title: Transcription and Cohesin Direct Genome Positioning and Domain Boundary Plasticity

city: Philadelphia

first: Ricardo

last: Linares Saldana

state: PA

address: 3400 civic center blvd

institute: University of Pennsylvania

summary: Spatial positioning of the genome and cellular identity have been correlated, but the mechanistic principles underlying 3D genome organization remain unclear. Consequently, our understanding of how compromised genome positioning leads to disease are limited. Here, we demonstrate that a cooperative relationship between gene transcription and cohesin activity directs lamina-associated domain (LAD) boundary plasticity and boundary-proximal gene spatial positioning. Transcription mediates LAD boundary fidelity and loss of transcription repositions LAD-boundary genes to the nuclear lamina. The transcriptional repression-mediated repositioning is dependent on cohesin’s loop extrusion activity and cannot be linked to heterochromatin modifiers or compaction status. Further, pathogenic transcriptional silencing of the LAD-boundary gene FXN in Friedrich’s Ataxia is associated with improper peripheral positioning of FXN. Strikingly, loss of cohesin activity is sufficient to reposition mutant FXN away from the nuclear periphery and partially restore FXN transcription. Taken together, we reveal how molecular regulators of distinct genome organization processes collaboratively orchestrate LAD boundary plasticity.

overall_design: LB1, H3K9me2, and RAD21 ChIP-seq in human fibroblasts. LB1 ChIP-seq in HCT116-mAID-RAD21 cells.

first: Ashley

last: Karnay

first: Parisha

last: Shah

first: Rajan

last: Jain


title: Paired CRISPR screens to map gene regulation in cis and trans (RNA-seq)

status: Public on Jun 24 2026

city: NEW YORK

first: Xinhe

last: Xue

state: New York

address: 101 Avenue of the Americas

country: USA

institute: New York Genome Center/New York University

type: Expression profiling by high throughput sequencing

summary: In this study, we develop a scalable approach that pairs discovery of cis- and trans-acting elements to systematically decipher the gene regulatory network. We explore the regulation of the immune checkpoint PD-L1 under both basal and IFNγ-stimulated contexts. PD-L1 expression on tumor cells serves as a clinically-actionable diagnostic for immune checkpoint blockade therapy across multiple cancer types.

overall_design: RNA-seq for BxPC-3 human pancreatic adenocarcinoma cells

first: Xiao

last: Wang

first: Zoran

last: Gajic

first: Christina

last: Caragine

first: Mateusz

last: Legut

first: Mari

last: Bell

first: Wen-Wei

last: Liang

first: Conor

last: Walker

first: James

last: Kim

first: Rachel

middle: E

last: Yan

first: Gina

middle: I

last: Hong

first: Hans-Hermann

last: Wessels

first: Congyi

last: Lu

first: Neil

last: Bapodra

first: Gamze

last: Gursoy

first: Neville

last: Sanjana


title: Myl1+ adipose progenitor cells (APCs) support brown adipose tissue (BAT) maintenance in adult mice

city: Minneapolis

first: Hai-Bin

last: Ruan

state: MN

department: Integrative Biology and Physiology

institute: University of Minnesota

summary: The ontogeny of brown adipose tissue (BAT) begins during embryogenesis and continues into the postnatal period and throughout adulthood. Distinct populations of adipose progenitor cells (APCs) have been identified to support BAT development and thermogenesis; however, the division of labor and temporal relationship between different APCs, particularly during adulthood and aging, remain undetermined. Using integrative single-cell analysis and lineage tracing, we identified a distinct population of Myl1-expressing cells that emerge in an age-dependent manner and function as committed BAT progenitors in adult and middle-aged mice. The blockade of Myl1+ APC differentiation leads to BAT paucity and impaired glucose metabolism in adult mice. Collectively, our results support a progenitor switching model in which distinct APC populations control sequential brown adipogenesis and shape BAT heterogeneity.

overall_design: To assess the physiological importance of the differentiation from Myl1+ APCs into adipocytes, we knocked out the master adipogenic transcription factor PPARγ driven by the Myl1-Cre. 7-month-old male Pparg-flox (wt) and Pparg-Myl1-Cre (ko) mice fed on normal chow were exposured to 4 degree cold in a CLAMS system for 24h and sacrified for interscapular BAT tissue dissection, RNA extraction, and RNA-sequencing.

first: Zan

last: Huang

first: Zengdi

last: Zhang


title: Increased Insulin Action, Glucose Metabolism and Muscle Function in Supervillin-knockout and Supervillin-mutant Mice

city: Gainesville

first: Yangyi

middle: Edward

last: Luo

state: FL

address: 1864 Stadium Road

institute: University of Florida

summary: We here describe mouse models with complementary homozygous Svil mutations. In skeletal muscle, Svil-Mut mice express the Svil-encoded N-terminus fused to the bgal-neo gene trap tag and lack the highly conserved archvillin C-terminus; Svil-KO mice lack expression of all known Svil-encoded proteins; and Svil-loxP mice contain loxP sites for tissue-specific disruption of protein expression. Older Svil-KO male mice showed decreased levels of markers for type 1, 2a and 2b muscle fibers. Male mice showed elevated pERK/ERK signaling during lengthening contractions, consistent with low-level muscle damage such as that seen in myofibrillar myopathy-10 in humans lacking SVIL proteins. Female mice lacking full-length Svil-encoded proteins, including supervillin and archvillin, exhibited reduced body weights and reduced fat mass. Females in both strains exhibited improved glucose tolerance and lower insulin levels following intraperitoneal glucose injections. Hyperinsulinemic-euglycemic clamp experiments showed increased insulin sensitivity in both strains and increased glucose metabolism in adipose tissues in female Svil-Mut mice. The GLUT4 glucose transporter was increased in skeletal muscle in breeder-aged female Svil-KO and Svil-Mut mice. RNA-Seq revealed increases in Rab7 and decreases in Mef2c mRNAs as potential mediators. A yeast two-hybrid screen identified new Svil candidate interactors, including CH1 domains of muscle Z-line proteins, a potential dimerization site and ARHGAP21 / RHO GTPase activating protein 21, a negative regulator of glucose-stimulated insulin secretion in pancreatic beta cells. We suggest that the Svil-Mut and Svil-KO strains described here will be useful models for understanding signaling within and between tissues regulating glucose metabolism.

overall_design: RNA Sequence was performed on purified RNA isolated from muscle tissue isolated from WT, Svil-Mut, and Svil-KO samples at 13months of age. Libarary were then generated and sequenced.

first: Tara

middle: C

last: Smith

first: Yanyi

first: Elisabeth

middle: R

last: Barton

first: Elizabeth

middle: J

last: Luna


title: Nicotine and tobacco smoke reshape neuronal signaling networks at a single-cell perspective

city: 杭州

first: XING

last: JI

state: State

address: 余杭塘路866号

country: China

institute: zhejiang university

summary: Nicotine and cigarette smoke exposure significantly impact brain function, yet their distinct cellular and molecular mechanisms remain unclear. To address this, we conducted comprehensive single-nucleus RNA sequencing (snRNA-seq) analysis on whole-brain samples and specifically on the ventral tegmental area (VTA) of adult C57BL/6 mice following nicotine or smoke exposure. Our study identified 18 major transcriptionally distinct cell populations across the whole brain and 27 distinct clusters within the VTA, covering major neuronal and glial cell types. Differential gene expression and KEGG pathway enrichment analyses revealed distinct transcriptional responses: nicotine prominently activated synaptic and addiction-related signaling pathways in neuronal populations, including dopaminergic and glutamatergic pathways, whereas smoke exposure triggered broader metabolic, immune, and endocrine responses. CellChat-based network analysis demonstrated significant remodeling of intercellular communication, notably enhanced oligodendrocyte-to-neuron signaling via the Neurexin (NRXN) pathway under nicotine exposure, contrasted with diffuse and attenuated signaling under smoke exposure. Additionally, oligodendrocytes exhibited pronounced metabolic adaptation, highlighted by upregulation of mitochondrial enzyme PISD, indicating lipid remodeling and stress adaptation in response to smoke exposure. Collectively, our findings provide novel insights into the cell-type-specific transcriptomic reprogramming and intercellular communication dynamics induced by nicotine and smoke, offering critical mechanistic understanding relevant to tobacco addiction and related neuroadaptations.

overall_design: ingle-cell nuclei from the brain and VTA were isolated by Dounce homogenization and debris removal, and analyzed using snRNA-seq.

first: Jian

last: Jiang

first: Anfu

last: Hu

first: Yixiao

last: Jin

first: Xia

last: Li

first: Guo-jun

last: Zhou

first: Yi

last: Shen

first: Chengyun

last: Xu

first: Xing

last: Ji

first: Ximei

last: Wu

first: Hong-Juan

last: Wang


title: PGC1α expression using targeted redox-responsive nanogels protects against prostate cancer in vivo

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

country: United Kingdom

institute: MRC London Institute of Medical Sciences

summary: Prostate cancer is among the most frequently diagnosed cancers in men in the UK and US. Increasing evidence implicates metabolic dysregulation as a critical driver of disease progression. Central to this process is peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PGC1α) that promotes oxidative metabolism and mitochondrial biogenesis while inhibiting metastatic programs. This work investigated the therapeutic potential of PGC1α overexpression via mRNA delivery. Here, we report a prostate-specific, targeted disulphide-crosslinked nanogel system for intracellular delivery of mRNA encoding the N-terminal isoform of PGC1α (NT-PGC1α). Functionalization of the NGs with a peptide targeting prostate-specific membrane antigen (PSMA) enabled selective delivery of NT-PGC1α mRNA in PCa cells and 3D spheroid models. We confirmed sustained PGC1α expression, and increased mitochondrial protein content, indicative of enhanced mitochondrial biogenesis. These nanogels, which were prepared in situ using a nanopolymerization technique, exhibited high mRNA loading capacity, low cytotoxicity, and redox-responsive cargo release, enabling controlled cytosolic delivery following intracellular glutathione-mediated degradation. In vivo, systemic administration of the PSMA-targeted NT-PGC1α mRNA-loaded nanogels resulted in tumour-preferential accumulation and significant suppression of xenograft growth (by 73.4% relative to untreated control), with minimal systemic toxicity. This study presents the first example of a prostate-targeted, disulfide-crosslinked nanogel system for mRNA-mediated metabolic reprogramming in prostate cancer, and highlights its promise as a platform for future RNA-based targeted and precision stimuli-responsive cancer therapies.

overall_design: RNA-seq profiling of C42 prostate cancer cells treated with NT-PGC1a mRNA loaded nanoparticles.

first: Rupali

last: Dabas

first: Lida

last: Kabir

first: Naveenan

last: Navaratnam

first: Hothri Ananyambica

last: Moka

first: Alessandro

last: Sardini

first: G

last: Mazzei

first: Nazila

last: Kamaly

first: David

last: Carling


title: Bulk RNA-seq of EO771 breast cancer cells with 3 conditions

city: Cold Spring Harbor

first: Yue

state: NY

address: One Bungtown Rd, Demerec RM 120

department: Cancer and Neuroscience

institute: Cold Spring Harbor Laboratory

summary: Bulk RNA sequencing was performed to compare mRNA expression profiles across six experimental conditions: monoculture of EO771 breast cancer cells; conditioned medium from DRG neurons applied to EO771 cells; and direct co-culture of EO771 and DRG neurons followed by fluorescence-activated cell sorting (FACS) to isolate EO771 cell populations. The aim was to identify transcriptional programs regulated by tumor–neuron interactions, including acute gene expression changes, intercellular signaling pathways, and broader pathway-level alterations. The dataset is intended for differential expression analysis, pathway enrichment, and hypothesis generation for downstream functional studies.

overall_design: Biological replicates: n = 3 independent samples per condition. RNA was extracted from each sample and processed for library preparation using standardized protocols. Differential expression of mRNAs were compared between three groups: mono-culture of EO771 (EO771_mono); conditioned medium (EO771_CM) and co-culture in EO771 population (EO771_co). Where feasible, sample processing was performed with the operator blinded to experimental groups.

first: Elena

last: Ghiban

first: Jeremy

last: Borniger


title: In vitro implantation model that recapitulates primary implantation events

city: Hirakata

first: Toru

last: Matsu-ura

state: Osaka

address: 2-5-1 Shin-mach

department: Pathology

country: Japan

institute: Kansai Medical University

summary: We established an in vitro implantation model (IVIM) with mouse endometrial organoids (EMOs), mouse endometrial stromal cells (ESCs), and mouse blastocysts. EMOs expressing endometrial epithelial markers were cultured in Matrigel domes. In the IVIM, the outer surface of endometrial epithelial cells (EECs) faced the blastocyst within a microwell. Under physiological conditions, blastocysts attach to the apical surface of EECs. Because the outer surface of EMOs cultured in Matrigel corresponds to the basal side, EMOs were retrieved from Matrigel and cultured for 4 days in an ultra-low attachment plate, inducing epithelial polarity inversion and generating apical-out EMOs. Microwells were fabricated in 7–8 mm glass-bottom wells by adding Matrigel containing ESCs and inserting a three-dimensional (3D) printed mold with multiple protrusions. After gelation at 37 °C, the mold was removed to form the microwells. Each microwell containing ESCs and an EMO was referred to as a mini-uterus, into which a blastocyst was placed and cultured using in vitro culture medium 2 (IVC2) medium. Confocal imaging demonstrated blastocyst invasion into the EMOs approximately 48–72 h after imaging began. Single-cell RNA sequencing (scRNA-seq) was performed on cells recovered from the IVIM after 72 h of co-culture to characterize their cellular composition and transcriptional profiles.

overall_design: In the IVIM system, blastocysts are placed in the artificial uterus for experimentation. The artificial uterus is constructed based on microwells fabricated on a glass-bottom dish. A microwell template sized for the millimeter-scale well, one well of a 4-well glass bottom dish (D141400, Matsunami), or one well of a 96-well plate was designed on Fusion 360 (Autodesk) and printed with a 3D printer (Onjet Eden260VS, Stratasys). A 50 µl drop of Matrigel containing 5×104 stromal cells was placed on the microwell template and then transferred into the millimeter-scale well filled with 50 µl of Matrigel containing 5×104 stromal cells, followed by incubation for 30 min to allow Matrigel solidification. After 100 µl of IVC2 medium (Advanced DMEM/F12 supplemented with 30% (vol/vol) KSR (10828010, ThermoFisher), ITS-X supplement (094-06761, FUJIFILM), L-Glutamine (16948-04, Nakalai tesque), 3 pg/ml E2 (E8875, Merck), 60 ng/ml P4 (Progesterone, P8783, Merck), and penicillin-streptomycin) was added, the microwell template was removed, leaving microwells filled with IVC2 medium. An EMO and a zona-free blastocyst were manually paired in a microwell to assess implantation-like events. EMOs and ESCs were extracted from female C57BL/6 mice. Embryos were recovered from B6D2F1 mice.

first: Matsu-ura

last: Toru

first: Pham

last: Tam Thi

first: Ikeda

last: Yoshiki

first: Yoshida

last: Naoko

first: Kobayashi

last: Tetsuya

first: Hashimoto

last: Yoshiko

first: Atsumi

last: Naho

first: Takeda

last: Hiroyuki

first: Kinoshita-Okabe

last: Miki

first: Takahashi

last: Keiichi

first: Okada

last: Hidetaka

first: Tsuta

last: Koji


title: RNA-seq Identifies FOS as a Potential Therapeutic Target Activating Neural Stem Cells via miR-21/SOX2 Pathway in Hypertensive Intracerebral Hemorrhage

city: shanghai

first: Zuopeng

last: Su

address: 170 Xinsong Road, Xinzhuang Town, Minhang District,

department: Department of Neurosurgery,

institute: Minhang Hospital, Fudan University

summary:
Objective: Intracerebral hemorrhage (ICH) is a severely devastating neurological disorder. At present, there is no specific effective therapy for ICH, and its pathophysiological mechanism remains incompletely elucidated. Herein, we attempted to identify blood mRNA biomarkers, potential therapeutic targets and pathways associated with ICH via RNA sequencing.
Results: Biological analysis of RNA-seq data screened numerous differentially expressed genes involved in various biological processes including inflammation, immunity and regeneration, which were systematically summarized in this study. Through bioinformatic analysis and experimental validation, we found that the expression level of FOS gene was upregulated after ICH, with the potential to participate in the proliferation and differentiation of neural stem cells and promote neural recovery. Our research further indicated that Fos may be involved in the regulation of biological behaviors of neural stem cells via the miR-21/SOX2 signaling pathway, although its exact mode of action requires further investigation.
Conclusion: Collectively, RNA-seq delineated the precise transcriptional alterations in peripheral blood between patients with hypertensive intracerebral hemorrhage and hypertensive control subjects. These findings establish a potential therapeutic target centered on the FOS gene, which is aimed at activating neural stem cells following intracerebral hemorrhage.

overall_design:
We enrolled patients diagnosed with hypertensive intracerebral hemorrhage (HICH) and hypertensive individuals undergoing routine physical examination at Minhang Hospital, Fudan University, between September 2025 and January 2026. Peripheral venous blood samples were collected from all subjects. For HICH patients, blood samples were obtained within 24 hours after ictus.
Inclusion criteria for HICH patients:
1.Admission blood pressure > 140/90 mmHg with a prior diagnosis of hypertension and poor blood pressure control;
2.Age between 18 and 85 years;
3.Radiologically confirmed hypertensive intracerebral hemorrhage.
Exclusion criteria for HICH patients:
1.Severe primary diseases involving cardiac, hepatic, renal, or hematopoietic dysfunction;
2.Psychiatric disorders;
3.Intracerebral hemorrhage caused by vascular malformation, trauma, brain tumor, or other etiologies.
Hypertensive control subjects were matched with the HICH group for age and sex, presented with poorly controlled blood pressure (> 140/90 mmHg) on physical examination, and had normal general examination results without obvious positive signs.

first: Wei

last: Dai

first: Jiarui

last: Du

first: Gang

last: Shen

first: Fulin

last: Xu


title: A database of extrachromosomal circular DNA (ecDNA) profiles across primary intracranial tumors

city: Wuhan

first: Haobin

last: Ren

state: Hubei

address: G9P7+CP8, Wuchang District

institute: Wuhan University

summary: Extrachromosomal circular DNAs (ecDNAs) have recently emerged as critical drivers of tumor evolution, distinct from linear chromosomal DNA. The presence of ecDNA often correlates with poor patient outcomes and rapid cancer progression, suggesting a potential role as a biomarker for early detection. Here, we present a dataset of ecDNA landscapes generated via extrachromosomal circular DNA sequencing (Circle-Seq) across four types of primary intracranial tumors: glioblastoma, meningioma, pituitary adenoma, and vestibular schwannoma. We provide comprehensive functional annotations of the derived ecDNA profiles, characterizing their genomic distribution and potential oncogenic content. This study characterizes the ecDNA population within these distinct brain tumor subtypes, offering a reliable resource for future biomarker identification and tumour-specific mechanistic investigations.

overall_design: ecDNA purification was performed on DNA extracted from meningioma, glioblastoma, pituitary adenoma and vestibular schwannoma. After confirming the successful enrichment of ecDNA from total DNA samples, Phi29-assisted ecDNA rolling circle amplification was performed before DNA library preparation. All DNA libraries were sequenced on the illumina NovaSeq 6000 platform in PE150 mode.

first: Gong

last: Hao

first: Du

last: Wu

first: Xin

last: Liu

first: Jichun

last: Shi


title: Jejunal gene expression in surfactant protein D (Sftpd) knockout and wild-type mice after doxorubicin-induced intestinal toxicity

city: Odense

first: Mark

last: Burton

address: J.B. Winsløvsvej 4

department: Clinical Genetics

country: Denmark

institute: Odense University Hospital

summary: Surfactant protein D (SP-D, gene Sftpd) is an anti-inflammatory host defence collectin produced by epithelial cells on mucosal surfaces. We investigated whether SP-D attenuates chemotherapy-induced gastrointestinal toxicity and inflammation in mice. Sftpd-/- (KO) mice and Sftpd+/+ (WT) littermates received a single intraperitoneal injection of doxorubicin (20 mg/kg) or isotonic saline and were sacrificed on day 3 or day 7. Genome-wide expression in the jejunum was profiled on the Affymetrix GeneChip Mouse Transcriptome Array 1.0.

overall_design: Two genotypes (Sftpd-/- KO vs Sftpd+/+ WT littermates) x two treatments (doxorubicin 20 mg/kg i.p. vs isotonic saline) x two timepoints (day 3, day 7) = 8 groups, n=5 per group, 40 jejunum samples, one array per animal.

first: Mathias

last: Rathe

first: Sebastian

last: von Huth

first: Grith

middle: L

last: Sørensen

first: Faisal

last: Fazli

first: Mads

last: Thomassen

first: Pingping

last: Jiang

first: Jesper

middle: B

last: Møller

first: Uffe

last: Holmskov

first: Steffen

last: Husby


title: Differential gene expression in Toxoplasma gondii-infected cells with modulated IFITM2/3 expression

city: Fuzhou

first: Yanlong

last: Gu

address: 15 Xiadian Road, Cangshan District, Fujian Agriculture and Forestry University

summary: Transcriptome sequencing (RNA-seq) was performed to investigate the global gene expression changes in host cells following Toxoplasma gondii infection, with a focus on the regulatory roles of interferon-induced transmembrane proteins 2 and 3 (IFITM2/3). Host cells were transfected with IFITM2 or IFITM3 overexpression vectors or empty vector controls, then infected with Toxoplasma gondii. Uninfected cells with corresponding vector transfections were included as controls.

first: Meng-Jie

last: Chu


title: Transcriptional response of A549 lung cancer cells to X-rays under normoxia, or chronic or transient hypoxia

city: Koeln

first: Christine

middle: Elisabeth

last: Hellweg

state: Nordrhein-Westfalen

address: Linder Hoehe

department: r, IInstitute of Aerospace Medicine

country: Germany

institute: German Aerospace Center

summary: The aim of this project was to study the X-ray-induced changes in A549 on the gene expression level under different oxygen conditions.

overall_design: For this purpose, the cells were incubated  under normoxia, or chronic or transient hypoxia for 48 h and were irradiated with 8 Gy of X-rays (0 Gy, 8 Gy) and RNA was extracted 4 h after irradiation.

first: Hasan

last: Nisar


title: Transcriptional response of A549 lung cancer cells to carbon ions under normoxia, or chronic or transient hypoxia

summary: The aim of this project was to study the radiation (carbon ions)-induced changes in A549 on the gene expression level under different oxygen conditions .

overall_design: For this purpose, the cells were incubated  under normoxia, or chronic or transient hypoxia for 48 h and irradiated with 8 Gy of carbon ions (0 Gy, 8 Gy) and RNA was extracted 4 h after irradiation.

first: Marie Denise

last: Hoffmann

first: Bikash

last: Konda

first: Jessica

last: Kronenberg


title: Comparative analysis of single-cell gene expression across the Saccharomycetacea

city: Ploen

first: Fernanda

last: Giersdorf

address: August-Thienemann 2

department: Theoretical Biology

institute: Max Planck Institute for Evolutionary Biology

summary: Gene expression noise is a fundamental driver of phenotypic variation, yet its evolutionary dynamics across species remain poorly understood. In this study, we used single-cell RNA sequencing to perform a comparative analysis of gene expression noise across multiple species of yeast. We quantified and compared single-cell transcriptional variability to identify conserved and divergent patterns of expression noise across these species. Our analysis revealed distinct noise profiles among orthologous genes, highlighting how selection operates on transcriptional fluctuation rather than just mean expression levels.

overall_design: scRNA-seq of Saccharomycetacea yeasts grown at 20C in nutrient rich GPY medium

first: David

middle: W

last: Rogers

first: Julien

middle: Y

last: Dutheil


title: Trained immunity links hematopoietic stem cell aging to aging-associated inflammation

city: Berkeley

first: Yibing

last: Chen

state: CA

address: Morgan Hall 335

department: Metabolic Biology & Nutrition

institute: University of California, Berkeley

type: Genome binding/occupancy profiling by high throughput sequencing

summary: SIRT3 is a mitochondrial NAD+-dependent deacetylase. To investigate the role of SIRT3 in hematopoietic stem cell aging, we generated and characterized mouse models overexpressing SIRT3.

overall_design: Cleavage Under Targets and Tagmentation sequencing (Cut&Tag-sequencing) of HSCs isolated from 2-year-old Mx1-T3 and Mx1-Cre control mice using an antibody against H3K4me3

first: Marine

last: Barthez

first: Danica


title: Multidimensional Exposure Architecture Shapes Vaping-Associated Transcriptomic Dysregulation in Oral Epithelium

city: Los Angeles

first: Ahmad

last: Besaratinia

address: 1450 Biggy Street

department: Population & Public Health Sciences

institute: University of Southern California

summary: Electronic cigarette (e-cig) use (vaping) has been associated with dysregulation of genes and molecular pathways in epithelial tissues. However, the relative contributions of dose and product characteristics to vaping-associated transcriptomic alterations have not been systematically evaluated. We performed RNA-sequencing of oral epithelial cells from e-cig users (vapers), cigarette smokers, and non-users. Differential gene expression was assessed using covariate-adjusted limma-voom modeling with false discovery rate control. We evaluated the extent to which exposure-specific dose metrics (including cumulative e-liquid, cumulative e-nicotine, years vaped, and plasma cotinine for vaping, and pack-years and plasma cotinine for smoking) explained transcriptional changes. Among vapers, we additionally examined whether device generation and flavor type contributed to variation in gene expression. Both vaping and smoking were associated with transcriptomic dysregulation relative to non-users, with partial overlap in differentially expressed genes (DEGs). Functional enrichment analyses revealed disruption of shared cancer- and signaling pathways, including RHO GTPase Cycle, as well as perturbation of pathways specific to vapers or smokers. Among vapers, 27.6% of DEGs showed concordant behavior across all dose metrics, indicating heterogeneous dose-response patterns for the remaining DEGs. Device generation and flavor type explained additional, largely non-overlapping components of gene expression variability. A much higher proportion of smoking-associated DEGs (54.1%) was consistently affected across dose metrics, reflecting more unified dose-dependent responses. These findings suggest that vaping-associated transcriptional dysregulation reflects combined influences of dose and product characteristics, highlighting structural differences in molecular perturbations between vaping and smoking. Incorporating multidimensional exposure metrics and product features into regulatory evaluation may better capture the biological complexity of e-cig exposure, thus informing clinical, public health practice, and regulatory decisions.

overall_design: Bulk RNA-sequencing of oral epithelial cells from e-cig users, cigarette smokers, and non-users

last: George

first: Stella

last: Tommasi

first: Niccolo

last: Pabustan

first: Daria

middle: M

last: Kessler

first: Zairah

last: Thomas

first: Lourdes

last: Baezconde-Garbanati

first: Kimberly

middle: D

last: Siegmund


title: Transcriptional Profiling of Otic Capsule and Femur in the oim Mouse Model of Osteogenesis Imperfecta

city: New york

first: Yurii

last: Chinenov

address: 535 E 71 str, Hospital for Special Surgery

department: Research Division

institute: Hospital for special surgery

summary: Hearing loss is a common and debilitating complication of the brittle bone disorder osteogenesis imperfecta (OI). Existing treatments that are designed to address age-related hearing loss in the broader population do not meet the needs of OI patients, who exhibit skeletal fragility and begin to lose their hearing when they are young-adults. The biologic mechanisms responsible for hearing loss in OI are unknown, hindering the development of preventative therapies. To identify potential mechanisms that drive this condition, we performed transcriptome profiling on femoral and otic capsule specimens obtained from the Col1a2oim mouse model at 12- and 25-weeks of age. We found that the bulk transcriptomes of femora and otic capsules were markedly different, regardless of mouse genotype. Further, bone formation-associated transcripts were reduced at 25-weeks, compared to 12-weeks. Mice homozygous for the oim mutation exhibited increased abundance of transcripts associated with osteoblast activity and type I collagen production compared to wild-type mice in both femoral and otic capsule specimens. The most notable difference between oim and wild-type mouse otic capsules was the depletion of the transcripts that encode mucin and keratin, suggesting dysregulation of epithelial cells, which has been previously linked to hearing loss. Our data offer new insights into the mechanisms that disrupt the middle ear in OI. Analysis of epithelial cells obtained from OI patients and additional models of OI could suggest novel strategies to prevent and/or treat hearing loss.

overall_design: RNA-seq profiling of femur and ossicle tissues from WT, OIM, and HET mouse models at 12 and 25 weeks of age, including both male and female animals.

first: Ugur

last: Ayturk

first: Miracle

first: Ketsia

last: Seide

last: Oliver

first: Ezgi

last: Aydin

first: Erin

last: Carter

first: Cathleen

last: Raggio


title: Caspase-11 Mediated Hyperinflammation Impairs CD8⁺ T Cell Immunity and Viral Clearance in Severe SARS-CoV-2 Infection

city: Columbus

first: Amy

last: Hite

state: OH - Ohio

address: 1800 Cannon Drive 250 Lincoln Tower

department: Biomedical Informatics

institute: The Ohio State University

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

overall_design: Refer to individual Series


title: Dermal fibroblasts attenuate osteoarthritis by restoring synovial fibroblast homeostasis

city: Shanghai

first: Lei

last: Shi

state: 请选择

address: 115 Jinzun Road, Pudong New Area, Shanghai

institute: Shanghai Jiaotong university

summary: Background: Managing early-to-mid-stage knee osteoarthritis (OA) remains an unmet clinical need. Synovitis drives OA progression, but current anti-inflammatory therapies offer limited efficacy. Disrupted fibroblast lineage homeostasis is central in chronic inflammation, and targeting this may attenuate synovitis and pathological synovium-cartilage crosstalk in knee OA. Methods: Synovial single-cell sequencing, clinical histological and transcriptomic data assessed fibroblast lineage changes and similarities between dermal fibroblasts (DFb) and synovial fibroblasts. Labeled DFb injection in rat knees evaluated cell retention. Rat anterior cruciate ligament transection (ACLT) model with intra-articular DFb injection assessed the therapeutic efficacy. Co-cultures characterized DFb paracrine effects on synovial fibroblasts and chondrocytes. Proteomics identified active components in DFb supernatants.  Results: OA synovium exhibits disrupted fibroblast lineage homeostasis, marked by a prominent pro-inflammatory phenotype in synovial fibroblasts. DFb show high transcriptomic and morphological similarity to synovial fibroblasts from healthy donors. Post-injection, DFb engrafted within the synovium with more than 3-week retention. Intra-articular DFb injection alleviated synovitis and cartilage degeneration in ACLT-induced OA rats. Co-cultures confirmed DFb alleviated cytokine-induced inflammatory responses in synovial fibroblasts and chondrocytes via paracrine mechanisms, and integrated proteomic/transcriptomic analyses identified apolipoprotein D (APOD) as a potential key mediator of these anti-inflammatory effects.  Conclusions: This study validates a novel cell therapy for OA that targets disrupted fibroblast lineage homeostasis in synovitis. By modulating pro-inflammatory synovial fibroblasts and alleviating synovitis through restoring lineage homeostasis, DFb ameliorate OA progression, providing a new theoretical basis and practical approach for OA cell therapy research.

overall_design: Three groups of rats were involved: the Sham group underwent sham surgery, the PBS group received a PBS injection into the right knee two weeks after ACLT modeling. The DFb group received GFP fibroblasts injection into the right knee two weeks after ACLT modeling. Each group consisted of three rats. On the fifth day after injection, the rats were sacrificed, and the knee joint synovial tissues were removed, digested into single-cell suspensions, and then processed on the machine.


title: The periphery of nuclear speckles defines a spatially and temporally regulated compartment of long-lived intron-retained RNAs that resolves during mitosis

city: Frankfurt am Main

first: Josep

last: Biayna Rodriguez

state: Hessen

address: Theodor-Stern-Kai 7

institute: Institute of Cardiovascular Regeneration

summary: RNA localization adds a fundamental layer to gene expression by determining when and where translation-ready mRNAs become available. Here, we identify a distinct subnuclear RNA niche at the nuclear speckle periphery that links intron retention to cell-cycle-timed RNA release. Using compartment-resolved transcriptional inhibition, sequence-based deep learning, and single-molecule and super-resolution RNA imaging in human pluripotent stem cells, we define a class of nuclear RNAs with long-lived retained introns (LL-IR-RNAs) that maintain stable intron retention for hours and are enriched in genome maintenance and mitosis regulators, including centromere and kinetochore assembly, DNA repair, and telomere maintenance. Long-lived retained introns are characterized by elevated GC content, predicted structural stability, and nuclear speckle-associated RBPs. In interphase, LL-IR-RNAs localize to a nuclear speckle-proximal niche conserved between cell types. During mitotic remodeling, they undergo coordinated, kinase-dependent splicing and populate the cytoplasm of early G1 daughter cells. These findings link cis-encoded intronic features, subnuclear organization and mitotic remodeling to temporal control of RNA fate.

overall_design: hiPSCs WTC-11 (Coriell Institute) were cultured on Vitronectin (Thermo Fisher Scientific) coated plates or 18 mm round glass coverslips (for smRNA FISH and IF) in StemFlex basal medium (Thermo Fisher Scientific) with StemFlex supplement (Thermo Fisher Scientific), RevitaCell supplement with Rock inhibitor (Thermo Fisher Scientific) and 2.5% penicillin-streptomycin. hiPSCs were passaged with 0.5 mM EDTA in dPBS.  Actinomycin D (ActD, Sigma-Aldrich) was used at a final concentration of 5 μg/mL in complete growth media. Cell pellets and coverslips were harvested at 0 h, 0.5 h, 2 h and 4.5 h after adding ActD

first: Gabrijela

last: Dumbovic

last: Biayna Rodríguez

first: Anusha

last: Chaudhuri


title: RNA Terminal Uridylyl-Transferases Are Druggable Vulnerabilities in AML, but are Dispensable for Normal Hematopoiesis [SLAM-Seq]

city: Edinburgh

first: Yuka

last: Kabayama

address: Max Born Crescent

institute: University of Edinburgh

summary: Acute myeloid leukemia (AML) is an aggressive hematological malignancy arising from hematopoietic stem and progenitor cells (HSPCs). Current treatments often fail to eradicate AML; therefore, new therapeutic strategies are essential. Here, we reveal that RNA Terminal-Uridylyl-Transferase-Enzymes 4 and 7 (TUT4/7) are druggable therapeutic targets, whose genetic deletion suppresses AML growth, induces apoptosis and improves the survival in leukemic mouse models. Notably, a pre-clinical TUT4/7 inhibitor promotes cell death in AML patient samples and synergizes with venetoclax. Mechanistically, TUT4/7 inactivation suppresses mevalonate pathway gene expression, compromising the cholesterol synthesis pathway. Current AML therapies often cause severe hematopoietic toxicity. Although Tut4/7 deletion results in inflammatory activation throughout the hematopoietic system, this is permissive to a normal lifespan and Tut4/7-deficiency does not compromise HSPC function. Together, these findings identify TUT4/7 as druggable targets, whose inactivation suppresses AML while sparing normal hematopoiesis. In combination with venetoclax this represents a promising therapeutic strategy.

overall_design: SLAM-seq profiling of control and Tut4/7 double conditional knockout murine acute preleukemic cells.

first: Christopher

last: Mapperley

first: Elise

last: Georges

first: Ali

middle: A

last: Azar

first: Hannah

last: Lawson

first: Iwo

last: Kucinsk

first: Derek

last: George

first: Joana

last: Campos

first: Corey

last: Fyfe

first: Jozef

last: Durko

first: Wei

last: Chan

first: Lewis

last: Allen

first: Babak

last: Jazayeri

first: Edward

last: Blacker

first: Louie

middle: N

last: van de Lagemaat

first: Aurelien

last: Tripp

first: Theodoros

last: Roumeliotis

first: Giulia

last: Guiducci

first: Eleanor

last: Herbert

first: Jasmin

last: Paris

first: Jyoti

last: Choudhary

first: George

last: Poulogiannis

first: Robert

last: Campbell

first: Marcos

last: Morgan

first: Lovorka

last: Stojic

first: Folkert

last: Van Werven

first: Douglas

last: Vernimmen

first: Berthold

last: G ttgens

first: D nal

last: O Carroll

first: Kamil

last: Kranc


title: Senescence inhibition by rapamycin mitigates radiation-induced atherosclerotic characteristics in human coronary endothelial cells

city: Didcot

first: christopher

last: Whiteman

address: UKHSA

institute: UK Health Security Agency

summary: Ionising radiation (IR) is a recognised risk factor for cardiovascular disease (CVD), yet the mechanisms linking it to exposure remain incompletely understood. We show that IR drives a pro-atherogenic phenotype in human coronary artery endothelial cells (HCAECs) through the induction of cellular senescence, and that rapamycin attenuates these effects. IR triggered hallmark senescence features, including elevated SA-β-galactosidase activity, nuclear enlargement, and increased CDKN1A and p53 expression. Functionally, irradiated HCAECs displayed impaired barrier integrity and heightened monocyte adhesion. Transcriptomic and proteomic profiling revealed broad IR-induced alterations enriched in DNA damage response, cell-cycle arrest, senescence, proteostasis, and immune-related pathways. These findings establish a mechanistic link between radiation-induced endothelial senescence and early atherogenic-associated dysfunction, demonstrating that senescence is a driver of vascular injury. Importantly, identifying mTOR inhibition as a promising strategy to counteract radiation-associated endothelial dysfunction. This work positions senescence as a tractable therapeutic target in radiation-induced vascular injury.

overall_design: RNAseq of human coronary artery endothelial cells 7 days post ionising radiation exposure with rapamycin treatment

first: Christopher


title: Transient YAP activation uncovers the neurogenic potential of proliferative mammlian Müller Glia

city: Houston

first: Justin

last: Dhindsa

state: TX

address: 1 Baylor Plz

institute: Baylor College of Medicine

summary: The Hippo pathway effector YAP promotes spontaneous proliferation of Müller glia (MG), suggesting that bypassing Hippo signaling and activating YAP could enhance retinal regeneration. However, whether proliferative adult MGs retain meaningful neurogenic competence remains unclear. Here, using viral delivery of a Hippo-resistant YAP variant to wild_x0002_type adult MGs, we achieved transient YAP activation in adult MGs, inducing proliferation followed by cell-cycle withdrawal and differentiation. Intersectional genetic lineage tracing and EdU labeling, combined with transcriptomic analyses, revealed that YAP-activated MGs predominantly regenerate MGs, whereas only a subset gives rise to bipolar neurons. These results indicate that proliferative MGs acquire a state resembling that of late-stage retinal progenitors, with limited neurogenic lineage potential. We conclude that YAP-activated cell_x0002_cycle re-entry inefficiently reprograms adult MGs toward photoreceptor or ganglion cell fates. These findings define the limited competence of proliferative adult MGs to contribute to neurogenic fates and provide a rigorous framework for assessing in vivo glial reprogramming strategies.

overall_design: FACS-purified tdTomato+ cells from AAV-control (n = 16 retinas pooled) and AAV-YAP5SA-infected retinas (n = 21 retinas pooled) at 56 days post-injection processed immediately after sorting.

first: English

last: Laserna

first: Irina

middle: V

last: Saltykova

first: Benjamin

last: Hall

first: Xufei

last: Tong

middle: S

first: Borna

last: Sarker

first: Ayrea

last: Hurley

first: Paul

middle: G

last: Swinton

first: William

last: Lagor

first: Nicholas

last: Tran

first: James

middle: F

last: Martin

first: Ross

last: Poche


title: Placental gene co-expression networks and mediation analysis identifies pathways and genes associated with birthweight

city: New York

first: Corina

last: Lesseur

address: 1 Gustave L. Levy Pl

institute: Icahn School of Medicine

summary:
The Developmental Origin of Health and Disease (DOHaD) concept postulates that birthweight (BW), a proxy of the in utero environment shaped by environmental and genetic factors, can impact future health. The placenta plays a key role in fetal growth and metabolic programming, thus essential to BW. However, the mechanisms by which intrauterine environment shapes BW, potentially via placenta, remain largely unknown.
To investigate the placental contribution to BW, we profiled the placental transcriptome from two large U.S. birth cohorts. We constructed weighted gene co-expression networks (WGCN) from all (N=673), female (N=331) and male (N=342) placentae, and identified 23, 24, and 22 modules, respectively. Pathway enrichment analyses of these networks revealed consistent functional processes related to signal transduction, lysosomes, brain development, immune, and HIF-1 hypoxia pathways. Seven modules were associated with BW in each network, and differential expression analysis within these modules identified 441, 467 and 227 genes in the overall, female, and male networks, respectively. We also identified 14, 12, and 8 genes mediating the impact of WGCN modules on BW, including genes related to oxidative stress (SLC25A27, MCTP1 and CD9), brain development (NFIA and SEMA3D) and maternal-fetal immune tolerance (TLR1 and TLR6).
Together, these placenta WGCNs revealed pathways and genes mediating the effect of placental transcriptome on BW offering mechanistic insights, including sex-specific mechanisms, on fetal programing. These findings support DOHaD and improve the understanding of how the intrauterine environment influences BW and later-life traits.

overall_design:
RNAseq profiling of 319 healthy placenta bulk samples

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

first: Ariadna

last: Cilleros Portet

first: Bushra

last: Amreen

first: Hachem

last: Saddiki

first: Amber

last: Burt

first: Karen

last: Hermetz

first: Maya

last: A. Deyssenroth

first: Diane

last: Gilbert Diamond

first: Margaret

last: R. Karagas

first: Ke

last: Hao

first: Carmen

last: J. Marsit

first: Jia

last: Chen


title: An mRNA vaccine confers enhanced protection against herpes sim-plex virus through a type I interferon-dependent pathway

city: Tianjin

first: Zhao

last: Wenying

address: 22 Qixiangtai Road, Heping District

institute: Tianjin Medical University

summary: Herpes simplex virus (HSV) types 1 and 2 cause widespread oral or genital infections, but no prophylactic or therapeutic HSV vaccine has been approved to date. In this study, we developed three mRNA vaccine candidates expressing key viral glycopro-teins: monovalent gD2, bivalent gD2-gC1, and bivalent gD2-gE1. We assessed their immunogenicity and protective efficacy in a murine model. All candidates elicited robust humoral and cellular immunity and provided significant protection against in-travaginal HSV challenge. Notably, the gD2-gE1 vaccine induced markedly stronger immune responses. Mechanistically, its superior immunoprotective efficacy was asso-ciated with the stronger IFN‑I response, which thereby enhanced the adaptive immune response. Collectively, our findings provide a scientific rationale and valuable insights for the future HSV vaccines development

overall_design: In this study, we developed three mRNA vaccine candidates expressing key viral glycopro-teins: monovalent gD2, bivalent gD2-gC1, and bivalent gD2-gE1. All candidates elicited robust humoral and cellular immunity and provided significant protection against in-travaginal HSV challenge.To comprehensively evaluate the innate immune response elicited by the candidates  vaccines, we performed RNA sequencing (RNA Seq) of dLNs collected at 24 hours post-vaccination. (n=3 mice per group)

first: Wenying

last: Zhao

first: Lingjin

last: Sun

first: Peng

last: Wang

first: Qian

first: Ying

last: Li

first: Yang

first: Hongyang

last: Shi

first: Man

last: Xing

first: Weiqian

last: Dai

first: Dongming

last: Zhou


title: Identifying severe COVID-19 risk variants modulating enhancer reporter activity in lung cells

first: Giovanna

last: Weykopf

address: Crewe Road

department: MRC Human Genetics Unit

summary: Common genetic variants contribute to risk for complex human diseases. However, despite thousands of associations, variants modulating disease risk and their functional impact remain largely unknown. This includes SARS-CoV-2 infection, where outcomes range from asymptomatic to fatal. Most host risk variants associated with COVID-19 disease, identified through genome wide association studies, are located in the non-coding genome and may function by altering gene expression in disease-relevant cells and tissues. To address this at scale, we tested >4800 severe COVID-19-associated variants to determine the impact of individual variants and variant combinations on regulatory activity using Self-Transcribing Active Regulatory Region sequencing, a massively-parallel reporter assay, in a lung epithelial cell line (A549). We identify 166 variants within active sequences, of which 29 modulate activity allele-specifically. Evaluating variant combinations, we observe both additive and non-additive effects on regulatory activity. We employ state-of-the-art deep learning models to interpret allele-specific variant effects on regulatory activity and endogenous genomic features. Our work provides a set of prioritised severe COVID-19-associated variants that modulate regulatory activity in lung epithelial cells, candidate transcription factors, and candidate target genes with potential to be disease modifying.

overall_design: STARR-seq experiments screening 170-bp candidate seqeunces centred on 4894 severe COVID-19 genetic risk variants to test for differential activity of reference compared to alternative allele (9788 candidate sequences). We additionally tested combinations of variants occuring within 100-bp genomic distance in all possible combinations of reference and alternative allele (3776 candidate sequences). As positive controls, we included 61x 170-bp sequences centred on the highest STARR-seq peaks in A549 lung adenocarcinoma cells (untreated condition, 0h) by sorting the bigwig signal in peaks from Johnson et al (2018) (NCBI GEO accession: GSE114063). We included 119x putative active sequences centred on the highest H3K27ac peaks in the H358 bronchioalveolar carcinoma cell line (NCBI GEO_GSM1635574), whereby each sequence required at least 30% overlap with ENCODE cCREs downloaded from https://api.wenglab.org/screen_v13/fdownloads/cCREs/GRCh38-ELS.bed (note that these are not used in this study and were excluded from the results presented). As negative controls, we included 10 scrambled sequences of A549 positive controls, 30 scrambled sequences of H358 putative active sequences, and 10 x 170 bp genomic sequences devoid of A549 chromatin modifications (A549 ENCODE H3K4me1, HeK4me3, H3K27ac, H3K9me3, ATAC-seq), or A549 STARR-seq enrichment from Johnson et al (2018). Lastly, we included 8x primer-amplified A549 controls from a previous test run of only controls sequences (total 238 control seqeunces, STARR-seq library of 13802 sequences). We performed 2 input (DNA) and 5 output (RNA) biological replicates, performed on different days.

first: Wendy

last: Bickmore

first: Simon

last: Biddie

first: Elias

middle: T

last: Friman


title: Isolinderalactone Suppresses the Progression of Cholangiocarcinoma by Modulating the CARMA1-BCL10-MALT1 Signalosome

city: Hangzhou

first: Wangyang

address: 261 Huansha Road, Hangzhou, Zhejiang, 310006, China

institute: Zhejiang University

summary: Cholangiocarcinoma (CCA) is a highly aggressive malignancy with poor prognosis and limited therapeutic options. While Isolinderalactone (ILL) has shown anticancer potential, its effects and underlying mechanisms in CCA remain unclear. This study investigated the anti-CCA activity of ILL and elucidated its molecular mechanisms. ILL significantly inhibited CCA cell viability, proliferation, migration, and invasion, while also inducing G0/G1 cell cycle arrest and promoting apoptosis. Transcriptomic and biochemical analyses revealed that ILL suppressed the NF-κB signaling pathway by inhibiting IκB phosphorylation and p65 activation. Mechanistically, ILL was found to directly bind to BCL10, a key adaptor protein. This interaction disrupted the formation of the CARMA1-BCL10-MALT1 (CBM) signalosome and consequently reduced BCL10 ubiquitination. Functional experiments confirmed this mechanism: BCL10 knockdown mimicked ILL's inhibitory effects, while a BCL10 mutation abolished them. Furthermore, activation of NF-κB with Diprovocim partially reversed ILL's suppressive effects. In a xenograft nude mouse model, ILL effectively reduced tumor growth without significant toxicity and suppressed NF-κB activation in tumor tissues. These findings demonstrate that Isolinderalactone suppresses CCA progression by modulating the CBM signalosome and BCL10 ubiquitination to regulate the NF-κB pathway, supporting its potential as a promising therapeutic candidate for CCA.

overall_design: RNA-seq profiling of HCCC9810 cells treated with 20 μM ILL or vehicle for 24 hours.


title: Proteomic and transcriptomic profiling identifies TIPRL as a potential target in multiple myeloma with 1q gain

city: Phoenix

first: Esteban

last: Braggio

state: AZ

address: 6161 E Mayo Blvd

department: Hematology

institute: Mayo Clinic

summary: Amplification or gain of chromosome 1q (+1q) is a common genomic alteration occurring in the plasma cells in nearly 40% of multiple myeloma patients. Although it is associated with inferior outcomes and is more common in the relapsed or refractory  advanced disease stages, the impact of +1q at the proteomic level remains unclear. Here, we studied  enriched CD138+ bone marrow plasma cells in newly diagnosed multiple myeloma to uncover molecular alterations associated with +1q. Differential expression analysis revealed significantly increased expression of several proteins encoded by 1q region indicating potential gene dosage effect. Pathway enrichment analysis identified enrichment of cell cycle  proteins. Further, protein-protein interaction network analysis showed enrichment of MYC transcriptional targets in +1q cases, including increased expression of TIPRL (located on 1q23). In agreement with these findings, increased TIPRL transcript expression was correlated with +1q across different cytogenetic subgroups in the CoMMPass dataset. High TIPRL protein expression was  associated with poor prognosis in  patients  from the hyperdiploidy subgroup. Overall, this study highlights the role of proteomics in understanding molecular events associated with chromosomal alterations in  MM and identifying potential targets for further functional analysis.

overall_design: 1q gain/amplification (+1q) is a common genomic alteration in multiple myeloma that is often associated with poor outcomes, and identifying genes dysregulated due to this copy number gain remains to be of significant interest.  A correlation analysis was performed on samples from 34 untreated multiple myeloma patients (14 cases with +1q and 20 cases without +1q) with 6,731 genes that were common to both RNA and proteome datasets.

first: Rafael

last: Fonseca

first: Leif

last: Bergsagel

first: Daniel

last: Binham


title: Fus interactions in muscle cells C2C12 ChIPseq - 2

city: Freiburg

first: Pierre

middle: Daniel

last: Cauchy

state: Baden-Württemberg

address: Breisacher Str. 115

department: Zentrum für Translationale Zellforschung

institute: University Medical Center Freiburg

summary: We would like to identify Fus interactions in muscle cells C2C12. In order to do this, we would like to identify FUS binding sites in C2C12 cells, and compare with RNApol2 sites. Our conditions for Chip-seq are thus C2C12 (input (N=1), without antibody (N=1), @FUS (N=3) , @RNApol 2 (N=3).

overall_design: FUS, RNAP2 ChIP-Seq in C2C12 myoblast cells

first: Gina

last: PICCHIARELLI

last: CAUCHY

first: Salim

last: MEGAT

first: Luc

last: DUPUIS


title: SIRT3 regulation of hematopoietic stem cell aging [ATAC-Seq]

city: BERKELEY

first: DANICA

last: CHEN

address: 119 Morgan Hall

department: NST

institute: UC BERKELEY

overall_design: ATAC-sequencing analyses of HSCs from 2-year-old Mx1-Cre and Mx1-T3 mice

first: Wei-Chieh

last: Mu

first: Paul

last: Lanhart

first: Danica

last: Chen


title: Aging Impairs Macrophage Phagocytosis through Mitochondrial ROS-Induced Collagen Production

first: Bowen

last: Wu

state: Zhejiang

address: NO.79 Qinchun Road

institute: The First Affiliated Hospital, Zhejiang University School of  Medicine

summary: Macrophages are pivotal immune cells due to their phagocytic capabilities, yet the impact of aging on macrophage phagocytosis remains poorly understood. Using comprehensive in vitro and in vivo phagocytic assays, we demonstrate significantly reduced phagocytic activity in monocyte-derived macrophages from aged humans and mice compared to young counterparts. RNA-seq analysis revealed upregulated expression of extracellular matrix protein genes, particularly collagens, in aged macrophages, manipulation of COL1A1 expression can significantly affect phagocytosis. Protein interaction assay identified binding between collagen and actin filaments, which inhibits F-actin turnover and consequently impairs phagocytic function. Also, we found that mitochondrial ROS is the driving force of collagen overproduction and MitoTEMPO rejuvenates macrophage phagocytosis via restoring actin dynamics. In mouse model, MitoTEMPO significantly boosted the phagocytosis of peritoneal macrophage against bacteria. These findings highlight the fundamental role of mitochondrial redox balance and collagen production in controlling macrophage phagocytic function, identifying them as targetable mechanisms for promoting healthy immune aging.

overall_design: Peripheral blood mononuclear cells were isolated from young and elderly people in vitro, induced with MSCF (20 ng/ml) for five days, and LPS (100 ng/ml) for two days for RNA-seq.

first: Yuming

last: Wang

first: Xin

last: Xu

first: Nuanqin

last: Shen

first: Ping

last: Han

first: Liuyi

first: Yiming

last: Sun

first: Lanlan

last: Xiao

first: Jinyou

last: Li

first: Lan

first: Qin

last: Zhang

first: Weiqian

first: Chaohui

last: Yu


title: The novel role of GADD45A in the etiology of autism: modulating neuronal excitability via TET1/R-loop dependent regulation of KCNQ5

city: CHENGDU

first: Tian

last: Tang

state: Sichuan

address: No. 20, Section 3,Renmin South Road

institute: Sichuan university

summary: The etiology of autism currently includes prenatal exposure factors and genetic variants, but it remains unclear how these factors converge on a common pathway. Through multiple autism transcriptome analyses of public data, we discovered that the disruption of Gadd45a may explain the pathogenesis of various types of autism, including the most established valproic acid (VPA) prenatal exposure and MECP2 gene-related autism. Subsequently, we generated Gadd45a knockout mice and found that these mice exhibit significant deficits in social ability, as well as autistic-like phenotypes such as increased digging behaviors. We demonstrated the preferential expression of Gadd45a in cortical excitatory neurons. Through in vivo electrophysiological recordings, we found that the firing frequency of excitatory neurons in the medial prefrontal cortex of knockout mice is abnormal in both resting and task states, which may explain the autistic-like phenotypes exhibited by these mice. Remarkably, we revealed that abnormal neuron firing may be due to the failure of TET1, a GADD45A-interacting protein, to be recruited to the promoter region of Kcnq5, thereby preventing normal DNA demethylation and transcription initiation in the absence of GADD45A. We also demonstrated that GADD45A can recognize R-loop structure to recruit TET1 to the CpG islands of KCNQ5 and regulate the transcription level of KCNQ5. This process also involved nearby antisense lncRNA in the formation of R-loops. Our study revealed a hub gene, GADD45A, and its epigenetic regulation of ion channels (GADD45A/TET1-KCNQ5 axis), which plays a critical role in the pathogenesis of autism.

overall_design: ChIP-seq of TET1 in prefrontal  cortices of two wildtype mice and two Gadd45a knockout mice.

first: Juncen

last: Guo


title: Sequencing of Rattus norvegicus chondrocytes under dermal fibroblast co-culture

first: Lei

last: Shi

summary: Knee osteoarthritis (KOA), as a degenerative multifactorial disease, affects the quality of life and mental health of patients, and also brings a huge socioeconomic burden. Treating synovitis have shown promise as anti-inflammatory therapeutics in mitigating OA symptoms and disease progression. Here, by analysing synovial single-cell sequencing (scRNA-seq) data from KOA, we found that synovial fibroblasts (FLS) in OA synovium showed a distinct pro-inflammatory phenotype. We collected synovial tissue from patients with clinical OA as well as from healthy donors, and histological examination was consistent with findings in scRNA-seq. Inspired by recent cross-tissue fibroblast lineage studies, we identified by sequencing that healthy FLS in synovial tissues share transcriptome-level similarities with dermal fibroblasts (DFb). Subsequently, we revealed the local as well as systemic distribution of intra-articular injected DFbs by constructing/extracting two types of rat fibroblasts (luciferase DFbs as well as GFP DFbs). The results demonstrate that DFbs can be locally retained in the synovium for up to three weeks following targeted engrafting on it. And intra-articular injection does not result in DFbs migration to vital organs or the occurrence of histological changes in these organs. A rat model of KOA was constructed by anterior cruciate ligament transection (ACLT) in order to study the therapeutic effect of DFbs on KOA. After injection, the rats showed improvement in painful gait. In addition, histological as well as imaging results showed reduced synovitis and improvement in articular cartilage. Finally we verified the protective effect of DFbs on cytokine-stimulated chondrocytes in a co-culture system.

overall_design: A transwell co-culture system was used, with chondrocytes seeded in the lower chamber and dermal fibroblasts in the upper chamber. The experiment included three groups: control (C), with routine culture; IL-1β-stimulated (CI), treated with IL-1β; and co-culture (DCI), where chondrocytes were co-cultured with dermal fibroblasts following IL-1β stimulation.

first: Kewei

last: Rong

first: Kexin

last: Liu

first: Jie

last: Zhao


title: Sequencing of Rattus norvegicus synovial fibroblasts

overall_design: A transwell co-culture system was used, with synovial fibroblasts seeded in the lower chamber and dermal fibroblasts in the upper chamber. The experiment included three groups: control (C), with routine culture; IL-1β-stimulated (FI), treated with IL-1β; and co-culture (DFI), where synovial fibroblasts were co-cultured with dermal fibroblasts following IL-1β stimulation.


title: DMAP1 promotes lung cancer progression by maintaining replication fork stability and suppressing IFN signaling-mediated anti-tumor immunity [scRNA-seq]

first: Kan

last: Huang

address: 130, Dongan Road

institute: Fudan University

summary: Despite substantial progress in targeted and immune therapies, lung cancer remains the leading cause of cancer-related mortality, highlighting the urgent need for novel therapeutic strategies. Through a CRISPR-based knock-out screen, we identified the DNA methyltransferase 1-associated protein 1 (DMAP1) as a critical regulator of tumor progression. Functional studies showed that loss of DMAP1 exerts its anti-tumor effects through attenuating tumor cell proliferation and activating T cell-mediated adaptive anti-tumor effects. Mechanistically, loss of DMAP1 causes replication fork retardance, disturbs genome stability, and induces endogenous DNA damage, thereby activating tumor-intrinsic immune signaling and enhancing anti-tumor immune response during cancer cell growth. Clinical data analyses revealed that high DMAP1 expression is associated with reduced immune infiltration, a “cold” tumor microenvironment, and poorer overall survival in lung cancer. These findings significantly advance our knowledge of DMAP1's function in lung cancer development and offer a scientific basis for designing novel treatment approaches.

overall_design: We inoculated wildtype and Dmap1 knockdown (shDmap1) KP cells into C57Bl/6 mice subcutaneously. Following the acquisition of samples from the subcutaneous tumor, we carried out single-cell sequencing (scRNA-seq) on the tumors.

first: Xi

last: Dai

first: Shuaihu

first: Yingxue

last: Chen

first: Yaxin

first: Lin

first: Kun

first: Chongyang

first: Yihua

first: Fei


title: DMAP1 promotes lung cancer progression by maintaining replication fork stability and suppressing IFN signaling-mediated anti-tumor immunity [RNA-seq]

overall_design: RNA-seq profiling of wildtype KP cells and their knockdown derivatives (shDmap1).

last: Wang


title: Elucidating the Mechanisms of SA-4-1BBL Immunoprevention Through Advanced Informatics Approaches

city: Huntington

first: Mohit

last: Verma

state: WV

address: 1676 3rd Ave, 4th Floor, Suite #4109

department: Department of Biomedical Sciences

institute: Marshall University

summary:
Cancer immunoprevention leverages the immune system’s surveillance mechanisms to mitigate tumor development. Vaccines constituting a tumor antigen and an immune adjuvant are perceived immunoprevention modalities.  However, relevant tumor antigens are unknown for non-viral cancers, which constitute the majority of human cancers. Our group has recently shown that SA-4-1BBL, a novel oligomeric recombinant agonist of CD137 costimulatory molecule, as a single agent, has robust immunoprevention efficacy against various tumor types.  In marked contrast, agonistic antibodies to CD137 lacked such function.  This study employs advanced informatics approaches for analyzing bulk RNA sequencing (RNA-seq) transcriptomics data to elucidate the molecular mechanisms driving SA-4-1BBL’s immunoprevention efficacy. Mice were treated subcutaneously with SA-4-1BBL or an agonistic antibody and injection site (IS) tissue and draining lymph nodes (LN) were analyzed for differentially expressed genes (DEGs).
Our findings reveal that SA-4-1BBL induces a compartmentalized and temporally dynamic immune program, characterized by early effector activation at IS and sustained immune regulation in draining LN. K-means clustering of 4,564 DEGs identified 8 functionally distinct clusters, with IS-enriched clusters (1 and 4) upregulating effector genes such as Cd28, Klra1, Cd4, Cd40, and Cd40l, supporting CD4+ T and NK cell activation. In contrast, LN-dominant clusters (2 and 5) were enriched for regulatory genes (Tnfaip3, Irf5, Col1a2), implicating roles in tissue remodeling and long-term immune memory.
Compared to agonistic antibody, SA-4-1BBL elicited a more selective and durable activation of adaptive immune pathways, including TCR signaling, Th1/Th2 differentiation, and NK cytotoxicity, while avoiding systemic inflammation. Agonistic antibody, in contrast, activated broader innate inflammatory programs, including Toll-like receptor and neurodegeneration-linked pathways. IMPRes analysis revealed that SA-4-1BBL engages sequential immune-regulatory circuits centered on Stat1, Cd247, and Ifng, and modulates the CD151–TGF-β axis, offering novel mechanistic insight into its immune-balancing effects.
These findings define a compartmentalized immune architecture that underlies SA-4-1BBL’s ability to provide safe, long-lasting cancer immunoprevention. Our study highlights the value of applying comprehensive informatics techniques in decoding the spatial and functional complexity of tissue-specific immune programming.

overall_design: RNA-seq samples were obtained from skin and draining lymph nodes of C57BL/6 mice (n=4/cohort) following subcutaneous injection with SA-4-1BBL, 3H3 agonist antibody, or PBS (control). Mice received either a single injection and were euthanized at Day 3 or Day 7, or two injections two weeks apart and were euthanized at Day 3 and Day 7 post-second injection.

first: Feyza

last: Nur Arguc

first: Pallav

last: Singh

first: Sameep

last: Dhakal

first: Yen

last: On Chan

first: Manish

last: Sridhar

first: Sabin

last: Dahal

first: Vahap

last: Ulkar

first: Mohammad

last: Tarique

first: Tariq

last: Malik

first: Lalit

last: Batra

first: Esma

last: S. Yolcu

first: Haval

last: Shriwan

first: Trupti

last: joshi


title: Upscaling generation of lung organoids

city: Essen

first: Bettina

last: Budeus

address: Virchowstrasse 173

department: Institute for Cell Biology

institute: University Hospital Essen

summary: Generation of lung organoids: manually versus bioreactor

overall_design: iPSC-derived lung organoids were generated either manually or via bioreactor culturing (d30-35) and then compared on single cell level

first: Chiara

last: Kroepel

first: Zehra Fatma

last: Sevindik

first: Luca

last: Buttler

first: Diana

last: Klein


title: Hormone-treatment (ABA, SA) timecourse of Arabidopsis thaliana root

city: Berkeley

first: Sharon

last: Greenblum

address: 1 Cyclotron Road

institute: DOE Joint Genome Institute

summary: Profiling of binding sites for hundreds of A. thaliana transcription factors genome-wide revealed an unexpected enrichment of conserved TF binding sites (TFBSs) in coding sequence (CDS) for specific TF families, yet little association with cell type-specific gene expression. To differentiate between possible explanations for this, gene expression was profiled using bulk RNA-seq in response to hormone-induced stress. Abscisic Acid (ABA) treatment time-course data revealed that TFs known to activate transcription in response to ABA were significantly up-regulated, and most target genes of these TFs were upregulated as well - with the exception being target genes with TFBSs exclusively in coding sequence, which showed no significant expression change. Salicylic acid (SA) treatment further confirmed that target genes of known SA-responsive activators were induced only when TFBSs were found outside the coding region. However a key SA-responsive repressor (ABR1) showed strong repression of genes with CDS binding sites, suggesting a mechanism for rapid antagonistic response. Moreover, integration with chromatin accessibility data from the same tissues revealed strong links between constitutive TFBS accessibility and stress-induced target gene expression, suggesting that rapid, tissue-wide regulatory responses might preferentially operate through constitutively accessible sites primarily located close to transcription start sites.

overall_design: A. thaliana seeds were sterilized and cold stratified, then planted on nylon mesh in agar plates. Seeds were sown on plates at a density of 3 rows per plate with ~30 plants per row and plates were placed vertically in a growth chamber under conditions of 16 h light at 22°C, 8 h dark at 19°C for 5 days. On the 5th day, the nylon mesh and plants were transferred using forceps to agar plates containing either 2 μM ABA, 150 μM SA, or the standard growth medium without added hormones to serve as a parallel, time-matched negative controlas a negative control. Samples for all three conditions (ABA, SA, and mock) were collected at time points of 0, 1, 2, 4, 7, 24, and 48 hours, separating root and shoot tissues with a single razor blade cut at the time of collection. At each time point, five biological replicates per treatment were collected and flash frozen in liquid nitrogen then stored at -80°C. Three of the biological replicates were used for bulk RNA-seq. Sequencing was performed on an Illumina NovaSeq 6000 S4 flow cell, using 2x150 bp paired-end sequencing.

first: Peng

last: Wang

first: Ronan

last: O'Malley

first: Abraham

last: Morales-Cruz

first: Leo

last: Baumgart

first: Jenifer

last: Johnson


title: NAD+ Deficiency Drives Metabolic Dysfunction-Associated Atrial Fibrillation

first: Paul

last: Zumbo

address: 1300 York Ave

department: Applied Bioinformatics Core

institute: Weill Cornell Medicine

summary: Atrial fibrillation (AF) is a cardiometabolic disease with obesity and diabetes as major risk factors. The cellular and molecular mechanisms by which obesity and metabolic stressors drive AF are poorly understood. Here we establish a new mouse model of spontaneous, obesity-induced AF. This two-hit model relies on genetic susceptibility coupled with an environmental factor of diet-induced obesity. Unbiased multi-omics analyses reveal cardiac conduction pathways, inflammation, and metabolic perturbations in AF. We demonstrate atrial NAD+ deficiency as a central pathological mediator in AF. Pharmacological replenishment of atrial NAD+ levels mitigates AF, protects against cardiac remodeling and fibrosis, reduces inflammation, and improves atrial metabolism. These results highlight the role of a metabolic pathway that could be therapeutically targeted for AF.

overall_design: NaV1.5 transgenic mice on regular diet (RD) or 4w high-fat diet (HFD) compared to Ctrl mice on RD or HFD. NaV1.5 transgenic mice on HFD vehicle compared to HFD supplemented with Nicotinamide Riboside (HFD&NR)

first: Lisa

last: Stoll

first: Elizabeth

middle: E

last: Ha

first: Odin

last: Schaepkens

first: Najla

last: Saadallah

first: Belem

last: Yoval-Sánchez

first: Iris

last: Bibolli

first: Ruiping

last: Ji

first: Renan

last: Pereira de Lima

first: Charles

last: Warren

first: Maiko

last: Matsui

first: Pavithran

last: Guttipatti

first: Dawson

last: Miller

first: Gabriel

last: Ayala

first: Joshua

last: Ip

first: Bruce

last: Lerman

first: Doron

last: Betel

first: Steven

last: Gross

first: Jacob

last: Geri

first: James

first: Yue

last: Yang

first: Alexander

last: Galkin

first: Qiuying

last: Chen

middle: O

last: Marx

first: Geoffrey

last: Pitt

first: Elaine

last: Wan

middle: C

last: Lo


title: ChIP-seq of GLTSCR1 and SS18::SSX fusion in HS-SY-II synovial sarcoma cells treated with the BRD9 PROTAC degrader WA-68 across a time course

city: Salt Lake City

first: Li

last: Li

state: Utah

address: 201 PRESIDENTS CIRCLE

institute: University of Utah

summary: Synovial sarcoma (SyS) is driven by the SS18::SSX fusion oncoprotein, which incorporates into GBAF chromatin remodeling complexes and creates a dependency on BRD9. To investigate the effects of BRD9 loss, we performed ChIP-seq, ATAC-seq, and RNA-seq in SyS models following BRD9 degradation. ChIP-seq shows reduced GBAF occupancy at target loci, while ATAC-seq reveals maintained or increased chromatin accessibility. RNA-seq demonstrates sustained or elevated expression of target genes. These results indicate that BRD9 is not required for GBAF assembly but instead restrains its remodeling activity, providing a mechanistic explanation for the limited efficacy of BRD9-targeted therapies in SyS.

overall_design: ChIP-seq for GLTSCR1 (a GBAF-specific subunit) and the SS18::SSX fusion oncoprotein (HA-tag) in HS-SY-II synovial sarcoma cells treated with the BRD9 PROTAC degrader WA-68 (100 nM) across a time course (DMSO, 12 h, 24 h, 48 h, 96 h). Matched input chromatin controls included for each time point.

first: Jinxiu

first: Kevin

last: Jones


title: ATAC-seq of synovial sarcoma cell lines treated with the BRD9 PROTAC degrader WA-68

overall_design: ATAC-seq (Omni-ATAC) was performed on synovial sarcoma cell lines SYO-1 and HS-SY-II treated with the BRD9 PROTAC degrader WA-68 (100 nM) or DMSO vehicle control. Time-course samples in HS-SY-II were collected at 12, 24, 48, and 96 hours post-treatment, with two biological replicates per condition.


title: Caspase-11 Mediated Hyperinflammation Impairs CD8⁺ T Cell Immunity and Viral Clearance in Severe SARS-CoV-2 Infection [FLOX]

city: Columbus

first: Amy

last: Hite

address: 1800 Cannon Drive 250 Lincoln Tower

institute: The Ohio State University

summary: Severe SARS-CoV-2 infection is characterized by lung hyperinflammation, impaired interferon responses, and defective T-cell activation, yet the molecular drivers of these immune dysregulations remain incompletely understood. Caspase-11 (CASP11), a key mediator of the non-canonical inflammasome, has been shown to mediate an innate hyperinflammatory response and cytokine release in a non-severe, non-lethal SARS-CoV-2 infection model. However, the role played by CASP11 in severe SARS-CoV-2 disease and how it impacts adaptive immunity is not identified. Here, we discover that CASP11 exacerbates severe SARS-CoV-2 pathogenesis by amplifying early innate immune responses while concurrently impairing antiviral CD8 T cell immunity. Using global knockouts, reciprocal bone marrow chimeras, and Cx3cr1-expressing mononuclear phagocyte system (MPS) cell-specific CASP11 deletion models, we show that targeting reduces lung inflammation, promotes early Natural Killer (NK) cell-mediated interferon-γ (IFN-γ) production, and enhances robust virus-specific effector CD8⁺ T cell responses. This was associated with enhanced viral clearance and improved survival, even under lethal infection conditions. Importantly, CASP11 KO mice also exhibited faster resolution of post-viral inflammation, suggesting a role in long-term immune remodeling. These findings position CASP11 as a promising immunomodulatory target for acute and delayed manifestations of severe SARS-CoV-2 infection.

overall_design: RNA sequencing was performed on lung tissue harvested from Cx3cr1-CreERT2; Casp11^WT/WT (Cx3cr1-Cre control) and Cx3cr1-CreERT2; Casp11^flox/flox (Cx3cr1-MPS-Casp11⁻/⁻) mice at day 4 post-infection with mouse-adapted SARS-CoV-2 (MA10 strain, 5×10⁵ TCID50, intranasal). Both groups are homozygous for the Cx3cr1-CreERT2 knock-in allele and received identical tamoxifen induction (75 mg/kg IP, 7 consecutive days) followed by a 3-day washout period prior to infection. The study design employed a two-group comparison (n = 5 per group) to identify transcriptional differences associated with cell-specific CASP11 deletion in Cx3cr1-expressing mononuclear phagocyte system cells during acute severe SARS-CoV-2 infection. The left lung lobe was used for RNA extraction from each mouse.

first: Amal

last: Amer

last: Webb

first: Mostafa

last: Eltobgy

first: Mohamed

last: Shamseldin


title: Caspase-11 Mediated Hyperinflammation Impairs CD8⁺ T Cell Immunity and Viral Clearance in Severe SARS-CoV-2 Infection [Casp11WT]

overall_design: RNA sequencing was performed on lung tissue harvested from WT chimeras (WT→WT) and Casp11⁻/⁻ chimeras (Casp11⁻/⁻→WT) at day 4 post-infection with mouse-adapted SARS-CoV-2 (MA10 strain, 1×10⁵ TCID50, intranasal). Bone marrow chimeric mice were generated by lethal irradiation of C57BL/6 wild-type recipient mice followed by reconstitution with bone marrow from either WT or Casp11⁻/⁻ donors, with a minimum 6-week reconstitution period prior to infection. The study design employed a two-group comparison (n = 4 per group, equal proportions of male and female mice) to identify transcriptional differences associated with CASP11 deficiency in hematopoietic cells during severe SARS-CoV-2 infection. The left lung lobe was used for RNA extraction from each mouse.


title: Haplotype-phased assemblies of the two poplar rust fungi species: Melampsora larici-populina and Melampsora allii-populina

city: Zurich

first: Cecile

last: Lorrain

state: Zurich

address: Universistätstrasse 2

department: Plant PAthology

country: Switzerland

institute: ETH Zurich

summary: Dikaryotic rust fungi maintain two distinct haploid nuclei for most of their life cycle, making their large, repeat-rich genomes difficult to assemble and phase. Here we present haplotype-phased, near chromosome-scale genome assemblies for the poplar rust pathogens Melampsora larici-populina 98AG31 and Melampsora allii-populina 12AY07, generated using PacBio HiFi sequencing and Hi-C-guided scaffolding. For each species, we resolve 18 chromosomes per haplotype, providing the first chromosome-level representations of poplar rust fungal species. M. larici-populina diploid assembly spans ~203 Mb, while M. allii-populina reaches ~416 Mb, with high completeness and strong collinearity between haplotypes.

sample_organism:
Melampsora laricis-populina
Melampsora allii-populina

overall_design: We used PacBio long-read sequencing combine with Hi-C to obtain haplotype-phased assemblies.

first: Emma

last: Corre

first: Emmanuelle

last: Morin

first: Jana

last: Sperschneider

first: Ammar

last: Abdalrahem

first: Igor

last: Grigoriev

first: Pascal

last: Frey

first: Sebastien

last: Duplessis


title: RNA-seq of HS-SY-II synovial sarcoma cells treated with the BRD9 PROTAC degrader WA-68 across a time course

overall_design: Bulk RNA-seq of HS-SY-II synovial sarcoma cells treated with the BRD9 PROTAC degrader WA-68 (100 nM) or DMSO vehicle control, harvested at DMSO control, 12 h, 24 h, 48 h, or 96 h post-treatment. Two biological replicates per time point.


title: CRISPR-Based Gene Dependency Screens reveal Mechanism of BRAF Inhibitor Resistance in Anaplastic Thyroid Cancer

city: Bethesda

first: Myriem

last: Boufraqech

state: Maryland

address: NIH campus, building 10 room 7S261

department: CCR

institute: NCI

summary: Anaplastic thyroid cancer (ATC) is the most aggressive form of thyroid cancer. Despite recent advances in treating BRAFV600E-driven ATC, therapy resistance remains a significant challenge, often resulting in disease progression and death. Leveraging a focused CRISPR/KO screen in parallel with a CRISPR/activation screen, both tailored on response to BRAFV600E inhibitor treatment, we identified TAZ (encoded by WWTR1 gene) deficiency as synthetically lethal with BRAF inhibitor in ATC. TAZ is overexpressed in ATC compared to well-differentiated thyroid tumors. We demonstrate that TAZ-deficient ATC cells display heightened sensitivity to BRAF inhibitors. Using gene essentiality score across cancer cell lines, we found that BRAFV600E-driven cancers are highly sensitive to TAZ loss, unlike their counterparts with wild-type BRAF and non-BRAFV600E. Mechanistically, we demonstrate that dabrafenib triggers the Unfolded Protein Response (UPR) under ER stress and suppresses protein synthesis. TAZ loss represses the UPR, reverses the inhibition of protein synthesis, and triggers increased cell death by ferroptosis in dabrafenib-treated ATC. Collectively, our findings unveil TAZ as a new target to overcome resistance to BRAF inhibitors in undifferentiated thyroid cancer.

overall_design: RNA profiling of shControl and shTAZ-8505c cells with and without dabrafenib treatment.

first: Shawn

last: Noronha

first: Alexei

last: Lobanov

first: Margaret

last: Cam


title: Caspase-11 Mediated Hyperinflammation Impairs CD8⁺ T Cell Immunity and Viral Clearance in Severe SARS-CoV-2 Infection [Lung4Day]

last: Hite

overall_design: RNA sequencing was performed on lung tissue harvested from WT and Casp11⁻/⁻ mice at day 4 post-infection with mouse-adapted SARS-CoV-2 (MA10 strain, 5×10⁵ TCID50, intranasal). The study design employed a two-group comparison (n = 4 per group, equal proportions of male and female mice) to identify transcriptional differences associated with CASP11 deficiency during acute severe SARS-CoV-2 infection. The left lung lobe was used for RNA extraction from each mouse.


title: Burn injury triggers distinct transcriptomic profiles in adipose tissue of adult and aged mice

city: Hamilton

first: Punit

last: Bhattachan

state: Ontario

address: 20 Copeland Avenue

department: Surgery

country: Canada

institute: McMaster University

summary: Severe burns are a major global health concern, and are associated with long-term physical and psychological impairments, multi-organ dysfunction, and substantial morbidity and mortality. While burn injuries in adults trigger systemic immuno-metabolic alterations—characterized by white adipose tissue browning, elevated resting energy expenditure, widespread catabolism and inflammation—these adaptive responses are considerably impaired in older adults, with molecular mechanisms behind these differences remaining largely unclear. As a key regulator of systemic metabolism, investigating the pathological role of adipose tissue (AT) post-burn may reveal novel targets that could potentially improve patient outcomes. In this study, we conducted bulk mRNA sequencing and analysis of AT from adult and aged mice, to elucidate the transcriptomic changes underlying the distinct post-burn responses in these populations. After examining differentially expressed genes in the adult and aged burn mice, the top six upregulated genes in adults (Ucp1, Lgr6, Dio2, Lncbate10, Fabp3, Kng2) were primarily associated with thermogenesis, whereas those in the aged mice (Car6, Spata25, Gm128, Btbd16, Lipm, Abca13) were linked to inflammation, tissue repair, and lipid metabolism. Furthermore, our gene co-expression and enrichment map analysis identified burn-associated modules related to thermogenesis and fatty acid oxidation in adults and leukocyte migration and tumor necrosis factor production in aged mice. Notably, Ppara and Sfpi1 emerged as potential master regulators of co-expressed genes in burn AT of adult and aged mice, respectively. Our findings highlight age-specific differences in burn-induced AT responses and uncover potential molecular regulators that may inform targeted therapeutic strategies to mitigate the post-burn stress response.

overall_design: mRNA-seq profiling of wildtype adipose tissue from adult and aged mice (Control, Scald burn injury).

first: Bhattachan

last: Punit

first: Vlavcheski

last: Filip

first: Wojtowicz-Piotrowski

last: Stephanie

first: Jeschke

last: Marc G


title: Multiomic sequencing identifies myeloid cell associations with neoadjuvant chemotherapy treatment response in pancreatic adenocarcinoma (PDAC)

city: Morgantown

first: Gangqing

last: Hu

address: 64 Medical Center Drive

institute: West Virginia University

summary: Pancreatic ductal adenocarcinoma (PDAC) is among the deadliest human malignancies with poor prognosis and limited therapeutic success. Despite significant advancements in therapeutic strategies over recent decades, the development of effective treatments for pancreatic ductal adenocarcinoma (PDAC) remains a major challenge due to its complex tumor microenvironment (TME). The PDAC TME is characterized by tumor-infiltrating immune cells, immunosuppressive cells, and cancer-associated fibroblasts (CAFs). The immune components, particularly the myeloid cells, play a role in the tumor microenvironment (TME). The myeloid compartment of the TME comprises a functionally diverse compartment of the TME, capable of exerting both pro-tumorigenic and antitumor effects depending on their phenotypic state and microenvironmental cues. In this study, we leveraged single-nucleus multiomic sequencing (snRNA-seq and snATAC-seq) of human pancreatic ductal adenocarcinoma (PDAC) tumors to dissect the immune landscape, particularly the myeloid subsets, in patients who received neoadjuvant chemotherapy, stratified as responders or non-responders based on histopathological evaluation. Our integrative analysis revealed striking differences in myeloid cell composition and transcriptional states, with a notable enrichment of lipid-associated macrophages (LAMs) in chemotherapy responders. LAMs exhibited a transcriptional program enriched for lipid metabolism, phagocytosis, and inflammatory signaling. Pseudotime and chromatin accessibility analyses from the ATAC-Seq data positioned LAMs as terminally differentiated, metabolically reprogrammed macrophages, shaped by immune and environmental cues. ChromVAR analysis identified AP-1, C/EBP, and metabolic transcription factor motif enrichment in LAMs from responders, indicating active immunometabolic states associated with treatment efficacy. These findings implicate LAMs as potential biomarkers and effectors of chemotherapeutic response in PDAC, providing new insights into myeloid cell plasticity and therapeutic reprogramming in the TME.

overall_design: To validate findings from snMultiomics analysis, nuclei were isolated from frozen pancreatic tissue from twelve (12)  patients who underwent surgical resection with pancreaticoduodenectomy for PDAC. Responders’ and non-responders’ PDAC tissue samples were obtained from the WVU Biospecimen and Translational Research Analysis Core (BioTRAC) upon surgical resection.  Patient received neoadjuvant chemotherapy.

first: Mercy

last: Ojetunde

first: Li

last: Ma

first: Hillary

last: Pratt


title: RNA Terminal Uridylyl-Transferases Are Druggable Vulnerabilities in AML, but are Dispensable for Normal Hematopoiesis

city: Edinburgh

first: Yuka

last: Kabayama

address: Max Born Crescent

institute: University of Edinburgh

type: Non-coding RNA profiling by high throughput sequencing

summary: Acute myeloid leukemia (AML) is an aggressive hematological malignancy arising from hematopoietic stem and progenitor cells (HSPCs). Current treatments often fail to eradicate AML; therefore, new therapeutic strategies are essential. Here, we reveal that RNA Terminal-Uridylyl-Transferase-Enzymes 4 and 7 (TUT4/7) are druggable therapeutic targets, whose genetic deletion suppresses AML growth, induces apoptosis and improves the survival in leukemic mouse models. Notably, a pre-clinical TUT4/7 inhibitor promotes cell death in AML patient samples and synergizes with venetoclax. Mechanistically, TUT4/7 inactivation suppresses mevalonate pathway gene expression, compromising the cholesterol synthesis pathway. Current AML therapies often cause severe hematopoietic toxicity. Although Tut4/7 deletion results in inflammatory activation throughout the hematopoietic system, this is permissive to a normal lifespan and Tut4/7-deficiency does not compromise HSPC function. Together, these findings identify TUT4/7 as druggable targets, whose inactivation suppresses AML while sparing normal hematopoiesis. In combination with venetoclax this represents a promising therapeutic strategy.

overall_design: small RNA-seq profiling of control and Tut4/7 conditional double knockout preleukemic cells.

first: Christopher

last: Mapperley

first: Elise

last: Georges

first: Ali

last: Azar

first: Hannah

last: Lawson

first: Iwo

last: Kucinsk

first: Derek

last: George

first: Joana

last: Campos

first: Corey

last: Fyfe

first: Jozef

last: Durko

first: Wei

last: Chan

first: Lewis

last: Allen

first: Babak

last: Jazayeri

first: Edward

last: Blacker

first: Louie

last: van de Lagemaat

first: Aurelien

last: Tripp

first: Theodoros

middle: I

last: Roumeliotis

first: Giulia

last: Guiducci

first: Eleanor

last: Herbert

first: Jasmin

last: Paris

first: Jyoti

last: Choudhary

first: George

last: Poulogiannis

first: Robert

last: Campbell

first: Marcos

last: Morgan

first: Lovorka

last: Stojic

first: Folkert

middle: J

last: Van Werven

first: Douglas

last: Vernimmen

first: Berthold

last: G ttgens

first: D nal

last: O Carroll

first: Kamil

middle: R

last: Kranc


title: Single-cell transcriptomic profiling reveals innate-like cytotoxic intraepithelial lymphocyte expansion during Salmonella Enteritidis infection in chickens

city: Wooster

first: Shuja

last: Majeed

state: OH

address: 1119 Townsview Place

department: Animal Sciences

summary: Salmonella is a major foodborne pathogen that causes approximately 1.35 million infections annually in the US and remains a leading cause of poultry-associated foodborne illness. To improve chickens' resistance to this pathogen, it is important to understand the mucosal immune mechanisms that govern intestinal defense. Intraepithelial lymphocytes (IELs) positioned between intestinal epithelial cells provide frontline immune surveillance against enteric pathogens. However, a comprehensive characterization of IEL subtype responses to Salmonella infection remains incomplete. Therefore, we conducted this study to examine IEL subtypes and their mechanisms in response to a Salmonella enterica serovar Enteritidis (S. Enteritidis) challenge using a combination of spectral flow cytometry and single-cell RNA sequencing (scRNA-seq). Fifty specific-pathogen-free (SPF) day-old chicks were reared to 21 days of age and then assigned to S. Enteritidis-challenged (SE; 1.62 × 10⁸ CFU/bird, oral gavage) or control (CN; PBS) groups (n = 25/group). On day 2 post infection (2 dpi) and 6 dpi, eight birds per group were euthanized by CO2 asphyxiation to collect liver and ceca for bacteriology and ileum for IEL acquisition. Body weights were recorded at 0, 2, and 6 dpi. Bacteriological findings confirmed the challenge: the SE group harbored S. Enteritidis at both time points, while body weight gain was only lower at 2 dpi in the SE group, indicating a transient dip in performance due to Salmonella infection. Flow cytometry results showed that Salmonella challenge increased the proportion of TCRγδ+CD8αβ+ cytotoxic IELs at 2 dpi, as well as the overall IEL proportion at 2 and 6 dpi. Notably, scRNA-seq identified clusters of progenitor T cells and innate-like cytotoxic T cells that significantly expanded in SE-challenged birds at 2 dpi, indicating rapid mobilization of an innate-like cytotoxic response. Integration of flow cytometry and scRNA-seq data provided evidence that cytotoxic T cells expressing CD8αβ acquire innate-like transcriptional signatures within the intestinal epithelial compartment, suggesting functional reprogramming that enables rapid antigen responses.  Trajectory analysis identified a robust differentiation pathway from progenitor T cells through activated CD8⁺ T cells to innate-like CTL as the terminal fate, with quiescent stem-like resident memory T cells serving as an upstream reservoir. These findings reveal a previously uncharacterized innate-like cytotoxic IEL response as a critical early defense mechanism against Salmonella in poultry and identify self-renewing stem-like Trm cells as a reservoir for rapid IEL effector differentiation.

overall_design: We challenged specific pathogen free layer chickens with Salmonella Enteritidis, following which approximately 10cm of promixal ileum was sampled on 2 and 6 days post infection (dpi) for intraepithelial lymphocyte (IEL) isolation. On 2dpi IEL was enriched with magnetic-activated cell sorting and 10x genomics (GEM-X Universal 3’ Gene Expression v4 kit ) was used for sc-RNA seq on IEL

first: Bikas

last: Shah

first: Bikash

last: Aryal

first: Nimra

last: Khalid

first: Tae

middle: H

last: Kim

first: Ali

last: Nazmi


title: Hnrnpa1 is essential for early zebrafish development and lipid metabolism

city: Munich

first: Bettina

last: Schmid

address: Feodor-Lynen-Str. 17

institute: DZNE

summary: RNA binding proteins have multiple diverse cellular functions and are often mis- regulated in disease. Despite their many cellular functions and implications in disease, very little is known about their physiological functions. Here we describe a novel zebrafish knockout model of the RNA binding proteins Hnrnpa1 and Hnrnpa3. Loss of Hnrnpa3 in zebrafish has no obvious morphological phenotype. Similarly, single mutants of the duplicated zebrafish hnrnpa1 genes, hnrnpa1a and hnrnpa1b, have no discernible phenotype, whereas the hnrnpa1a; hnrnpa1b double mutants are embryonic lethal. They display muscle, vascular and developmental defects with a reduced volume of the yolk extension. Metabolic profiling revealed severe changes in lipid metabolism in the hnrnpa1a; hnrnpa1b double mutants. Our analysis identified the involvement of Hnrnpa1 in many cellular pathways including the regulation of lipid metabolism and opens the door for future therapeutic studies in HNRNPA-associated diseases.

overall_design: Bulk RNA sequencing of whole hnrnpa1 dKO larvae at 30 hpf compared to wildtype control larvae

first: Lara

middle: U

last: Jansen

first: Alexander

last: Hruscha

first: Özge

middle: P

last: Burhan

first: Ting

last: Sun

first: Stefan

last: Bonn


title: FXR-induced PC-5p-694_11238 promotes CAF activation in NSCLC

city: SHANGHAI

first: Shufang

last: Chen

address: 2800 Gong Wei Road

institute: Shanghai Pudong Hospital

summary: MicroRNA sequencing identified an increase of newly discovered PC-5p-694_11238 in FXR-overexpressing NSCLC exosomes. In NSCLC cells, FXR increased the packaging of exosomal PC-5p-694_11238 from tumor cells, which might be a potential therapeutic target for NSCLC patients.

overall_design: To investigate FXR’s role in NSCLC exosomal miRNA regulation, A549 cells were transduced with lentiviral vectors to stably overexpress FXR. Exosomes were isolated from conditioned media via ultracentrifugation, followed by miRNA sequencing .

first: Wenjie

last: You

first: Ruilin

last: Yao


title: Integrating transcription factor networks with chromatin accessibility as markers of survival outcome and drug response in triple-negative breast cancer

city: Toronto

first: Mathieu

last: Lupien

address: 101 College Street

institute: University Health Network

summary: Triple-negative breast cancer (TNBC) is an aggressive and heterogeneous breast cancer subtype with few effective targeted therapies and frequent resistance to chemotherapy. Here, we integrated transcriptional regulatory network inference with chromatin accessibility across a large-scale multi-system collection of primary tumors, patient-derived xenografts (PDXs) and model cell lines to quantify Transcription Factor (TF) activity and identified regulators that underpin TNBC identity. This approach prioritized 94 high-confidence TNBC TFs whose activity scores capture inter-tumor heterogeneity and independently stratify patient outcome across clinical endpoints. Linking TF activity to pharmacogenomics drug sensitivity profiles identifies reproducible drug-TF associations across independent datasets, including NFE2L3 and CBFB activity as predictors of sensitivity to mTOR inhibition, which we validated in everolimus-treated TNBC PDX models. Collectively, we establish a transcriptional and chromatin-informed framework to capture TNBC regulatory state and expand TF-guided precision medicine to this breast cancer subtype.

overall_design: ATAC-seq of untreated breast cancer cell lines

first: Shalini

last: Bahl

first: Ankita

last: Nand


title: RNA Terminal Uridylyl-Transferases Are Druggable Vulnerabilities in AML, but are Dispensable for Normal Hematopoiesis [RNA-seq]

first: Yuka

last: Kabayama

overall_design: RNA-seq profiling of control and Tut4/7 double conditional knockout murine acute preleukemic cells, and those treated with the TUT4/7 inhibitor 2266 or vehicle control. Technical replicates were performed for MLL-AF9/Flt3-ITD and NPM1/Flt3-ITD cells. Individual biological replicates generated from indipendent foetal livers were analysed for Mesi1/HoxA9 cells.

first: Christopher

last: Mapperley

first: Elise

last: Georges

middle: A

last: Azar

first: Hannah

last: Lawson

first: Iwo

last: Kucinsk

first: Derek

last: George

first: Joana

last: Campos

first: Corey

last: Fyfe

first: Jozef

last: Durko

first: Wei

middle: Y

last: Chan

first: Lewis

last: Allen

first: Babak

last: Jazayeri

first: Edward

last: Blacker

first: Louie

last: van de Lagemaat

first: Aurelien

last: Tripp

first: Theodoros

last: Roumeliotis

first: Giulia

last: Guiducci

first: Eleanor

last: Herbert

first: Jasmin

last: Paris

first: Jyoti

last: Choudhary

first: George

last: Poulogiannis

first: Robert

middle: M

last: Campbell

first: Marcos

last: Morgan

first: Lovorka

last: Stojic

first: Folkert

last: Van Werven

first: Douglas

last: Vernimmen

first: Berthold

last: G ttgens

first: D nal

last: O Carroll

first: Kamil

last: Kranc