title: Antimicrobial activity of canine adipose tissue-derived Mesenchymal Stromal Cells lyosecretome

city: Brescia

first: Martina

last: Tambassi

state: Italy

address: Via Bianchi, 9

department: Risk Analysis and Genomic Epidemiology Unit

country: Italy

institute: Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia-Romagna, VAT IT00284840170

summary: Mesenchymal Stromal Cells (MSCs) are widely studied in regenerative medicine because of their unique biological properties. The MSC-derived secretome is a cell-free product containing soluble factors and extracellular vesicles that mediate many of the biological properties of MSCs, including immunomodulatory and antimicrobial activities. This study aimed to evaluate the antimicrobial activity of a freeze-dried secretome derived from canine adipose tissue MSCs (canine lyosecretome, c-Lyo) against pathogens relevant to canine infections. The antimicrobial activity of c-Lyo was assessed using minimal inhibitory concentration (MIC) assays against six bacterial species (Escherichia coli, Salmonella enterica subsp. enterica serovar Typhimurium, Staphylococcus aureus, methicillin-resistant Staphylococcus aureus (MRSA), Staphylococcus pseudintermedius and Pseudomonas aeruginosa) and one yeast (Malassezia pachydermatis). Potential interactions between c-Lyo and commonly used veterinary antimicrobials (gentamicin, amoxicillin, enrofloxacin, and ketoconazole) were evaluated using checkerboard assays (CkA). Proteomic characterization of the c-Lyo and transcriptomic analysis of canine MSCs were also conducted to explore molecular mechanisms underlying antimicrobial activity. The results demonstrated that c-Lyo exerts antimicrobial activity against all tested microorganisms, with variable sensitivity among species. CkA exhibited predominantly additive interactions with conventional antimicrobials and occasional synergistic effects, with no evidence of antagonism. Proteomic and transcriptomic analyses supported the presence of antimicrobial peptides and immune-related pathways that potentially contribute to both direct antimicrobial activity and the modulation of host defense mechanisms. These findings indicate that c-Lyo may represent a promising cell-free biologic approach for antimicrobial strategies in veterinary medicine.

overall_design: RNA-seq profiles of primary adipose-derived canine mesenchymal stromal Cells

first: Valentina

last: Andreoli

first: Costanza

last: Spadini

first: Nicolò

last: Mezzasalma

first: Priscilla

last: Berni

first: Melissa

first: Laura

last: Mazzera

first: Virna

last: Conti

first: Roberto

last: Ramoni

first: Elia

last: Bari

first: Silvia

last: Dotti

first: Rossana

last: Rossi

first: Ishak

last: Yosuf

first: Pierluigi

last: Mauri

first: Dario

last: Di Silvestre

first: Giuseppina

last: Basini

first: Clotilde Silvia

last: Cabassi

first: Maria Luisa

last: Torre

first: Stefano

last: Grolli


title: GPR34 regulation of disease-associated microglial states in mice

status: Public on Apr 09 2026

city: Cambridge

first: Joshua

last: Levin

state: MA

address: 75 Ames St

department: Stanley Center

country: USA

institute: Broad Institute

type: Expression profiling by high throughput sequencing

summary: We investigated the role of the microglia-enriched G protein–coupled receptor GPR34 in regulating cell states for microglia and other cell types under physiological and disease conditions using single-cell RNA sequencing (scRNA-seq) and single-nuclei RNA sequencing (snRNA-seq). Microglia isolated from Gpr34 knockout (KO) and wild-type mice, with or without the 5xFAD Alzheimer’s disease background, were profiled to assess transcriptional changes associated with GPR34 loss, as were other cell types in the hippocampus. Our findings indicate that GPR34 plays a critical role in maintaining microglial homeostasis and restraining disease-associated transcriptional responses in vivo.

overall_design: For single cell data: Six-month-old male mice of four genotypes (wild-type, Gpr34 KO, 5xFAD, and Gpr34 KO;5xFAD) were used to assess the impact of GPR34 loss on microglial transcriptional states. Hippocampal tissue was collected following perfusion and dissection. Microglia were isolated using CD11b-based magnetic enrichment and subjected to scRNA-seq using the 10x Genomics platform. Comparative analyses were conducted across genotypes to identify differential gene expression and changes in microglial transcriptional programs associated with GPR34 deficiency. For single nucleus data:  Six-month-old male mice of four genotypes (wild-type, Gpr34 knockout, 5xFAD, and Gpr34 KO;5xFAD) were used. Hippocampal tissue was collected following perfusion and dissection, and nuclei were isolated for single-nucleus RNA sequencing (snRNA-seq). Comparative analyses were performed across genotypes to identify transcriptional changes and shifts in cell-type composition associated with GPR34 deficiency.

first: Ana

last: Geller

first: Min Jee

last: Kwon

first: Sean

last: Simmons

first: Qihong

last: Xu

first: William

last: Martenis

first: Jordan

last: Doman

first: Sahana

last: Natarajan

first: Katherine

last: Stalnaker

first: Constanze

last: Depp

first: Steven

last: Carr

first: David

last: McKinney

first: Alexandra

last: Gould

first: Evan

last: Lebois

first: Michel

last: Weiwer

first: Matthew

last: Johnson

first: Yan-Ling

last: Zhang

first: Nader

last: Morshed

first: Deeksha

last: Misri

first: Diana

last: Bohannon

first: Elena

last: Longhi

first: Hasmik

last: Keshishian

last: Demers

first: Donovan

last: Batzli

first: Antia

last: Valle-Tojeiro

first: Christy

last: Biji

first: Sameer

last: Aryal

first: Horai

last: Pribiag

first: Jixiang

first: Xian

last: Adiconis

first: Trang

last: Nguyen

first: Morgan

last: Sheng

first: Prabhat

last: Kunwar


title: Effect of the poly-ICLC vaccine adjuvant on prostate cancer patients’ PBMC

status: Public on Apr 10 2026

city: Acton

first: Manuel

middle: Xavier

last: Duval

address: 12 Abel Jones Pl

institute: double-strand

summary:
Identify PBMC RNA quantities whose level might predict response to prostate HIT-IT treatment
Phase I Peripheral Blood Mononuclear Cell from 12 high risk prostate cancer patients

overall_design:
Patients’ PBMC under HIT-IT treatment were collected at baseline and at five time points (week 3, week 6, week 9, week 6 post surgery and week 12 post surgery.
study protocol: Open-label Phase I clinical trial using a dose-escalation strategy of poly-ICLC in patients with clinically-localized prostate cancer.

first: Sujit

middle: S

last: Nair

first: Dimple

last: Chakravarty

first: Ashutosh

middle: K

last: Tewari


title: Motif-directed chromatin repression by BCL11B shapes ectopic targeting and lineage commitment [RNA-seq]

city: MEMPHIS

first: QINGSONG

last: GAO

state: Tennessee

address: 262 DANNY THOMAS PLACE

institute: ST JUDE CHILDREN'S RESEARCH HOSPITAL

summary: BCL11B encodes a critical T-lineage transcription factor that is implicated as both an oncogene and a tumor suppressor in acute leukemia. Despite its central role in development and malignancy, a basic understanding of the sequence determinants of BCL11B activity remains obscure. Here, we define two functionally distinct modes of BCL11B engagement with chromatin: Most detectable BCL11B binding events are determined by pre-existing patterns of chromatin accessibility and RUNX1 occupancy. In contrast, BCL11B directs chromatin closing at genomic regions enriched for DNA motifs containing the core “TGACC” sequence, which are most prevalent in non-T lineages. These BCL11B-closed target sites cannot be identified from conventional BCL11B chromatin profiling approaches yet represent the primary mechanism by which BCL11B regulates gene expression. We provide evidence that cell of origin impacts the ability of BCL11B to repress lineage-inappropriate gene programs, thereby promoting lineage skewing. Together, these findings define a motif-centered determinant of BCL11B repression and explain how BCL11B controls lineage specification.

overall_design: This submission includes RNA-seq data generated in human cord blood-derived CD34+ HSPCs transduced with lentiviral constructs encoding BCL11B, BCL11B-dTAG, or an empty vector (control), and BRU-seq data generated in Jurkat cells genetically engineered to express FKBP12F36V-HA-BCL11B (BCL11B-dTAG) or unedited control cells. Cells were either untreated, treated with DMSO (control) or treated with dTAGV-1 for 1 (Jurkat) or 6 (CD34+ HSPCs) hours to induce BCL11B degradation. Three replicates were generated for each experimental condition for RNA-seq in CD34 cells; two replicates were used for BRU-seq in Jurkat cells. For CD34 experiments, RNA-seq was performed on day 7 of CD34+ expansion, representing 4 days post-transduction.

first: Lindsey

middle: E

last: Montefiori

first: Qingsong

last: Gao

first: Charles

middle: G

last: Mullighan


title: BAF complexes maintain accessibility at stimulus-responsive chromatin and are required for transcriptional stimulus responses [ATAC-seq]

city: Atlanta

first: Alexander

middle: O. D.

last: Gulka

state: Georgia

address: 1510 Clifton Rd NE

institute: Emory University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Gene regulation relies on cis-regulatory sequence elements (cREs), including enhancers, to alter gene expression in response to developmental and environmental cues. BRG1/BRM-Associated Factors (BAF) chromatin remodeling complexes are required to maintain an “accessible” chromatin state at many cREs, which enables binding by transcription factors (TFs) and other regulatory proteins. However, cREs exhibit a broad range of sensitivity to loss of BAF function, and the basis of this variable dependence on BAF remains unclear. To identify the characteristics of cREs that rely on BAF complexes to maintain chromatin accessibility, we generated time- and dosage-resolved maps of chromatin accessibility changes following acute BAF inhibition in the lymphoblastoid cell line GM12878. We then integrated these results with ChIP-seq data on more than one hundred TFs and histone modifications available for this cell line and used machine learning to identify features that predict changes in chromatin accessibility upon BAF inhibition. We found that several TFs were associated with sensitivity to BAF inhibition, including widely expressed Activator Protein 1 (AP-1) factors and lymphoid lineage-defining TFs such as RUNX3 and PU.1. Surprisingly, we also found that cREs bearing the chromatin signature of “primed” enhancers – characterized by H3K4me1 enrichment in the absence of the “active” enhancer mark H3K27ac – were significantly more sensitive to BAF inhibition than typical active enhancers. Nearly all primed enhancers lost chromatin accessibility within 30 minutes of BAF inhibition. Notably, primed enhancers are known to facilitate transcriptional responses to external stimuli. Thus, we reasoned that BAF function may be required for cells to mount transcriptional stimulus responses. To test this theory, we assessed the effect of acute BAF inhibition on responses to two orthogonal stimuli, interferon gamma and dexamethasone. We found that BAF inhibition was sufficient to prevent chromatin and transcriptional responses to these stimuli. cREs which normally gained accessibility in response to stimulation failed to do so with BAF inhibition, and these cREs were linked to genes with suppressed transcriptional induction upon stimulation. Collectively, our results demonstrate a requirement for continuous BAF activity to enable stimulus response and suggest that defective signal responsiveness may be a pathogenic mechanism in disease states caused by loss-of-function mutations in BAF subunits.

overall_design: ATAC-seq profiling of : GM12878 cells after treatment with BRM014 for various timepoints (0.5h-24h) and doses (10nM - 10uM); GM12878 cells after 24h treatment with 1uM ACBI1; GM12878 cells after stimulation with interferon gamma or dexamethasone (1h or 6h), with or without BRM014 pretreatment; or HepG2 cells treated for 24h with 10uM BRM014.

middle: O

first: Kihoon

middle: A

last: Kang

first: Ziben

last: Zhou

first: David

middle: U

last: Gorkin


title: Motif-directed chromatin repression by BCL11B shapes ectopic targeting and lineage commitment

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

overall_design: Refer to individual Series


title: Epitranscriptomic analysis reveals clinical and molecular signatures in glioblastoma

city: Miami

first: Glaucia Maria

middle: de

last: Mendonça Fernandes

state: FL

address: 4060 SW 97th PL

department: HWCOM Cellular and Molecular Medicine

institute: Florida International University

summary: Retrospective GB patient data of patients that were eventually deemed to have progressive disease or pseudoprogressive disease was captured from the electronic health record , and RNA from the first resection specimen was utilized to evaluate Arraystar Human m6A Single Nucleotide resolution microarray analysis  biomarkers from FFPE samples

overall_design: 92 patients were categorized into psPD and PD groups: psPD was identified by new or progressive enhancement within 6 months of ChemoRT, confirmed treatment reaction, and no prior progression. PD classification relied on clinic-pathologically confirmed cancer recurrence with no previous progression history

first: Fernandes

last: Glaucia Maria de Mendonça Fernandes

first: Wang

last: Wesley

first: Jones

last: Daniel

first: Peng

last: Jing

first: Giglio

last: Pierre

first: Venere

last: Monica

first: Otero

last: Jose Javier


title: Motif-directed chromatin repression by BCL11B shapes ectopic targeting and lineage commitment [ATAC-seq]

overall_design: This submission includes ATAC-seq data generated in human cord blood-derived CD34+ HSPCs transduced with lentiviral constructs encoding BCL11B, BCL11B-dTAG, or an empty vector (control), and Jurkat cells genetically engineered to express FKBP12F36V-HA-BCL11B (BCL11B-dTAG) or unedited control cells. Cells were either untreated, treated with DMSO (control) or treated with dTAGV-1 for 1 (Jurkat) or 6 (CD34+ HSPCs) hours to induce BCL11B degradation. Two replicates were generated for each experimental condition. For CD34 experiments, ATAC-seq was performed on day 7 of CD34+ expansion, representing 4 days post-transduction.


title: Identification and integration of LRG1-Induced differentially Expressed Gene (DEG) Hub Profiles in breast cancer cell

city: Tlaxcala

first: Federico

last: Osorio Antonio

state: Puebla

address: 11 Pte av.

department: Faculty of biotechnology

country: Mexico

institute: Popular Autonomous University of the State of Pueb

summary: Breast carcinoma is a major cause of cancer-related mortality among women worldwide. Identifying novel molecular targets remains essential, particularly for aggressive triple-negative breast cancer (TNBC). Leucine-rich alpha-2-glycoprotein 1 (LRG1) has been linked to tumor progression and angiogenesis, but its molecular mechanisms in breast cancer are poorly defined. We evaluated the effects of recombinant human LRG1 (rhLRG1) on cell viability and migration in MDA-MB-231 TNBC cells and performed transcriptomic profiling followed by functional enrichment analyses using GenArise, Cytoscape, and R-based tools. RhLRG1 treatment significantly increased cell viability and migration. Transcriptomic analysis revealed activation of key oncogenic cascades, including the PI3K/AKT, MAPK, and RAS signaling pathways.

overall_design: Two conditions assay. Control vs RhLRG1 treatment.  Biological replicates. 2 control. 2 treated with RhLRG1. independently grown and harvested. One replicate per array

last: Osorio-Antonio

first: Daniela

middle: M

last: Díaz-González

first: Gabriela

last: Campos-Viguri

first: José

last: Sánchez-López

middle: L

last: Cortez-Sánchez

first: Francisco

last: Castelán

first: Jesús

middle: R

last: Chávez-Ríos

first: Paola

last: Maycote-González

first: Paulina

last: Cortés-Hernández

first: Oscar

last: Peralta-Zaragoza

first: Elizabeth

middle: B

last: Rodríguez


title: Triggering mouth-resident antiviral CD8+ T cells potentiates experimental periodontitis

city: Cleveland

first: Michael

last: Stolley

state: Ohio

address: 9620 Carnegie Ave N Bldg

department: Department of Inflammation and Immunity

institute: Cleveland Clinic Lerner Research Institute

summary: Emerging evidence indicates that gingival-resident helper CD4+ T cells are major drivers of periodontal inflammation in response to commensal and pathogenic oral microorganisms. Whether tissue-resident memory CD8+ T cells (TRM), which principally safeguard against viruses and cancer but also drive certain autoimmune and inflammatory conditions, impact periodontitis progression and severity remain unknown. We asked whether local reactivation of oral CD8+ TRM of a defined antigen specificity could exacerbate ligature-induced periodontitis (LIP), a well-established model of periodontal disease in mice. Topical application of virus-mimicking peptides to the oral mucosa concurrent with LIP 1) intensified alveolar bone loss, 2) amplified gingival and cervical lymph node inflammation, and 3) stimulated gingival transcriptional changes in genes related to innate immune sensing and cell-mediated cytotoxicity. Therapeutic depletion of CD103-expressing oral CD8+ TRM in advance of LIP prevented exacerbation of disease. These observations provide evidence that oral CD103+ CD8+ TRM have the potential to participate in gingival inflammation, alveolar bone loss, and periodontitis.

overall_design: RNA-seq profiling of maxilla gingival tissue from mice subjected to ligature-induced periodontitis (LIP) with or without oral CD8+ TRM activation via topical virus-mimicking peptides applied to the oral mucosa, collected three and seven days post-LIP.

first: Flávia

last: M Saavedra

first: Danielle

last: Barbosa Brotto

first: Courtney

last: A Matson

first: Pavel

last: P Nesmiyanov

first: Mark

last: C Herzberg

first: Vaiva

last: Vezys

first: David

last: Masopust

first: J Michael


title: Epigenetic analysis of murine normal mammary gland fibroblasts (mNFs) and MMTV-PyMT cancer-associated fibroblasts (mCAF1) (H3K27ac ChIP-seq)

city: Santander

first: Fernando

last: Calvo

state: Cantabria

address: C. Albert Einstein, 22

country: Spain

institute: IBBTEC

summary: In comparison with normal tissue fibroblast (normal fibroblasts, NFs), cancer-associated fibroblasts (CAFs) have pathologically activated phenotypes that impact in a wide variety of tumoral processes including cancer cell growth and invasion, extracellular matrix (ECM) remodelling, angiogenesis and immune suppression. These phenotypes result from the establishment of altered gene expression programs that may be further sustained through epigenetic alterations. However, how epigenetic rearrangements influence CAF behaviour is not well delineated. Here, we identify aspartoacylase (ASPA) as a metabolic enzyme consistently repressed in tumour stroma and CAFs. We report a reciprocal crosstalk between ASPA and Transforming Growth Factor Beta (TGFβ) signalling that influences fibroblast behaviour. TGFβ suppresses ASPA expression in fibroblasts, whereas ASPA restrains TGFβ-dependent myofibroblast conversion, ECM remodelling, angiogenesis and pro-tumoral macrophage phenotypes. TGFβ/SMAD3-dependent transcriptional repression may require the activity of histone deacetylases (HDACs), which participate in epigenetic rearrangements modulating gene expression. Epigenomic analysis of the 3’ regulatory regions at the Aspa locus in murine MMTV-PyMT-derived breast cancer CAFs (mCAF1) as compared to normal murine mammary gland fibroblasts (mNFs), revealed a selective loss of H3K27Ac, an epigenetic mark of active enhancers. As expected, bona fide CAF marker genes such as Acta2, Fap, Lrrc15 and others presented increased H3K27Ac signal at regulatory regions in mCAF1, whereas peaks at NF marker genes (Cxcl1 and Pi16) were decreased. Our findings unveil ASPA expression in fibroblasts as a previously unknown gatekeeper of TGFβ responses and activation in cancer progression.

overall_design: ChIP-Seq of the histone modification H3K27ac of murine normal mammary gland fibroblasts (mNFs) and MMTV-PyMT cancer-associated fibroblasts (mCAF1). Primary NFs/CAFs were isolated and immortalized, and processed for epigenetic analyses

first: Miguel

last: Juliá


title: Differential impact of FLASH and conventional radiotherapy on a pivotal metabolic organ: White Adipose Tissue

city: Pisa

first: Giulia

last: Furini

address: Via Giuseppe Moruzzi 1

department: Institute of Clinical Physiology (IFC)

institute: National Research Council (CNR)

summary: Subcutaneous white adipose tissue (scWAT), a key metabolic and endocrine organ, is inevitably exposed during radiotherapy (RT). Although RT is a cornerstone of cancer treatment, its clinical use is limited by damage to surrounding healthy tissues. Ultra-high-dose-rate FLASH-RT has emerged as a promising approach that preserves tumor control while reducing normal tissue toxicity. Notably, conventional (CONV) RT has been associated with long-term metabolic dysfunction and white adipose tissue (WAT) impairment, particularly following childhood exposure; however, the impact of FLASH-RT on WAT remains unknown. Here, we compared the effects of FLASH- and CONV-RT on adipocyte function and scWAT homeostasis, integrating molecular, structural, and functional analyses. Experiments were conducted using the human SGBS preadipocyte/adipocyte cell line and a mouse model of proximal hind limb irradiation, employing a dedicated linear accelerator capable of delivering both modalities. In vivo analyses were performed 70 days after irradiation. In vitro, RT impaired adipogenic differentiation in a dose-dependent manner, with a relative sparing effect of FLASH-RT at 4–8 Gy, while mature adipocytes exhibited radioresistance with partial protection at 8 Gy. In vivo, both irradiation modalities reduced fat mass without affecting body weight, with a more pronounced loss following CONV-RT.  Transcriptomic profiling of inguinal scWAT by RNA sequencing revealed a marked divergence between treatments. CONV-RT induced extensive transcriptional reprogramming of scWAT. Upregulated genes were enriched in inflammatory and immune-related pathways, as well as processes associated with chemotaxis, oxidative stress, and macrophage recruitment. Conversely, downregulated genes were linked to neuronal function, angiogenesis, and differentiation-related pathways, indicating a compromised neurovascular and adipogenic environment. In contrast, FLASH-RT elicited minimal transcriptional changes, with only three genes differentially expressed and no significant enrichment of biological processes. These molecular findings were supported by histological and ultrastructural analyses, which showed increased cellular damage, vacuolization, lipid spill-over, and reduced PLIN1 expression, predominantly in CONV-treated mice. In conclusion, our data suggest that WAT homeostasis is highly sensitive to conventional RT, which induces extensive transcriptional remodeling associated with inflammation and tissue dysfunction, whereas FLASH-RT largely preserves the scWAT transcriptome, tissue structure, and function, supporting its potential to mitigate long-term metabolic complications in cancer survivors.

overall_design: C57BL/6J mice were exposed to 33.3 Gy electron irradiation to the left hindlimb by either FLASH-RT or conventional (CONV-RT) modality. Sham, not irradiated mice served as controls. 70 days post  treatment, inguinal subcutaneus WAT from the irradiated area was collected and the trascriptomic profile investigated by RNA-Seq.

first: Gaia

last: Scabia

first: Alice

last: Usai

last: Asero

first: Eduarda

last: Mota Da Silva

first: Claudia

last: Kusmic

first: Filippo

last: Rossi

first: Roberto

last: Cusano

first: Riccardo

last: Berutti

first: Jessica

last: Milia

first: Margherita

last: Maffei


title: Concurrent genetic and non-genetic resistance mechanisms to KRAS inhibition in CRC

city: Houston

first: Salvador

last: Alonso

state: Texas

address: 1400 Holcombe Blvd, FC10.3030

department: GI Medical Oncology

institute: MD Anderson Cancer Center

summary:
Whole exome sequencing and single cell spatial transcriptomics (CosMx) of patient biopsies show that genetic and non genetic resistance mechanisms often coexist in the same tumor.
We show that targeting the early adaptive changes, characterized by inflammatory reprogramming, synergizes with KRAS inhibition.

overall_design: To identify genetic and non-genetic adaptive programs to KRAS inhibition, we prospectively collected 12 matched pre-treatment and on-treatment (day 7 to day 21) biopsies, as well as 8 post-progression biopsies from CRC patients treated with combined KRASG12C plus EGFR inhibition. Patients received treatment in one of two clinical trials combining sotorasib plus panitumumab, or testing adagrasib with or without cetuximab.

first: Lukas

last: Dow


title: PI-5-P links the Hippo Pathway and PI5P4K signaling [PIP4K2A/B shRNA]

city: La Jolla

first: Brooke

middle: M.

last: Emerling

state: CA

address: 10901 North Torrey Pines Road

department: Cell and Molecular Biology of Cancer Program

institute: Sanford Burnham Prebys Medical Discovery Institute

summary: The phosphoinositide PI-5-P is a signaling lipid that mediates cellular responses to oxidative stress and DNA damage, however it is unclear how PI-5-P participates in these processes. Intracellular pools of PI-5-P are regulated by PI5P-Kinases (PI5P4Ks), but how PI5P4K activity is controlled has also remained elusive. Here, we used an unbiased screen to discover the core Hippo pathway kinases MST1/2 phosphorylate and inhibit PI5P4K signaling in vitro and in cells. We further show PI5P4Ks regulate several Hippo/YAP-related phenotypes in human cells, such as the interaction between the key Hippo proteins MOB1-LATS, and the genetic program governing epithelial-to-mesenchymal transition. Mechanistically, we show that MOB1 binds PI-5-P with high specificity and potency, providing a signaling connection between the Hippo Pathway and PI5P4Ks. These discoveries shed new light on how these two important evolutionary conserved signaling pathways are integrated to regulate metazoan development and human disease.

overall_design: Transcriptomics comparison of scrambled control shRNA versus PIP4K2A/B shRNA in HCC1806 cell line using RNA-seq

first: Lavinia

last: Palamiuc

first: Ryan

last: Loughran


title: The H3K4 methyltransferase KMT2D is an essential cofactor for GATA1 at erythroid gene enhancers

city: Suzhou

first: Peng

last: Xu

state: Jiangsu

address: Office3625 Building703, RENAI ROAD No.199, INDUSTRIAL PARK DISTRICT

department: Suzhou Medical College

country: China

institute: Soochow University


title: Hypoxia-responsive interaction between Cyclin T1, BHLHE40, and Tim8-Tim13 regulates RNA Polymerase II

city: Chicago

first: Ali

last: Shilatifard

state: IL

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

summary: P-TEFb regulates the pause release checkpoint on transcription by RNA Polymerase II. We sought hypoxia-specific interactions that could direct PTEF-b activity to hypoxia-responsive genes. Using a biochemical purification approach, we discovered a hypoxia-specific, chromatin-associated interaction between the P-TEFb subunit Cyclin T1 (CCNT1), the mitochondrial chaperone Tim8-Tim13 complexes, and the hypoxia-inducible, DNA-binding transcription factor BHLHE40. This interaction is conserved across diverse cell line models. Tim8-Tim13 complex disruption and BHLHE40 silencing both impair the transcriptional response to acute hypoxia by RNAPII in DLD-1 cells. HIF is not involved in the CCNT1/BHLHE40/Tim8-Tim13 interaction, and BHLHE40 expression is not entirely HIF-dependent: neither genetic HIF-1β knockout nor pharmacological inhibition of HIF-2α using belzutifan eliminates BHLHE40. Finally, BHLHE40 depletion compromises the proliferation of 786-O clear cell renal carcinoma cells, which constitutively express HIF-2α and hypoxia-responsive genes. Together, these findings reveal a HIF-independent regulatory axis in which Tim8a-Tim13 complexes and BHLHE40 that modulate PTEF-b activity in the transcriptional response to hypoxia.

overall_design: ChIP-seq of RNAPII, BHLHE40, and HIF-1A in a colorectal cancer cell line (DLD-1) with sgRNA-induced KO and shRNA-KD modifications to analyze impact of genetic background on response to hypoxia.

first: Shimaa

middle: H

last: Soliman

first: Simone

last: De Fabritiis

first: Lawrence

last: Lin

first: Marta

last: Iwanaszko

first: Navdeep

last: Chandel


title: Studing chemo- and immuno-resistance in non-small cell lung cancer (NSCLC) NCI-H2228 cell line

status: Public on Apr 13 2026

city: Torino

first: Raffaele

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

institute: University of Torino

summary: Non-small cell lung cancer (NSCLC) has a chemo-immuno-resistant phenotype. This study aims to elucidate druggable molecular pathways underlying such chemo-immuno-resistance.

overall_design: This study includes wild-type (wt), IRAK1-silenced (sh),TFEB-silenced (sh), C/EBP-β LAP-overexpressing NCI-H2228 cells, all inoculated in Hu-CD34+ mice, which are characterized by a reconstituted human immune system. From previous in vitro experiments and observations on patients cohorts, IRAK1-silenced  NSCLCs were more chemosensitive and immunosensitive, TFEB-silenced and C/EBP-β LAP-overexpressing NSCLCwere more chemosensitive and immunosensitive. Mice were randoized and treated with: 1) saline solution as control group), 2) cisplatin, the first-line treatment for NSCLC; 3) drugs targeting pathaways controlled by IRAK1 (synthetitic IRAK1 inhibitors or IRAK1 shRNA), by TFEB (zoledronic acid) or by C/EBP-β LAP (Etomoxir); 4)  their combinations, namely: cisplatin + IRAK1 inhitors/IRAK1 shRNA (for  tumors wt and with tunable IRAK1); cisplatin + zoledronic acid (for  wt and shTFEB tumors); cisplatin + Etomoxir (for wt and C/EBP-β LAP tumors). Two tumors per each treatment groups were analyzed. The endpoints were: i) the evalaution of tumor growth; ii) the changes in tumor immune-environment. Our data provide indications on different molecular pathways involved in the chemo-immuno-resistant phenotype of NSCLC, and on new combination treatments that may overcome chemo-immuno-resistance in NSCLC refractory to cisplatin alone.

first: Tatiana

last: Chontorotzea

first: Elisa

last: Balmas

first: Alessandro

last: Bertero

first: Simona

last: Fontana

first: Sabrina

last: Digiovanni

first: Joanna

last: Kopecka

first: Iris

middle: C

last: Salaroglio

first: Luca

last: Alessandri

first: Chiara

last: Riganti


title: Spatial transcriptomic atlas of aggressive osteosarcomas reveals shared gene surface expression and immune landscape.

city: Villejuif

first: Gaël

last: Moquin-Beaudry

address: 114, rue Édouard-Vaillant

country: France

institute: Gustave Roussy

summary: Osteosarcoma remains a highly aggressive malignancy with limited advancements in treatment efficacy and survival rates over the past four decades. Current therapeutic strategies fail in a significant proportion of patients, leading to metastatic relapse and poor prognosis. The substantial genomic instability and cellular plasticity of osteosarcoma contribute to its complex biology, necessitating innovative approaches for improved diagnosis and treatment. In this study, we applied spatial transcriptomics (ST) to 26 osteosarcoma samples, primary tumors and metastatic or local relapse samples. We described diverse differentiation phenotypes, ranging from mostly undifferentiated to metaphyseal-like organized highly differentiated phenotypes. Despite the phenotypic variability within and across samples, a comprehensive surfaceome analysis identified 306 cancer-specific membrane protein genes, among which nine formed a robust osteosarcoma-specific theranostic signature validated in multiple bulk RNAseq datasets. Additionally, spatial analysis of immune cell dynamics confirmed the systemic lymphoid cell exclusion and distinguished between cancer-excluded and -infiltrating myeloid populations. This identified three distinct populations along the osteoclastic lineage, with a systematic cancer-infiltration capacity. Cancer-infiltrating potential was also associated with type I interferon response and specific integrin-mediated adhesion mechanisms. This study provides a valuable resource to improve the understanding of osteosarcoma biology. We also suggest new clinically relevant targets in osteosarcoma, enabling the development of adapted and targeted treatment strategies for patients with the hope of improving clinical outcomes in the future.

overall_design: 26 FFPE samples of primary (n=9) and relapse (n=17) osteosarcoma tumors were analyzed by spatial transcriptomics using the Visium V1 FFPE protocol.

first: Maria Eugénia

last: Marques Da Costa

first: Pierre

last: Knheisser

first: Corentin

last: Thuilliez

first: Baptiste

last: Audinot

first: Hanane

last: Zair

first: Nicolas

last: Signolle

first: Michael

last: McDermott

first: Marie-Dominique

last: Tabone

first: Jean-Yves

last: Scoazec

first: Birgit

last: Geoerger

first: Damien

last: Drubay

first: Nathalie

last: Gaspar

first: Antonin

last: Marchais


title: AMPK inhibition and elevated angiogenin are associated with tRNA fragmentation in the male germline exposed to a high-fat diet

city: Seoul

first: Yoon Jung

last: Park

address: 52 Ewhayeodae-gil, Seodaemun-gu

country: South Korea

institute: Ewha Womans University

type: Non-coding RNA profiling by high throughput sequencing

summary: The existence of an inherent intergenerational rewiring of metabolic regulation has been demonstrated through studies of obese mice that are fed a normal diet and produce offspring with metabolic disorders. tRNA-derived fragments (tRFs) have been suggested as a potential mediator of this inheritance. To explore a mechanism underlying metabolic stress-induced tRNA fragmentation, we examined the effects of a HFD on tRFs in sperm. Small RNA sequencing on sperm revealed that HFD-induced metabolic changes affect the tRF profiles, showing a trend of decreased 5’-derived tRFs and increased 3’-derived tRFs, suggesting a shift in tRNA cleavage patterns under HFD feeding. In conjunction with the alteration of tRFs, the expression of Ang, which encodes the ribonuclease angiogenin, was significantly increased in the testis. Transcriptome and metabolome analyses indicated that AMPK-mTOR signaling pathway was the possible mediator of these effects, with decreased AMPK activity and increased mTOR activity confirmed at the protein level in the testis. Moreover, in vitro experiments showed that AMPK inhibition led to increased angiogenin expression level and alterations in tRF profile. In vitro angiogenin induction experiments, designed to mimic HFD conditions, produced changes in tRF profiles similar to those observed in HFD-fed mice, although the resulting tRF profiles did not completely recapitulate the in vivo HFD-induced profiles. Our findings suggest that AMPK inhibition by HFD may induce Ang expression and tRF remodeling, potentially acting as a mediator of intergenerational transmission of diet-induced metabolic dysregulation.

overall_design: smallRNA-seq profiling of mouse sperm exposed to CD and HFD, and TM4 cells with CC treatment and Ang OE.

first: Eunbi

last: Lee

first: Seo Yoon

last: Choi

first: Seung Min

last: Song

first: Anders

last: Lindroth


title: IRF7 links HK1-dependent histone lactylation to fibroblast activation and cardiac fibrosis [RNA-Seq]

city: Nanjing

first: yujia

last: xue

address: Longmian Avenue 639

institute: China Pharmaceutical University

summary: In response to a myriad of stimuli quiescent resident cardiac fibroblasts undergo metabolic, morphological, and functional alterations to transition to myofibroblasts and mediate cardiac fibrosis. In the present study we investigated the contribution of interferon regulatory factor 7 (IRF7) to fibroblast activation and cardiac fibrosis. IRF7 knockdown in quiescent cardiac fibroblasts potentiated whereas IRF7 over-expression suppressed myofibroblast transition. Consistently, targeted deletion of IRF7 fibroblasts/myofibroblasts similarly exacerbated cardiac fibrosis and dampened heart function in animal models of heart failure. Integrated transcriptomic analysis uncovered Hexokinase 1 (Hk1) as a downstream target for IRF7. Congruently, genetic deletion or pharmaceutical inhibition of HK1 protected the mice from adverse cardiac remodeling. Mechanistically, HK1 contributed to cellular lactate pool to promote histone H3K9 lactylation thus licensing the transcription of pro-fibrogenic molecules. Finally, the relevance of the IRF7-HK1 axis was authenticated in human heart specimens. In conclusion, our data unveil a previously unrecognized IRF7-HK1 axis that contributes to metaboloepigenetic reprogramming of fibroblast activation and cardiac fibrosis. Targeting this axis might yield novel therapeutic solutions for the intervention of heart failure.

overall_design: Mouse primary cardiac fibroblasts were induced to undergo IRF7 overexpression by transfection with adeno-associated virus, followed by TGF-β treatment.

first: Ming

last: Kong

first: Chenghao

last: Zhu

first: Yujia

last: Xue

first: Wenxuan

last: Hong

first: Guoqing

last: Zhang

first: Dingsheng

last: Jinag

first: Yong

last: Xu

first: Junli

last: Guo


title: Divergent Roles of SPOP and CHD1 in ACSL4 Regulation Reveal Context-dependent Vulnerabilities for Targeting Ferroptosis in Prostate Cancer

first: Di

last: Zhao

state: Tx

address: Zayed Building Z7. 4018

summary: Genetic heterogeneity contributes to the variable therapeutic responses in prostate cancer (PCa). Frequent SPOP mutations and recurrent CHD1 deletions define distinct molecular subtypes of PCa with differential responses to anti-androgen therapy. Ferroptosis, an iron-dependent cell death driven by lipid peroxidation, has emerged as a promising anticancer strategy. Here, we identify SPOP mutations and CHD1 deletion as key genetic determinants of ferroptosis susceptibility in PCa.

overall_design: ChIP-seq was performed in WT and SPOPW131G LNCaP cells using IgG control or CHD1 antibodies; SPOPW131G/CHD1KO LNCaP cells were treated with or without atorvastatin (10 𝜇M) for 48h, followed by ChIP-seq using IgG control or SP1 antibodies.

first: Feiyu

last: Chen

first: Qidong

last: Li

first: Yue

last: Lu

first: Boyi

last: Gan


title: Macrophage–Fibroblast Signaling Network Identified by Single-Cell RNA Sequencing in Juvenile Systemic Sclerosis

city: Pittsburgh

first: Kathryn

last: Torok

email: TRH107@pitt.edu, kst7@pitt.edu

state: PA

address: 4401  Penn Ave

institute: University of Pittsburgh

summary: Juvenile systemic scleroderma (SSc) is a rare autoimmune disease characterized by excessive fibrosis and vascular involvement. Adult-onset SSc and inflammatory-driven multi-organ fibrosis are similar; interstitial lung disease was recently found in 40% of SSc patients in an international cohort. While recent single-cell studies have explored different types of fibroblasts that are involved in juvenile systemic scleroderma, less is known about the specific immune interactions with fibroblasts that maintain their activation. This study aims to address that gap by mapping macrophage-fibroblast signaling using interaction analyses. The current abstract describes the single-cell RNA sequencing (scRNA-seq) profile of 9 SSc patients’ skin compared to 9 healthy subjects. ScRNA-seq was performed on the skin of 9 SSc patients and 9 healthy age-matched subjects. Samples were dissociated into single-cell suspensions and processed using the 10x Genomics® Chromium platform for single-cell RNA sequencing. Data preprocessing and clustering were performed in R using Seurat and Harmony for normalization and batch correction, followed by visualization with UMAP. Cell-to-cell communication was investigated using NicheNet and CellChat to predict ligand–receptor interactions between macrophage and fibroblast populations, including associated signaling pathways and target gene networks. Analysis of scRNA-sequenced data revealed specific fibroblast and macrophage populations driving fibrosis in systemic scleroderma (SSc). Clustering led to 11 unique groups of fibroblasts. Clusters COL11A1+/POSTN+ and STC1+/FZD9+ were markedly expanded in SSc skin and showed activation of TGFβ, WNT, and FGF pathways associated with extracellular matrix (ECM) production. The STC1+/FZD9 cluster was a novel finding, with pathway involvement in pulmonary and hepatic fibrosis signaling and TGFβ pathway activation. Macrophage subsets MMP19+/CTSL+ and MERTK+ emerged as important profibrotic sender cells, expressing ligands such as TGFB1, AREG, and COL6A2 that signal to fibroblast receptors TGFBR1, TGFBR2, FGFR1, FGFR2, and FZD9. NicheNet and CellChat analyses identified a coordinated macrophage–fibroblast signaling network integrating TGFβ, FGF, WNT, IGF, NOTCH, and TNF pathways. Notably, TGFβ signaling persisted through accessory activators (ITGAV, THBS1, and SDC2), suggesting a self-sustaining loop of fibroblast activation independent of accessory inflammatory input.  Analysis of scRNA-sequenced data revealed specific fibroblast and macrophage populations driving fibrosis in systemic scleroderma (SSc). Clustering led to 11 unique groups of fibroblasts. Clusters COL11A1+/POSTN+ and STC1+/FZD9+ were markedly expanded in SSc skin and showed activation of TGFβ, WNT, and FGF pathways associated with extracellular matrix (ECM) production. The STC1+/FZD9 cluster was a novel finding, with pathway involvement in pulmonary and hepatic fibrosis signaling and TGFβ pathway activation. Macrophage subsets MMP19+/CTSL+ and MERTK+ emerged as important profibrotic sender cells, expressing ligands such as TGFB1, AREG, and COL6A2 that signal to fibroblast receptors TGFBR1, TGFBR2, FGFR1, FGFR2, and FZD9. NicheNet and CellChat analyses identified a coordinated macrophage–fibroblast signaling network integrating TGFβ, FGF, WNT, IGF, NOTCH, and TNF pathways. Notably, TGFβ signaling persisted through accessory activators (ITGAV, THBS1, and SDC2), suggesting a self-sustaining loop of fibroblast activation independent of accessory inflammatory input. These findings define a macrophage-driven signaling circuit that reinforces chronic fibrosis and identify novel molecular targets that may disrupt this feedback loop. Consistent with adult SSc, fibroblast–macrophage interactions likely sustain fibrosis in SSc, yet the specific fibroblast populations involved are different. TGFβ, FGF, and WNT pathways form an interconnected network that drives fibroblast persistence and ECM accumulation, while NOTCH and TNF signaling amplify immune–fibrotic crosstalk. Targeting key ligand–receptor interactions or accessory activators such as ITGAV, THBS1, and SDC2 may provide novel therapeutic strategies to disrupt chronic fibrotic signaling in SSc. By characterizing these ligand–receptor interactions, our study provides a detailed picture of macrophage–fibroblast communication in juvenile systemic scleroderma.

overall_design:
4mm punch bx from skin was collected from 2 jSSc patients These bx were then embedded into FFPE and then underwent flex sequencing where 6 scrolls each of 25um was sectioned and dissociated to yeild viable cells which was then subjected to V3 sequerncing protocol. these sequences were then normalised in an object with other trasitional single cell data to yeild a data set of 9 jSSc patients compared to 9 healthy contols.
4mm punch bx from skin was collected from 7 jSSc patients and 2 healthy controls. These bx were then either cryo preserved till dissociation or disscoatiated fresh to yeild cells which was thenn subject to traditional single cell sequncing on a 10x genomics platform. The data obtaiened were added onto a single object with other healthy samples and 2 j SSc samples with flex seq and analysed.

first: Aneri

last: Shethji

first: Theresa

last: Hutchins

first: Tianhao

last: Liu

first: Anwesha

last: Sanyal

first: Wei


title: The gene regulations by AGR2 in the lung cancer cell line PC9 under Gefitinib treatment.

city: Taipei

first: Kang-Yi

last: Su

address: Rm507, Bldg.Lab.Med., NTU Hospital, No.1, Chang-Te St., Taipei 10048, Taiwan

department: Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine

country: Taiwan

institute: National Taiwan University

summary: We treated the AGR2 silencing (shAGR2) and its control groups with 300nM Gefitinib for 24 hours, while treating the AGR2 overexpression (oeAGR2) and its control groups for 72 hours. We used RNA-seq data to investigate the dynamics of AGR2 expression and its related pathway under drug treatment.

overall_design: RNA-seq profile of PC9 cells with AGR2 knockdown (24 hr gefitinib), AGR2 overexpression (72 hr gefitinib), and their corresponding time-matched controls.

first: Jung-Hsuan

last: Chang


title: Diet-induced phospholipid remodeling dictates ferroptosis sensitivity and tumorigenesis in the pancreas

city: New Haven

first: Mandar

middle: Deepak

last: Muzumdar

state: CT

address: 333 Cedar Street

department: Genetics

institute: Yale University

summary: High-fat diet (HFD) intake has been linked to an increased risk of pancreatic ductal adenocarcinoma (PDAC), a lethal and therapy-resistant cancer. However, whether and how specific dietary fats drive cancer development remains unresolved. Leveraging an oncogenic Kras-driven mouse model that closely mimics human PDAC progression, we screened a dozen isocaloric HFDs differing solely in fat source and representing the diversity of human fat consumption. Unexpectedly, diets rich in oleic acid – a monounsaturated fatty acid (MUFA) typically associated with good health – markedly enhanced tumorigenesis. Conversely, diets high in polyunsaturated fatty acids (PUFAs) suppressed tumor progression. Relative dietary fatty acid saturation levels (PUFA/MUFA) governed pancreatic membrane phospholipid composition, lipid peroxidation, and ferroptosis sensitivity in mice, concordant with circulating PUFA/MUFA levels being linked to altered PDAC risk in humans. These findings directly implicate dietary unsaturated fatty acids in controlling ferroptosis susceptibility and tumorigenesis, supporting potential “precision nutrition” strategies for PDAC prevention.

overall_design: RNA-seq profiling of pancreata isolated from KrasLSL-G12D/+; Pdx1-Cre (KC) and (KrasLSL-G12D/+;Pdx-Cre;Leptinob/ob (KCO) mice fed a high-fat diet (HFD). KC mice  were fed an HFD for either 12 weeks or 3 weeks beginning at 6 weeks of age. KCO mice  were fed an HFD for 8 weeks beginning at 6 weeks of age. All mice were maintained on ad libitum high-fat diet.

first: Christian

last: Ruiz

middle: D


title: Reprogramming the pancreatic ductal adenocarcinoma microenvironment: A novel integrin-targeted cytotoxin, ProAgio, potentiates chemotherapy [scRNA-seq]

city: Birmingham

first: Sujith

last: Sarvesh

state: Alabama

address: 1824 6th Ave S

department: Medicine

institute: University of Alabama at Birmingham

summary: Pancreatic ductal adenocarcinoma (PDAC) growth and metastasis are influenced by the tumor microenvironment (TME), which includes immune cells, endothelial cells, macrophages, and cancer-associated fibroblasts (CAFs). Since the novel integrin-targeted cytotoxin ProAgio can modulate the TME, we investigated its combination with various conventional chemotherapies in genetically engineered (GEM) and murine models of PDAC. The combination of ProAgio plus chemotherapy significantly modulated TME, improving hypoxia, reducing tumor weight, and eliminating metastasis to the lung and liver. Notably, the combination therapy with gemcitabine also increased overall survival in GEM model animals compared to either treatment alone. Single-cell RNA sequencing (scRNA seq; acquired from GEM model animals), flow cytometry, immunofluorescence, and immunohistochemistry analyses suggested that ProAgio plus chemotherapy treatment reprogrammed the PDAC- TME by changing activated CAFs toward a qCAFs (quiescent CAFs), macrophages from protumor to proinflammatory polarization, and activating natural killer (NK) cells, CD4⁺, and CD8⁺ T cells. Combination therapy inhibited PDAC stemness. ProAgio-treated CAFs in vitro exhibited reduced secretion of glycine and cysteine, vital metabolites that support stemness and tumor progression. These results highlight the potential of ProAgio to potentiate the efficacy of chemotherapy through modulating the PDAC-ME and improving hypoxia.

overall_design: GEM-KPC mice (LSL-KrasG12D/+; LSL-Trp53 R172H/+; Pdx-1-Cre) were obtained from Jackson Laboratory (Bar Harbor, Maine). These mice were created by mating LSL-KrasG12D/+ with LSL-Trp53R172H/+ and then breeding the resulting heterozygotes with Pdx-1-Cre. GEM-KPC mouse treatments began at 14 weeks of age. Experimental details were described and depicted in Table 1 and Figure 4A. Initially, they were treated with ProAgio (10mg/Kg; IP) for 10 consecutive doses, trailed by 10 doses every other day. Gemcitabine (50mg/Kg; IP) treatment was initiated after 5 doses of ProAgio and administered once every 2 days.

first: Ganji Purnachandra

last: Nagaraju

first: Zhi-Ren

first: Bassel

last: El-Rayes


title: G-quadruplexes regulate chromatin accessibility and gene expression in Bloom Syndrome [ChIP-seq]

city: Tübingen

first: Yingguang Frank

last: Chan

address: Max Planck Ring 9

department: Chan group

country: Germany

institute: Friedrich Miescher Laboratory of the Max Planck Society

summary: Bloom Syndrome (BS) is a recessive genetic disorder characterized by hyper-recombination and genome instability. It is caused by mutations in the conserved RecQ helicase gene, BLM, which is essential in maintaining genome integrity and unwinds various aberrant DNA structures. One such structure is DNA G-quadruplexes (G4s), which have broad regulatory functions. Although putative G4-forming sequences have been previously implicated in BS, it remains unclear what (dys)regulatory role, if any, endogenous G4 structures may play in BS. Here, we profiled chromatin accessibility and gene expression via ATAC-seq and RNA-seq and mapped endogenous G4 via ChIP-seq in wild-type (WT) vs. BS cell lines. We observed that in BS, differential G4 formation positively correlated with both chromatin accessibility and gene expression. Stabilizing G4 in WT cells with pyridostatin partially phenocopied BS. Additionally, data from a BS family showed that regions with increased chromatin accessibility in BS individuals were also enriched for G4-forming sequences. Our data showed that G4 formation is associated with higher chromatin accessibility and gene expression; likely in BS, unresolved G4 increases focal chromatin accessibility, thereby upregulating gene expression. In summary, our results revealed a central role of G4 in the molecular etiology of BS and provide a new perspective on BLM’s regulatory function through G4s.

overall_design: To characterize the G4 formation changes caused by BLM-/- , we  compared  endogenously formed G4 in BLM-/- and wildtype cells.

first: Dingwen


title: G-quadruplexes regulate chromatin accessibility and gene expression in Bloom Syndrome  [ATAC-seq]

overall_design: To characterize the chromatin accessiblity changes caused by BLM-/- , we  profiled the open chromatin landscape via ATACseq and identified alterations in BLM-/- vs. wildtype cells. To characterise the impacts of a small G4 stablizing molecule, PDS, on open chromatin landscape and if PDS treatment mimics BLM-/-, we  profiled the genome-wide chromatin accessiblity via ATACseq in wildtype cells treated with 0.4%DMSO (as the control) and with 10uM PDS and dentified alterations invoked by PDS treatment.


title: Reprogramming the pancreatic ductal adenocarcinoma microenvironment: A novel integrin-targeted cytotoxin, ProAgio, potentiates chemotherapy [RNA-seq]


title: Transcriptomic Profiling of RAW264.7 Cells During RANKL-Induced Osteoclast Differentiation

city: Hefei

first: sijie

last: bian

address: Huaihai Avenue

department: Department of Orthopaedics

institute: The First Affiliated Hospital of Anhui Medical Universit

summary: Osteoclast differentiation is primarily driven by RANKL stimulation, yet the transcriptional remodeling associated with this process remains incompletely characterized. This dataset profiles global gene expression changes in RAW264.7 macrophages under two conditions: untreated control and RANKL-induced osteoclast differentiation. The transcriptomic comparison reveals key pathways associated with osteoclast formation, including osteoclast-related gene activation, metabolic remodeling, and oxidative stress–related signaling. These data serve as the baseline reference for subsequent uridine-intervention analyses.

overall_design: This study analyzed six RNA-seq samples from RAW264.7 murine macrophages. Two experimental conditions were included: untreated control and RANKL-stimulated osteoclast differentiation. Each condition contained three biological replicates. Total RNA was collected after 3 days of culture and subjected to high-throughput sequencing to compare transcriptomic changes associated with RANKL-induced osteoclastogenesis.

first: Sijie

last: Bian


title: Cohesin acetylation and ATPase activity control cohesion and loop architecture through distinct mechanisms

city: berkeley

first: lorenzo

last: costantino

state: california

address: berker hall

department: MCB

institute: University of California, Berkeley

summary: Cohesin is a conserved protein complex that mediates sister chromatid cohesion, chromosome condensation, gene regulation, and DNA repair. These processes rely on cohesin’s ability to tether sister chromatids and form chromatin loops, which depend on cohesin’s ATP hydrolysis activity and Eco1-mediated acetylation of two lysines (K112 and K113 in budding yeast) in its Smc3 subunit. How cohesin’s ATPase activity and acetylation integrate to control cohesin functions remains poorly understood. To address this, we analyzed chromatin architecture in yeast mutants with altered cohesin acetylation and/or ATPase activity. We find that acetylation of either K112 or K113 is sufficient to form a wild-type pattern of loops anchored at cohesin-associated regions (CARs), whereas loss of acetylation at both residues abolishes positioned loops, indicating that acetylation of either lysine is sufficient for loop positioning. We found that a cohesin acetylation mutant lacking the tethering activity required for cohesion was able to form loops similar to wild type, while cohesion-competent mutants lacked positioned loops. Together, these results suggest that the activities required for cohesion and loop formation are mechanistically separable, arguing against loop formation through passive loop capture. Moreover, a mutant with reduced ATPase activity showed a wild-type loop profile, indicating that lowering ATPase activity does not dictate loop size or positioning. However, hyper-ATPase mutants exhibited an accumulation of positioned loops, suggesting that ATPase levels contribute to loop processivity. Together, our findings reveal a multilayered regulatory logic in which acetylation fine-tunes ATPase output and cohesin functions to shape genome architecture.

overall_design: Micro-C XL in a panel of budding-yeast mutants affecting cohesin acetylation and ATPase activity

first: Lorenzo

last: Costantino

first: Tiantian

last: Ye

first: Kevin

last: Boardman

first: Siheng

last: Xiang

first: Jonathan

last: Luo

first: Yudi

last: Mu

first: Wenxiu

last: Ma

first: Douglas

last: Koshland


title: A circuit of mechanically regulated transcription factors balances regenerative and fibrotic memory of mesenchymal stromal cells

city: Charlottesville

first: Andrew

last: Miller

state: Virginia

address: 415 Lane Rd.

department: Biomedical Engineering

institute: University of Virginia

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

overall_design: Refer to individual Series


title: The H3K4 methyltransferase KMT2D is an essential cofactor for GATA1 at erythroid gene enhancers

first: Peng

last: Xu

summary: Gene expression during cellular differentiation is coordinated by combinatorial interactions between transcription factors (TFs) and cofactors at promoters and enhancers. The “master TF” GATA1 coordinates gene transcription in a subset of hematopoietic lineages, including erythroid, megakaryocytic, mast and eosinophil, while repressing the development of other blood lineages. However, the specific cofactors required for GATA1-activated gene expression during hematopoiesis are incompletely defined. We identified the cofactor KMT2D in an unbiased CRISPR/Cas9 screen for epigenetic regulators of erythropoiesis. Loss of KMT2D in human erythroid precursors caused developmental arrest with impaired expression of numerous erythroid genes. Mechanistically, KMT2D belongs to a family of H3K4 methyltransferases that collaborate with H3K27 acetyltransferases to activate transcription. KMT2D colocalized with GATA1 on more than one thousand erythroid enhancers associated with over two hundreds erythroid genes. In general, co-occupancy of GATA1 and KMT2D at erythroid enhancers was associated with stronger transcriptional activity than occupancy by GATA1 alone. Acute depletion of KMT2D in erythroid precursors caused rapid reductions of H3K4me1 and H3K27ac on a subset of GATA1-bound enhancers and impaired the expression of canonical erythroid genes including ZFPM1, SLC4A1, and EPOR. Moreover, acute depletion of GATA1 or KMT2D individually caused downregulation of overlapping genes. Thus, KMT2D controls erythropoiesis by selectively activating GATA1-dependent erythroid enhancers. Our studies identify KMT2D as a novel cofactor for transcriptional activation by GATA1 during erythropoiesis. More generally, our findings demonstrate how a lineage-specific TF cooperates with a ubiquitous epigenic regulator to drive lineage-specific gene expression during cellular differentiation.

overall_design: The K562 and HUDEP2 cells used in the experiment were knock in cell lines of GFP-P2A-miniAID-KMT2D constructed by ourselves. We treated the two cell lines with drugs for 0 hours, 6 hours, 12 hours, and 24 hours, with two replicates at each time point. The drugs used included DMSO and 5-Ph-IAA.


title: Cross-platform Hi-C meta-analysis identifies functional insulators that actively block enhancer-promoter interactions

city: Boston

first: Wanying

state: MA

address: Karp Family Research Building

department: Hematology

institute: Boston Children's Hospital & Broad Institute

summary:
Insulator protein CTCF controls genome architecture through forming thousands of cohesin-dependent structural loops. However, genome-wide studies only found mild transcriptional consequences upon acute CTCF-depletion, raising confusions about how CTCF regulates enhancer-promoter (E-P) interactions and gene expression. Here we reanalyze independent Hi-C, in situ Hi-C, and micro-C data in mouse embryonic stem cells upon acute CTCF-, RAD21-, and WAPL-depletion; DeepLoop is used to enable robust comparison of orthogonal Hi-C data at kb-resolution regardless of sequencing depth. All datasets show that most loops are lost upon CTCF depletion, but E-P interactions are enriched among the retained loops, and interestingly a small number of newly gained loops repressed by CTCF.
From multiplatform Hi-C data, we identified several hundred recurrent events in which new E-P interactions form after the insulating CTCF loops disappear. We therefore define FINs (functional insulators) as CTCF sites that actively insulate their flanking sequences. In CTCF-depleted cells these newly gained E-P interactions require cohesin activity. WAPL-depletion causes relaxation of FIN loops and abolish insulator functions. Importantly, CTCF-repressed genes are enriched near FINs, but CTCF-dependent genes are enriched near TAD-boundaries. We also validated the transcription regulatory functions of several FINs with CTCF-blocking assays. Taken together, DeepLoop meta-analysis unifies multiplatform Hi-C data and demonstrated that FINs, but not TAD-boundaries, are bona fide insulators.

overall_design:
We achieve gobal identification and characterization of functional insulators that rewire local chromatin interactions

Third-party reanalysis:  We reanalyzed 16 GSM samples derived from GSE98671, including Hi-C data (without washoff condition) and RNA-seq data (without washoff condition). We reanalyzed 12 GSM samples derived from GSE94452, including Hi-C data and RNA-seq data. We reanalyzed 41 GSM samples derived from GSE178982, including Hi-C data, mNET-seq data and RNA-seq data. We reanalyzed 6 GSM samples derived from GSE135180, including Hi-C data and RNA-seq data. We reanalyzed 12 GSM samples derived from GSE144834, including Hi-C data and RNA-seq data. We reanalyzed 4 SAMEA Hi-C data derived from E-MTAB-7816. We reanalyzed 8 SAMEA RNA-seq data derived from E-MTAB-7818

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The table below lists GEO accessions reused/reanalyzed for this study.
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The table below lists GEO accessions reused/reanalyzed for this study.
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first: Jian

last: Cui

first: Shanshan

last: Zhang

first: Leina

last: Lu

first: Xiaoxiao

last: Liu

first: Yan

last: Li

first: Fulai

last: Jin


title: Harnessing Viral Strategies to modulate the ISR and Reverse Cognitive Dysfunction

city: Redwood City

first: Jin

last: Chen

address: 2400 Bridge Parkway

department: Institute of Science

institute: Altos Labs

summary: The integrated stress response (ISR) is essential for cellular homeostasis and cognitive function. Here, we investigated how persistent ISR activation impacts cognitive performance by studying the PPP1R15BR658C genetic variant associated with intellectual disability. To model this condition, we generated a knock-in mouse line carrying the pathogenic allele. We found that this variant destabilizes the PPP1R15B•PP1 phosphatase complex, causing persistent ISR activation, impaired protein synthesis, and long-term memory deficits. Importantly, we demonstrated that the cognitive and synaptic impairments in Ppp1r15bR658C mice arise directly from ISR activation. Furthermore, we characterized DP71L, a viral orthologue of PPP1R15B, revealing new molecular and structural insights as a potent pan-ISR inhibitor. Remarkably, DP71L reversed the cognitive and synaptic deficits across diverse conditions—including Down syndrome, Alzheimer’s disease and aging—and enhanced synaptic plasticity and memory in healthy mice. Our findings illustrate how human genetics and viral adaptations converge to unlock potential innovative therapeutic strategies for cognitive disorders.

overall_design: To investigate the role of persistent integrated stress response in brain function and long term memory, we generated Ppp1r15b mutant (ISR on) mice that resulted in persistent ISR and long term memory deficits.  We then performed gene expression analysis by Ribo-Seq and RNA-seq of wild type and Ppp1r15b mutant cortical tissue from male animals.

first: Chen

first: Reineke

last: Lucas

first: Costa-Mattioli

last: Mauro


title: RNA-seq analysis of human CD19 CAR T cells overexpressing RAB5

city: Philadelphia

first: Kaitlin

middle: Adele

last: Read

state: Pennsylvania

address: 3600 Civic Center Blvd, Bldg 421, Rm 8-184

institute: University of Pennsylvania

summary: Chimeric antigen receptor (CAR) T cells (CARTs) are engineered T cells designed to target specific molecules on the surface of cancer cells. Using a continuous antigen exposure (CAE) assay to model this interaction, we observed that tumors can capture CAR molecules, leaving the CARTs devoid of surface-expressed CARs and unable to kill tumors after repeated challenges. Overexpression of Rab5, a key regulator of endocytosis, prevents the loss of CARs and enhances CARTs activity. Rab5 significantly increased the endocytic recycling of T cells without causing other perturbations to CART function. Interestingly, we observed membrane protrusions on the CART cell surface, which disappeared after multiple tumor challenges. Rab5 overexpression maintained these protrusions after multiple tumor engagements, and the presence of membrane protrusions correlated with tumor clearance. In vivo, Rab5-expressing CARTs demonstrated improved activity and were able to clear an otherwise recalcitrant mesothelin-expressing solid cancer. These findings suggest that engineering CARTs with Rab5 overexpression could enhance the clinical efficacy of CAR T cell therapy.

overall_design: Human CD4+ and CD8+ T cells from four different healthy donors were used simultaneously for CART generation. Cells were transduced with either 19BBz-tEGFR or 19BBz-Rab5 vectors. To profile baseline differences between these two populations, CARTs expanded in vitro for 9 days were collected for analysis. To profile differences under repeated tumor challenges, beginning at day 9, CARTs were co-cultured with K.19.GFP cells at a 1:2 ratio (CARTs effector:target). Every 2 days, target cells were replenished to rechallenge CARTs. After the third round of target replenishment, at 48 hours post-plating, CD3+CAR+ cells were enriched. Dead cells were removed using the Dead Cell Removal Kit (Miltenyi Biotec). T cells were isolated from target K562 cells with using the Dynabeads™ Untouched™ Human T Cells Kit (Invitrogen). Surface CAR-positive cells were sorted by flow cytometry. A portion of each sample was reserved to test Rab5 overexpression via immunoblotting. For RNA-sequencing analysis, while another portion with 1x106 cells from each sample were flash-frozen in liquid nitrogen and sent to BGI Genomics for sample QC, mRNA isolation, RNA library preparation and sequencing. To address potential variability in genes with low read count, filtering was performed to omit genes in which more than 4 samples had a read count <10. Genes with an adjusted p-value <0.05 were considered significant, and those with fold changes of >3 were defined as differentially expressed genes (DEGs) for the present study.

first: James

last: Riley

first: Meidi

last: Gu


title: Exploring life-long tissue homeostasis through lineage tracing and cell transplantation

city: Jerusalem

first: Itamar

last: Harel

address: Givat Ram

country: Israel

institute: The Hebrew University of Jerusalem

summary: Using lineage tracing and fate mapping strategies to study vertebrate aging has lagged behind developmental studies, primarily due to of the relatively long lifespans of classical models. Here, we introduce the Killibow, an inducible transgenic model for in-vivo multicolor lineage tracing in the naturally short-lived turquoise killifish (N. furzeri). We demonstrate that Cre-mediated recombination in transgenic fish can generate robust and stochastic labeling that remains stable during aging and regeneration. In addition, to achieve inducible control of recombination, we either utilize in-vivo Cre electroporation or use the tamoxifen system in Killibow-derived cells. To further enable transplantation assays, we establish the first immunocompromised killifish model by mutating rag2. RNA sequencing reveals that rag2 mutants exhibit severely compromised expression of V(D)J recombination products, including immunoglobulins. Accordingly, we demonstrate that clearance of transplanted Killibow-derived cells is delayed in rag2 recipients, and present a proof-of-principle for a KRAS G12D cancer model that is compatible with lineage tracing. Our platform provides the opportunity to examine tissue homeostasis, stem cell function, cancer dynamics, and tissue regeneration at unprecedented temporal resolution during vertebrate aging and disease.

overall_design: We compared the transcriptome of the killifish head kidney, the equivalent of the mammalian bone marrow, from three wild-type and three rag2 mutants.

first: Itai

last: Rozenberg

first: Tehila

last: Atlan

first: Roman

last: Franek

first: Eitan

last: Moses

first: Adi

last: Oron-Gottesman

first: Henrik

last: Chrzanowski


title: FINE-EM-seq: a rapid isothermal amplification method enabling comprehensive methylome profiling of zebrafish early embryos

city: Wuhan City

first: Zhiyuan

last: Hu

address: No. 115 East Lake Road (Donghu Road), Wuchang District

department: Medical Research Institute

institute: Wuhan University

type: Methylation profiling by high throughput sequencing

summary: DNA methylation plays a crucial role in development and disease. Bisulfite-free methods such as enzymatic methyl sequencing (EM-seq) offer gentle approaches for whole-genome analysis, but they typically depend on PCR-based library amplification, which distorts coverage and methylation quantification. Here, we introduce FINE (Fast Isothermal amplification via Nicking Enzyme), a robust isothermal amplification strategy that leverages a nicking enzyme-assisted strand displacement reaction and can amplify methylation libraries from sub-nanogram inputs in 20 minutes. FINE-EM-seq increases library efficiency and coverage uniformity compared to PCR-based approaches, minimizing amplification bias and improving methylation calling accuracy. Applied to zebrafish embryos at four early developmental stages, FINE-EM-seq characterized stage-associated methylation dynamics through blastulation and early gastrulation. Furthermore, our analysis revealed blastulation-associated differentially methylated regions (DMRs) overlapping with AT-rich regions that were previously under-covered. These results illustrate that FINE-EM-seq is a rapid, robust solution for low-input whole-genome methylation sequencing with broad utility in developmental biology and clinical epigenomics.

sample_organism:
Danio rerio
Homo sapiens

platform_organism:
Danio rerio
Homo sapiens

overall_design:
Genome-wide DNA methylation profiling of HeLa genomic DNA across three input amounts (1 ng, 100 pg, 10 pg), benchmarking FINE-EM-seq with PCR-amplified EM-seq.
Genome-wide DNA methylation profiling of zebrafish embryos at four developmental stages (64-cell, 128-cell, 1k-cell, germ-ring) using FINE-EM-seq, with two biological replicates per stage.

first: Chenyang

last: Ding

first: Qifeng

last: Zhang

first: Jing

last: Wang

first: Yanbo

last: Xu

first: Tiantian

last: Huang

first: Yanfang

last: Du

first: Junjie

first: Xiang

last: Zhou

first: Yibin


title: Motif-directed chromatin repression by BCL11B shapes ectopic targeting and lineage commitment [CUT&RUN]

city: MEMPHIS

first: QINGSONG

last: GAO

state: Tennessee

address: 262 DANNY THOMAS PLACE

institute: ST JUDE CHILDREN'S RESEARCH HOSPITAL

summary: BCL11B encodes a critical T-lineage transcription factor that is implicated as both an oncogene and a tumor suppressor in acute leukemia. Despite its central role in development and malignancy, a basic understanding of the sequence determinants of BCL11B activity remains obscure. Here, we define two functionally distinct modes of BCL11B engagement with chromatin: Most detectable BCL11B binding events are determined by pre-existing patterns of chromatin accessibility and RUNX1 occupancy. In contrast, BCL11B directs chromatin closing at genomic regions enriched for DNA motifs containing the core “TGACC” sequence, which are most prevalent in non-T lineages. These BCL11B-closed target sites cannot be identified from conventional BCL11B chromatin profiling approaches yet represent the primary mechanism by which BCL11B regulates gene expression. We provide evidence that cell of origin impacts the ability of BCL11B to repress lineage-inappropriate gene programs, thereby promoting lineage skewing. Together, these findings define a motif-centered determinant of BCL11B repression and explain how BCL11B controls lineage specification.

overall_design: This submission includes CUT&RUN data generated in human cord blood-derived CD34+ HSPCs transduced with lentiviral constructs encoding BCL11B, BCL11B-dTAG, or an empty vector (control), and Jurkat cells genetically engineered to express FKBP12F36V-HA-BCL11B (BCL11B-dTAG) or unedited control cells. Cells were either untreated, treated with DMSO (control) or treated with dTAGV-1 for 1 (Jurkat) or 6 (CD34+ HSPCs) hours to induce BCL11B degradation. Two replicates were generated for each experimental condition. For CD34 experiments, CUT&RUN was performed on day 7 of CD34+ expansion, representing 4 days post-transduction. Data sets annoated as "CD34-018" refer to an experiment that tested the effect of untagged BCL11B expression on RUNX1 chromatin occupancy. Data sets annotated as "CD34-016" refer to an experiment that tested BRG1 recrutiment following acute BCL11B degradation.

first: Lindsey

middle: E

last: Montefiori

first: Qingsong

last: Gao

first: Charles

last: Mullighan


title: The genetic basis for DNA methylation variation across tissue and development

first: Batia

last: Azria

state: Israel

address: Jerusalem

institute: Hebrew university of Jerusalem

summary: DNA methylation regulates gene expression and cell identity through development. By analyzing genome-wide methylation patterns in multiple tissues from genetically distinct mouse strains, we identify thousands of differentially methylated regions (DMRs) linked to sequence variants. These DMRs reveal key factor-binding regulatory motifs that govern methylation programming, with ubiquitous DMRs established early in embryogenesis, whereas cell-type-specific DMRs emerge later during tissue differentiation. Extending this approach to human data, we map over 21,000 methylation-associated SNPs, pinpointing genetic variants that regulate DNA methylation ubiquitously or in specific cell types. These findings highlight the role of transcription factor binding in shaping epigenetic landscapes and provide mechanistic insights to how genetic variation influences gene regulation and disease susceptibility. Our study establishes a systematic developmental framework for deciphering the genetic determinants of DNA methylation programming, offering a foundation for understanding epigenetics and phenotypic diversity with clinical implications in health and disease.

overall_design: DNA methylation profile  in multiple tissues from genetically distinct mouse strains

first: Jonathan

last: Rosenski

first: Ofra

last: Sabag

first: Howard

last: Marcus

first: Netanel

last: Loyfer

first: Yuval

last: Dor

last: Cedar

first: Tommy

last: Kaplan


title: JAX Study 13- RNA-seq of male KOLF2.2J hiPSC-derived endoderm and mesoderm homozygous null for ten different transcription factors

city: Hinxton

first: MorPhiC

last: Consortium

address: Wellcome Genome Campus

country: United Kingdom

institute: EMBL-EBI

summary: This study aims to phenotype iPSC-derived early endoderm and mesoderm that contain homozygous null alleles for the following transcription factors: CITED1, HOXB8, GATA6, GSC, HES6, SP5, TBXT, LHX1, SOX17 and MSX1. Null alleles were generated using insertion of a premature termination codon with frameshift (PTC+1) in the case of CITED1, HOXB8, GATA6, SP5, TBXT, LHX1 and SOX17 or full protein coding region deletion (KO) for HES6 and MSX1. RNA-seq data was generated after 5 days of initiating differentiation from iPSCs. This analysis allowed the investigation of early embryonic development, cell fate mapping, and lineage analysis.

overall_design: The study involved the generation of RNA-seq on 45 samples. Four of the transcription factors were analyzed in the endoderm differentiation scheme and six in the early mesoderm scheme. Three biological replicates were run for each gene. Additionally, three biological replicates were run of wild-type KOLF2.2J cells (the parental male cell line in which the KOs were generated) under the same differentiation conditions. This comprehensive design allowed the investigation of the effects of transcription factor manipulation during early embryonic development.

first: Juliana

last: Diniz

first: Bill

last: Skarnes

first: Paul

last: Robson


title: Plasma exosomal circRNA profiling in diffuse large B-cell lymphoma by Arraystar microarray

city: Changzhou, Jiangsu

first: yue

last: cao

address: juqian street

department: The Third Afiliated Hospital of

institute: Soochow University

summary: Diffuse large B-cell lymphoma (DLBCL) lacks reliable liquid biopsy biomarkers. This study identifies plasma exosome-derived circular RNAs (circRNAs) as novel diagnostic and prognostic tools.

overall_design: **Cohort Design:**  - Discovery phase: Plasma exosomes from 3 treatment-naive DLBCL patients vs. 3 age/sex-matched healthy controls (Arraystar circRNA microarray)  - Validation phase: Independent cohort of 55 DLBCL patients and 25 controls (qRT-PCR)    **Sample Processing Workflow:**  1. Plasma exosome isolation: Sequential centrifugation (500g/5min → 2,000g/10min → 10,000g/10min) → 0.22-μm filtration → Ultracentrifugation (100,000g × 2h) with TEM validation (Tecnai G2 Spirit)  2. Total RNA extraction: TRIzol reagent (Thermo Fisher) from exosomal pellets  3. circRNA enrichment: RNase R digestion (Epicentre MRR092; 3U/μg RNA, 37°C, 15min)  4. Microarray hybridization: Arraystar Super RNA Labeling → Hybridization (Arraystar Human circRNA Array V2, 65°C/17h)    **Analytical Strategy:**  - Differential expression: limma R package (v3.54.0) with thresholds: |log₂FC| ≥ 0.263 (FC≥1.2), Benjamini-Hochberg FDR < 0.05  - Diagnostic validation: ROC analysis of candidate circRNAs (AUC calculation)  - Clinical correlation: Student's t-test for clinicopathological parameters (age, stage, IPI, β₂M, remission status)  - Longitudinal monitoring: Paired t-test for pre-/post-chemotherapy hsa_circ_001393 expression  - ceRNA network: miRanda/pita for miRNA target prediction → Cytoscape visualization

first: Yue

last: Cao

first: Yan

last: Lin


title: Skin-resident Langerhans Cells Drive Neuropathic Pain via Chemokine-Dependent Neuron-Immune Communication

city: chicago

first: Daniela

middle: Maria

last: MEnichella

state: illinois

address: 303 E Superior

department: Neurology

institute: Northwestern University

summary: Single-cell RNA sequencing of paw epidermis from male and female C57BL/6J mice fed regular diet (RD) or high-fat diet (HFD) for 10 weeks, to investigate the role of Langerhans cells in painful diabetic neuropathy.

overall_design: scRNAseq was performed on paw epidermis from RD and HFD male mice (n=3 per group) and RD and HFD female mice (n=3 per group). Cells were sequenced using the 10x Genomics Chromium Single Cell 3' v3 platform and aligned to the mouse transcriptome (mm10-2020-A) using Cell Ranger 7.2.0.

first: Pacifico

last: Paola

first: George

last: Dale S.

first: Jayaraj

last: Nirupa D.

first: Ren

last: Dongjun

first: Coy-Dibley

last: James S

first: Veronesi

last: Sofia

first: Baldamani

last: Abdelhak

first: Andelic

last: Mirna

first: Cartelli

last: Daniele

first: Devigili

last: Grazia

first: Lombardi

last: Raffaella

first: Lauria

last: Giuseppe P

first: Paller

last: Amy S

first: Miller

last: Richard J

first: Menichella

last: Daniela M


title: The mechanism of circular RNA circ0061693 and its encoded peptide P385 in improving neural injury in Parkinson's disease

city: suzhou

first: zhaotong

last: liu

address: renailu

summary: Parkinson’s disease (PD) is the second most common neurodegenerative disorder, pathologically characterized by the loss of dopaminergic neurons and abnormal accumulation of α-synuclein (α-syn). Circular RNAs (circRNAs) are a unique class of stable closed-loop RNA molecules that exert biological functions via molecular sponging, transcriptional regulation, peptide translation, and other mechanisms. Accumulating studies have demonstrated that circRNAs are differentially expressed between PD patients and healthy controls; however, their precise mechanistic roles in PD pathogenesis remain incompletely understood. Therefore, in-depth investigation of the functions and regulatory mechanisms of circRNAs in PD is critical for elucidating disease etiology and identifying novel diagnostic biomarkers and therapeutic targets.

overall_design: Establishment of PD cell model: SH‑SY5Y cells were treated with 500 μM 1‑Methyl‑4‑phenyl‑1,2,3,6‑tetrahydropyridine (MPTP) for 24 h to establish an in vitro PD model.Screening and validation of circ0061693: High throughput sequencing was performed to profile circRNA expression in the midbrain substantia nigra of wild type (WT) and A53T transgenic PD mice, followed by bioinformatic analysis to identify differentially expressed circRNAs. The authenticity and expression pattern of circ0061693 were verified by polymerase chain reaction (PCR), Sanger sequencing, quantitative real time polymerase chain reaction (RT qPCR), Northern blot, and fluorescence in situ hybridization (FISH).Functional exploration of circ0061693 in PD regulation: circ0061693 overexpression vector and small interfering RNA (siRNA) targeting the back splice junction were constructed and transfected into MPTP treated SH SY5Y cells. PD related markers (α syn, tyrosine hydroxylase, TH) and autophagy related markers (microtubule associated protein 1 light chain 3 beta, LC3B; p62/SQSTM1) were detected by RT qPCR and Western blot (WB). Lentiviral vector overexpressing circ0061693 was injected into A53T transgenic mice via the tail vein. Motor function was evaluated by pole test and open field test. Structural changes in the substantia nigra and levels of TH and LC3B were examined by hematoxylin–eosin (HE) staining and immunofluorescence (IF). Protein levels of α syn, TH, LC3B, and p62 in the substantia nigra were measured by WB.Analysis of the translational activity of circ0061693 and its encoded polypeptide P385: The internal ribosome entry site (IRES) sequence of circ0061693 was predicted using the IRESbase database (http://reprod.njmu.edu.cn/cgi-bin/iresbase/index.php). Dual luciferase reporter plasmids were constructed, and IRES activity was measured by dual luciferase reporter assay. A plasmid with a mutation in the start codon of circ0061693 (ATG MUT) was generated. Total proteins were extracted from cells transfected with circ0061693 overexpression plasmid or ATG MUT plasmid, then subjected to SDS PAGE, Coomassie blue staining, and mass spectrometry to confirm the identity and expression of P385.Functional investigation of polypeptide P385 in PD regulation: P385 overexpression vector was transfected into MPTP treated SH SY5Y cells. Levels of α syn, TH, LC3B, and p62 were detected by RT qPCR and WB. Lentiviral vector overexpressing P385 was injected into A53T transgenic mice via the tail vein. Motor function, substantia nigra morphology, TH and LC3B expression, and PD  and autophagy related protein levels were assessed as described above.Verification that P385 mediates the regulatory effect of circ0061693 in PD: circ0061693 and ATG MUT vectors were transfected into MPTP treated SH SY5Y cells separately, and α syn, TH, LC3B, and p62 levels were detected by RT qPCR and WB. ATG MUT and circ0061693 lentiviral vectors were injected into A53T transgenic mice via the tail vein. Motor function, substantia nigra structure, TH and LC3B levels, and related protein expression were evaluated.Screening and validation of P385 interacting proteins: HA tagged P385 overexpression vector was transfected into cells, and total proteins were extracted for pull down assay with anti HA antibody to identify candidate interacting protein ADP ribosylation factor 1 (ARF1). ARF1 overexpression plasmid was constructed and co transfected with P385 plasmid into 293T cells. Co immunoprecipitation (Co IP) and IF were performed to verify the interaction between P385 and ARF1.Molecular mechanism by which P385–ARF1 interaction regulates PD: ARF1 overexpression plasmid and ARF1 siRNA were transfected alone or co transfected with P385 plasmid into MPTP treated SH SY5Y cells. Protein levels of PI3K/AKT/mTOR axis components, α syn, TH, LC3B, and p62 were detected by WB. Furthermore, the AKT agonist SC79 was applied alone or combined with P385 and ARF1 overexpression in MPTP treated SH SY5Y cells, and α syn and TH levels were examined.In vivo functional validation of P385–ARF1 interaction in A53T transgenic mice: ARF1 lentiviral vector was injected alone or combined with P385 lentiviral vector into A53T transgenic mice via the tail vein. Motor function, substantia nigra morphology, TH and LC3B levels, PI3K/AKT/mTOR axis proteins, α syn, TH, LC3B, and p62 were measured. Mice overexpressing both P385 and ARF1 were further intraperitoneally injected with SC79, and the above indicators were detected.


title: Functional redundancy between UTY and UTX in regulating the localization of transcription factors involved in pluripotency [ATAC-seq]

city: Yokohama

first: Tomohiko

last: Akiyama

state: Kanagawa

address: 3-9 Fuku-ura

department: School of medicine

country: Japan

institute: Yokohama city university

summary: The Y chromosome retains a limited number of protein-coding genes, yet their biological significance remains poorly understood. Here, we find UTY, a Y-linked homolog of the histone demethylase UTX, plays an essential regulator of pluripotency in human embryonic stem cells. Despite its low expression and weak enzymatic activity, UTY co-localizes with UTX at active cis-regulatory elements and contributes to the regulation of core pluripotency genes such as NODAL and LEFTY. Through genome-wide occupancy and transcriptome analyses of knockout cell lines, we show that UTY and UTX function redundantly to maintain proper localization of key transcription factors including OCT4 and SOX2. Dual loss of UTY and UTX leads to their mislocalization, widespread transcriptional dysregulation, and loss of pluripotency, without changes in H3K27 methylation. Instead, these effects are associated with changes in histone acetylation and altered chromatin accessibility, likely driven by recruitment of ATP-dependent chromatin remodelers, pointing to a non-enzymatic mechanism. Our findings uncover a novel role for UTY in stabilizing transcription factor binding and maintaining cell identity, demonstrating that even the evolutionarily compact Y chromosome retains critical regulatory functions in early human development.

overall_design: ATAC-seq to identify open chromatin regions in WT and UTX/UTY-KO hES cells


title: miRNA expression profiles of exosomes extracted from C8-D1A supernatants in heatstroke

city: Foshan

first: Yahong

last: Chen

state: Guangong

address: No. 1, Jiazhi Road, Licun Village Committee, Lunjiao Subdistrict Office

department: pediatric

institute: The Eighth Affiliated Hospital of Southern MedicalUniversity(The First People's Hospital of Shunde Foshan)

summary: To determine the changes in miRNA levels in exosomes secreted by C8-D1A after heatstroke

overall_design: Exosomes were isolated from the supernatant of non-heat-stressed C8-D1A cells (control group) and heat-stressed C8-D1A cells (heat stress group), followed by high-throughput miRNA sequencing. Each group consisted of two biological replicates.


title: Evolutionary transfer learning of the regulatory grammar of mammalian genomes

city: Hanover

first: Chengxiang

last: Qiu

state: NH

address: Vail 604, 74 College St

department: Department of Molecular and Systems Biology

institute: Dartmouth College

summary: Mammalian development is orchestrated by the interplay of trans-acting factors and cis-regulatory elements. However, while genome sequences evolve rapidly, the regulatory grammar that governs their interpretation evolves far more slowly. We hypothesized that this pronounced mismatch in evolutionary tempos creates a powerful opportunity for “evolutionary transfer learning”, in that models trained to learn cell type-specific cis-regulatory grammars in one mammalian species should generalize to the orthologous cell types of other mammals. To test this, we generated a time-resolved atlas of chromatin accessibility across mouse development from embryonic day 10 (E10) to birth (P0). Using single-cell combinatorial indexing, we profiled 3.9 million nuclei from 36 precisely staged embryos, resolving dynamic accessibility landscapes across 36 cell classes and 140 cell types. From these data, we applied a multi-output deep learning model, CREsted, to predict cell type-specific chromatin accessibility from DNA sequence. However, while “evolution-naive” models performed well within peak-defined regions, genome-wide inference revealed systematic failure modes, including overprediction at tandem repeats and conflation of promoter and distal enhancer grammars. To address this, we introduced an “evolution-aware” framework that isolates distal enhancer grammars by requiring both syntenic persistence and functional coherence across mammals, defined as sequence-intrinsic regulatory behavior that is concordant across enhancer orthologs and robust to in silico tandem repeat disruption. This updated CREsted model produced refined genomewide regulatory maps whose predicted enhancer activity scaled with enhancer score and enhancer–promoter proximity to explain cell type-specific gene expression. Incorporating syntenic enhancer orthologs from up to 240 placental mammals directly into training expanded the effective regulatory corpus by more than two orders of magnitude. Finally, applying the fully evolution-augmented model to the human genome yielded distal enhancer maps for orthologous human cell types. Taken together, our results unify advances in single-cell molecular profiling, deep learning, and comparative genomics into a framework for model-driven reconstruction of human cis-regulatory landscapes, including for cell types that emerge during the embryonic, fetal, and pediatric stages of human development that are largely inaccessible to molecular profiling. More broadly, our work supports the view that model organisms and evolutionarily diverse non-human genomes are indispensable resources for accelerating the AI-enabled exploration of human biology.

overall_design: To profile chromatin accessibility across mouse embryogenesis, 36 frozen embryos were selected from a staged collection of 523 embryos spanning late gastrulation to birth (E8–P0), targeting one embryo per 6-hour interval from E10 to P0 (with the exception of E17.75). Female embryos were preferentially selected (29 female, 7 male) to minimize sex-related mapping artifacts. Whole frozen embryos — without tissue dissection — were processed using sci-ATAC-seq3 across six experiments grouped by gestational age range (E10–E13.75, E14–E15.75, E16–E18, E18.25–P0). Sequencing was performed on five Illumina NovaSeq runs, followed by demultiplexing, embryo assignment, trimming, alignment to mm10, and fragment profile generation.

first: Riza

last: Daza

first: Ian

last: Welsh

first: Rupali

last: Patwardhan

first: Beth

last: Martin

first: Tony

last: Li

first: Shizhao

last: Yang

first: Niklas

last: Kempynck

first: Megan

last: Taylor

first: Olivia

last: Fulton

first: Truc-Mai

last: Le

first: Diana

last: O’Day

first: Jean-Benoît

last: Lalanne

first: Silvia

last: Domcke

first: Stephen

last: Murray

first: Stein

last: Aerts

first: Cole

last: Trapnell

first: Jay

last: Shendure


title: JAX Study 12- RNA-seq of male KOLF2.2J hiPSC-derived trophoblast cell lines homozygous null for five different transcription factors

first: MorPhiC

last: Consortium

summary: This study aims to phenotype iPSC-derived trophoblast lines that contain homozygous null alleles for transcription factors expressed within the trophoblast lineage and favoring either primitive syncytium formation or mesenchymal cell formation, depending on the TF being analyzed. Null alleles were generated by insertion of a premature termination codon with frameshift (PTC+1). RNA-seq data was generated after 6 days of initiating differentiation from iPSCs. The study included the homozygous null alleles for the following transcription factors: SNAI2, ELK3, SOX7, ZNF175 and TFEB. This analysis provided insight into the impact of loss of function for these transcription factors in trophoblast lineage differentiation.

overall_design: The study involved the generation of RNA-seq on 21 samples. Two of the transcription factors were analyzed in the primitive syncytium differentiation scheme and three in the extra-embryonic mesenchymal cell scheme. Three biological replicates were run for each gene. Additionally, three biological replicates were run of wild-type KOLF2.2J cells (the parental male cell line in which the KOs were generated) under the same differentiation conditions. This comprehensive design allowed for a robust comparison of the effects of transcription factor manipulation on cell fate decisions within the extra-embryonic lineage.

first: Juliana

last: Diniz

first: Bill

last: Skarnes

first: Paul

last: Robson


title: Vacuolar ATPase subunit Atp6v0c transgene promotes neuroprotection and long-distance axon regeneration in injured retinal ganglion neurons

city: Farmington

first: Jacob

last: Brady

state: Connecticut

address: 263 Farmington Avenue

department: Neuroscience

institute: UConn School of Medicine

summary: Central nervous system (CNS) projection neurons’ failure to repair/regenerate injured axons has devastating consequences for those who have sustained CNS injuries. Thus, there is a need for translatable factors capable of promoting long-distance axon regeneration in the CNS. We hypothesized that supporting lysosomes in injured neurons by supplementing their structural factors through gene therapy may foster axon regeneration. To test our hypothesis, we selected Atp6v0c for experimental regulation because it plays roles in lysosomal acidification and degradation of misfolded proteins in response to endoplasmic reticulum (ER) stress in injured neurons. We tested in a rodent optic nerve crush (ONC) model of traumatic optic neuropathy (TON) in which injured prototypical CNS projection neurons, the retinal ganglion cells (RGCs), do not regenerate damaged axons and eventually degenerate. Atp6v0c transgene expression was achieved using intravitreally-injected adeno-associated virus serotype 2 (AAV2), which transduces the RGCs. For benchmarking, we compared efficacy to AAV2-targeting of prominent regulators of axon regeneration, Pten and Klf9. We found that Atp6v0c transgene promoted RGC survival and long-distance axon regeneration, comparable to targeting Pten and Klf9. Thus, Atp6v0c is an axon regeneration-promoting factor with a potential for treating CNS injury and disease.

overall_design: Uninjured and injured (2 weeks post-ONC) RGCs from 12-week old wild-type (129S1/SvImJ (JAX strain 002448)) mice of both sexes were immunopanned and FACS-isolated from the retinal single cell suspension. After sorting, cells were processed by 10X Chromium scRNA-seq.

first: Ephraim

middle: F

last: Trakhtenberg


title: Sodium Channel Isoform Diversity Underlies Chamber-Specific Cardiac Excitability [Spatial Transcriptomics]

city: Iowa City

first: Jared

last: McLendon

state: Iowa

address: 180 South Grand Ave, CPB 554

department: Pharmaceutical Sciences and Experimental Therapeutics

institute: University of Iowa - College of Pharmacy

summary: Sodium channels are essential for cardiac conduction and excitability. The sodium current is primarily carried by the voltage gated sodium channel isoform NaV1.5. Using a novel NaV1.5 chimeric construct, our study reveals a unique chamber-specific distribution of non-NaV1.5 sodium channel isoforms, and we performed spatial sequencing of murine hearts to assess the transcriptional changes associated with our chimeric channel.

overall_design:
Spatial sequencing was performed on hearts from three wild type mice and three mutant mice. Of note, the Scn5a mutant was not able to be detected because the target of the probe based sequencing method was located in the mutated region.
This is a spatial RNAseq dataset, a complement to GSE319426 bulk RNA-seq records

first: Christian

last: Anderson

first: Omar

last: Rabab'h


title: circRNA microarray data of IL4 and IL13 treated prostal stromal fibroblasts

first: Susan

last: Patalano

address: 100 Morrissey Blvd.

department: Center for Personalized Cancer Therapy

institute: UMASS Boston

summary: Interleukin IL-4 and IL-13 JAK/STAT signaling increases fibrosis-related extracellular membrane (ECM) protein production in prostate fibroblasts, which contributes to aging-associated lower urinary tract dysfunction (LUTD).To interrogate the role of circRNAs in this regulation, human stromal prostate fibroblasts were treated with IL4, IL13, or Vehicle and RNA extracted and subjected to microarray analysis with ArrayStar Mouse circRNA microarray v2.