title: Stem cell derived spinal cord chips reproduce disease biomarkers in sporadic ALS patients [snRNAseq]

first: Shaughn

last: Bell

state: CA

address: 8700 Beverly Blvd

department: Regenerative Medicine Institute

institute: Cedars-Sinai Medical Center

summary: Amyotrophic Lateral Sclerosis (ALS) is a fatal neurodegenerative disorder with complex origins. Familial monogenetic causes of ALS make up a small percentage of patients overall, and the cause of the majority of idiopathic (sporadic) form remains unknown. Frequently utilized for disease modeling, human induced pluripotent stem cell (iPSC)-derived motor neuron cultures lack cellular maturity in vitro and rarely recapitulate clinically relevant phenotypes of ALS. Microfluidic organ-on-chip systems enable co-culture of multiple disease-relevant cell types and enhance cellular maturity. Here, we describe the generation of spinal cord (SC)-chips from 8 sporadic ALS (sALS) patients and 10 non-diseased controls. Transcriptomic and proteomic analyses of SC-Chips revealed changes in expression of targets known to be disrupted in ALS patients. Particularly, intermediate filaments (IF) neurofilament heavy (NEFH), medium (NEFM), and light (NEFL) were upregulated in SC-Chips from sALS patients. Single nuclei RNAseq (sNucseq) of SC-Chips revealed two subpopulations of motor neurons and cell-specific changes related to ALS pathogenesis and mimicking conditions in vivo.

overall_design: iPSC-derived cells grown in organ-on-chip format (3D) or 96 well plate (2D).  Comparitive gene expression of cells from control and ALS patients.  Library preps were done in 3 batches. Each batch was run on a single 10x chip and prepped on a different day.

first: Deepti

last: Lall

first: Samuel

last: Sances

last: Workman

first: Briana

last: Ondatje

first: George

last: Lawless

first: Amanda

last: Woodbury

first: Dylan

last: West

first: Kareem

last: El-Ghazawi

last: Meyer

first: Nur

last: Yucer

first: Andrea

last: Matlock

first: Vineet

last: Viabhav

first: Jennifer

last: Van Eyyk

first: Clive

last: Svendsen


title: Stem cell derived spinal cord chips reproduce disease biomarkers in sporadic ALS patients [bulk RNAseq]

status: Public on Jun 24 2025

city: Los Angeles

country: USA

type: Expression profiling by high throughput sequencing

overall_design: iPSC-derived cells grown in organ-on-chip format or 96 well plate.  Some comparison of gene expression under flow vs no flow conditions.  Comparitive gene expression of cells from control and ALS patients.

first: Michael


title: Thyroid hormone, but not photoperiod, is a potent modulator of the chroroid plexus transciptome in the ewe

city: Nouzilly

first: Hugues

last: Dardente

address: INRA

department: INRAE - Centre Val de Loire

country: France

institute: INRAE

summary:
Three groups of adult ewes were initally submitted to short days. One group remained in short days (Short), the other two were transferred to long days - one was intact (Long), the other had been subject to thyroidectomy before the photoperiodic transfer (THX). At the end of the treatment (see Lomet et al 2018 CelMolLifeSci 75:905-918) ewes were killed and extracts from the choroid plexus (from lateral ventricles) were taken and analyzed.

Abstract: The photoperiodic control of seasonal functions requires the action of melatonin at the pars tuberalis of the pituitary and subsequent control of local thyroid hormone (TH) signaling by tanycytes lining the basolateral part of the third ventricle. Therefore, TH supply of tancytes through the cerebrospinal fluid (CSF) is central to photoperiodism and the choroid plexuses (CP), which produce the CSF, play a pivotal role. Here, the transcriptome of the CP of the lateral ventricles was established by RNAseq in ewes maintained under three experimental conditions: ewes exposed to a short photoperiod (SP), intact ewes submitted to an acute 3-week exposure to a long photoperiod (LP-Sham) and ewes thyroidectomized prior to the LP exposure (LP-THX). Statistical analysis of the data revealed 1169 genes impacted by photoperiod (SP vs LP comparison) and 575 genes sensitive to the TH status (LP vs LP-THX comparison). Even though twice as numerous as the genes impacted by TH, genes responsive to photoperiod comparatively displayed rather weak transcriptional changes associated with a lower statistical significance. In line with this, validation of a few candidate DEG by RT-qPCR confirmed the impact of the TH status, but not that of photoperiod. We further showed that the expression level of the melatonin MT1 receptor is at best very low in the ewe CP, which provides a functional rationale for the lack of impact of photoperiod. In conclusion, while the CP is responsive to TH, which it provides to distant target tissues through the CSF, it is unlikely to be a major target of melatonin.

overall_design: The study was performed in 24 ewes - 8 per group (except THX - 7 ewes). RNA was individually extracted from each sample of choroid plexus. Then, 6 equimolar pools were prepared by mixing RNA from 3-4 individuals for each condition (i.e. duplicate for each condition).

first: Didier

last: Lomet

first: Olivier

last: Lasserre

first: Anne-Alicia

last: Gonzalez

first: Xavier

last: Mialhe

first: Juliette

last: Cognié


title: The effects of Baz2b-knockout on doxorubicin-induced cardiotoxicity

city: Shanghai

first: Fei

last: Xu

state: Shanghai

address: 1609 Xietu Road

country: China

institute: Zhongshan Hospital, Fudan University

summary: The study used wild type (WT) and Baz2b-knockout (KO) mice to establish a subacute doxorubicin (DOX)-induced cardiotoxicity model by intraperitoneal injection for 6 times in 2 weeks. Mice injected with equivalent PBS were used as the control group.

overall_design: Wild type (WT) and Baz2b-knockout (KO) mice were intraperitoneally injected with doxorubicin (DOX) for 6 times in 2 weeks to induce subacute cardiotoxicity. Mice injected with equivalent PBS were used as the control group.

first: Tongtong

last: Zang


title: An organ-chip model of sporadic ALS using iPSC-derived spinal cord motor neurons and an integrated blood-brain-like barrier

first: Shaughn

last: Bell

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

overall_design: Refer to individual Series


title: Keratin15 Regulates Cell Proliferation in Outer Enamel Epithelium

city: Sendai

first: Yuta

last: Chiba

state: Miyagi

address: 4-1 Seiryo-cho, Aoba-ku

country: Japan

institute: Tohoku University

summary: The keratins are the typical intermediate filament proteins of epithelia, presenting with highly specific expression patterns related to the epithelial type and stage of cellular differentiation. They are important for the cytoplasmic stability and integrity of epithelia, and also involved in various intracellular signaling pathways. Several keratins have been proved to be associated with enamel formation. However, there is still lack of information on the expression patterns of keratins during tooth morphogenesis. In the present study, we analyzed the spatiotemporal expression of the keratin family members using cap analysis gene expression and single-cell RNA-sequence analysis, revealing that Krt15 and Krt17 were not only highly expressed during tooth development, but also specifically expressed in non-ameloblasts. Immunostaining of both embryotic and postnatal mouse tooth germs showed that keratin 15 was mostly expressed in outer enamel epithelium, whereas keratin 17 was mainly found in stratum intermedium. Microarray analysis discovered that a core set of proliferation related genes were upregulated in Krt15-knockdown dental epithelial cells. The results of both CCK8 assay and EdU staining indicated that the loss of keratin 15 resulted in a higher cell proliferation activity. Our findings suggested that Krt15 could be a marker gene of outer enamel epithelium, and might take a part in regulating cell proliferation of dental epithelial cells.

overall_design: The mouse cervical loop-derived dental epithelial cell line CLDE was  transfected with ON-TARGETplus non-targeting control siRNAs or siKrt15 for 72h. Gene expression was analyzed.

first: Tian

last: Tian

first: Xin

last: Wang

first: Hiroshi

last: Sato

first: Fu

last: Yao

first: Keigo

last: Yoshizaki

first: Satoshi

last: Fukumoto


title: Whole genome sequencing of ccrZ-, yabA::cat, and ccrZ- yabA::cat in Bacillus subtilis.

city: Ann Arbor

first: Lyle

middle: A.

last: Simmons

state: MI

address: 1105 N. University Ave.

department: Molecular, Cellular, & Developmental Biology

institute: University of Michigan

summary: We obtained whole genome sequencing data as a measure of chromosome replication to see the effects of combining ccrZ deletion with yabA deletion, as well as the effect of making a phosphotransferase dead ccrZ

first: Katherine

middle: J

last: Wozniak


title: CRISPR screens uncover CRTC3 as a regulator of IFN-γ induced ferroptosis in hepato-cellular carcinoma [RNA-seq]

city: Beiing

first: TAO

last: XING

state: Beiing

address: Beiing

institute: Peking University Cancer Hospital

summary: Gamma interferon (IFN-γ) was reported to exhibit anti-tumor effects via inducing ferroptosis. Based on genome-wide CRISPR/Cas9 knockout screens, we discovered that cAMP response ele-ment binding protein (CREB) regulated transcription coactivator3 (CRTC3) protects tumor cells from drug induced ferroptosiis and is a significant resister of IFN-γ treatment in hepatocellular car-cinoma (HCC). Mechanically, CRTC3 knockout alters tumor cell lipid pattern and increases the abundance of polyunsaturated fatty acids (PUFAs), which facilitates lipid peroxidation and renders HCC cells susceptible to ferroptosis inducers. To scavenge accumulated lipid peroxides (LPO) and maintain redox equilibrium, HCC cells upregulate SLC7A11 expression to enhance the activity of glutamate-cystine antiporter (system xc-). As IFN-γ inhibiting system xc-, simultaneously treatment of IFN-γ disrupts the compensatory mechanism, and generates a synergistic effect with CRTC3 knockout to facilitate ferroptosis. The sensitizing effect of CRTC3 depletion was further confirmed in typical ferroptosis inducers including RSL3, Erastin and Sorafeinib. Here, we reported a hitherto unexpected role of CRTC3 in regulating PUFAs metabolism and ferroptosis. Targeting the CRTC3 signaling in combination with ferroptosis inducers may represent a viable approach to treat cancer and overcome drug resistance in HCC.

overall_design: To gain biological insight into global transcriptome affected by CRTC3 knockout, we per-formed RNA sequencing (RNA-seq) analysis in Hep3B-CRTC3-KO and Hep3B-vehicle cells.

first: Li

last: Li

first: Tao

last: Xing

first: Yiran

last: Chen

first: Jun

last: Liang

first: Xiubao

last: Ren


title: Whole genome sequencing of overexpressed ccrZ and overexpressed ccrZ-D166A in Bacillus subtilis.

summary: We obtained whole genome sequencing data as a measure of chromosome replication to see the effects of a phosphotransferase dead ccrZ (amyE::Pxyl-ccrZ-D166A, ccrZ-)

overall_design: Overexpressed ccrZ and overexpressed ccrZ-D166A in Bacillus subtilis


title: CRISPR screens uncover CRTC3 as a regulator of IFN-γ induced ferroptosis in hepato-cellular carcinoma


title: Affinity-based controlled release of interleukin-4 from scaffolds via biotin-avidin interactions for immunomodulation

status: Public on Jun 23 2025

city: Philadelphia

first: Kara

last: Spiller

state: Pennsylvania

address: 3141 Chestnut Street, Bossone 718

institute: Drexel University

summary: Abstract: Controlled release of immunomodulatory cytokines like interleukin-4 (IL-4) from biomaterials can modulate host immune cell behavior to improve tissue integration, however options for modifying complex biomaterials remain limited. Bioconjugation strategies using biotin-avidin interactions offer a promising approach since biotin can be conjugated to proteins, biomaterials, and even cells, without compromising their function. Although it is known that conjugation of biotin to large biomolecules reduces its binding affinity for avidin and avidin variants, the potential to control release of biotinylated molecules via leveraging affinity interactions has not been thoroughly investigated. Moreover, the effects of biotin and avidin variants on innate immunity are poorly understood. Therefore, the goal of this study was to determine if biotin-avidin interactions could be manipulated to control the release of IL-4 from biomaterials and to investigate the subsequent effects on primary human macrophage phenotype. First, we characterized the effects of soluble biotin, avidin, and avidin variants, streptavidin and CaptAvidin, on the phenotype of primary human macrophages using RNA sequencing and found that CaptAvidin significantly influenced macrophage gene expression while other variants did not. Then, after evaluating how bioconjugation parameters influenced biotin density and avidin variant binding to porous gelatin scaffolds, we found that biotin-avidin affinity interactions influenced the spontaneous release of biotinylated IL-4 (bIL-4) from biotinylated and desthiobiotinylated scaffolds bound with either avidin or streptavidin for up to ten days in vitro. Finally, we measured the response of primary human macrophages (8 donors) cultured on modified scaffolds, finding an increase in IL-4 driven genes when bIL-4 was released via biotin-streptavidin affinity interactions compared to desorption-based release. These results highlight how biotin-avidin interactions can be leveraged for spontaneous release to achieve an immunomodulatory drug delivery system.

overall_design: RNA-seq profile of primary human macrophages from 4 male and 4 female donors treated with soluble biotin, avidin, stretpavidin, or CaptAvidin for 24 hours on day 5 of culture

first: Victoria

last: Nash

first: Juan

last: Cortes-Troncoso

first: Phoebe

last: Chua


title: CRISPR screens uncover CRTC3 as a regulator of IFN-γ induced ferroptosis in hepato-cellular carcinoma [CRISPR screen]

overall_design: we conducted genome-scale CRISPR/Cas9 knockout screens using HCC cells under stimulation of IFN-γ, and identified CRTC3 as a critical mediator of IFN-γ resistance.


title: Drug and single-cell gene expression integration identifies sensitive and resistant glioblastoma cell populations [RNA-Seq]

city: Washington, DC

first: Nagi

last: Ayad

state: District Of Columbia

address: 3970 Reservoir Rd NW

department: Department of Oncology

institute: Georgetown University

summary: Glioblastoma (GBM) remains the most common and lethal adult malignant primary brain cancer with few treatment options. One of the most significant issues hindering GBM therapeutic development is intratumor heterogeneity. GBM tumors consist of multiple neoplastic cell types with distinct transcriptional profiles. Identifying compounds that target these different cell types requires a platform that predicts differential sensitivity and resistance of cells within GBM tumors. To address this, we developed a novel framework to generate tumor cell-type-specific disease signatures and their predicted drug sensitivity. We performed single-cell RNA sequencing of newly diagnosed and recurrent GBM tumors and identified compounds from the LINCS L1000 database with transcriptional response signatures selectively discordant with distinct single-cell transcriptional states within GBM tumors. We then validated in silico predictions with in vivo findings in mice as the aurora kinase inhibitor alisertib induced a shift from NPC-like to MES-like transcriptional states upon treatment. To allow other investigators to predict selective tumor cell type drug sensitivity in silico we developed a platform termed ISOSCELES (Inferred cell Sensitivity Operating on the integration of Single-Cell Expression and L1000 Expression Signatures).  Our studies suggest that ISOSCELES is a novel platform to identify cell populations that are sensitive and resistant to targeted therapies in GBM, which can inform treatment decisions in future clinical trials.

overall_design: RNA sequencing of GBM8 PDX Cells (Mayo Clinic) treated with DMSO, 100nM CT-179, or 200nM CT-179.

middle: G

first: Robert

middle: K

last: Suter


title: The Tumor Microenvironment Imposes Persistent ATF4 in CD8+ TILs to Obstruct Cancer Control

city: Chapel Hill

first: Office of Genomics Research

last: UNC Lineberger Comprehensive Cancer Center

state: NC

address: 125 Mason Farm Road, CB #7599 5105-5106 Marsico Hall

institute: University of North Carolina at Chapel Hill

summary: The T cell-intrinsic element that responds to tumor microenvironment (TME) stress to shape CD8+ tumor infiltrating lymphocyte (TIL) fate and function in solid cancers remains elusive. Here we report that the hypoxic TME imprints persistent activity of the central transcriptional node of the integrated stress response (ISR), activating transcription factor 4 (ATF4), in CD8+ TILs that results in metabolic polarity, mitochondrial oxidative stress, and cell death. Chronic ATF4 expression replicated the terminal exhaustion cell state in CD8+ T cells and high Atf4 expression in bulk tumor or peripheral T cells of patients with melanoma predicted poor response to PD-1 inhibition. Genetic or pharmacologic attenuation of ATF4 reduced mitochondrial oxidative stress and promoted viability among CD8+ TILs, enabling complete responses to PD-1 inhibition and conferring protection from re-emergent disease. Our multidisciplinary approach identifies chronic ATF4 activity as a barrier to immune checkpoint inhibitors, positioning ISR therapeutics as novel treatment strategies to improve efficacy of immunotherapy combinations.

overall_design: RNA-seq data from CD8+ T cells isolated from spleens of naïve ATF4Tg/Tg or E8IcreATF4Tg/Tg mice

first: Coral del Mar

last: Alicea Pauneto

first: Brian

middle: P

last: Riesenberg

first: Evelyn

last: Gandy

first: Andrew

middle: S

last: Kennedy

first: Genevieve

middle: T

last: Clutton

first: Jessica

middle: W

last: Hem

first: Katie

middle: E

last: Hurst

first: Elizabeth

last: Hunt

first: Jarred

middle: M

last: Green

middle: C

last: Miller

first: Steven

last: Angus

first: Gary

middle: L

last: Johnson

last: Esther

first: Jennifer

last: Guerriero

first: Peng

last: Gao

first: David

middle: R

last: Soto-Pantoja

last: Ferris

last: Modliszewski

first: Michael

middle: F

last: Coleman

first: H

last: Kay Chung

first: Justin

last: Milner

first: Stergios

last: Moschos

first: R

last: Wiseman

last: Thaxton


title: Comparative transcriptomics across photoperiod in the Siberian hamster and Japanese quail brains

city: Glasgow

first: Tyler

last: Stevenson

address: Jarret Building

department: School of Biodiversity, One Health, and Comparative Medicine

country: United Kingdom

institute: University of Glasgow

summary: Seasonal morphological brain plasticity plays a key role in driving adaptive behavioural responses. Structural changes in the brain including the hippocampus and amygdala (nucleus taeniae in birds), across photoperiods are thought to underlie seasonal shifts in emotional state. For humans, this includes manifestations of short photoperiod seasonal affective disorder (SAD). While morphological brain changes are well documented, the associated transcriptomic dynamics remain poorly understood. Here, we examined the transcriptomes of the hippocampus and amygdala or nucleus taeniae in two highly photoperiodic species, the Siberian hamster (Phodopus sungorus) and the Japanese quail (Coturnix japonica), to identify transcriptomic changes underpinning seasonal shifts in emotional state. Hamsters and quail exhibited robust physiological changes between long and short photoperiod treatment. Under short photoperiod, hamsters displayed anxiety-like behaviour (increased grooming) in the open field test, consistent with a SAD-like phenotype. Transcriptomic analysis of the amygdala in hamsters identified 76 significantly differentially expressed (DE) transcripts (including transthyretin, TTR) and prolactin receptor, PRLR as differentially expressed, but not significantly. In the quail nucleus taeniae, we found 54 DE transcripts (including tenascin-C, TNC). In the hamster hippocampus, 14 DE transcripts were found, including mahogunin ring finger-1 (MGRN1), and 31 in the quail hippocampus, including eyes absent-2 (Eya2). These findings provide novel insights into the transcriptomic mechanisms underpinning seasonal affective states and suggest conserved roles for prolactin and thyroid hormone signalling in mediating seasonal changes in physiology and affective behaviour, particularly in the Siberian hamster.

sample_organism:
Phodopus sungorus
Coturnix japonica

platform_organism:
Phodopus sungorus
Coturnix japonica

overall_design: Oxford Nanopore RNA-sequencing files for hippocampus and amygdala brain tissue for Japanese quail and Siberian hamsters held under a long (16L:8D) or short (8L:16D) photoperiod (day length). Adult male Japanese quail (Coturnix japonica) were maintained in photoperiodic, temperature-controlled rooms (390 (l) x 400 (w) x 250 (h) cm) at 27 °C and 39 % relative humidity (at the National Avian research Facility (NARF) Roslin Institute, The University of Edinburgh. Rooms were illuminated by Aquaforce Pro/AQFPRO S LED 4300 - 840, providing 25 - 30 lux at floor level. The quail were kept in pens with wooden frames and wire mesh walls (175 (l) x 128 (w) x 195 (h) cm) containing deep litter (wooden shavings, Stevenson Brothers Avonbridge, U.K.) and furniture (wooden logs, boxes, and perches) enrichment. Food (quail breeder diet; Target Feeds U.K.) and water was provided ad libitum and was replenished daily. Male quail (n = 12) were held on a long photoperiod (18L:6D), for 6 weeks and either remained on 18L:6D (n = 5) or were transferred to a short photoperiod (6L:18D, n = 6) for 4 weeks.  Adult male Siberian hamsters (Phodopus sungorus), were singly housed in polypropylene cages in the Veterinary Research facility at the University of Glasgow (PPL PP5701950). Hamsters were provided with rodent chow (SDS [BK001]) and cool tap water ad libitum, as well as cotton wool and cardboard tubes for enrichment and housing. The hamsters (n=12) were either housed in long photoperiod (16L:8D, n = 6) or initially housed in long photoperiod then transferred to short photoperiod (8L:16D, n = 6) for 12 weeks. Hamsters were age-matched where possible, to between 9 and 14 months at the time of collection, to account for age effects on photoperiod manipulation. After 12 weeks, animals were killed using cervical dislocation, and whole brains were collected onto dry ice.

first: Timothy

middle: A

last: Liddle

first: Calum

last: Stewart

first: Jonathan

middle: H

last: Pérez

first: Simone

last: Meddle


title: Injury-induced niche factors Cxcl12 and Shh/Ihh coordinate suture stem cell activation during calvarial bone regeneration

city: Boston

first: Yuchen

last: Liu

state: Massachusetts

address: 188 Longwood Avenue, REB 514B

institute: Harvard school of dental medicine

summary: Suture stem cells (SuSCs) are important for homeostasis and regeneration of cranial bone and can be used as a model to understand stem cell regulation for bone regeneration at a distance. Using a mouse cranial bone injury model, we identified the chemokine Cxcl12 and the Hedgehog family ligands Shh and Ihh as injury-induced interacting niche factors that coordinately regulate Gli1+ SuSC expansion, directional migration,and osteoblastic differentiation. Cxcl12 increased in the early inflammatory phase after injury, and Cxcl12-mediated activation of its cognate receptor, Cxcr4, in Gli1+ SuSCs promoted bone regeneration by stimulating SuSC proliferation and migration. Cxcl12-Cxcr4 signaling induced Shh and Ihh expression, which promoted Gli1+ SuSC proliferation and osteoblastic differentiation.

overall_design: RNA-seq was profiled of the cranial suture tissues, including coronal, sagittal, and lambdoid sutures of new-born wildtype mouse pups.

first: Takehito

last: Ochi

first: Bo

last: Li

first: Yingzi

last: Yang


title: Mechanobiological proximal tubular defects in ARC syndrome: A VPS33B CRISPR knockout study

city: London

first: Maria

last: Caluianu

address: Gower Street

institute: University College London

summary: ARC syndrome (arthrogryposis-renal dysfunction-cholestasis) is a rare autosomal recessive multisystem disorder affecting the kidneys. The disease is caused by mutations in either VPS33B or VIPAS39. ARC syndrome is currently incurable, with patients rarely surviving beyond their first year of life. The renal component of this disorder is characterised by proximal tubular dysfunction. Here, a proximal tubular cell line, RPTEC-TERT1, was CRISPR-edited to knock out (KO) VPS33B expression. Characterisation of VPS33B-KO cells was performed using brightfield imaging, immunostaining, RNA sequencing, and cell detachment assays. The VPS33B-KO RPTEC-TERT1 cells demonstrated a 'peeling' phenotype and altered cell adhesion. This, along with altered transcription of genes associated with cell adhesion, suggests that VPS33B KO results in cell-matrix attachment defects. These findings provide the first insights into the cause of proximal tubular dysfunction in ARC syndrome.

overall_design: RNA-seq profiling of control RPTEC-TERT1 (with wild-type VPS33B) cells and two VPS33B-knockout RPTEC-TERT1 clones (KO1 and KO2)

first: Kimberley

last: Owen


title: Nerve-associated macrophages control adipose homeostasis across lifespan and restrain age-related inflammation

city: New Haven

first: Vishwa

middle: Deep

last: Dixit

state: CT

address: 310 Cedar Street, BML330

department: Pathology

institute: Yale School of Medicine

summary: Age-related inflammation or ‘inflammaging’ is a key mechanism that increases disease burden and may control lifespan. How adipose tissue macrophages (ATMs) control inflammaging is not well understood in part because the molecular identities of niche-specific ATMs are incompletely known. Using intravascular labeling to exclude circulating myeloid cells and subsequent single-cell sequencing with orthogonal validation, we define the diversity and alterations in niche resident ATMs through lifespan. Aging led to depletion of vessel-associated macrophages (VAMs), expansion of lipid-associated macrophages (LAMs), and emergence of a unique subset of CD38+ age-associated macrophages (AAMs) in visceral white adipose tissue (VAT). Interestingly, CD169+CD11c- ATMs are enriched in a subpopulation of nerve-associated macrophages (NAMs) that declines with age. Depletion of CD169+ NAMs in aged mice increases inflammaging and impairs lipolysis suggesting that they are necessary for preventing catecholamine resistance in VAT. These findings reveal specialized ATMs control adipose homeostasis and link inflammation to tissue dysfunction during aging.

overall_design: Stromal vascular fraction (SVF) cells were isolated via enzymatic digestion of visceral white adipose tissue (VAT) from young (2-month) and aged (21-month) WT C57B/6J male and female mice. Adipose tissue macrophages (ATMs) residing in the tissue parenchyma (CD45+CD45.2iv-CD3-CD19-SiglecF-F4/80+CD11b+) were isolated by fluorescence-activated cell sorting (FACS) and analyzed using scRNA-seq.

first: Elsie

last: Gonzalez-Hurtado

first: Claire

last: Leveau

middle: D


title: Splicing of erythroid transcription factor is associated with therapeutic response in myelodysplastic syndromes [ChIP-Seq]

city: Bronx

first: Kith

last: Pradhan

state: ny

address: 1300 Morris Park Ave

institute: Einstein College of Medicine

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Anemia is the primary clinical manifestation of myelodysplastic syndromes (MDS), but the molecular pathogenesis of ineffective erythropoiesis remains incompletely understood. Luspatercept, an activin receptor 2B (ACVRIIB-Fc) ligand trap, has been approved to treat anemia, however its molecular mechanism of action is unclear. We found that the ACVR2B, its ligand GDF11, and effector, SMAD2, are upregulated in MDS patient samples. GDF11 inhibited human erythropoiesis in vitro and caused anemia in zebrafish, effects that were abrogated by luspatercept. Upon GDF11 stimulation of human erythroid progenitors, SMAD2 binding occurred in the erythroid regulatory regions, including at GATA1 intron. Intronic SMAD2 binding led to skipping of exon 2 of GATA1, resulting in a shorter, hypomorphic isoform (GATA1s). CRISPR deletion of the SMAD2 binding intronic region decreased GATA1s production upon GDF11 stimulation. Expression of gata1s in a mouse model led to anemia, rescued by a murine ActRIIB-Fc (RAP-536). Finally, RNA-seq analysis of samples from the Phase 3 MEDALIST trial revealed that responders to Luspatercept had a higher proportion of GATA1s compared to non-responders. Moreover, the increase RBCs post-treatment was linked to a relative decrease in GATA1s isoform. Our study indicates that GDF11-mediated SMAD2 activation results in an increase in functionally impaired GATA1 isoforms, consequently contributing to anemia and influencing responses to Luspatercept in MDS.

overall_design: A total of 25 million cells were treated with GDF11 and TGF-β1. After a 2-hour treatment, the cells were pelleted at 350 x g for 15 minutes at 4°C. They were then washed once with ice-cold PBS. The following steps were followed using the Diagenode HighCell ChIP Kit (Cat# C01010060), according to the manufacturer's protocol.

first: Srinivas

last: Aluri

first: Amit

last: Verma


title: Glucagon controls obesity-specific energy expenditure via persistent cAMP/PKA signaling

city: Zurich

first: Genome

last: Informatics

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich (FGCZ)

country: Switzerland

institute: ETH ZURICH / University of Zurich


title: Chromatin occupation changes associated with IRF4 silencing

city: Rochester

first: Surendra

last: Dasari

state: MN

address: 200 First Street SW

department: Quantitative Health Sciences Research

institute: Mayo Clinic

summary: TMD8 cells were treated with either shIRF4 or control shRNA. Cells were lysed and the DNA was subjected to ATAC-sequencing to assess the changes in chromatin occupation.

overall_design: TMD8 cells treated with shIRF4 or scrambled shRNA

first: Mondello

last: Patrizia

first: Dasari

last: Surendra


title: Activation of a bacterial flow sensor by stimulated neutrophils

city: Irvine

first: Albert

last: Siryaporn

address: 4129 Reines Hall

institute: University of California Irvine

summary: RNA-seq profiling of wild-type Pseudomonas aeruginosa (PA14) and the ΔfroR mutant strain under the stimulation of NaOCl, hydrogen peroxide, or untreated.

overall_design: Mid-exponential strains cultured in MinA medium were treated with 1 µM NaOCl, 4 µM H2O2, or untreated for 30 minutes and processed using the NucleoSpin RNA kit. Libraries were prepared using the NEBNext rRNA Depletion kit and NEBNext Ultra II Directional Library kit (NEB) and sequenced using a Illumina NovaSeq X Plus. Data were processed using Trimmomatic, Bowtie2, Subread, and DeSeq2.

first: Ilona P.

last: Foik

first: Runhang

last: Shu

first: Serena

last: Abbondante

first: Summer

middle: J

last: Kasallis

first: Lauren

last: Urban

first: Andy

last: Huang

first: Leora

last: Duong

first: Michaela

last: Marshall

first: Eric

last: Pearlman

first: Timothy

last: Downing


title: STAMP: Single-Cell Transcriptomics Analysis and Multimodal Profiling through Imaging [CosMx Spatial]

city: Memphis

first: Jasmine

last: Plummer

state: TN

address: 262 Danny Thomas Pl

department: Developmental Neurobiology

institute: St. Jude Children's Research Hospital

summary: Single-cell RNA sequencing (scRNA-seq) has revolutionized our understanding of cellular diversity, but remains constrained by scalability, high costs, and the destruction of cells during analysis. To overcome these challenges, we developed STAMP (Single-Cell Transcriptomics Analysis and Multimodal Profiling), a highly scalable approach for the profiling of single cells. By leveraging transcriptomics and proteomics imaging platforms, STAMP eliminates sequencing costs, enabling single-cell genomics of hundreds to millions of cells at an unprecedented affordability. Immobilizing (‘stamping’) cells in suspension onto imaging slides, STAMP supports single-modal (RNA or protein) and multimodal (RNA, protein and H&E) profiling, while retaining cellular structure and morphology. Its flexible, ultra-high-throughput formats facilitate the analysis of single or multiple samples in the same experiment, enhancing experimental scalability and adaptability. We demonstrate STAMP's versatility across diverse experimental contexts, including the profiling of peripheral blood mononuclear cells (PBMCs), cell lines and stem cells. We also stamped cells and nuclei from dissociated tissues from mouse organs to simulate the generation of cell atlases. Accessibility was further enlarged by analyzing nuclei from archival formalin fixed and paraffin embedded (FFPE) tissue samples. Combining RNA and protein profiling, we applied STAMP for high-throughput immuno-phenotyping of millions of blood cells, providing multimodal insights into cellular heterogeneity. We highlight the capability of STAMP to identify ultra-rare cell populations, simulating clinical applications for detecting circulating tumor cells (CTCs). By capturing lineage dynamics during stem cell differentiation and subtle changes in in vitro activated PBMCs, we further showed its utility for large-scale perturbation studies. These results validate STAMP as a first-of-its-kind single-cell imaging analysis strategy. We present data for 10,962,092 high quality cells/nuclei and 6,030,429,954 high quality transcripts. By replacing sequencing with imaging, STAMP enables high-resolution cellular profiling that is more accessible, scalable, and cost-effective. STAMP has the potential to transform our ability to map biological diversity and dynamics, significantly advancing research and clinical applications.

overall_design: In this study, we transformed four advanced imaging platforms—Xenium Analyzer (10X Genomics), CosMx Spatial Molecular Imager (NanoString Technologies/Bruker), MERSCOPE (Vizgen), and PhenoCyler Fusion (Akoya Biosciences)—into scalable, flexible single-cell profiling tools. We termed this approach Single-Cell Transcriptomics Analysis and Multimodal Profiling (STAMP) through imaging.    STAMP leverages single-molecule imaging to analyze hundreds to millions of individual cells with unprecedented flexibility and scalability. The platform supports both single-modal (RNA or protein) and multimodal (RNA, protein, and H&E) profiling in single- or multi-sample configurations. We validated its performance across diverse sample types and experimental conditions, comparing its quality control metrics to classical single-cell analysis methods.    To assess scalability, STAMP was applied to cell populations ranging from hundreds to millions, demonstrating adaptability to varying sample sizes. It successfully profiled both whole cells and nuclei (from fresh-frozen and FFPE samples), enabling the analysis of archival tissues. Functional applications included:    -Immunophenotyping millions of peripheral blood mononuclear cells (PBMCs), capturing subtle compositional and transcriptional shifts induced by in vitro perturbations.  -Detection of ultra-rare cell populations, such as circulating tumor cells (CTCs), which are often undetectable using conventional scRNA-seq methods.  -Cellular differentiation and lineage tracing, where STAMP was used to study human embryonic stem cell (hESC) differentiation induced by bone morphogenetic protein 4 (BMP4), effectively modeling early embryonic gastrulation.  -Application to induced pluripotent stem cells (iPSCs), highlighting STAMP’s potential for large-scale perturbation and drug screening studies.

first: Emanuele

last: Pitino

first: Anna

last: Reguant

first: Felipe

last: Dezem

first: Kellie

last: Wise

first: Irepan

last: Martinez

first: Helena

last: Crowell

first: Maycon

last: Marção

first: Sara

last: Ruiz

first: Elise

last: Courtois

first: William

last: Flynn

first: Santhosh

last: Sivajothi

first: Emily

last: Soja

first: Ginevra

last: Caratù

first: German

last: Mora Roldan

first: B

last: Dredge

first: Yutian

last: Liu

first: Hannah

last: Chasteen

first: Monika

last: Mohenska

first: Juan

last: Nieto

first: Raymond

last: Yip

first: Ruvimbo

last: Mishi

first: José

last: Polo

first: Adrienne

last: Sullivan

first: Holger

last: Heyn

first: Luciano

middle: G

last: Martelotto


title: Hybrid lizards with introgressed mtDNA show resistance to DNA damage from Reactive Oxygen Species

city: Elon

first: Gregory

last: Haenel

address: CB 2625, Elon University

department: Biology

institute: Elon University

summary: Hybrids can experience genetic incompatibilities that lead to cellular dysfunction and infertility. Previous analyses of mitochondrial function in the lizards Urosaurus graciosus and Urosaurus ornatus found that hybrids, which had introgressed mtDNA, experienced higher ATP production which increases reactive oxygen species (ROS) production, one of the main causes of damage to DNA. Hybrid populations of these lizards have persisted so we predicted they may have mechanisms for protecting their DNA from damage. To test this, we exposed liver cells of these lizards to hydrogen peroxide, a source of ROS, and compared DNA damage using single-cell gel electrophoresis. Hybrid cells showed significantly less DNA damage. We then examined potential mechanisms to explain this result by comparing melanin content of livers and expression levels of antioxidant genes. If functioning to deal with ROS, these should be expressed higher in hybrids. Melanin content of livers was highly variable among U. graciosus individuals and therefore not highest in hybrids as expected. Eighteen antioxidant genes showed significant differential expression but were not expressed consistently higher in hybrids. The overall gene expression profiles of hybrids and U. graciosus were very similar while that of the mtDNA donor species, U. ornatus, was highly divergent from both. Three antioxidant genes with different expression levels in hybrids and that warrant further study were SOD2, SOD3, and PRDX2. These results show how species can compensate for mtDNA introgression and highlight the complexity of genetic interactions encountered when closely related species exchange genetic material in zones of secondary contact.

sample_organism:
Urosaurus graciosus
Urosaurus ornatus

platform_organism:
Urosaurus graciosus
Urosaurus ornatus

overall_design: To investigate the differences in antioxidant gene expression in hybrid lizards, lizards (both parental species and hybrids) were held for 48 hours at 36C or 40C. Total RNA was extracted from liver tissue and sequenced. Sequences were aligned to the Sceloporus undulatus genome and then expression levels were calculated and compared for 40 antioxidant genes using DEseq2.


title: Prenatal diagnosis, ultrasound results, pregnancy outcomes and follow-up information analysis of xp22.31 deletion duplication syndrome

city: Shenzhen

first: xiaojin

last: luo

state: China (Mainland)

address: 6 Ailong Road SHENZHEN

institute: Longgang District maternity & Child Heal

summary: Objective: Analyze the ultrasound features, single nucleotide polymorphism microarray (SNP-array) outcomes, pregnancy results, and follow-up data of fetuses with Xp22.31 deletions or duplications in mid to late pregnancy.    Methods: A retrospective analysis was carried out on 10 cases diagnosed with Xp22.31 deletions and 11 cases with duplications, identified through single nucleotide polymorphism microarray (SNP-array) testing. The analysis focused on assessing ultrasound abnormalities, tracing parental origins, pregnancy outcomes, and postnatal follow-up conditions.    Results: The deletion sizes in the 10 deletion cases ranged from 913 Kb to 1.81 Mb, while the duplication sizes in the 11 duplication cases ranged from 1.29 Mb to 2.35 Mb, encompassing 9 OMIM genes including STS, ANOS1, DXS1283E, VCS3B, and HDHD1A. Among the fetuses with deletions, four cases (40.0%, 4/10) exhibited ultrasound abnormalities, which included cardiovascular system malformations, lateral ventriculomegaly, clubfoot, increased nuchal translucency, and polyhydramnios. Notably, Case 5 involved a fetus with complex multi-organ malformations, including bilateral ventriculomegaly, a ventricular septal defect, and clubfoot. Among the 11 cases of duplications, three cases (27.3%, 3/11) exhibited ultrasound abnormalities, primarily featuring cardiovascular malformations, ventriculomegaly, and polyhydramnios. Of the 10 deletion cases, eight underwent parental origin testing, with seven cases inherited (six maternal and one paternal) and one case of de novo mutation. Among the 11 duplication cases, eight underwent parental origin testing, with seven cases being inherited (four maternal and three paternal) and one case representing a de novo mutation. Of the 10 deletion cases, six chose to terminate the pregnancy, while four decided to continue. Follow-up revealed that Case 6 was diagnosed with STS ichthyosis shortly after birth, and the sbling of Case 3 and Case 10 exhibited delayed walking and speech development. In the duplication group, one case opted for termination of pregnancy, while 10 continued with their pregnancies. Follow-up identified that Case 18 exhibited delayed walking and speech development.    Conclusion: This study provides a preliminary assessment of the genotypes and phenotypes of fetuses with Xp22.31 deletions /duplications, expanding the phenotypic spectrum of Xp22.31 deletions /duplications syndrome. The findings indicate that prenatal Xp22.31 deletions in male fetuses are likely to manifest as STS ichthyosis after birth. Xp22.31 deletions and duplications may be associated with cardiovascular malformations. For fetuses with Xp22.31 deletions /duplications that appear phenotypically normal prenatally, postnatal monitoring of their neurological development is crucial.

first: Xiaojin

last: Luo

first: Fengxiang

last: Wei


title: Sugarcane streak mosaic virus P1 protein targets the BES1 transcription factor to subvert DAMP-induced immunity in plant

city: Yangzhou

first: Zhen

last: He

state: Jiangsu province

address: Wenhui East Road No 4

department: Plant pathology

institute: Yangzhou University

summary: Sugarcane streak mosaic virus (SCSMV) is the most important cause of sugarcane mosaic disease in the main production region. The SCSMV-encoded protein 1 (P1SCSMV) plays a vital role in disease development. However, the molecular mechanisms by which P1SCSMV participates in plant immunity remains unknown. Here, we found that the relative expression levels of P1SCSMV were negatively correlated with the xyloglucan endotransglucosylase/hydrolase gene (XTH) in a linear relationship. P1SCSMV directly interacts with the transcription factor, NbBES1, in vivo and in vitro. P1SCSMV-NbBES1 interaction interferes the binding of NbBES1 to the E-box element on the promoter region of NbXTH1 gene and inhibits the normal transcription of NbXTH1 gene. Furthermore, we found that down-regulation of the NbXTH1 directly resulted in enhanced infection of different plant pathogenic fungi and viruses, disrupted compositions of xyloglucan and xylan in the cell wall, and thinner middle lamellae in cell walls. We found that xyloglucan is a direct trigger of damage-associated molecular pattern- (DAMP) induced plant innate immunity. Moreover, the decrease in xyloglucan content in the cell wall caused by down-regulation of NbXTH1 leads to a reduction in DAMP-triggered immunity. Our study revealed the molecular mechanism of how a plant virus manipulates plant cell wall-mediated plant innate immunity, and identified NbXTH1, a wide-spectrum disease resistance protein for both plant pathogenic fungi and viruses. Our research also provides the basis for the application of the small molecule xyloglucan and the wide-spectrum disease resistance gene, XTH, in wide-spectrum resistance improvement in the future crop molecular breeding.

overall_design: Transcriptome sequencing analysis of healthy sugarcane plants and sugarcane plants infected with SCSMV.

first: Xiaolong

last: Deng

first: Xiaowei

last: Xu

first: Mengyan

last: Tang

first: Yanhong

last: Hua

first: Lang

last: Qin

first: Kun

last: Zhang


title: Spatial transcriptomics from paired pancreas and associated draining lymph nodes reveals a lymphotoxin-beta signature in human type 1 diabetes

city: Gainesville

first: Miguel

last: Medina-Serpas

state: FL

address: 1275 Center Dr

institute: University of Florida

summary: This study explores the inflammatory response involved in type 1 diabetes (T1D) using multi-cell resolution spatial transcriptomics (ST) to assay paired pancreas and pancreatic lymph node (pLN) samples from human donors across the natural history of T1D. Integration of ST with public single-cell RNA sequencing data enabled interrogation of transcriptional alterations in T1D across both tissues at the cellular scale. In the T1D pancreas, we identified global upregulation of inflammation-associated transcripts, including multiple regenerating islet-derived (REG) family genes, complement factor 3 (C3), SOD2, and OLFM4, and highlighted cellular candidates potentially contributing to these signatures. Within the T1D pLN, we observed spatially restricted upregulation of lymphotoxin- (LTB) alongside follicular dendritic cell (FDC)-associated transcripts including FDCSP, CLU, and FCER2. Collectively, these findings highlight a distinct inflammation signature in the pancreas and evidence of enhanced follicular activity in the associated pLN.

overall_design: Spatial transcriptomics using the 10x Genomics Visium spatial gene expression assay performed on human donor pancreas and associated pancreatic lymph node sections from non-diabeitc controls, non-diabetic islet autoantibody positive donors at high risk, and T1D donors.

first: Todd

last: Brusko


title: Effect of depletion of Dnmt3a on gene expression during the appearance of endometriosis

city: Houston

first: Nuri

last: Sung

state: Texas

address: One Baylor plaza, Houston, Rm807

department: Molecular and Cellular biology

institute: Baylor college of Medicine

summary: Endometriosis is a benign yet invasive condition in which endometrial-like tissue grows outside the uterus. Recent evidence highlights the role of epigenetic mechanisms—particularly DNA methylation—in its development. DNA methyltransferases (DNMTs), including DNMT1, DNMT3B, and DNMT3A—regulate these modifications. DNMT3A is uniquely upregulated in the eutopic endometrium of women with endometriosis and may affect reproductive potential via altered gene expression.  To investigate DNMT3A's role, we compared the incidence of endometriosis and transcriptomic profiles in Dnmt3a knockout (KO) mice and wild-type controls. RNA sequencing of KO samples revealed upregulation of pathways such as E2F_TARGETS, MYC_TARGETS_V1, G2M_CHECKPOINT, and UNFOLDED_PROTEIN_RESPONSE, and downregulation of NOTCH_SIGNALING, COAGULATION, HEDGEHOG_SIGNALING, ANGIOGENESIS, and ADIPOGENESIS. Several immune-related genes were also differentially expressed, including IL-6, CXCL1, CXCL2, IL-1β, TNFα, CCL5, CXCL5, TGFβ1, IL-10, CXCL9, CXCL10, CX3CL1, CCL2, CCL22, CCL17, and CXCL12.  These findings suggest that elevated DNMT3A expression may contribute to immune suppression in endometriosis, and its loss leads to reactivation of immune response genes, highlighting DNMT3A as a potential therapeutic target.

overall_design: RNA-seq profiling was conducted on endometriosis samples using both wild-type DNMT3A and its knockout mice, four weeks post-disease onset.

first: Sang Jun

last: Han


title: Splicing of erythroid transcription factor is associated with therapeutic response in myelodysplastic syndromes

first: Kith

last: Pradhan

summary: Anemia is the primary clinical manifestation of myelodysplastic syndromes (MDS), but the molecular pathogenesis of ineffective erythropoiesis remains incompletely understood. Luspatercept, an activin receptor 2B (ACVRIIB-Fc) ligand trap, has been approved to treat anemia, however its molecular mechanism of action is unclear. We found that the ACVR2B, its ligand GDF11, and effector, SMAD2, are upregulated in MDS patient samples. GDF11 inhibited human erythropoiesis in vitro and caused anemia in zebrafish, effects that were abrogated by luspatercept. Upon GDF11 stimulation of human erythroid progenitors, SMAD2 binding occurred in the erythroid regulatory regions, including at GATA1 intron. Intronic SMAD2 binding led to skipping of exon 2 of GATA1, resulting in a shorter, hypomorphic isoform (GATA1s). CRISPR deletion of the SMAD2 binding intronic region decreased GATA1s production upon GDF11 stimulation. Expression of gata1s in a mouse model led to anemia,rescued by a murine ActRIIB-Fc (RAP-536). Finally, RNA-seq analysis of samples from the Phase 3 MEDALIST trial revealed that responders to Luspatercept had a higher proportion of GATA1s compared to non-responders. Moreover, the increase RBCs post-treatment was linked to a relative decrease in GATA1s isoform. Our study indicates that GDF11-mediated SMAD2 activation results in an increase in functionally impaired GATA1 isoforms, consequently contributing to anemia and influencing responses to Luspatercept in MDS.

overall_design:
RNA-seq analysis of:
In vitro HSC cultures were either treated with GDF11 (100 ng/mL) or TGFb1 (20 ng/mL)
Medalist trial patient Non-responder to Luspatercept
Medalist trial patient Responder to Luspatercept

first: Srinivas

last: Aluri

first: Amit

last: Verma


title: Glucagon controls obesity-specific energy expenditure via persistent cAMP/PKA signaling [RNA-Seq 2]

first: Genome

last: Informatics

summary: Background & Aims: Glucagon (GCG) analogues are gaining attention as promising components in incretin-based therapeutics for obesity and metabolic dysfunction-associated steatohepatitis. However, the biology of chronic glucagon treatment, in particular, the molecular underpinnings of GCG-induced energy expenditure and lipid metabolism, remain poorly defined. Methods: We utilized a long-acting GCG analogue (LA-GCG) in conjunction with hepatic and adipose glucagon receptor knockout mouse models. Through an integrative approach that combined metabolic, biochemical and omics techniques, we investigated the molecular mechanisms underlying GCG-induced energy expenditure and metabolic benefits. Results: We demonstrate that the LA-GCG enhances energy expenditure in diet-induced obese mice with an essential role of hepatic, but not adipose, GCGR signaling. Intriguingly, the enhancement in energy expenditure is observed only in obese but not in lean mice. The preferential efficacy is plausibly found in a prolonged activation of cAMP/PKA signaling through PDE4B/4D downregulation by LA-GCG. Conversely, the cAMP/PKA signaling is promptly attenuated by the PDE4B/4D activity in lean mice. Interestingly, unlike the EE phenotype, the lipid-clearing capacity of LA-GCG is independent of the PDE4/cAMP/PKA axis. Conclusions: These findings provide the molecular basis for GCG-induced energy expenditure and metabolic benefits and suggest the phenotypic segregation of cAMP/PKA-dependent and independent effects.

overall_design: Liver tissue was collected from lean wild-type mice after a 6-day treatment with long-acting glucagon to assess transcriptional changes

first: Fen

last: Long

first: Falko

last: Noé

first: Adhideb

last: Ghosh

first: Christian

last: Wolfrum


title: Glucagon controls obesity-specific energy expenditure via persistent cAMP/PKA signaling [RNA-Seq 1]

overall_design: Liver tissue was collected from obese liver glucagon receptor knockout  mice and wild-type controls after a 6-day treatment with long-acting glucagon to assess transcriptional changes.


title: Adipocytes-derived β-hydroxybutyrate confers the resistance of myeloma cells to metabolic stress

city: Hefei

first: Rui

last: Li

state: Anhui

address: Yuhuangshan Road, Thirty Head Street

department: cell biology

institute: Anhui Medical University

summary: Albeit being recognized as one of the major mesenchymal cells and a dangerous accomplice in myeloma, the roles of adipocytes in different stages of myeloma pathogenesis remain elusive. Here we showed that glucose metabolic stress impairs protein stability of interferon regulatory factor 4 (IRF4), an oncoprotein essential for myeloma cell survival, while adipocytes-derived β-hydroxybutyrate (β-OHB) preserves IRF4 stability and cell survival. Mechanistically, glucose deficiency activates the AMP-activated protein kinase (AMPK) to disrupt the interaction of IRF4 with heat shock protein 90 (HSP90), enabling the E3 ligase TRIM21-mediated IRF4 ubiquitination degradation. The presence of β-OHB drives 3-oxoacid CoA-transferase 1 (OXCT1)-mediated ketolysis and facilitates N-acetyltransferase 10 (NAT10)-mediated IRF4 acetylation at lysine 87, which restores IRF4’s interaction with HSP90 and precludes TRIM21-mediated IRF4 degradation. Notably, targeting OXCT1 or NAT10 to interfere with β-OHB utilization displays a synergistic anti-myeloma effect in combination with AMPK activator both in vitro and in vivo. Our study thus positions adipocytes-derived β-OHB as a pivotal contributor that enables myeloma cells to overcome glucose metabolic stress and suggests viable therapeutic targets to be exploited for multiple myeloma treatment.

overall_design: Addition of glucose, glucose deficiency, β - OHB, and combined treatment to ARP1 cells，Collect cells for cuttaq detection after processing

first: Zongwei

last: LI

first: Chen

last: Song

first: Peng

last: Yang

first: Tao

last: Xia

first: Yu

first: Wenjun


title: IRF4 silencing gene expression study

first: Surendra

last: Dasari

summary: A gene expression study was conducted to understand the role of IRF4 in ABC like lymphomas. For this, IRF4 was silenced in TMD8 cell line alongside a control vector. Treated and control cell lines were subjected to gene expression measurement. Pathway analysis of differentially expressed gens showed antigen presentation pathways to be differentially regulated.

first: Patrizia

last: Mondello


title: Gene expression profile at single cell level of mouse wound tissue cells from Mrc1-DTR mice treated with PBS and diphtheria toxin (DTX)

city: Bunkyo-ku

first: Hiroyuki

last: Koike

state: Tokyo

address: 1-5-45 Yushima

department: Department of Medical Biochemistry

institute: Institute of Science Tokyo

summary: Our finding that granulation tissue formation and wound closure were significantly attenuated by the reduction of CD206(Mrc1)+ macrophages. We used single-cell RNA sequencing (scRNA-seq) to analyze intracellular communication of the wound site.

overall_design: Live cells (7AAD-negative) were sorted by Fluorescence-activated cell sorting (FACS) from mouse wound tissues 5 days after wounding and processed for droplet-based scRNA-seq

first: Azusa

last: Honda

first: Yumiko

last: Oishi


title: Mutational profiling of HIV-associated diffuse large B-cell lymphomas from Malawi

city: Chapel Hill

first: Yuri

last: Fedoriw

address: 160 Medical Drive

institute: University of North Carolina

type: Genome variation profiling by high throughput sequencing

summary: To investigate the biological differences between HIV-, HIV+/ART-experienced and HIV+/ART-naive diffuse large B-cell lymphoma, we performed whole exome sequencing of 30 pre-treatment formalin-fixed paraffin-embedded (FFPE) whole lymph node biopsies of diffuse large B-cell lymphoma.

overall_design:
We performed whole exome sequencing of 30 pre-treatment formalin-fixed paraffin-embedded (FFPE) whole lymph node biopsies of HIV- and HIV+ (with and without prior antiretroviral therapy exposure) diffuse large-B cell lymphoma, 24 of which had paired germline (whole blood).

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

first: Sophia

last: Roush

first: Tamiwe

last: Tomoka

first: Matthew

last: Painschab


title: LARP-1 maintains the structure and function of mitochondria by regulating mitochondrial crista-related proteins

status: Public on Jun 22 2025

city: Kunming City

first: Jiangyang Li

last: Jingyang Li

state: Yunnan Province

address: School of Life Science, Yunnan University, Chenggong District

department: School of Life Science

institute: Yunnan Universiity

summary: Mitochondria are the metabolic center and powerhouses of cells by coordinating the tricarboxylic acid (TCA) cycle, oxidative phosphorylation (OXPHOS) and electron transport to generate ATP, which provide energy for cell survival and functional maintenance. This is attributed to the key structure of mitochondria cristae, which are formed by the inward folding of inner mitochondrial membranes. Numerous studies have demonstrated that RNA-binding proteins play an important role in maintaining the normal structure and function of mitochondria. However, the relevant mechanism remains unclear. Here, we report that the RNA-binding protein LARP-1 affects the structure and function of mitochondria by disrupting crista-related proteins, including the MICOS complex, respiratory chain complexes, and the proton-transporting ATP synthase complex. Using APEX-based proximity labeling assays, we pulled down mRNAs associated with LARP-1::APEX2, and determined the identities of mRNAs by sequencing. Among the 653 LARP-1::APEX2-enriched mRNAs, 37.5% (245/653) encode mitochondrial proteins, of which 71.8% (176/245) were identified to be down-regulated in larp-1 mutants by LC-MS analysis of purified mitochondria. In addition, mRNAs encoding components of the MICOS complex, respiratory chain complexes, and ATP synthase complex were strongly enriched, suggesting that they were associated with LARP-1.

overall_design: RNA-seq of immunoprecipitation results of fusion proteins LARP-1::GFP (knock in) or LARP-1::APEX2 (knock in).

first: Yan

last: Bai

first: Tengfei

last: Ma

first: Jingyang

first: Shunkai

last: Chen

first: Chonglin


title: The RNA-Binding Protein DDX39B Promotes Colorectal Adenocarcinoma Progression by Stabilizing DCLK1

city: jinan

first: Guixi

last: Zheng

address: 107 Wenhua West Road, Lixia District, Jinan City, Shandong Province

institute: Qilu Hospital of Shandong University

summary: As an RNA-binding protein (RBP), DDX39B increased the stability of DCLK1-B mRNA, a variant highly expressed in colorectal cancer known to promote cancer stemness, thereby augmenting its protein expression. Notably, silencing of DCLK1-B effectively abrogated the pro-metastatic effects induced by DDX39B overexpression.

overall_design: RNA-seq was performed after overexpression of DDX39B in colorectal adenocarcinoma cells SW480, and differentially expressed genes were screened compared with control cells.

first: Shichao

last: Liu

first: Shoucai

last: Zhang

first: Hongxi

last: Zhao

first: Yingjie

first: Zeyu

first: Xueyan

last: Geng

first: Maopeng

last: Yin

first: Yongyuan

last: Liang


title: The specificity of exoCasMINI for gene editing.[Tag-seq]

city: Guangzhou

first: Kechen

state: Guangdong

address: Shatai South Road

institute: Southern Medical University

summary: The exoCasMINI exhibits similar specificity for gene editing. Compared to SpCas9, exoCasMINI also exhibited higher specificity for genomic DNA cleavage at the tested sites.

overall_design: We evaluated the specificity of exoCasMINI-mediated gene editing in human cells using Tag-seq. Within the 10 tested sites, exoCasMINI exhibited about 2.5-fold increased activity and similar specificity compared to CasMINI. we also compared the DNA cleavage activity of SpCas9, LbCas12a, CasMINI, and exoCasMINI across four genomic sites at the same location and five sites at adjacent locations, exoCasMINI also exhibited higher specificity for genomic DNA cleavage at the tested sites.

first: Kaitong

last: Liao

first: Ying

last: Lin


title: Single-cell sequencing of plasma cell mastitis

city: Taizhou

first: Qingtao

last: Ni

state: State...

address: hailingnanlu No 399

institute: Jiangsu Taizhou People's Hospital

overall_design: one sample from plasma cell mastitis tissue

first: Chi

last: Pan


title: Overexpression of SLC2A1, ALDOC and PFKFB4 in the glycolysis pathway drives strong drug resistance in 3D HeLa tumor cell spheroids.

city: Shanghai

first: Wang

last: tong

address: meilong road 130,Shanghai,China

institute: East China University of Science and Technology

summary: The three-dimensional (3D) tumor spheroid model exhibits enhanced fidelity in  replicating the tumor microenvironment and demonstrates exceptional resistance to  clinical drugs compared to the two-dimensional (2D) monolayer model. In this study, we used multi-omics (transcriptome, proteomics, and metabolomics) tools to explore the molecular mechanisms and metabolic differences of the two culture models. Analysis of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment pathways revealed that the differentially expressed genes between the two culture models were mainly enriched in cellular components and biological processes associated with extracellular matrix, extracellular structural organization and mitochondrial function. A combined analysis of three omics data revealed 11 possible drug resistance targets. Among these targets, 7 genes, AKR1B1, ALDOC, GFPT2, GYS1, LAMB2, PFKFB4 and SLC2A1, exhibited significantly up-regulation. Conversely, 4 genes, COA7, DLD, IFNGR1 and QRSL1, were significantly down_x0002_regulated. Clinical prognostic analysis using the TCGAsurvival database indicated that  high expression groups of SLC2A1, ALDOC and PFKFB4 exhibited a significant negative correlation with patient survival. We further validated their involvement in chemotherapy drug resistance, indicating their potential significance in improving prognosis and chemotherapy outcomes. These results provide valuable insights into potential therapeutic targets that can potentially enhance treatment efficacy and patient outcomes.

overall_design: The 2D sample had three biological replicates, named S2D1, S2D2, and S2D3. And the 3D sample had three biological replicates, named S3D1, S3D2, and S3D3.

first: Tong

last: Wang

first: Xueting

first: Xuli

first: Zhongfang

last: Guo

first: Ali

last: Mohsin

first: Yingping

last: Zhuang

first: Guan


title: The liver-specific long noncoding RNA FAM99B inhibits ribosome biogenesis and cancer progression through cleavage of dead-box Helicase 21

first: Xianghuo

last: He

address: No 270, Dong An Road

institute: Fudan University

summary: The evidence we provide highlights a novel mechanism by which FAM99B and DDX21 regulate HCC,  and we provide a new approach for the application of  lncRNA in gene therapy.

overall_design: Whole-transcriptome sequencing (RNA-Seq) was performed to identify the downstream target genes regulated by both FAM99B and DDX21 in Huh7 cells.   Chromatin immunoprecipitation followed by sequencing (ChIP-seq) was performed using indicated antibodies to study the DDX21 status and binding sites of RPs in Huh 7 cells.

first: Yifei

first: Shenglin

last: Huang

first: Zhiao

last: Chen


title: The Cdc42 effector and non-receptor tyrosine kinase, ACK defines a distinct STAT5 transcription signature in a chronic myeloid leukaemia cell model [RNA-Seq]

status: Public on Jun 21 2025

city: cambridge

first: Jessica

last: Corry

address: 80 Tennis court road

institute: University of Cambridge

summary: Activated Cdc42-associated kinase (ACK) is a Rho family effector that is widely implicated in cancer. This work investigates how ACK affects the signal transducer and activators of transcription (STAT) family. ACK is shown to interact with STAT5 in the K562 CML cell line, and contribute to the pool of nuclear phosphorylated STAT5. By Cleavage Under Targets and Release Using Nuclease (CUT&RUN) and RNA-sequencing experiments using ACK KO K562 cells we have identified ACK driven STAT5 transcriptional targets.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for K562s, WT vs ACK KO, with 3 biological replicates of each

first: Corry

last: Jessica

first: Daniel

last: Jachimowicz

first: Benjamin

last: Keith

first: Jose

last: Julio Vicente-Garcia

first: Helen

last: R Mott

first: Kate

last: Wickson

first: Darerca

last: Owen


title: Downregulation of miR-182-5p by NFIB promotes NAD+ salvage synthesis in colorectal cancer by targeting NAMPT

city: Chongqing

first: Li

last: Zhou

address: 1, Medical College Road, Yuzhong District, Chongqing

institute: Chongqing Medical University

type: Non-coding RNA profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: NSD1-916aa encoded by CircNSD1 contributes to AKI-to-CKD transition through inducing ferroptosis in tubular epithelial cells

city: Heifei

first: Gao

last: Li

address: Meishan Road

institute: The First Affiliated Hospital of Anhui Medical University

summary: Acute kidney injury (AKI) is characterized by a rapid decline in renal function. In severe or recurrent cases, AKI can progress to chronic kidney disease (CKD), marked by renal inflammation and fibrosis. Despite the severity of these outcomes, early-stage diagnostic tools and pharmacological interventions for AKI-to-CKD progression remain limited. In this study, we examined circular RNA (circRNA) expression profiles in mouse renal cortex tissues 14 days post-ischemia/reperfusion (I/R) injury using circRNA sequencing. The renal biopsy samples of patients from AKI patients exhibited reduced CircNSD1 expression, which was inversely associated with inflammation and fibrosis. Overexpression of CircNSD1 attenuated ferroptosis in vivo and in vitro, thereby slowing AKI-to-CKD progression. Mechanistically, CircNSD1 downregulated ACSL4 and SlC39A14 expression through histone H3 lysine 36 (H3K36) methylation, a critical pathway regulating ferroptosis during AKI or hypoxia/reoxygenation (H/R) injury. Furthermore, we identified that CircNSD1 encoded a NSD1-916aa peptide, which may functionally contribute to its observed effect. Collectively, these findings demonstrated that CircNSD1 may serve as a diagnostic and therapeutic target for early detection of AKI-to-CKD transition.

overall_design: Renal cortex tissues from male C57BL/6J mice 14 days post-ischemia/reperfusion (I/R) were subjected to high-throughput circRNA sequencing

last: Gao

first: Junsheng

last: Zhang

first: Chaoyi

first: Sai

last: Zhu

first: Ling

last: Jiang

first: Yonggui

last: Wu


title: Downregulation of miR-182-5p by NFIB promotes NAD+ salvage synthesis in colorectal cancer by targeting NAMPT [ChIP-Seq]

summary: Nuclear factor IB (NFIB) plays an important role in tumors. Our previous study found that NFIB can promote colorectal cancer (CRC) cell proliferation in acidic environments. However, its biological functions and the underlying mechanism in CRC are incompletely understood. Nicotinamide adenine dinucleotide (NAD+) effectively affects cancer cell proliferation. Nevertheless, the regulatory mechanism of NAD+ synthesis in cancer remains to be elucidated. Here we show NFIB promotes CRC proliferation in vitro and growth in vivo, and down-regulation of NFIB can reduce the level of NAD+. In addition, supplementation of NAD+ precursor NMN can recapture cell proliferation in CRC cells with NFIB knockdown. Mechanistically, we identified that NFIB promotes CRC cell proliferation by inhibiting miRNA-182-5p targeting and binding to NAMPT, the NAD+ salvage synthetic rate-limiting enzyme. Our results delineate a combination of high expression of NFIB and NAMPT predicted a clinical poorest prognosis. This work provides potential therapeutic targets for CRC treatment.

overall_design: The gene information of NFIB binding in HT29 cells was investigated by chromatin immunoprecipitation DNA-sequencing (ChIP-seq)

first: Song

last: He

first: Zhihang

first: Shu


title: The DNA cleavage efficiency of the exoCasMINI system.[Deep-seq]

first: Kechen

last: Chen

summary: The fusion of a T5 exonuclease to the C-terminus of CasMINI (exoCasMINI) could indeed enhance the DNA cleavage efficiency in mammalian cells.

overall_design: To investigate the potential of exoCasMINI in genomic DNA cleavage, we transfected CasMINI or exoCasMINI or SpCas9 or LbCas12a into MCF7 cells and HEK292T cells with gRNA targeting different genomic sites. The results indicated that exoCasMINI significantly improved editing efficiency at all the tested sites compared to CasMINI.When compared to SpCas9 and LbCas12a, exoCasMINI displayedsimilar DNA cleavage activity at 5 of tested sites，while the other loci remain lower activity.

first: Kaitong

last: Liao

first: Ying

last: Lin


title: Altered gene expression by C1orf106 in endometrial cancer cells.

city: tianjin

first: qiaoling

last: zhang

address: 154 Anshan Road, Heping District

institute: Tianjin Medical University General Hospital

summary: Chromosome 1 open reading frame 106 (C1orf106) has been shown to be elevated in lung adenocarcinoma. However, its expression and function in endometrial cancer (EC) are totally unknown. To explore the role of C1orf106 in EC, we analyzed the gene expression in HEC-1A cells with or without C1orf106 knockdown.

overall_design: The mRNA profiles of NC and RNAi cells were generated by sequencing, in duplicate, using an Illumina NovaSeq 6000.

first: Qiaoling


title: TRPML3 regulates expression of development-related neuronal genes, and augments starvation-induced autophagy mediated transcriptional regulation in HEK cells

status: Public on Jun 20 2025

city: Delhi

first: Tapan

middle: Kumar

last: Nayak

address: IIT Delhi, Hauz Khas

department: KSBS

country: India

institute: Indian Institute of Technology Delhi

summary: Autophagy (self-eating) involves sorting of cargo like aggregated or misfolded proteins and damaged organelles, and their degradation via the endo-lysosomal system. It is a conserved process that is crucial in survival, cell stress response, and differentiation. Transient Receptor Potential Mucolipin-3 (TRPML3) is an endolysosomal calcium channel largely implicated in the mechanisms of endocytosis and autophagy.  Overexpression and channel activation of TRPML3 has been reported to induce autophagy in cell-line models. However, its effect on the gene expression patterns, both before and during autophagy induction, is not clearly understood. Here, we have explored the changes in the transcriptomic profile of an in vitro serum starvation model of autophagy by RNA sequencing experiments in an over-expression background of TRPML3. We report that serum-starvation induced autophagy leads to downregulation of development-related neuronal genes and gene sets. TRPML3 overexpression during autophagy induction further amplifies the effect of starvation in downregulating neuronal gene sets. But, when nutrition is not a limiting condition, TRPML3 overexpression upregulates neuronal genes that promote development. In summary, overexpression of TRPML3 promotes neuronal development under ‘fed’ conditions, while significantly arresting development by augmenting the effects of starvation-induced autophagy in HEK293T cells.

overall_design: RNA-seq of polyA RNA from Vector control/TRPML3 transfected HEK293T cells under either serum-fed or serum-starved (4hrs) conditions

first: Sushanth

last: Adusumilli

first: Mahesh

last: Mathe

first: Jayasha

last: Shandilya

middle: K


title: The Cdc42 effector and non-receptor tyrosine kinase, ACK defines a distinct STAT5 transcription signature in a chronic myeloid leukaemia cell model [CUTnRUN]

first: Jessica

last: Corry

summary: Activated Cdc42-associated kinase (ACK) is a Rho family effector that is widely implicated in cancer. This work investigates how ACK affects the signal transducer and activators of transcription (STAT) family. ACK is shown to interact with STAT5 in the K562 CML cell line, and contribute to the pool of nuclear phosphorylated STAT5. By Cleavage Under Targets and Release Using Nuclease (CUT&RUN) and RNA-sequencing experiments using ACK KO K562 cells we have identified ACK driven STAT5 transcriptional targets. This also revealed global losses in H3K4me3 and H3K27ac in ACK KO cells.

overall_design: CUT&RUN on K562 WT and ACK KO cells, 3 replicates for STAT5, H3K4me3, H3K27ac and IgG.

first: Corry

last: Jessica

first: Daniel

last: Jachimowicz

first: Benjamin

last: Keith

first: Jose

last: Julio Vicente-Garcia

first: Helen

last: R Mott

first: Kate

last: Wickson

first: Darerca

last: Owen


title: Inhibitor of DNA binding-1, a master regulator of vasculogenic mimicry by cancer cells.

city: Adelaide

first: John

last: Toubia

address: Frome Rd

country: Australia

institute: Centre for Cancer Biology

summary: Cancer cells within solid tumours routinely access the blood supply by promoting endothelium-dependent angiogenesis, but tumour vasculature can also be formed by the cancer cells themselves via vasculogenic mimicry (VM). With increasing evidence that VM correlates with cancer progression, understanding the regulatory factors that underpin VM could provide new therapeutic strategies to improve patient outcomes. Herein we investigate changes to the gene expression profile of breast cancer cells during the early stages of VM formation. Results identify the transcriptional regulator Inhibitor of DNA binding 1 (ID1) to be elevated ~10-fold within the first two hours of VM formation by MDA-MB-231-LM2 cells. A role for ID1 in promoting VM was supported by ID1-targeting siRNA in breast and pancreatic cancer cells. Similarly, administration of the pan-ID inhibitor AGX-51, interrupted VM formation by MDA-MB-231-LM2 and BxPC-3 cells. Inhibition of ID1 also reduced the production of pro-angiogenic and pro-cancerous proteins, e.g. DKK-1, VEGF, CD31, MMP9, PDGF-AA, angiogenin, and IL-8. Regulatory control of these genes by ID1 was further implicated through identification of the requisite DNA binding motifs upstream of the gene start site. Finally, in silico analysis of barcoded VM-competent MDA-MB-231 cells injected into the mammary fat pad of mice enabled gene expression profiling of cancer cells in the primary tumour and metastatic sites. Elevated expression of ID1 was observed in the cancer cells that has metastasised to the lung and the liver and was associated with an enrichment of pro-angiogenic genes. Taken together, this study further implicates ID1 as an important master regulator of cancer progression via its role in the formation of VM structures, protein production and metastasis.

overall_design:
This study aims to identify genes of early VM regulatory events.
To address this, the human TNBC cell line MDA-MB-231-LM2 was cultured in either two-dimensions (2D, tissue culture flasks) or in 3D as VM-structures in Matrigel and harvested at early time points of VM formation (i.e.  two and six hours) followed by bulk RNA sequencing and comparative gene expression analysis.

first: Emma

last: Thompson

first: Claudine

last: Bonder


title: EDNRB2 regulates fate determination, migration and maturation of hair-cell precursors in regenerating avian auditory epithelia

city: Kyoto

first: Mami

last: Matsunaga

state: Kyoto

address: Kawahara cho 54, Shogoin, Sakyo-ku

department: Department of Otolaryngology, Head and Neck Surgery

institute: Kyoto university

summary: The mammalian cochlea loses the ability for hair cell (HC) regeneration after birth, while in the avian auditory epithelium, namely the basilar papilla (BP), supporting cells (SCs) retain the capability for HC regeneration throughout life. Our previous study using single-cell RNA sequencing indicated stepwise fate conversion of SCs to HCs via the precursor state, in which EDNRB2 exhibited specifically high expression, in the process of HC regeneration in chick BP. The present study aimed to reveal a distinct role of EDNRB2 in HC regeneration in chick BP. During HC regeneration in chick BP explant cultures, EDNRB2 expression emerged in a part of ATOH1-expressing SCs immediately after HC loss and decreased according to the progress of HC regeneration process. In embryonic chick BP, EDNRB2 expression was specifically identified in the precursor cell state, which confirmed that mature SCs were reprogrammed to the precursor state in response to HC loss. Pharmacological inhibition of endothelin receptor type B (EDNRB) signaling decreased regenerated HCs in chick BP explant cultures. RNA sequencing revealed that inhibition of EDNRB signaling downregulated genes for HC differentiation and maturation together with genes for cell migration. Histological assessments clarified the deterioration of migration of HC precursors and the delay of HC regeneration processes by inhibition of EDNRB signaling. These results indicate that the expression of EDNRB2 contributes to the fate determination of HCs and that EDNRB signaling regulates the migration and maturation of HC precursors during chick HC regeneration.

overall_design: Bulk RNA-seq of chick basilar papaillae during hair cell regeneration using an explant culture

first: Takeuchi

last: Marie

first: Matsunaga

last: Mami

first: Nakagawa

last: Takayuki


title: GATA Transcription Factors Coordinate Developmental Progression in the Arabidopsis Root

city: Tuebingen

first: Marja

last: Timmermans

address: Morgenstelle 32

country: Germany

institute: University of Tuebingen

summary: For proper organ development, cell proliferation and cellular differentiation must balance in a tightly regulated spatiotemporal manner. Here, we show that a phased gene expression profile from meristematic cells at the Arabidopsis root niche, to differentiating cortex- and endodermis cells, is defined by the action of distinct transcription factor (TF) families. We show that while chromatin accessibility serves as a strong predictor of the activation of developmental genes, a key expression ‘switch’ from dividing- to elongating/differentiating cells is underpinned by a considerable level of chromatin rearrangement. Within this structure, a GATA TF subfamily is proposed to sit at the heart of a mutually antagonistic regulatory module, acting to promote differentiation and feedback on cell proliferation through the regulation of both lineage specific differentiation processes and general maturation programs. Key to this is integration of the auxin- and cytokinin responsive PLT- and ARR-B TF families. This model provides a level of coordination in the regulation of meristem size and the timing of differentiation, at both the tissue- and organ levels.

overall_design: Roots of six day old seedlings or A. thaliana Col-0 were cut 0.5 - 0.7 cm from their tip and a total of 180 mg of root tissue was collected. Single cell ATAC-seq libraries were produced from freshly isolated nuclei in accordance with the 10X Genomics Chromium Single Cell ATAC-seq kit protocol (v 1.1 protocol, Rev D).

first: Tom

last: Denyer

first: Pavel

last: Solansky

first: Francesco

last: de Martino

first: Efthymia

last: Symeonidi

first: Arvid

last: Herrmann

first: Valentin

last: Brösamle


title: m5C-MeRIP-seq of HHL5 cells

first: Jin

last: Hou

address: 800 Xiangyin Road

institute: Second Military Medical University

summary: We discovered the  YBX1 in the lipid-induced particles assembled by DDX49,  YBX1 is an m5C reader and constitutively associates with Timp2 mRNA in hepatocytes, we examined whether their association was dependent on the m5C modification of Timp2 mRNA, then we  performed m5C-MeRIP-seq.

overall_design: After treating HHL5 cells with OA/PA for 24 hours, the cells were lysed.Total RNA was subjected to immunoprecipitation with the GenSeq® m5C MeRIP Kit (GenSeq Inc.) following the manufacturer’s instructions.


title: Genome-wide maps of chromatin state in U251 cells expressing VASN.

first: Zixi

last: Qin

address: Department of Pathology, Medical College, Jinan University, Guangzhou, 510632, P. R. China

institute: Jinan university

summary: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for VASN in U251 cells expressing VASN.

overall_design: Examination of VASN overexpression U251 cells.

first: Lihui

last: Wang


title: Overexpression of NPY leads to a progressive, cutaneous inflammatory fibrotic response in mouse skin.

city: Birmingham

first: Alex

middle: Dwight

last: Dawson

state: Alabama

address: 902, 14th st. South

institute: University Of Alabama At Birmingham

summary: Neuropeptide Y (NPY) is a pleiotropic peptide produced in the central nervous system and peripheral organs and is upregulated in some human skin conditions like atopic dermatitis. We reported previously that a knock-in mouse with entopic NPY overexpression (NPYtet/tet) exhibits significantly elevated NPY gene and protein expression in the skin, accompanied by premature and progressive hair graying. However, the question remained whether NPY overexpression induces other skin pathologies. RNA-seq was used to show changes in the transcriptome in 35-week-old NPY overexressing mice, allowing us to highlight transcriptional changes using downstream analysis. Using a cross-sectional approach focused on timepoints before and after the onset of graying, we find that overexpression of NPY results in transcriptomic changes associated with inflammation and fibrosis. The histopathology of NPYtet/tet mice following hair graying included increased epidermal proliferation and an increase in CD3+ dendritic epidermal T cells. The dermis of NPYtet/tet mice exhibited enhanced fibrotic changes with abnormal rearrangement of collagen bundles and widespread dermal infiltration of degranulated mast cells and CD206+ M2 macrophages. NPYtet/tet mice also showed a thinning of the intradermal fat layer with focal areas of panniculitis. These results provide long-awaited evidence of NPY’s involvement in skin pathology, a background for defining the precise role of NPY in the regulation of skin homeostasis, and highlights its potential impact in inflammatory and/or fibrotic disorders.

overall_design: B6;129S4-Npytm2Rpa/J mice (NPY tet/tet) and their wildtype siblings (NPY +/+) were aged to 35 weeks of age before being euthanized, with whole skin being harvested for RNA extraction and analysis

first: Dawson

last: Alex

first: Harris

last: Melissa


title: A PLURIPOTENT STEM CELL PLATFORM FOR IN VITRO SYSTEMS GENETICS STUDIES OF MOUSE DEVELOPMENT [ATAC-seq]

city: New York

first: Richard

last: Koche

state: New York

institute: Memorial Sloan Kettering Cancer Center

summary: The directed differentiation of pluripotent stem cells (PSCs) from panels of genetically diverse individuals is emerging as a powerful experimental system for characterizing the impact of natural genetic variation on developing cell types and tissues. Here, we establish new PSC lines and experimental approaches for modeling embryonic development in a genetically diverse, outbred mouse stock (Diversity Outbred mice). We show that a range of inbred and outbred PSC lines can be stably maintained in the primed pluripotent state (epiblast stem cells) and establish the contribution of genetic variation to phenotypic differences in gene regulation and directed differentiation. Using pooled in vitro fertilization, we generate and characterize a genetic reference panel of Diversity Outbred PSCs (n = 250). Finally, we demonstrate the feasibility of pooled culture of genetically diverse PSCs as “cell villages”, which can facilitate the differentiation of large numbers for forward genetic screens. These data can complement and inform similar efforts within the stem cell biology and human genetics communities to model the impact of natural genetic variation on phenotypic variation and disease-risk.

overall_design: We converted embryonic stem cells (ESCs) from the 7 of the 8 Diversity Outbred founder strains (129S1/SvImJ, C57BL/6J, NOD/ShiLtJ, NZO/HiLtJ, CAST/EiJ, PWK/PhJ, WSB/EiJ) to epiblast stem cells (EpiSCs) and collected them for ATAC-sequencing at low passage.  We then performed directed differentiation to definitive endoderm (DE) from these cells.  Following 40 hours of differentiation, cells were collected and sorted using magnetic activated cell sorting (MACS) to perform ATAC-sequencing on the CXCR4-positive population.

first: Rachel

last: Glenn

first: Thomas

last: Vierbuchen

middle: P


title: RNA-seq samples of Escherichia coli  MG1655 for regulatory network analysis

city: La Jolla

first: Heera

last: Bajpe

state: CA

address: 9500 Gilman Dr.

institute: UC San Diego

summary: Transcriptomic data is accumulating rapidly. We assembled a top-down expression and regulation knowledge base for Escherichia coli. High-quality RNA-seq compendium consisting of data generated in the lab using a single experimental protocol.

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

overall_design: RNA-seq profiling of wild type and knock out strain (yfeC) in E. coli K-12 MG1655

first: Ye

last: Gao

last: Szubin

first: Ying

last: Hefner

first: Bernhard

middle: O

last: Palsson


title: Downregulation of miR-182-5p by NFIB promotes NAD+ salvage synthesis in colorectal cancer by targeting NAMPT [miRNA-seq]

first: Li

last: Zhou

overall_design: To study the regulatory effect of NFIB on miRNA in colon cancer

first: Song

last: He

first: Zhihang

first: Shu

last: Chen


title: mRNA-Engineered CRISPR-Cas Epigenetic Editors Enable Durable and Efficient Gene Silencing in Vivo [RNA-seq]

city: Shenzhen

first: Jian-Kang

last: Zhu

address: 1088 Xueyuan Blvd, Nanshan

institute: Southern University of Science and Technology

summary: Programmable epigenetic editors that achieve long-term gene expression modulation hold immense therapeutic potential. However, the large size of current CRISPR-based epigenome editors has limited their widespread application. This study describes the engineering of compact, mRNA-delivered epigenetic repressors, termed CRISPR OFF-EE, using SpyCas9, intein-based split-SpyCas9 or the smaller SF01 Cas variant, to achieve highly efficient and durable silencing of endogenous genes. We developed "superfolder" V2 mRNA constructs with optimized codon usage, UTRs, and nuclear localization signals, which enhanced mRNA stability, translational output, and LNP packaging. These CRISPR OFF-EE V2 editors demonstrated significantly improved and durable gene silencing across multiple targets in variable cell lines. Remarkably, a single intravenous administration of lipid nanoparticles (LNPs) encapsulating the optimized OFF-EE-V2 mRNA and selected sgRNAs targeting PCSK9 in mice led to an approximately 90% reduction in circulating PCSK9 protein and a 55% reduction in LDL-C levels, with effects persisting for at least 180 days. Whole-genome bisulfite sequencing confirmed the high specificity of these editors, with SF01-based editors exhibiting fewer off-target methylation events than SpCas9-based editors. The platform also demonstrated multiplexing capability and a favorable safety profile with liver-restricted activity. These findings establish a robust foundation for advancing in vivo therapeutics based on precise and durable epigenetic silencing using transiently delivered mRNA editors.

overall_design: RNA-seq profiling of the same liver and cell-line samples to assess transcriptomic changes caused by long-term Pcsk9 silencing at the 180-day time-point (n = 3/group).

first: Chao

last: Xu

first: Chen

last: Zeng

first: Mengge

first: Xiaofei

last: Wei

first: Minglei

last: Song

first: Xiaoyi

last: Liu

first: Weiping

first: Qitong

first: Xingkun

last: Ji

first: Pengyu

last: Luo

first: Hanlin

last: Gou

first: Yan

last: Sun

first: Liyong

last: Ma

first: Qianchuan

last: Shi

first: Xiaohua

last: Li

first: Yuxuan

last: lyu

first: Pengpeng


title: A PLURIPOTENT STEM CELL PLATFORM FOR IN VITRO SYSTEMS GENETICS STUDIES OF MOUSE DEVELOPMENT [RNA-seq]

first: Richard

last: Koche

overall_design: We converted embryonic stem cells (ESCs) from the 7 of the 8 Diversity Outbred founder strains (129S1/SvImJ, C57BL/6J, NOD/ShiLtJ, NZO/HiLtJ, CAST/EiJ, PWK/PhJ, WSB/EiJ) to epiblast stem cells (EpiSCs) and collected them for RNA-sequencing at low passage.  We then performed directed differentiation to definitive endoderm (DE) from these cells.  Following 40 hours of differentiation, cells were collected and sorted using magnetic activated cell sorting (MACS) to perform RNA-sequencing on the CXCR4-positive population.

first: Rachel

last: Glenn

first: Thomas

last: Vierbuchen


title: Identification of the immune enhancement effect of CpG ODN on periodontitis genetic vaccine by RNA sequencing

city: zunyi

first: Huijie

last: zhang

address: No. 1, Daxue Road, Honghuagang District, Zunyi City

institute: ZunyiMedicalUniversity

summary: Periodontitis is one of the main causes of tooth loss in adults. Early diagnosis and intervention can effectively control the progression of periodontitis. The research group constructed a periodontitis genetic vaccine in the early stage and improved the immunogenicity of the body by adding CpG oligonucleotide (CpG ODN). The purpose of this study was to analyse the potential mechanism by which CpG ODN adjuvants enhance the preventive effect of periodontitis genetic vaccines at the molecular level by transcriptome sequencing and to screen out key genes and signaling pathways for follow-up research.

overall_design: Nine 4- to 6-week-old male Sprague–Dawley (SD) rats were randomly divided into 3 groups, namely, the blank group, pVAX1-HA2-fimA control group, and pVAX1-HA2-fimA + CpG ODN experimental group. At the 1st, 2nd, and 4th weeks, the rats were immunized by intranasal instillation, and three groups of rats were sacrificed at the 7th week. After total RNA was extracted from the spleen, RNA-seq library construction and sequencing were performed.

last: Zhang

first: Fengjiao

first: Hang

last: Yu

first: Bin

last: Chen

first: Xiaohong

last: Zhou

first: Mingwei

last: Wang

first: Guohui

last: Bai


title: 5-HT regulates resistance to aumolertinib by attenuating ferroptosis in lung adenocarcinoma

city: Tianjin

first: Feng

middle: Yuan

last: Ying

address: Tianjin

institute: Tianjin Medical University Cancer Institute and Hospital

summary: Resistance to epidermal growth factor receptor (EGFR) -tyrosine kinase inhibitor (TKI) remains a critical clinical challenge in EGFR mutant lung adenocarcinoma (LUAD). Therefore, it is urgent to explore personalized treatment strategies based on distinct resistance mechanisms to reverse EGFR-TKI resistance. Herein, we found that HER2 S310F mutation contributes to third-generation EGFR-TKI resistance, driven by the accumulation of neurotransmitter 5-hydroxytryptamine (5-HT). Mechanistically, 5-HT interacted with 5-HT3 receptor, triggering calcium ion (Ca²⁺) influx and subsequent activation of the Ca²⁺/CAMKK2/AMPK pathway. This pathway activation conferred ferroptosis resistance, thereby driving aumolertinib resistance. 5-HT3 receptor  (HTR3) antagonists were pinpointed as potential agents for reversing aumolertinib resistance through drug library screening and transcriptomics analysis. We demonstrated that pharmacologically targeting 5-HT/HTR3 signaling with the clinically approved HTR3 antagonist palonosetron effectively restores aumolertinib sensitivity. Importantly, we showed that elevated 5-HT levels in patient plasma play a potential role in predicting EGFR-TKI resistance. Ourdata highlight the critical role of 5-HT and ferroptosis in the development of aumolertinib resistance, and propose HTR3 antagonists as a novel combination therapy strategy for LUAD treatment with aumolertinib.

overall_design: RNA-seq profiling of H1975 EV (Empty vector) cells and H1975 HER2 S310F mutant stable cells

first: Yuanying

last: Feng

first: Hua

last: Guo


title: Age-associated Tissue Organization Shifts Retinal Pigmented Epithelium Actomyosin Plasticity in Phagocytosis

city: Aachen

first: Teodora

last: Piskova

address: Wendlingweg 2

institute: RWTH Aachen University

summary: Mechanical homeostasis in healthy tissues relies on a dynamic balance of mechanical properties essential for maintaining tissue integrity and function. Over time, this integrity decays due to structural reorganization from extracellular remodelling or an imbalance of cell death and proliferation. This is particularly challenging in postmitotic tissues such as the retina, where lack of proliferation requires age-dependent structural adaptation. The retinal pigment epithelium exemplifies this adaptation, compensating for apoptotic events through morphological reconfiguration and cytoskeletal remodelling. To explore the connection between age-related structural changes and mechanical homeostasis, we developed an in vitro model simulating cell density reduction observed in the human retinal pigmented epithelium during ageing. This model is characterized by reduced cell height, shortened apical microvilli, and alterations in the actin cytoskeleton. The resulting age-associated phenotype leads to significant biomechanical changes, including tissue stiffening, enhanced junctional contractility, and apical cell cortex remodelling. Transcriptional profiling revealed notable shifts in actin-associated gene expression, indicating reduced plasticity when remodelling is necessary for phagocytosis of photoreceptor outer segments. Structurally aged monolayers exhibit changes in phagocytic activity that mirror those seen in aged individuals. Additionally, we observed an impaired capacity for apico-lateral remodelling while internalizing photoreceptor outer segments. This altered activity can be partially corrected by regulating actin network remodelling capacity with inhibitors targeting the actin nucleators Arp2/3 and formins. Overall, our findings suggest that age-related structural changes in the postmitotic outer retina shift its mechanical homeostasis, impacting physiological functions that are crucial for healthy vision.

overall_design: RNAseq profiling of 3 weeks mature hiPSCs-derived RPE (iCell-RPE, iRPE) cells 4 days after cell density reduction after on demand apoptosis via FKBP/casp8 activation (AgeD for Apoptosis-genereated Density) and time-matched control hiPSCs-derived RPE cells (Ctrl)

first: Aleksandra

middle: N

last: Kozyrina

first: Giedrė

last: Astrauskaitė

first: Mohamed

last: Elsafi Mabrouk

first: Sebastian

last: Schepl

first: Stacy Lok Sze

last: Yam

first: Ragul

last: Ravithas

first: Wolfgang

last: Wagner

first: Massimo

last: Vassalli

first: Jacopo

last: Di Russo


title: The Cdc42 effector and non-receptor tyrosine kinase, ACK defines a distinct STAT5 transcription signature in a chronic myeloid leukaemia cell model

first: Jessica

last: Corry

institute: University of Cambridge

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

overall_design: Refer to individual Series


title: mRNA-Engineered CRISPR-Cas Epigenetic Editors Enable Durable and Efficient Gene Silencing in Vivo [WGBS]

first: Jian-Kang

last: Zhu

type: Methylation profiling by high throughput sequencing

overall_design: Whole-genome bisulfite sequencing of mouse liver tissue and Hepa1-6 hepatocyte lines 180 days after a single LNP delivery of CRISPR OFF-EE mRNA/sgRNA targeting Pcsk9, compared with vehicle controls (n = 3/group).

first: Chao

last: Xu

first: Chen

last: Zeng

first: Mengge

first: Xiaofei

last: Wei

first: Minglei

last: Song

first: Xiaoyi

last: Liu

first: Weiping

first: Qitong

last: Chen

first: Xingkun

last: Ji

first: Pengyu

last: Luo

first: Hanlin

last: Gou

first: Yan

last: Sun

first: Liyong

last: Ma

first: Qianchuan

last: Shi

first: Xiaohua

last: Li

first: Yuxuan

last: lyu

first: Pengpeng


title: snRNA-seq analysis of dorsal striatum in a mouse model of 22q11 deletion syndrome

city: Memphis

first: Stanislav

last: Zakharenko

state: Tennessee

address: 262 Danny Thomas Pl, M2426

institute: St. Jude Children's Research Hospital

summary: We performed snRNA-seq on dorsal striatum of young adult (postnatal day 64) Df(16)1/+ mice and wildtype littermates. Nuclei were isolated from frozen tissue as previously described (PMID 30371670), and libraries were prepared using the 10× Genomics Chromium Next GEM Single Cell Kit (v3.1).

overall_design: Mice were heterozygotes or wildtype littermates from the Df(16)1 line and a mixture of males and females. Heterozygotes are hemizygous in a region homologous to the human 22q11.2 locus.

first: Mary

last: Patton

first: Brett

last: Teubner

first: Kristen

middle: T

last: Thomas

first: Sharon

last: Freshour

first: Alexandra

last: Trevisan

first: Andrew

middle: B

last: Schild

first: Cody

last: Ramirez

first: Jay

last: Bikoff

middle: S


title: Dynamic transcriptional landscape of canine hematopoiesis and cross-species comparisons revealed by single-cell RNA sequencing

city: Fort Collins

first: Robert

middle: Adam

last: Harris

state: CO

address: 1601 Campus Delivery

department: MIP

institute: Colorado State University

summary: We used single-cell RNA sequencing to characterize the heterogeneity of canine hematopoieitic cells collected from bone marrow.

overall_design: The complete dataset consists of 150bp paired end sequnecing data obtained using a 10x genomics single-cell RNA sequencing platform. The final dataset consists of 5 samples (3 whole bone marrow and 2 fluorescence activated cell sorted CD34+ cells) acquired from 3 healthy dogs.

first: Dylan

last: Ammons