron, Tre-act, and Tacute) in four donors

first: Erica

last: Pledger

first: Navya

last: Ambavaram

first: Lucas

last: Ferguson


title: Effect of chronic mechanical compression on immortalized human astrocytes

first: Christopher

last: Patzke

summary: Immortalized human astrocytes were subjected to a controlled in vitro model of chronic mechanical compression to investigate how solid stress—similar to that exerted by growing brain tumors—directly affects astrocyte transcriptional programs. RNA sequencing was performed after 24 hours of compression to measure sustained mechanotransductive responses. Compressed astrocytes showed robust induction of AP-1-associated immediate-early genes and activation of NF-κB–dependent inflammatory pathways. These data define the transcriptional signatures by which human astrocytes detect and respond to mechanical stress, providing a resource for understanding mechanobiology and neuroinflammatory signaling in diseases featuring mass effect, including glioblastoma and traumatic brain injury.

overall_design: RNA-seq profiling of immortalized human astrocytes cultured under control conditions or subjected to 24 hours of chronic mechanical compression equivalent to 0.14 kPa of stress.

first: Maksym

last: Zarodniuk

first: Anna

last: Wenninger

first: Julian

last: Najera

first: Jihaeng

first: Jack

last: Markillie

first: Cameron

last: MacKenzie

first: Jenny

last: Bergqvist-Patzke

first: Bianca

last: Batista

first: Megna

last: Panchbhavi

first: R’nld

last: Rumbach

first: Alice

last: Burchett

first: Charles

last: Sander

first: Meenal

last: Datta


title: Exercise alleviates cognitive dysfunction in Alzheimer’s disease mice via skeletal muscle-derived extracellular vesicles which enhance plaque clearance by microglia [RNA-Seq]

first: Jiaquan

last: Lin

address: Hankou road

institute: nanjing university

summary: Exercise confers cognitive benefits in Alzheimer’s disease (AD), yet the underlying mechanisms remain incompletely understood. The skeletal muscle functions as an endocrine organ that secretes myokines which affect the homeostasis of extra-muscular organs, including the brain. Here, we found that swimming exercises promoted the secretion of skeletal muscle-derived extracellular vesicles (SKM-EVs), which subsequently pinocytosis by microglia. Gain- and loss-of-function experiments showed that exercised SKM-EVs activated the polarization of disease-associated microglia (DAM) and enhanced the clearance of amyloid-beta (Aβ) plaques. Furthermore, miR-378a-3p was identified as the key miRNA in SKM-EVs and promoted lipid metabolism in DAM by targeting p110α. Importantly, the therapeutic administration of EVs derived from mir-378a overexpressing myotubes alleviated cognitive impairment in AD mice. Together, our findings demonstrate that exercised SKM-EVs could serve as a novel myokine mediating communication from skeletal muscle to the brain and develop alternative therapeutic strategies for exercise in AD treatment.

overall_design: In order to further understand the potential mechanism of miR-378a-3p's involvement in skeletal muscle movement to delay cognitive function in AD mice, especially its regulatory effect on microglia, we pre treated primary microglia with A β oligomers, and then transfected them with negative control (nc) or miR-378a-3p mimetics (mimic), and collected the cells for RNA sequencing analysis.

first: Xiaoyan

last: Shao

first: Tianshu

last: Shi


title: Overcoming ADC resistance in advanced colorectal cancer by dual targeting of TROP2 and PERK to suppress Wnt/β-catenin signaling [TROP2+GSK RNA-Seq]

city: Ganzhou

first: zhou

last: dongdong

address: hexie avenue

institute: Gannan Medical University

summary: Targeted therapy for advanced colorectal cancer (CRC) remains a significant clinical challenge. In this study, we systematically examined the anti-tumor efficacy and underlying mechanisms of IMMU132, an FDA-approved anti-TROP2 antibody conjugate linked to the topoisomerase I inhibitor SN-38, both as a standalone treatment and in combination with the PERK inhibitor GSK2606414 in TROP2-positive advanced CRC. We first established that TROP2 expression was markedly elevated in CRC cohorts and correlated with poor patient prognosis. In vitro experiments demonstrated that IMMU132 inhibited CRC cell proliferation and viability in a dose-dependent manner. In patient-derived xenograft (PDX) models, IMMU132 monotherapy significantly inhibited tumor growth. Mechanistically, transcriptomic analysis indicated that PERK, a key factor in endoplasmic reticulum stress (ERS), may serve as a critical synergistic target for IMMU132’s anti-tumour activity. Subsequent screening of various ERS inhibitors revealed that the specific PERK inhibitor GSK2606414 significantly enhanced the effects of IMMU132. In diverse experimental models, including cell lines, organoids, and PDX models, combination therapy exhibited superior anti-tumor effects compared to monotherapy, highlighting a pronounced synergistic effect. Furthermore, transcriptomic analysis showed that combination therapy notably inhibited the Wnt/β-catenin signaling pathway. Gene set enrichment analysis confirmed significant upregulation of Wnt pathway-related genes, while Western blot analysis showed downregulation of key molecules in the Wnt pathway, including β-catenin, GSK3B, JUN, and WNT2B, following combination therapy. These findings suggest that the synergistic anti-tumour effects of IMMU132 and GSK2606414 may arise from their dual modulation of ERS and Wnt signalling pathways, offering novel insights for targeted therapy in advanced CRC and informing strategies for combining antibody-drug conjugates (ADCs).

overall_design: This study systematically characterized TROP2 expression in colorectal cancer through integrated bioinformatics and tissue microarray analysis, with validation across multiple preclinical models. The TROP2-targeting antibody-drug conjugate IMMU132 demonstrated potent monotherapeutic efficacy across diverse molecular subtypes in cell lines, patient-derived organoids and xenografts. Transcriptomic analysis identified PERK, a key endoplasmic reticulum stress regulator, as crucial to IMMU132's mechanism. The specific PERK inhibitor GSK2606414 significantly enhanced IMMU132's anti-tumor effects through synergistic modulation of both endoplasmic reticulum stress and Wnt/β-catenin signaling pathways. These findings elucidate IMMU132's mechanism of action and propose a novel combination strategy with strong translational potential for advanced colorectal cancer therapy.

first: Jie

last: Liu

first: Mei

last: Li

first: Jianming

last: Huang


title: Translational Downregulation of 5’ TOP mRNAs During T Cell Exhaustion [RNA-Seq]

first: Jamie

last: Cate

overall_design: RNA-Seq on human CD8+ T cells (Tchron, Tre-act, and Tacute) in four donors

first: Erica

last: Pledger

first: Navya

last: Ambavaram

first: Lucas

last: Ferguson


title: Exercise alleviates cognitive dysfunction in Alzheimer’s disease mice via skeletal muscle-derived extracellular vesicles which enhance plaque clearance by microglia [miRNA-Seq]

type: Non-coding RNA profiling by high throughput sequencing

overall_design: In order to further understand the potential mechanism of SKM-EVs involved in delaying cognitive function in AD mice during exercise, especially the biological role of their contents. We constructed a skeletal muscle ex vivo exercise model using the Aurora Scientific 2000A skeletal muscle isolation system, simulated exercise (EX) and sedentary (ST) states through pulsed electrical stimulation, and collected their SKM-EVs for microRNA sequencing analysis.


title: Overcoming ADC resistance in advanced colorectal cancer by dual targeting of TROP2 and PERK to suppress Wnt/β-catenin signaling


title: NanoString CosMx SMI (human) on ten human MASLD samples

city: Leuven

first: Olivier

last: Govaere

address: ON6 Herestraat 49

country: Belgium

institute: KU Leuven

summary: CosMx SMI is a high-plex in situ analysis platform to provide spatial multiomics with formalin-fixed paraffin-embedded (FFPE) and fresh frozen (FF) tissue samples at cellular and subcellular resolution. CosMx SMI is an integrated system with mature cyclic fluorescent in situ hybridization (FISH) chemistry, high-resolution imaging readout, interactive data analysis and visualization software. Herein we used the CosMx SMI with the CosMxTM Human Universal Cell Characterization RNA Panel (1000-plex) supplemented with 14 custom genes of interest to probe different disease stages of MASLD/MASH, previously known as NAFLD.

overall_design: n=1 normal biopsy, n=2 MASL biopsies, n=1 F1 biopsy, n=4 F3 biopsies,  n=1 F4 biopsy, n=2 end-stage explants.

first: Markus

last: Boesch

first: Dania

last: El Abyad


title: Simultaneous Targeting of KRAS and CDK4 Synergistically Induces Durable Growth Arrest in Pancreatic Cancer Cells

city: Göttingen

first: Adi

last: Mackay

address: Robert-Koch-Straße 40

department: Pathology

country: Germany

institute: University Medical Center Göttingen

summary: Mutant Ras oncoproteins, particularly KRAS, are among the most prevalent drivers of cancer. Small-molecule KRAS inhibitors have emerged as promising cancer therapeutics, yet resistance development remains a major hurdle. To overcome this challenge, we explored rational combination strategies aimed at enhancing therapeutic efficacy and durability. We show that the KRAS-G12C inhibitor Sotorasib synergizes with the CDK4/6 inhibitor Palbociclib to eliminate pancreatic ductal adenocarcinoma (PDAC) cells and organoids harboring KRAS-G12C mutations. This synergy was especially pronounced following drug washout, indicating a durable cellular response. Similar synergistic effects were observed in non-small-cell lung cancer (NSCLC) cells. Additionally, the KRAS-G12D inhibitor MRTX1133 cooperated with Palbociclib to suppress KRAS-G12D-mutant PDAC cells. Mechanistically, the combinations induced sustained cell cycle arrest, marked by reduced RB phosphorylation, decreased E2F1 expression, and increased levels of CDKN1B/p27. Deletion of CDKN1B largely reversed the growth-inhibitory effect, highlighting its essential role in mediating the observed synergy. In an orthotopic, immunocompetent mouse model of PDAC, MRTX1133 significantly delayed tumor growth and extended survival; however, despite its ability to suppress RB phosphorylation, Palbociclib failed to enhance these effects. This might be due to increased tumor vascularization upon Palbociclib treatment, as revealed by single cell RNA sequencing. In summary, our findings demonstrate the therapeutic potential of enhancing cell cycle restriction point activation in KRAS inhibitor-based therapies, while emphasizing the importance of precisely adjusting the drug combinations to the in vivo situation.

overall_design: 1.5 x 10^5 KrasG12D;Trp53R172H/+ (KPC) cells in culture medium and 50 % matrigel were injected into the pancreatic tail of C57BL/6J mice aged 4 to 6 months. Upon successful tumor detection, mice were assigned to treatment groups: Vehicle-control, Palbociclib (25 mg/kg, PZO199, Sigma-Aldrich) and/or MRTX1133 (30 mg/kg, HY-134813, Medchem Express). The treatments were administered i.p. once a day within weekly cycles of three consecutive treatmens followed by four recovery days until humane endpoint.


title: DeCAF redefines fibroblast states uncovering multidimensional tumor-stroma relationships driving clinical tumor progression and immunotherapy response [scRNA-Seq]

city: Chapel Hill

first: Jen Jen

last: Yeh

state: North Carolina

address: 450 West drive

institute: The University of North Carolina at Chapel Hill

summary: Cancer-associated fibroblast (CAF) heterogeneity within pancreatic ductal adenocarcinoma (PDAC) has been previously assessed through single-cell RNA sequencing (scRNAseq) to discover distinct CAF populations such as myCAFs and iCAFs. While useful as a biological framework, no studies have conclusively and robustly demonstrated a correlation of CAF subpopulations with clinical prognosis or therapy response. We define restraining (rest) and promoting (pro) CAFs in patient samples that are both prognostic and predictive of therapy response in disparate tumor types. Using a single sample classifier, DeCAF, we uncover distinct clinical and spatial interactions between pro- and restCAF subtypes and basal-like and classical tumor subtypes that support tumor stroma crosstalk where basal-like tumors are enriched in proCAFs and classical tumors are enriched in restCAFs. Finally, we find striking differences in the immune contexture of pro- and restCAF tumors where restCAF dominant tumors are enriched in patients who respond to immune checkpoint inhibition (ICI) in two large clinical trials, and proCAF dominant tumors are enriched in patients who respond to myeloid inhibition. This work is the first to define CAF subtypes that are clinically robust, prognostic, predictive of immunotherapy response, and associate with tumor molecular subtype.

overall_design:
129 de-identified primary PDAC patient samples were collected from the IRB-approved University of North Carolina Lineberger Comprehensive Cancer Center Tissue Procurement Core Facility and were flash frozen in liquid nitrogen.  FFPE samples were prepared, hematoxylin and eosin stained.

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

first: Xianlu

middle: L

last: Peng

first: Ian

middle: C

last: McCabe


title: DeCAF redefines fibroblast states uncovering multidimensional tumor-stroma relationships driving clinical tumor progression and immunotherapy response [Spatial Transcriptomics]


title: DeCAF redefines fibroblast states uncovering multidimensional tumor-stroma relationships driving clinical tumor progression and immunotherapy response [RNA-Seq]


title: Identifying membrane-bound transcriptional regulatory proteins from rare but evolutionarily conserved domain combinations

city: Austin

first: Muyoung

last: Lee

state: TX

address: 2506 Speedway

department: Molecular Biosciences

institute: University of Texas at Austin

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Transcriptional regulatory proteins, including transcription factors (TFs) and chromatin modifiers, perform their crucial cellular functions inside cell nuclei. However, unlike most TFs, membrane-bound transcription factors (MBTFs) are first anchored in membranes before nuclear translocation. Known MBTFs are vital for processes from myelin expression (MYRF) to cholesterol homeostasis (SREBP), yet their overall diversity remains uncharted. We hypothesized that additional membrane-bound transcriptional regulators (MBTRs) might exist and developed a bioinformatics screen that prioritizes membrane proteins likely to regulate transcription. Our approach leverages domain composition, assuming that surprising domain combinations suggest novel biological functions. We searched for rare but evolutionarily conserved combinations of transmembrane domains paired with domains likely involved in transcriptional regulation. Our method rediscovered known MBTFs and membrane-bound histone kinases, and identified novel MBTR candidates, including histone N-acetyltransferases and the prolactin regulatory element-binding protein PREB. Experimental validation indicates that PREB may undergo cleavage. Without its transmembrane domain, PREB exhibits nuclear localization and chromatin association in mouse embryonic stem cells. Furthermore, we identified a putative class of new MBTFs that share MYRF's DNA-binding domain. These findings underscore the utility of our method and provide a framework for investigating MBTRs that likely facilitate the integration of extracellular signals with transcriptional responses.

overall_design: bioChIP-seq was performed on PREB- and PREBΔTM-expressing ES cells treated with 0.5 µg/mL Dox for 24 hours as previously described (21). Cells were cross-linked with 1% formaldehyde (Fisher Bioreagents, BP531-500) for 7 minutes at room temperature, and the reaction was quenched by adding glycine (Fisher Scientific, BP381-1) to a final concentration of 0.125 M. The chromatin was sheared to an average fragment size of ~200 bp using a Bioruptor sonicator (Diagenode). Cross-linked chromatin was pre-cleared with Protein A agarose beads (Thermofisher, 10008D) and subsequently subjected to immunoprecipitation using Dynabeads MyOne Streptavidin T1 (Invitrogen, 65602). Immunoprecipitated complexes were washed twice with 2% SDS, once with buffer A (0.1% Deoxycholate, 1% Triton X-100, 1mM EDTA, 50mM HEPES pH 7.5, 500mM NaCl), once with buffer B (250mM LiCl, 0.5% NP-40, 0.5% Deoxycholate, 1mM EDTA, 10mM Tris-Cl pH 8.1), and twice with TE buffer. The crosslinked protein-DNA complexes were reversed with an elution buffer (1% SDS, 10mM EDTA, 50mM Tris-Cl 8) to the washed beads and were incubated at 65°C overnight. RNase A (Thermo Scientific, EN0531) was then treated for 30 minutes, followed by treatment of proteinase K (NEB, P8107S) for 2 hours. DNA was extracted with phenol:chloroform:isoamyl alcohol (Invitrogen, 15593031), then precipitated and re-suspended in the TE buffer. Library preparation was performed using the NEBNext Ultra DNA Library Prep Kit (NEB, 7103L), and sequencing was conducted on an Illumina NovaSeq 6000 platform to generate 50-bp paired-end reads. Comparison of the samples with the BirA-only control allowed identification of target-specific binding sites, and IgG ChIP served as a negative control, providing a background signal.

first: Yeejin

last: Jang

first: Qingqing

last: Guo

first: Jonghwan

last: Kim

first: Edward

last: Marcotte


title: High-dimensional profiling uncovers heterogeneity, lineage-specific precursors and inflammation-induced changes in the mononuclear phagocyte compartment of the human intestine

city: Copenhagen

first: William

middle: Winston

last: Agace

address: Blegdamsvej 3B

department: Skin Immunology Research Center

country: Denmark

institute: Copenhagen University

summary: With use of single-cell omics this study explore mononuclear phagocyte complexity of the human intestinal lamina propria in health and IBD. The study identifies distinct dendritic cell and macrophage subsets, lineage specific precursors and state specific signatures.

overall_design:
Healthy controls consist of resection material from colorectal cancer patients undergoing surgery, samples are taken away from cancer site. IBD samples are similarly taken from patients undergoing surgery, material is from inflamed areas in this case.

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

first: Thomas

last: Fenton

first: Line

last: Wulff

first: Venla

last: Väänänen

first: Gareth-Rhys

last: Jones

first: Camilla

middle: K

last: Lemvigh

first: Lene

last: Riis

first: Mads

last: Wewer

first: Julien

last: Vandamme

first: Peter

last: Jørgensen

first: Calum

last: Bain

first: Julie

first: Kirstine

last: Belling

first: Gwo-Tzer

last: Ho

first: Tune

middle: H

last: Pers

first: Anja

last: Poulsen

first: Gorm

last: Madsen

first: Ole

last: Nielsen

first: Henrik

last: Jakobsen

first: Jose

last: Izarzugaza

first: Flemming

last: Bendtsen

first: Søren

last: Brunak

first: Allan

last: Mowat

first: Lars

last: Olsen

first: Urs

last: Mörbe

middle: W


title: Distinct chromatin regulators downmodulate meiotic axis protein deposition and DNA break induction at chromosome ends [MNAse-seq]

city: New York

first: Andreas

last: Hochwagen

state: NY

address: 24 Waverly Place

department: Department of Biology

institute: New York University

summary: In many organisms, meiotic crossover recombination is suppressed near the extreme ends of chromosomes. Here we show that multiple, often chromosome-specific, suppressive mechanisms with differing ranges combine to achieve the consistently low enrichment of recombination-promoting axis proteins and downregulation of DNA double-strand breaks (DSBs) within 20 kb of telomeres in Saccharomyces cerevisiae. Suppression of axis proteins is associated with cis-encoded signals, including reduced coding density and the subtelomeric Y’ elements, which are present at many chromosome ends, but also requires chromatin modifiers, including the histone methyltransferase Dot1 and the Sir silencing complex. We show that Dot1 suppresses Sir complex activity at least in part independently of its canonical target, H3K79, to downmodulate axis protein deposition near chromosome ends. In parallel, the Sir complex, but not Dot1, suppresses the induction of DSBs by limiting the openness of promoters, the preferred sites of meiotic DSB formation. The separable downmodulation of axis protein deposition and DSB induction likely contributes to the robust reduction of meiotic recombination effectors near chromosome ends.

overall_design: We mapped MNase-sensitive chromatin complexes in budding yeast by profiling DNA fragments generated upon micrococcal nuclease (MNase) cleavage. Protected fragments correspond to nucleosomes, and cleavage patterns were used to assess chromatin organization genome-wide.

first: Adhithi

last: Raghavan

first: Kieron

last: May

first: Vijayalakshmi

middle: V

last: Subramanian

first: Hannah

last: Blitzblau

first: Neem

last: Patel

first: Jonathan

last: Houseley


title: Phosphite promotes the growth of the filamentous fungus Trichoderma atroviride by activating genes involved in cell cycle and cell division

city: IRAPUATO

first: ALFREDO

last: HERRERA ESTRELLA

state: GUANAJUATO

address: Libramiento Norte León Km 9.6

department: UGA-LANGEBIO

country: Mexico

institute: CINVESTAV

summary: Phosphite (Phi) is widely used in agriculture due to its biostimulant effects on plants and its ability to control various phytopathogens. However, its impact on beneficial soil microorganisms remains poorly understood. In this study, we evaluated the effect of Phi on the growth and transcriptional response of the beneficial fungus Trichoderma atroviride. Our results show that low concentrations of Phi, in the presence of phosphate (Pi), promote the growth of T. atroviride, whereas higher concentrations inhibit its development. Transcriptomic analysis via RNA-Seq revealed the activation of genes associated with growth, amino acid biosynthesis, and siderophore transport. Furthermore, Phi enhanced the antagonistic capacity of T. atroviride against Rhizoctonia solani. These findings reveal a novel role of Phi in stimulating beneficial fungi and suggest its combined use with T. atroviride as a sustainable strategy for phytopathogen biocontrol in agricultural systems.

overall_design: RNA-Seq profile of the wild strain of Trichoderma atroviride IMI206040 under different concentrations of phosphite (Phi) in the presence of phosphate (Pi) in the medium: control (1 mM Pi), treatment 1 (1 mM Pi + 0.1 mM Phi), treatment 2 (1 mM Pi + 0.5 mM Phi).

first: C

last: Pérez-Salazar

first: S

last: Esparza-Reynoso

first: E

middle: E

last: Enríquez-Félix

first: A

last: Herrera-Estrella


title: DeCAF redefines fibroblast states uncovering multidimensional tumor-stroma relationships driving clinical tumor progression and immunotherapy response

first: Jen Jen

last: Yeh

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

overall_design: Refer to individual Series


title: Advancing Lung Tissue Engineering Through the Discovery of Factors that Control Alveolar Epithelial Cell Fate (AT2 scRNA-seq)

city: Durham

first: Laila

last: Roudsari

state: NC

address: 2 Maughan Drive

institute: United Therapeutics

summary: The objective of this study was to compare uncultured primary human alveolar epithelial type 2 cells (AT2s) isolated from lungs to AT2s that were expanded in large-scale.

overall_design: Alveolar type 2 cells were isolated from human lung tissue and expanded for 3 passages. Isolated cells (uncultured, UC, or isoAT2), passage 0, and passage 2 cells from 3 donors were analyzed using scRNA-seq.

first: Lauren

last: Rochelle

first: Rachael

middle: S

last: Van

first: Richard

last: Ottman

first: Daren

middle: F

last: Robinson

first: Ashley

last: Dockham

first: Amy

last: Smith

first: Daniel

middle: P

last: Keeley

first: Darell

last: McCoy

first: Tyler

last: Zimmerman

first: Bryan

last: Fioret

first: Ryan

last: Bonvillain

first: Thomas

last: Petersen

first: Sarah

last: Hogan


title: Advancing Lung Tissue Engineering Through the Discovery of Factors that Control Alveolar Epithelial Cell Fate (snRNA-seq from recellularized scaffolds)

summary: The objective of this study was to evaluate primary, human AT2 cells following seeding into decellularized lung scaffolds.

overall_design: Alveolar type 2 cells were isolated from human lung tissue, expanded in large-scale, and seeded onto decellularized porcine lung scaffolds. Cell culture media was used to promote AT1 differentiation, and samples were taken down over a time-course study. SnRNA-seq analysis was performed on the recellularized lung tissue.


title: Sperm RNA landscape during sexual maturation in Duroc boars

city: Hamar

first: Asmita

last: Shrestha

state: Innlandet

address: Holsetgata 22

department: Department of Biotechnology

country: Norway

institute: University of Inland Norway

summary:
Sexual maturation in boars impacts reproductive efficiency in swine production, yet the molecular mechanisms underlying this developmental transition remain poorly understood. This study aimed to investigate the transcriptomic changes in sperm from Duroc boars during sexual maturation, conducting a longitudinal analysis. The total RNA and miRNA profiles from the same individuals (n = 6) at puberty (7.24 ± 0.39 months) and sexual maturity (10 ± 0.40 months) were compared, identifying molecular signatures associated with reproductive development. Total RNA sequencing (Illumina NovaSeq-6000) and miRNA sequencing (Illumina NextSeq-500) were performed on all 12 paired samples (6 boars at 2 time points), followed by differential expression analysis using a paired statistical model in DESeq2 to account for repeated measures.
Differential expression analysis identified 60 differentially expressed genes using stringent criteria (adj P < 0.05, |log₂FC| ≥ 0.5), with 65% upregulated in sperm of boars 10-months versus 7-months of age. Key upregulated genes included NCLN, RGS12, CIB2, FOXP4, PHC1, CDC25B and AKAP1, while HSP90AA1, EVI5, FSIP2, VDAC3, and ALMS1 were key downregulated genes. Furthermore, Gene ontology analysis revealed significant enrichment of 11 biological processes, mostly related to reproductive development, and four molecular functions (transferase activity, transferring phosphorus-containing groups, protein serine/threonine kinase activity, protein kinase activity and signal sequence binding). Additionally, our miRNA analysis identified six differentially expressed miRNAs (adj P < 0.05 & |log2FC| ≥ 0.5); ssc-miR-193a-5p, ssc-miR-574-3p, ssc-miR-126-3p, ssc-miR-196a, ssc-miR-210 were upregulated, and ssc-miR-338 showed downregulation in 10-months age. Integrated analysis of differentially expressed mRNA and predicted miRNA targets identified 18 miRNA-mRNA regulatory pairs, enriched in pathways related to cell cycle processes and chromatin binding, suggesting coordinated regulation across RNA biotypes in sperm during sexual maturation.
Our study reveals coordinated transcriptomic shifts in boar sperm during sexual maturation. Most genes show increased abundance at 10 months of age, with enrichment in terms of reproductive development. Several miRNAs appear to regulate these changes through targeted mRNA interactions. These findings expand our understanding of the

overall_design: Total RNA-seq and miRNA-seq profiling of sperm samples from six Duroc boars collected at pubertal (~7 months) and mature (~10 months) ages using a longitudinal paired design.

first: Maren

last: Son

first: Adnan

last: Hashim

first: Soudabeh

last: Rouzbehani

first: Gregor

middle: D

last: Gilfillan

first: Urszula

last: Berge

first: Elisabeth

last: Kommisrud

first: Anne

last: Alm-Kristiansen


title: Specific SLC25 carriers regulate mitochondrial protein synthesis

city: Nedlands

first: Danielle

middle: Louise

last: Rudler

state: WA

address: 6 Verdun Street

department: Mitochondrial Medicine and Biology

country: Australia

institute: The Kids Research Institute

summary: A genome-wide knock out screen identified members of the SLC25 family of mitochondrial carrier proteins as important regulators of the rate of de novo mitochondrial protein synthesis. To elucidate this relationship, we generated human cell knockouts for SLC25A25, SLC25A44, SLC25A45, and SLC25A48, which have been shown to exchange ATP and magnesium, branched-chain amino acids, methylated basic amino acids, and choline, respectively.  Multi-omic and functional analyses identified that these four carriers are crucial for mitochondrial translation, biogenesis and function of the oxidative phosphorylation system, as well as mitochondrial morphology. Thermostability screens showed that SLC25A48 is specifically stabilised by choline and changes in the mitochondrial metabolome and lipidome indicated defects in choline biosynthetic pathways and remodelling of mitochondrial membranes, both consistent with SLC25A48 being a choline transporter. These results highlight the essential roles of specific SLC25 transporters in maintaining mitochondrial structure and function and show that of mitochondrial translation is sensitive to local concentrations of branched chain amino acids, methylated basic amino acids, ATP, magnesium, and choline.

overall_design: Total RNA from CAL51 cells were isolated from three control cells (WT) and three of each knockout (SLC25A44KO, SLC25A45KO, SLC25A48KO) and was sequenced and analysed for differential expression.

first: Aleksandra

last: Filipovska


title: A Cellular Basis for Heightened Gut Sensitivity in Females

city: San Francisco

first: Holly

middle: A

last: Ingraham

address: 1550 4th Street Rock Hall 284F

department: Cellular and Molecular Pharmacology

institute: University of California, San Francisco

summary: Visceral pain disorders, such as irritable bowel syndrome, exhibit a marked female prevalence. Enhanced signaling between enterochromaffin (EC) cells in the gut epithelium and mucosal sensory nerve fibers likely contributes to this sex bias. Here, we identify a novel estrogen-responsive paracrine pathway in which two enteroendocrine cell types, PYY-expressing L-cells and serotonergic EC cells, communicate to increase gut sensitivity in females. We demonstrate that ERα estrogen signaling upregulates the bacterial metabolite SCFA receptor Olfr78 on colonic L-cells, increasing PYY release and their sensitivity to acetate. Elevated PYY acts on neighboring EC cells via NPY1R, thereby enhancing serotonin release and gut pain. We propose that hormonal fluctuations, in conjunction with internal (stress) or environmental (diet) factors, amplify this local estrogen-responsive colonic circuit, resulting in maladaptive gut sensitivity.

overall_design: RNA-seq was performed on L-cells and EC cells isolated from colons of 10–14-week-old ovariectomized (OVX) female mice. L-cells were obtained from OVX Cck-Cre;R26LSL-tdTomato mice treated with sesame oil vehicle (VEH) or estradiol benzoate (EB) 4 hours prior to isolation. Approximately 7,000 L-cells were collected per treatment group (OVX + VEH and OVX + EB). EC cells were obtained from OVX ECFLTG mice treated with VEH or EB, with at least 500 EC cells isolated per sample and processed in the same manner.

first: Archana

last: Venkataraman

first: Eric

last: Figueroa

first: Joel

last: Castro

first: Fernanda

middle: M

last: Castro Navarro

first: Deepanshu

last: Soota

first: Stuart

last: Brierley

first: David

last: Julius


title: miRNA sequencing of exosomes generated from young and old muscle

city: Cardiff

first: NATHAN

last: HARMSTON

address: Museum Avenue

country: United Kingdom

institute: Cardiff University

summary: Sarcopenic muscles exhibit reduced EV secretion and altered EV cargoes, promoting cancer progression. Her we performed miRNA-seq of exosomes secreted by young muscle (12-week-old NOD/SCID mouse) and old muscle (>12 month old NOD/SCID old mouse) to identify miRNAs that are potentially involved in this process.

overall_design: miRNA-sequencing of Evs from young and old mouse muscle

first: Harmston

last: Nathan

first: Goh

last: Kah Yong

first: Tang

last: Hong-Wen


title: Tenascin C+ myofibroblasts exacerbate vascular neointimal hyperplasia by propagation of nerve-macrophage interactions

city: Shanghai

first: Guangzheng

last: Shi

state: Shanghai

address: No. 197 Ruijin 2nd Road, Huangpu District, Shanghai

institute: Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University

summary: Neointimal hyperplasia (NIH) is a major pathological feature of vascular injury, yet the underlying cellular and molecular drivers remain poorly understood. Here, we combine lineage tracing, single-cell transcriptomics, genetic mouse models and live imaging to identify a population of Tenascin C-expressing (Tnc+) myofibroblasts (MFs) that emerges in both a ligation-induced mouse model of carotid artery NIH and clinical NIH specimens.

overall_design: Carotid arteries from Tnc-cKO mice were harvested two weeks post vascular ligation. Arteries were enzymatically digested to single-cell suspension, and then scRNA-seq libraries were built with the 10x Genomics platform.

first: Qun

last: Li


title: Activating mutations in ESR1 contribute to an immunosuppressive breast tumor microenvironment.

city: Montreal

first: Alain

last: Pacis

state: QC

address: 1010 Sherbrooke #1800

country: Canada

institute: Canadian Centre for Computational Genomics (C3G)

summary: Estrogen receptor (ER, ESR1)-positive breast cancer patients are most at risk of long-term relapse, where activating somatic mutations in ESR1 promote metastasis and therapeutic resistance. ER+ patients are also disadvantaged in receiving and responding to immunotherapies, the mechanisms of which remain to be elucidated. Here, we engineered a novel transgenic mouse model carrying either Y541S or D542G point mutation in ESR1, mirroring the two most common mutations in ER+ metastatic breast cancer patients. End-stage ESR1mut tumors do not differ in the total number of immune cells yet display downregulation in immune-mediated pathways and decreased immune-modulatory cytokines, including IL-17a and IL-1b. Furthermore, T cells and macrophages have lower IFNγ activity and antigen presentation, respectively. Mechanistically, ESR1mut negatively regulates immune modulator expression compared to wild-type ESR1 and upregulates Stat5 to further dampen cytokine expression. In concordance, clinical validation on ESR1mut patient tumors shows decreased IL-17a and IL-1b. Collectively, our findings reveal that activating mutations in ER contribute to an immunosuppressive tumor microenvironment by dampening cytokine secretion and immune cell activity, supporting clinical observations where hormone receptor patients, especially ER mutant patients, respond poorly to immunotherapies.

overall_design: RNA-seq profiling MIC WT, MIC ESR1-Y541S, and MIC ESR1-D542G endpoint mammary tumors.

first: Yu

last: Gu

first: William

middle: J

last: Muller


title: Hypoxia-activated scleraxis a mediates epicardial progenitor differentiation into a unique cardiac perivascular cell type

first: Jingli

last: Cao

department: Cell & Developmental Biology

institute: Weill Cornell Medical College

summary: The epicardium is a crucial source of progenitor cells and paracrine signals that support heart development and regeneration. However, the molecular mechanisms that guide epicardial cell fate decisions remain incompletely understood. Here, we identify the transcription factor Scleraxis a (encoded by scxa) as a key regulator of epicardial progenitor differentiation in zebrafish. Through single-cell transcriptomics, genetic lineage tracing, and cardiac injury models, we show that scxa is transiently induced in activated epicardial progenitor cells (aEPCs) during both heart regeneration and developmental coronary angiogenesis. scxa+ epicardial cells primarily give rise to a previously uncharacterized cardiac population of perivascular cells marked by col18a1a, molecularly distinct from classical pericytes and vascular smooth muscle cells. We refer to this population as epicardial-derived perivascular mesenchymal cells (Epi-PMCs). These Epi-PMCs closely associate with coronary vessels and may contribute to vascular stabilization and remodeling, potentially through the anti-angiogenic but vessel-stabilizing activity of endostatin derived from collagen XVIII. Loss of scxa increases coronary vessel density. Mechanistically, we identify hypoxia and Hif1a signaling as upstream regulators of scxa, with systemic hypoxia or Hif factor stabilization robustly inducing scxa expression in the epicardium. Together, these findings uncover a hypoxia-responsive Scxa-Col18a1a axis that drives epicardial differentiation toward a vascular-supportive fate, offering new insight into the regulation of coronary vessel development and the regenerative potential of the epicardium.

overall_design: CUT&Tag of histone modification H3K4me1 of epicardial progenitor cells. Heart amputation surgery was performed on adult fish (6 months of age) carrying tcf21:nucEGFP and ptx3a:mScarlet reporters. Hearts were isolated at 3 days post injury together with the uninjured control (2 biological replicates each). Ventricles were digested and EGFP+ cells (uninjured) and EGFP+mScarlet+ (3 dpa) cells were isolated for CUT&Tag processing.

first: Jun

last: Yao

last: Xia


title: MiR-302 regulates pancreatic progenitor pool and pancreatic size [mRNA-seq]

city: Houston

first: Ziyue

last: Yang

address: 1 Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

summary: Disruptions in pancreatic development lead to health issues such as pancreatic agenesis and congenital diabetes mellitus. Understanding pancreatic organogenesis is critical for identifying disease mechanisms and developing regenerative therapies. The pancreas consists of endocrine and exocrine cells, both of which are derived from multipotent progenitor cells (MPCs). MPC proliferation and differentiation are tightly controlled by multiple mechanisms, including post-transcriptional regulation by miRNAs. However, these regulatory factors are not fully understood. Here, we profiled miRNA expression in MPCs and identified that miR-302 was highly enriched during the earliest stages of pancreatic development. Loss of miR-302 resulted in reduced pancreatic size without altering the proportions of endocrine and exocrine cells at E17.5, suggesting that miR-302 regulates MPC number rather than differentiation. Transcriptomic analysis at E10.5 revealed that miR-302 modulates genes involved in the Wnt signaling pathway and cell cycle progression. Notably, miR-302 prolonged S phase in MPCs, leading to slower cell proliferation and a smaller MPC pool at E10.5. These findings provide the first comprehensive miRNA profile during early pancreatic development and establish miR-302 as a critical regulator of MPC number and pancreas size.

overall_design: Pdx1-Cre, miR-302+/- animals were crossed with tdtomato, miR302+/- animals. Embryos were dissected at E10.5 and Pdx1-labelled cells were isolated from trunk region

middle: Z

first: Caroline

middle: G

last: Snider

first: Ronald

last: Parchem


title: Phage-encoded small RNA hijacks host replication machinery to support the phage lytic cycle

city: Urbana

first: Ido

last: Golding

address: 1110 W Green St.

department: Physics

institute: University of Illinois Urbana-Champaign

summary: Bacteriophages (phages) significantly influence bacterial populations in their natural environment. However, one aspect that has not been thoroughly explored in the context of phage-bacteria interactions is the post-transcriptional regulation of gene expression, despite the growing attention it has received for bacterial physiology over the last two decades. Important players in this process are small RNAs (sRNAs) that regulate target mRNAs via base-pairing, typically using RNA chaperones like Hfq to facilitate this regulation. Here, we apply RIL-seq, to map in-vivo the sRNA-RNA network in Escherichia coli upon lambda phage infection. We highlight changes in the bacterial transcriptome and sRNA interactome while uncovering a novel phage-encoded sRNA that regulates key genes in E. coli. We decipher the molecular mechanism of the sRNA-mediated regulation and illustrate how it hijacks the host replication machinery and helps the infection cycle. Overall, we uncover an RNA-level regulatory layer that shapes the E. coli - lambda interactions.

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

overall_design: Total RNA-seq was performed on E. coli MG1655 wild-type cells infected with phage lambda at high or low multiplicity of infection (MOI), or mock-infected with buffer, at multiple time points post-infection. As controls, libraries were similarly generated from uninfected MG1655 host cells and lambda lysogens. Two biological replicates were done for each condition.

first: Tianyou

first: Yuncong

last: Geng

first: Ehsan

last: Homaee

first: Susan

last: Born


title: Visualize and quantify rDNA instabilities in mammalian cells and mouse models

last: Liang

address: Yueyang Road 320

department: SIBCB

institute: CEMCS, CAS

summary: Ribosomal DNA (rDNA) encodes the 18S, 5.8S, and 28S RNA components of ribosomes, accounting for up to 70% of cellular transcription. Despite its central role in cellular function and known association with cancer and aging, quantifying rDNA instability in mammals remains challenging due to its repetitive organization and inherent heterogeneity. In this study, we developed murine rDNA FISH probes and genomic tools tailored for laboratory strains. The results confirmed the locations of rDNA clusters, uncovered marked inter-/intra-strain and inter-cell heterogeneity at rDNA loci in inbred mice and unstressed cells, and identified sources of spontaneous, replication-associated DNA double-strand breaks within rDNA. Focused mini-screens using DNA repair-deficient cells uncovered distinct contributions of homologous recombination, non-homologous end-joining, and the ATM-mediated DNA damage response in safeguarding rDNA stability. Together, these findings and tools provide a robust framework for assessing rDNA instability in mammalian cells and animal models with applications in aging and cancer research.

overall_design: Using RPA ChIP-seq in cytokine-activated B cells to identified recurrent, unidirectional DSBs in rDNA region.

first: Xiaolu

last: Zhu

first: Wenxia

last: Jiang

first: Wei

last: Wu

first: Brian J.

last: Lee

first: Demis

last: Menolfi

first: Anthony

last: Tubbs

first: Olivia

last: Cupo

first: Eli

last: Malkovskiy

first: Mattie

last: Nester

first: Xiaobin S.

last: Wang

first: Peter A.

last: Sims

first: Richard

last: Baer

first: Chyuan-Sheng

last: Lin

first: Lorraine

last: Symington

first: Andre

last: Nussenzweig

first: Brian

last: MsStay

first: Shan

last: Zha


title: An inflammatory and quiescent HSC subpopulation expands with age in humans

city: Boston

first: Ksenia

last: Safina

address: 4 Blackfan St

institute: Brigham and Women's Hospital

summary: Aging of the blood system impacts systemic health and can be traced to hematopoietic stem cells (HSCs). Despite multiple reports on human HSC aging, a unified map detailing their molecular age-related changes is lacking. We developed a consensus map of gene expression in HSCs by integrating seven single-cell datasets. This map reveals previously unappreciated heterogeneity within the HSC population. It also links inflammatory pathway activation (TNF/NFκB, AP-1) and quiescence within a single gene expression program. This program dominates an inflammatory HSC subpopulation that increases with age, highlighting a potential target for further experimental studies and anti-aging interventions.

overall_design:
Sternum bone marrow samples from young (<40 y.o.) and aged (>60 y.o.) individuals were analysed with scRNA-seq.
Bone marrow cells from nine donors were collected from the iliac crest of patients undergoing cardiac surgery under an excess sample banking and sequencing protocol that covers all study procedures and was approved by the Institutional Review Board (IRB) of Mass General Brigham. Donors were confirmed negative for common CHIP mutations using targeted sequencing. Mononuclear cells were isolated using Ficoll or lymphoprep and cryopreserved in liquid nitrogen storage. Cells were thawed using standard procedures, and viable (DAPI negative) cells were sorted on a Sony SH800 flow cytometer. Next, 10,000-15,000 cells were loaded onto a 10x Genomics chip. Further processing was done using the recommended procedures for the 10x Genomics 3’ v3.0, v3.1, or v4 chemistry. Libraries were sequenced on the NovaSeq SP 100 cycle with the following parameters (Read 1: 28 + Read 2: 75 + Index 1 (i7): 10 + Index 2 (i7): 10). Count matrices were generated using CellRanger v.7.1.0 with default settings and GRCh38 as the reference genome.

middle: R

first: Jonathan

last: Good

first: Peter

last: van Galen


title: Delayed transcriptional response of Daphnia pulex to thermal stress

city: West Lafayette

first: Nathan

last: Backenstose

state: Indiana

address: 915 Mitch Daniels Blvd

institute: Purdue University

summary: Changing global climates present threats to aquatic ecosystems with events such as heatwaves and prolonged increased temperatures altering habitats and affecting species survival. Aquatic organisms are particularly vulnerable to these elevated temperatures often due to a lack of suitable migration routes. A decrease in population abundance and survival in species occupying lower trophic levels may have cascading effects on the health of an ecosystem. In this study, we investigated the fitness (fecundity) and transcriptional response of Daphnia pulex, a common grazer in lentic freshwater systems, to sublethal temperature stress. D. pulex were exposed to control (20℃) and elevated sublethal (25℃) temperature to simulate an increased water temperature from a mild heat wave for 168 hours. Our findings indicate a dynamic transcriptional response to elevated temperatures. Notably, differential gene expression between the control and temperature-elevated treatment increased throughout the experiment with a three-fold increase in counts of DEGs at 168 hours as compared to 96 hours. D. pulex within the experimental treatment had higher mean cumulative offspring produced compared to the control treatment. Given D. pulex’s role as a foundational species in aquatic food webs, the observed transcriptional response provides insight into the potential for both plastic and adaptive responses in the face of environmental change.

overall_design: RNA-Seq profiling of Daphnia pulex reared at 20 and 25C at day 4 and day 7.

first: Backenstose

last: Nathan

first: Christie

last: Mark


title: Safeguarding Genome Integrity: Polo-like kinase Cdc5 and phosphatase Cdc14 Orchestrate Topoisomerase II-Mediated Catenane Resolution in Mitosis

city: Edinburgh

first: Lucia

last: Massari

address: 6.22 Michael Swann Building, Max Born Crescent

department: Discovery Research Platform for the Hidden Cell Biology, Institute of Cell Biology

institute: University of Edinburgh

summary: Resolution of sister chromatid intertwine in mitosis is vital for safeguarding genome integrity. While cohesin, condensin, the polo-like kinase Cdc5, and the phosphatase Cdc14 have all been implicated in this process, the underlying molecular mechanisms remain elusive. Our study unveils a coordination between spindle elongation and the timely resolution of DNA linkages orchestrated by Cdc14 and Cdc5. We show that Cdc14 and Cdc5 collaborate to facilitate the resolution of DNA catenanes, the predominant species of DNA intertwines in mitosis, by regulating Topoisomerase II (Top2) function, both through SUMOylation and via phosphorylation. Our findings contribute to unraveling a redundant mechanism wherein Cdc5 and Cdc14 work together to ensure the timely removal of all sources of cohesion between sister chromatids, thereby preserving the integrity of chromosome segregation and genome stability.

overall_design: Calibrated Top2-PK ChIP-seq for TOP2 cdc20, TOP2-PK cdc20, TOP2-PK cdc5 cdc14 S. cerevisiase strains arrested in metaphase (cdc20) in presence or absence of nocodazole, in or in minianaphase (cdc4 cdc15). S. pombe is used as calibration genome

first: Rosella

last: Visintin


title: Transcriptomic changes in the hypothalamus of gasping mice by high concentration of sevoflurane.

city: Toyama

first: Jun-Dal

last: Kim

state: Toyama

address: 2630 Sugitani

department: Department of Complex Biosystem Research (CBR), Institute of National Medicine (INM)

country: Japan

institute: University of Toyama

summary: Gasping respiration is a terminal pattern that occurs after anoxia effort in response to severe hypoxia, and has been known to increase the chances of survival in patients with cardiac arrest. During severe hypoxia, increased activity of upper airway muscles would be essential for self-resuscitation in association with gasping respiration. Previously, we reported that high concentration of sevoflurane, one of the volatile anesthetics, causes a gasping-like respiration pattern in mice. Herein, to extend understanding of the molecular mechanism involving the gasping respiration, we performed a comprehensive analysis of the changes in hypothalamic transcripts of sevoflurane-induced gasping mice.

overall_design: mRNA profiles of hypothalamic tissues were generated by RNA sequencing using the NextSeq 500 (Illumina).

first: Yoko

last: Irukayama-Tomobe

first: Koichiro

last: Tatsumi


title: Spaceflight induces systemic effects on extracellular matrix and immune system in different age-stages

city: Saarbrücken

first: Friederike

last: Grandke

address: Saarbrücken Campus

institute: Saarland University

summary: Spaceflights significantly impacts astronaut health, causing muscle atrophy, bone loss, cardiovascular deconditioning and immune system dysregulation, especially during long missions. To explore molecular changes, we generated a single-cell RNA sequencing dataset, of 216 samples from 28 mouse organs and tissues under spaceflight and control conditions. Since spaceflight effects closely resemble aspects of aging, we included two age groups (3 and 8 months) to assess age-related influences. Our data revealed that spaceflight drives age-independent systemic changes, primarily affecting tissue remodeling and alterations in cytoskeleton, membrane and extracellular matrix (ECM), particularly in endothelial cells. In contrast, aging has a weaker impact, mainly altering immune regulation in an age-dependent manner. These findings suggest that cytoskeletal and ECM changes may contribute to immune Dysregulation.

overall_design: We performed single-cell RNA-sequencing (scRNA-seq) on organ samples from four female Balb/C mice exposed to 40 days of spaceflight on the ISS, alongside four age-matched controls housed under identical conditions on earth (Figure 1A, 1B). Our study design incorporated two age groups, 3-months-old (young adult) and 8-months-old (mature adults), capturing the typical age range of astronauts. Three days after splashdown, the mice were taken down, and the tissues were immediately processed for single-cell RNA sequencing.

first: Nicholas

last: Schaum

first: Fabian

last: Kern

first: Jérémy

last: Amand

first: Thomas

last: Ambrosi

first: Teni

last: Anbarchian

first: Karl

last: Annusver

first: Reza

last: Ashrafi

first: Kruti

last: Calcuttawala

first: Shubhangi

last: Das Barman

first: Antoine

last: de Morree

first: Angela

last: Detweiler

first: Hala

last: Dhowre

first: Annika

last: Engel

first: Tobias

last: Fehlmann

first: Virginia

last: Ferguson

first: Matthias

last: Flotho

first: Astrid

last: Gillich

first: Michael

last: Haney

first: Yan

last: Hang

first: Pascal

last: Hirsch

first: Taichi

last: Isobe

first: Joanna

last: Kalucka

first: Maria

last: Kasper

first: Seung

last: Kluiver

first: Davis

last: Lee

first: Song

first: Olivia

last: Leventhal

first: Ling

last: Liu

first: Catriona

middle: Y

last: Logan

last: Lugo-Fagundo

first: Luca

last: Mannino

first: Maxim

last: Markovic

first: Maurizio

last: Morri

first: Shravani

last: Mukherjee

first: Norma

last: Neff

first: Patricia

last: Nguyen

first: Róbert

last: Pálovics

first: Weng

middle: C

last: Peng

first: Maksim

last: Plikus

first: Ermelinda

last: Porpiglia


title: MiR-302 regulates pancreatic progenitor pool and pancreatic size [miRNA-seq]

first: Ziyue

last: Yang

first: Caroline

last: Snider

first: Ronald

last: Parchem


title: Distinct chromatin regulators downmodulate meiotic axis protein deposition and DNA break induction at chromosome ends [TrAEL-Seq]

first: Andreas

last: Hochwagen

address: 24 Waverly Place

institute: New York University

summary: In many organisms, meiotic crossover recombination is suppressed near the extreme ends of chromosomes. Here we show that multiple, often chromosome-specific, suppressive mechanisms with differing ranges combine to achieve the consistently low enrichment of recombination-promoting axis proteins and downregulation of DNA double-strand breaks (DSBs) within 20 kb of telomeres in Saccharomyces cerevisiae. Suppression of axis proteins is associated with cis-encoded signals, including reduced coding density and the subtelomeric Y’ elements, which are present at many chromosome ends, but also requires chromatin modifiers, including the histone methyltransferase Dot1 and the Sir silencing complex. We show that Dot1 suppresses Sir complex activity at least in part independently of its canonical target, H3K79, to downmodulate axis protein deposition near chromosome ends. In parallel, the Sir complex, but not Dot1, suppresses the induction of DSBs by limiting the openness of promoters, the preferred sites of meiotic DSB formation. The separable downmodulation of axis protein deposition and DSB induction likely contributes to the robust reduction of meiotic recombination effectors near chromosome ends.

overall_design: ChIP-seq Analysis: Input and ChIP samples were prepared to assess the binding dynamics of meiotic and nonmeiotic factors. Each bedgraph file represents the results from Input and ChIP samples. To normalize SK1 reads between genotypes, 20% SK288C yeast spike-in controls were included.  mRNA-seq Analysis: RNA-seq was conducted to detect changes in transcription levels during meiosis in wild-type and mutant S. cerevisiae strains.  TrAEL-seq Analysis: Genome-wide DSBs were mapped during meiosis in S. cerevisiae wild-type and mutant strains using TrAEL-seq.

first: Adhithi

last: Raghavan

first: Kieron

last: May

first: Vijayalakshmi

last: Subramanian

first: Hannah

last: Blitzblau

first: Neem

last: Patel

first: Jonathan

last: Houseley


title: Integrative blood profiling uncovers inflammatory network signatures in high-altitude pulmonary edema

city: Delhi

first: Aastha

last: Mishra

state: Delhi

address: Mall Road, Delhi-110 007

department: Genomics and genome biology

country: India

institute: Council Of Scientific And Industrial Research–Institute Of Genomics And Integrative Biology (CSIR–IGIB)

summary: Despite the well-known role of hypoxia-driven inflammatory mediators in the pathogenesis of hypoxic pulmonary hypertension, their involvement in high-altitude (HA) illnesses, particularly high-altitude pulmonary edema (HAPE), remains unclear. The present study uses an integrated clinical, transcriptomic, proteomic, and long noncoding RNA (lncRNA) profiling of 83 individuals, including HAPE patients segregated into mild, moderate, and severe categories, HAPE-free sojourners, and long-term HA residents, to highlight the molecular and immunological changes associated with HAPE and its severity. Clinical assessments revealed significantly reduced peripheral oxygen saturation and elevated respiratory parameters in HAPE patients. Differential gene expression and functional enrichment analyses identified 515 significantly differentially expressed genes, with marked enrichment of inflammatory and hypoxia-associated pathways. Protein-protein interaction network analysis revealed eighteen hub genes, including toll-like receptor (TLR) 2 and Forkhead box O3 (FOXO3), with strong diagnostic potential. Immune cell deconvolution analysis and hematological profiling indicated a prominent increase in neutrophil proportion. Interestingly, oncostatin M (OSM), a hypoxia-regulated predominant cytokine produced by neutrophils, was revealed in the cytokine and transcriptomic profiling, highlighting its role in inflammation and extracellular matrix degradation. Co-expression network analysis notably revealed significant alterations that formed a gene module exhibiting a strong correlation with immune response, leukocyte adhesion, and ncRNA processing pathways. Interestingly, these co-expressed partners, LINC01093 and immune-regulatory genes like interleukin-18 receptor 1 and TLR5, appear to regulate the NF-κB signaling pathway, one of the positively enriched pathways in our analysis. Overall, this multiomics approach highlighted a strong inflammatory signature and lncRNA-mRNA interactions associated with HAPE.

overall_design: The study included 83 participants aged between 18 - 70 years and were classified into three distinct study groups: healthy HA sojourners or controls ( n=19), HAPE patients segregated into mild (n=15), moderate (n=13), and severe categories (n=14), and healthy highlanders (HLs, n=22). HAPE patients included sojourners from low-altitude regions (< 200 m) who traveled to Leh, Ladakh, and developed HAPE within 2 to 5 days of HA exposure. Healthy HA sojourners or controls included sojourners from low-altitude regions (< 200 m) who visited HA under similar conditions as the HAPE group but did not develop any HA related disorders. The HLs group comprised healthy individuals who are permanent residents of Leh, Ladakh, at the altitude of 3500m asl.

first: Kanika

last: Singh

first: Krishna

last: Kumar G

first: Manzoor

last: Ali

first: Raushni

last: Choudhary

first: Mohit

last: Khadia

first: Stanzen

last: Rabyang

first: Tashi

last: Thinlas

first: Rahul

last: Kumar


title: Distinct chromatin regulators downmodulate meiotic axis protein deposition and DNA break induction at chromosome ends [RNA-Seq]

city: New York


title: MicroRNAs shape mouse age-independent tissue adaptation to spaceflight via ECM and developmental pathways

first: Friederike

last: Grandke

summary: As human space exploration accelerates, understanding the organism-wide molecular effects of longer spaceflight in mammals becomes increasingly critical. Non-coding RNAs like miRNAs are key to regulating this landscape. We thus analyzed 686 small RNA samples of mice from 13 solid organs at 3 and 8 months of age, after at least 3 weeks on the ISS and compared them to earth-bound controls. We observed significant spaceflight effects in systemic tissue remodeling pathways along the Fat-Liver-Pancreas axis and in heart, brain, spleen and thymus. The MIR-17/92 and MIR-1/133 families drive distinct molecular changes through specific gene targeting. Age-dependent changes, smaller in magnitude compared to age-independent changes, primarily involved tissue remodeling through MIR-8, MIR-154 and MIR-15 families in MAT, pancreas, and diaphragm. Our findings provide evidence on how spaceflight regulates mammalian gene expression in preparation for interplanetary spaceflight.

overall_design: We sequenced 686 samples across 13 organs of young (3 months) and middle-aged (8 months) mice that were sent to the ISS (Flight). We compared them against mice living in standard conditions (Vivarium Ground Control) and mice living in an environment matched to ISS conditions (Habitat Ground Control). We euthanized mice at two time-points (matching timelines for controls and flight mice), one before returning to earth (TERM) and one after (LAR) in order to distinguish spaceflight-induced effects from the reentry-induced stress

first: Shusruto

last: Rishik

first: Viktoria

last: Wagner

first: Annika

last: Engel

first: Nicole

last: Ludwig

first: Kruti

last: Calcuttawala

first: Fabian

last: Kern

first: Verena

last: Keller

first: Marcin

last: Krawczyk

first: Louis

last: Stodieck

first: Virginia

last: Ferguson

first: Amanda

last: Roberts

first: Eckart

last: Meese

first: Nicholas

last: Schaum

first: Steven

last: Quake

first: Tony

last: Wyss-Coray


title: Genome wide DNA methylation of colon low grade and high grade adenoma

city: Besançon

first: Alexis

last: Overs

address: 16 route de Gray

country: France

institute: University of Franche-Comte

summary: Introduction: The dynamics of colorectal epigenetics during early carcinogenesis remain undocumented. In this study, we explore the DNA methylation dynamics in colorectal cancer oncogenesis from non-tumor colon tissues to low-grade, high-grade adenoma and adenocarcinoma.  Methods: The methylome of 13 low-grade and 19 high-grade colorectal adenomas was determined using the EPIC v1 Human Methylation Beadchip. These methylation profiles were complemented with the methylomes of 206 non-tumor colon and 24 colon adenocarcinomas from GSE149282, GSE132804 series and the HCMI study. Differentially methylated CpG were identified by Student's t-test and used to monitor the evolution of the colon methylome during carcinogenesis. The differentially methylated promoters were used to infer the associated biological process using gene ontology.  Results: 4.9% of the colon methylome is significantly altered (p < 10-4) during carcinogenesis with two thirds corresponding to DNA demethylation. 56.6% of the methylation changes occurs at the transition from non-tumor colon tissues to low-grades adenomas. 18.2% of the DNA methylation changes are transitory during low-grade and/or high-grade adenomas. The biological pathways sensory perception of odor and stimulus were early unmethylated, nervous system development and homophilic cell adhesion were early methylated, and chemical synaptic transmission and cell adhesion were transiently methylated.  Conclusion: This study provides insight into the dynamics of colonic epigenetics during carcinogenesis, with early DNA methylation changes in the low-grade adenomas associated with transient DNA methylation changes. However, the causality of these changes remains to be elucidated.

overall_design: We aimed to profile the colon methylome during oncogenesis. Tissue DNA was analyzed using the Infinium Methylation Epic v1 array in a cohort of 13 low-grade colon adenomas and 19 high-grade colon adenomas.

first: Jean-Paul

last: Feugeas

first: Zohair

last: Selmani

first: Paul

last: Peixoto

first: Eric

last: Hervouet

first: Chloé

last: Molimard

first: Laurent

last: Arnould

first: Frédéric

last: Bibeau

first: Jules

last: Durand


title: Distinct chromatin regulators downmodulate meiotic axis protein deposition and DNA break induction at chromosome ends [ChIP-Seq]

first: Andreas

last: Hochwagen

overall_design: ChIP-seq Analysis: Input and ChIP samples were prepared to assess the binding dynamics of meiotic and nonmeiotic factors. Each bedgraph file represents the results from Input and ChIP samples. To normalize SK1 reads between genotypes, 20% SK288C yeast spike-in controls were included.

first: Adhithi

last: Raghavan

first: Kieron

last: May

first: Vijayalakshmi

last: Subramanian

first: Hannah

last: Blitzblau

first: Neem

last: Patel

first: Jonathan

last: Houseley


title: RNA-seq analysis of gene expression profile of wildtype and Oxsr1 knockout HEK293T cells

city: Xiamen

first: Xiawei

last: Huang

state: Fujian

address: Xiang an nan lu 4221

institute: Xiamen university

summary: Our study aims to identify the potential signaling pathways regulated by osmosensor OXSR1. Animals activate regenerative processes to repair injuries and restore homeostasis following tissue damage. A central question in regeneration is how damage signals are sensed and translated into regenerative growth. Tissue injuries lead to the release of intracellular contents and bodily fluids and disturb osmotic balance. However, the role of osmolarity in regeneration remains largely unexplored. Using Drosophila and mouse intestine, and samples from inflammatory bowel disease (IBD) patients, we identify a key role for the osmolarity-sensing WNK-OXSR1 signaling pathway in intestinal regeneration. Mechanistically, upon intestinal injury, OXSR1 phosphorylates the RhoB GTPase at threonine 37, disrupting its interaction with ARHGAP17, increasing GTP-bound RhoB, enhancing F-actin polymerization, and activating YAP to drive regeneration. We further show that pharmacologically inhibiting WNK or OXSR1 reduces the oncogenic potential of intestinal regeneration. These findings reveal osmolarity as a critical damage signal in regeneration and position WNK-OXSR1 as a potential therapeutic target to promote intestinal repair.

overall_design: RNA was extracted using Trizol Reagent (Invitrogen) and purified using RNeasy Mini Kit (Qiagen) following the kit manual. Library construction, sequencing and bioinformatics analysis were performed by MegaGenomics Inc. (Beijing, China). The P value was calculated by Deseq2 (v1.26.0). The differentially expressed genes (DEGs) were defined as adjusted p-value < 0.05 and |log2(FoldChange)|>0.5 Three biological replicates were performed for WT and Oxsr1 KO HEK293T cells.

first: Bo

last: Liu

first: He ming

last: Cao

first: Xiaobing

last: Jiang

first: Jingrong

last: Deng

first: Chengfang

last: Wu

first: Jiahui

last: Wang


title: Endothelial transcription factor EB protects against doxorubicin-induced endothelial toxicity and cardiac dysfunction

city: Columbus

first: Wa

last: Du

state: OH

address: 460 West 12th Avenue, Biomedical Research Tower, Rm 360A

department: Department of Surgery, Division of Vascular Diseases and Surgery

institute: The Ohio State University

summary: Doxorubicin (DOX) has been demonstrated to induce cardiovascular toxicity in cancer survivors. Endothelial cell dysfunction is recoginized to play a critical role in the onset and severity of cardiotoxicity associated with DOX. Endothelial TFEB protects against EC damage and cardiac dysfunction. Cardiac single cells isolated from vehicle and doxorubicin treated wild type and EC-Tfeb Tg mice were collected for scRNA-seq analysis.

overall_design: Mouse heart tissues from male EC-Tfeb Tg mice and WT mice treated with DOX (5 mg/kg, iv, once a week) or vehicle for 2 weeks (n = 4-5 / group). Cardiac single cells isolated from wild type and EC-Tfeb Tg mice treated with vehicle or doxorubicin were collected for scRNA-seq analysis.

first: Yanbo

last: Fan


title: RNA sequencing on  liver samples from wild type C57BL/6J mice exposed to the vandetanib

city: Hangzhou

first: Wu

middle: Wen

last: Tong

state: Zhejiang

address: 866 Yuhangtang Road

institute: Zhejiang University

summary: Purpose: The aim of this study was to  demonstrate the hepatotoxicity mechanism induced by vandetanib. Methods: Liver mRNA profiles of C57BL/6J mice exposed to the vandetanib  were generated by RNA sequencing. Results: We analyzed the results of high-throughput transcriptome sequencing on liver samples from C57BL/6J mice exposed to the vandetanib and identified that vandetanib increased apoptosis-related genes expression apoptosis and  the JAK-STAT signaling pathway was significantly enriched.

overall_design: RNA was isolated from mice administered with CMC-Na or 100 mg/kg/day vandetanib using the TRIzol reagent (15596026, Invitrogen). The subsequent RNA sequencing (RNA-seq) was performed by LC-Bio.

first: Peihua

last: Luo

first: Hao

last: Yan

first: Wentong


title: Integrated meta-omics uncovering the mechanisms of Lactobacillus salivarius to improve Oreochromis niloticus intestine health

city: Chengdu

first: Ying

last: JP

address: No.17, Section 3, Renmin South Road

institute: sichuan University

summary: Oreochromis niloticus represents a critically important species in the aquaculture industry due to its economic significance. Probiotics used as feed additives are known to enhance the growth performance and health of tilapia. However, the underlying mechanisms by which these benefits are conferred remain poorly understood. Here, we demonstrate that Lactobacillus salivarius exhibits significant growth performance-enhancing effects when used as a feed additive. Utilizing multi-omics approaches, our results revealed that L. salivarius significantly modulates the composition and abundance of the intestinal microbiota. Bile acids, choline, and tryptophan were identified as pivotal factors in the microbial-mediated modulation of systemic metabolism. Additionally, we have delineated a single-cell atlas of the tilapia intestine for the first time, discovering that L. salivarius_01 increases the populations of intestinal epithelial cells, immune cells, and epithelial stem cells. A broad spectrum of developmentally relevant genes and pathways were found to be activated. This study significantly advances the application of probiotics in promoting sustainable aquaculture practices.

overall_design: Single-cell transcriptomics of tilapia gut tissues were determined for probiotic-treated and untreated groups, respectively.

first: Qilin

last: Zhang

first: Jianping

last: Ying


title: Multiomic ATAC + Gene Expression sequencing on E8.75 wild type and Nr6a1 null mouse embryos

city: Kansas City

first: Andrew

middle: Joseph

last: Price

state: MO

address: 1000 E. 50th Street

department: Computational Biology

institute: Stowers Institute for Medical Research

summary: Mouse embryos from 2 different litters were collected at E8.75. 3-4 Nr6a1 null embryos and 3-4 wild type embryos were pooled into one sample per genotype. Nuclei was then isolated using the 10X Genomics Nuclei Isolation Kit. Samples were then processed and analyzed using 10X Genomics Multiomic ATAC + Gene Expression single nuclei profiling.

overall_design: Two samples, each containing 3-4 embryos, were collected from 2 litters of E8.75 mouse embryos according to genotype and analyzed with 10 Multiomic ATAC + Gene Expression single cell profiling.

first: Emma

middle: L

last: Zajic

first: Paul

last: Trainor