title: Defect in hematopoiesis and embryonic lethality at midgestation of Vps13a/Vps13c double knockout mice

city: West Haven

first: Francesc

last: Lopez

state: CT

department: Department of Genetics

institute: Yale University

summary: VPS13 is the founding member of a family of proteins that mediate lipid transfer at intracellular membrane contact sites by a bridge-like mechanism. Mammalian genomes comprise 4 VPS13 genes encoding proteins with distinct localizations and function. The gene duplication resulting in VPS13A and VPS13C is the most recent in evolution and, accordingly, these two proteins are the most similar to each other.  However, they have distinct subcellular localizations and their loss of function mutations in humans are compatible with life but result in two different age-dependent neurodegenerative diseases, chorea-acanthocytosis and Parkinson’s disease, respectively. Thus, it remains unclear whether these two proteins have overlapping functions. Here, we show that while Vps13a KO and Vps13c KO mice are viable, embryonic development of Vps13a/Vps13c double knockout (DKO) mice is arrested at midgestation. Prior to death, DKO embryos were smaller than controls, were anemic and had a smaller liver, the key erythropoietic site at this developmental stage. Further analyses of erythroid precursor cells showed that their differentiation was impaired and that this defect was accompanied by activation of innate immunity as revealed by upregulation of interferon stimulated genes (ISGs). Additionally, the RIG-I and MDA5 components of dsRNA triggered innate immunity were found upregulated in the DKO fetal liver. Activation of innate immunity may result from loss of integrity of the membranes of intracellular organelles, such as mitochondria and autophagic lysosomes, due to the absence of these lipid transport proteins. The surprising and striking synthetic effect resulting for the combined loss of VPS13A and VPS13C suggests that despite of the different localization of these two proteins, the lipid fluxes that they mediate are partially redundant.

overall_design: RNAseq profiling of isolated S0 cells (erythroid precursors) from E12.5 WT and Vps13a/Vps13c DKO fetal livers

first: Peng

last: Xu

first: Rubia

last: Isler Mancuso

first: Marianna

last: Leonzino

first: Caroline

last: Zeiss

first: Diane

last: Krause

first: Pietro

last: De Camilli


title: YAP and TAZ loss of function in the neural crest broadly affects olfactory ensheathing cells, olfactory-vomeronasal neurons, but not GnRH-1 neuronal migration.

status: Public on Jul 15 2025

city: Albany

first: Paolo

middle: Emanuele

last: Forni

state: NY

address: 1400 Washington Avenue

department: Biology

country: USA

institute: University at Albany

type: Expression profiling by high throughput sequencing

summary: Olfactory Ensheathing Cells (OECs) originate from the neural crest and are critical for bundling olfactory axons to the brain. Their development is vital for the migration of Gonadotropin-Releasing Hormone-1 (GnRH-1) neurons, which are essential for puberty and fertility. OECs are of particular interest for potential treatments of central nervous system lesions, though their development is not fully understood. Our single-cell RNA sequencing of mouse embryonic nasal tissues suggests that OECs and Schwann cells share a common origin from Schwann Cell Precursors (SCPs). However, OECs and SCs have significant genetic differences. Wnt1 is highly expressed in pre-migratory neural crest cells, while Sox10 expression occurs later and is lost in most derivatives, except for nasal cartilage, SCPs, SCs, melanocytes, and OECs. Rosa26 lineage tracing revealed that the Wnt1Cre2 mouse line recombines extensively in non-neural crest-derived tissues, while Sox10 Cre more selectively recombines in neural crest derivatives. We used Sox10 Cre mice to manipulate the Yap and Taz genes in migrating neural crest cells. Our analyses showed reduced Sox10+ cells in the nasal region and alterations in gene expression of SCs, melanocytes, and OECs. However, GnRH-1 neuronal migration remained unaffected. Notably, the loss of Yap and Taz in neural crest derivatives led to significant secondary effects in olfactory structures, reducing both olfactory sensory neurons and vascularization in the vomeronasal organ (VNO). Our findings highlight the importance of the Hippo pathway in OEC development and its implications for the olfactory vasculature.

overall_design: Whole embryonic noses were dissected from E14.5 yap flox/flox;taz flox/flox and Sox10cre;yap flox/WT;taz flox/flox mice, cells were isolated then analyzed using scRNAseq.

first: Ed Zandro

middle: M

last: Taroc

first: Enrico

last: Amato Jr

first: Alexis

last: Semon

first: Nikki

last: Dolphin

first: Brianne

last: Beck

first: Sophie

last: Belin

first: Yannick

last: Poitelon

middle: E


title: Gut-derived metabolites drive Th17 cell pathogenicity in Multiple Sclerosis

city: 1066 Epalinges

first: Jessica

last: Rebeaud

address: Chemin des Boveresses 155

country: Switzerland

institute: University of Lausanne

summary: The gut-brain axis is an emerging factor in promoting multiple sclerosis (MS). However, the underlying mechanisms and strategies to target this axis are not established. Here, we investigated how the gut environment influences myelin-specific Th17 cell pathogenicity. We used the adoptive Th17 cell transfer experimental autoimmune encephalomyelitis (EAE) model and antibiotic treatment to modulate the intestinal microbiome. We observed a reduced pathogenic Th17 cell signature in the colon of antibiotics-treated mice. Treatment with fecal filtrates enhanced myelin-specific Th17 cell encephalitogenic properties both in vitro and in vivo. Feces metabolomic profiling identified altered tryptophan-derived metabolites, including indole-3-carboxylate (I3CA). Oral I3CA supplementation accelerated EAE development and I3CA concentration in blood samples from persons with MS (PwMS) was associated with increased disease severity mirrored by increased serum neurofilament light chain levels. Altogether, our study shows that microbiota-derived metabolites play a key role in the intestine during neuroinflammation, offering potential therapeutic insights for PwMS.

overall_design: Comparative gene expression profiling analysis of RNA-seq data of colonic lamina propria lymphocytes isolated from wild-type mice (n = 4-6) four days after the adoptive transfer of pathogenic Th17 cells for EAE induction. Cells were FACS sorted based on viable cells and their expression of CD45.1+ CD45.2+, which characterizes the population of injected myelin-specific Th17 cells.

first: Solenne

last: Vigne

first: Valentine

last: Bressoud

first: Roméo

last: Carre

first: Florian

last: Ruiz

first: Benjamin

last: Peter

first: Nicholas

last: Phillips

first: Lena

last: Siewert

first: Tim

last: Roloff

first: Jens

last: Kuhle

first: Tinh-Hai

last: Collet

first: Anne-Katrin

last: Proebstel

last: Pot


title: Molecular Subtypes of Human Skeletal Muscle in Cancer Cachexia

city: Edmonton

first: Sambasivarao

last: Damaraju

state: Alberta

address: 11560 University Avenue

department: Laboratory Medicine and Pathology

country: Canada

institute: University of Alberta

type: Non-coding RNA profiling by high throughput sequencing

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

sample_organism:
Homo sapiens
Rattus norvegicus

platform_organism:
Homo sapiens
Rattus norvegicus

overall_design: Refer to individual Series

first: Bhumi

middle: J

last: Bhatt

first: Vickie

last: Baracos


title: Heparanase 2 Modulates Vascular Permeability via Heparan Sulfate-Dependent Growth Factor Signaling

city: Bar Harbor

first: Yannic

last: Becker

state: Maine

address: 159 Old Bar Harbor Road

institute: Mount Desert Island Biological Laboratory

summary: Heparan sulfate (HS) glycans attached to the apical surface of vascular endothelial cells (ECs) play an important role in regulating endothelial permeability and ligand recognition by cell-surface receptors. Shedding of HS from the EC surface increases vascular leakage and is associated with vascular diseases. Recently, heparanase 2 (Hpa2) was described as a novel regulatory molecule that controls HS shedding. However, its role in regulating HS physiology in the vascular endothelium is largely unknown. Here, we characterize the role of endogenous Hpa2 in the vertebrate vascular system using zebrafish as our primary research model. We detected Hpa2 expression in hepatic tissue and localized the protein in blood vessels. Hpa2 loss-of-function (LOF) larvae exhibited increased vascular permeability, occasional hypersprouting, and altered EC and extracellular matrix (ECM) morphology. Hpa2-LOF also reduced HS levels and caused changes in the endothelial transcriptome characterized by dysregulated genes involved in ECM-receptor interaction and signal transduction regulation. Recombinant Hpa2 rescued the Hpa2-LOF phenotype in zebrafish. Hpa2 competes with fibroblast growth factor 2 (FGF2) and vascular endothelial growth factor A165 (VEGFA165) for binding on the EC surface and consequently reduces the cellular response these factors elicit. Pharmacological inhibition of these pathways alleviated the Hpa2-LOF phenotype in zebrafish. We conclude that Hpa2 is a circulating molecule that maintains vascular integrity by regulating HS-dependent processes on the EC surface. These results may translate into novel strategies applying recombinant Hpa2 to treat microvascular diseases.

overall_design: To investigate the effect of heparanase 2 (Hpa2) on endothelial cells in zebrafish larvae, we induced a Hpa2 loss-of-function scenario and isolated endothelial cells from pooled larvae. Bulk RNA sequncing from EC-derived RNA was perfromed comparing the expression profile of Hpa2 loss-of-fuction vs. control larvae.

first: Sergey

last: Tkachuk

first: Yulia

last: Kiyan

first: Hermann

last: Haller

first: Anne

last: Jörns

first: Ahmad

last: Alwakaa

first: Nelli

last: Shushakova

first: Song

last: Rong


title: Maintenance of histone crotonylation by YEATS2 and GCDH drives EMT in head and neck cancer [RNA-seq]

city: Bhopal

first: Sanjeev

last: Shukla

state: Madhya Prades

address: Bhopal Bypass Road, Bhauri Bhopal 462 066 Madhya Pradesh, INDIA

department: Biological Sciences

country: India

institute: Indian Institute of Science Education and Research Bhopal

summary: Regulation of gene expression is an integral cellular process, fine-tuned by epigenetic marks like histone modifications. Perturbations in the activity or abundance of epigenetic factors can lead, or contribute to tumorigenesis in healthy cells. Remarkably, the addition of epigenetic marks is dependent on the metabolites produced during several essential cellular pathways. Here, we have explored the interplay between a highly expressed epigenetic factor YEATS2, and a metabolic enzyme GCDH in regulating epithelial to mesenchymal transition in head and neck cancer. We report the results of RNA-seq in YEATS2-silenced BICR10 cells to investigate the effect of YEATS2 in influencing gene expression globally. We have also performed ChIP-seq using YEATS2 antibody in BICR10 cells to obtain the globally occupied sites of YEATS2. Lastly, we report the changes in crotonylation at histone 3 lysine 27 (H3K27Cr) upon YEATS2 downregulation in BICR10 by performing ChIP-seq in shControl vs. shYEATS2 cells.

overall_design: RNA-seq was performed using RNA extracted from shControl and shYEATS2 BICR10 cells

first: Deepak

last: Pant


title: SGK3 Orchestrates Glucocorticoid Signaling to Facilitate Chromatin Remodeling During Adipogenesis

city: 上海市

first: Ben

last: Zhou

address: 岳阳路320号

country: China

institute: shanghai institude of nutrition and health, CAS

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Excessive glucocorticoid exposure is associated with significant metabolic side effects, partly attributed to the transcriptional regulation of adipogenesis by the Glucocorticoid receptor (GR). However, emerging evidence suggests the involvement of alternative pathways beyond GR activation, which are inadequately explored. Through quantitative phosphoproteomics analysis, we identified a significant enrichment of rapidly phosphorylated proteins harboring the RxxS motif following glucocorticoid exposure. Notably, a subset of these proteins undergoes phosphorylation at the RxxS motif by Serum- and glucocorticoid-induced kinase 3 (SGK3) upon glucocorticoid stimulation in preadipocytes. SGK3 emerges as a critical mediator of glucocorticoid-induced preadipocyte differentiation, supported by genetic ablation and pharmacological inhibition experiments that demonstrate impaired adipogenesis both in vitro and in vivo. Mechanistically, upon glucocorticoid stimulation, SGK3 translocates to the nucleus and directly interacts with the core ATPase subunit of the BAF chromatin remodeling complex, BRG1, leading to phosphorylation at threonine 428 and serine 1417 residues. This phosphorylation event prevents proteasomal degradation of BRG1, facilitating chromatin remodeling essential for adipogenesis. Furthermore, Sgk3 knockout mice exhibit resistance to obesity induced by either glucocorticoids or a high-fat diet (HFD). These findings illuminate novel roles of glucocorticoids beyond GR-mediated transcriptional control, highlighting SGK3 as a promising therapeutic target for mitigating metabolic side effects associated with glucocorticoid therapy.

overall_design: BRG1 CUT&TAG profiling and chromatin accessibility profiling via ATAC-Seq were conducted on stromal vascular fraction (SVF) cells treated with either vehicle or SGK3 PROTAC at D-3 or D2 during adipocyte differentiation induction.

first: Qilong

last: Chen


title: A postnatal molecular switch drives the activity-dependent maturation of parvalbumin interneurons.

city: London

first: Monika

last: Moissidis

address: New Hunt's House, Newcomen St

department: Centre for Developmental Neurobiology

country: United Kingdom

institute: King's College London


title: Impact of phosphate limitation on PHBV production and microbial community dynamics fed with synthetic fermentation digestate [18S]

status: Public on Jul 14 2025

city: Pisa

first: Giulio

last: Petroni

address: Via A. Volta n°4/6

department: Department of Biology

country: Italy

institute: University of Pisa

summary: This study investigates the role of carbon-to-phosphorus (C/P) ratios in shaping microbial community dynamics and polyhydroxyalkanoates (PHA) production in sequencing batch reactors (SBR) fed with volatile fatty acids. Three conditions, characterized by fixed organic loading rates but varying C/P ratios (Run 1 = 170 Cmol Pmol-1; Run 2 = 235 Cmol Pmol-1; Run 3 = 400 Cmol Pmol-1), were tested to explore their impact on PHA accumulation, biomass growth, and reactor stability. Results indicate that the moderate phosphorus limitation of Run 2 achieves the best overall performance, with a PHA volumetric productivity of 2.02 g PHA L-1 d-1 and process stability. Conversely, higher C/P ratio increased the storage yield but lowered the productivity (1.55 gPHA L-1 d-1), compromising sludge settleability and reactor stability, indicating impaired microbial functionality. Full-length 16S/18S rRNA gene sequencing using PacBio technology enabled high-resolution profiling of microbial communities, revealing ecological shifts across conditions. Run 2 exhibited the highest bacterial and eukaryotic diversity, featuring multiple PHA-accumulating bacteria (mainly Sphaerotilus, Leadbetterella, and uncultured Rhodobacteraceae) and a well-structured eukaryotic community dominated by K-strategist bacterivorous protists, e.g. Rhogostoma (Rhizaria) and Vorticella (Ciliophora, Oligohymenophorea) and predatory protozoa, e.g. Tokophrya (Ciliophora, Suctoria). In contrast, Sphaerotilus dominated under suboptimal conditions and may be linked to bulking. These results suggest that eukaryotic diversity may support system stability through selective predation. Transmission electron microscopy (TEM) further confirmed the presence of intracellular PHA granules and polyphosphate reserves, reinforcing the connection between nutrient limitation and adaptive microbial strategies. Overall, these findings highlight the critical role of the C/P ratio in shaping the performance of mixed microbial cultures, demonstrating that a well-balanced nutrient supply can enhance PHA production while maintaining microbial community stability. The results contribute to optimizing the selection process for mixed microbial cultures, offering valuable insights into the impact of carbon-to-nutrient ratios in the feeding strategy.

overall_design: Total DNA was extracted from activated sludge and mixed microbial cultures grown under three C/P conditions, then amplified for full-length 18S rRNA gene sequencing using the PacBio platform

first: Alessio

last: Castagnoli

first: Sitihaya

last: Malibo

first: Tianshi

last: Li

first: Serena

last: Falcioni

first: Letizia

last: Modeo

first: Prawit

last: Kongjan

first: Isabella

last: Pecorini


title: Tetrandrine regulates the gut microbiota-associated CYP51 metabolism and improves cognitive dysfunction in SAH rats through the TLR4/NF-κB pathway

city: Hengyang

first: Rui

address: No. 336 Dongfeng Road

institute: Nanhua Hospital Affiliated to University of South China

summary: Tet restored gut microbiota imbalance in SAH rats

overall_design: Considering that Tet improved cognitive function in SAH rats, potentially involving the gut microbiota, fecal samples were collected to determine differences in gut microbiota composition among the experimental groups.

first: Huan

last: Liu

first: Qin

last: Zou

first: Tao

last: Xiang

last: Zhu

first: Zigui


title: Neurobehavioral phenotypes in the pan-neuronal GAL4 zebrafish line Tg(elavl3:KalTA4) - Addition of a second elavl3:KalTA4 bulk RNA-sequencing dataset.

city: Worcester

first: Summer

last: Thyme

state: MA

address: 364 Plantation St

institute: UMass Chan Medical School

summary: The Gal4/UAS system is used across model organisms to overexpress target genes in precise cell types and relies on generating transgenic Gal4 driver lines. In zebrafish, the Tg(elavl3:KalTA4) (HuC) line drives robust expression in neurons. We observed an increased prevalence of swim bladder defects in Tg(elavl3:KalTA4) zebrafish larvae compared to wildtype siblings, which prompted us to investigate whether transgenic larvae display additional neurobehavioral phenotypes. Tg(elavl3:KalTA4) larvae showed alterations in brain activity, brain morphology, and behavior, including increased hindbrain size and reduced activity of the cerebellum. Bulk RNA-seq analysis revealed massive dysregulation of the transcriptome and suggested an increased ratio of neuronal progenitor cells compared to differentiated neurons. To understand whether these phenotypes derive from Gal4 toxicity or from positional effects related to transgenesis, we used economical low-pass whole genome sequencing to map the Tol2-mediated insertion site to chromosome eight. Reduced expression of the neighboring gene gadd45ga, a known cell cycle regulator, is consistent with increased proliferation and suggests a role for positional effects. Challenges with creating alternative pan-neuronal lines include the length of the elavl3 (HuC) promoter (9 kb) and random insertion using traditional transgenesis methods. To facilitate the generation of alternative lines, we cloned five neuronal promoters (atp6v0cb, elavl3, rtn1a, sncb, and stmn1b) ranging from 1.7 kb to 4.3 kb and created KalTA4 lines using Tol2 and the phiC31 integrase-based pIGLET system. Our study highlights the importance of using appropriate genetic controls and establishes a roadmap for identifying positional effects in new transgenic lines.

overall_design: RNA-sequencing of dissected heads of larval zebrafish of the Tg(elavl3:KalTA4; 4xUAS:hmgn6) zebrafish versus Tg(4xUAS:hmgn6) siblings. There are likely multiple 4xUAS insertions, but the purpose of this data is to define the elavl3:KalTA4 effect on the brain.

first: Thyme

last: Summer


title: Impact of phosphate limitation on PHBV production and microbial community dynamics fed with synthetic fermentation digestate [16S]

overall_design: Total DNA was extracted from activated sludge and mixed microbial cultures grown under three C/P conditions, then amplified for full-length 16S rRNA gene sequencing using the PacBio platform


title: A postnatal molecular switch drives the activity-dependent maturation of parvalbumin interneurons [scRNA-seq]

summary: Cortical neurons are specified during embryonic development but often only acquire their mature properties at relatively late stages of postnatal development. This delay in terminal differentiation is particularly prominent for fast-spiking parvalbumin-expressing (PV+) interneurons, which play critical roles in regulating the activity of the cerebral cortex. We found that the terminal differentiation of PV+ interneurons is triggered by neuronal activity and mediated by the transcriptional coactivator peroxisome proliferator-activated receptor-gamma coactivator 1-alpha (PGC-1a). Developmental loss of PGC-1a prevents PV+ interneurons from acquiring their unique structural, electrophysiological, synaptic, and metabolic features and disrupts PV+ interneuron subtype specification. PGC-1a exerts its function as a master regulator of the differentiation of PV+ interneurons by directly controlling gene expression through a transcriptional complex that includes ERRg and Mef2c. Our results uncover a molecular switch that translates neural activity into transcriptional programs promoting the maturation of PV+ interneurons at the appropriate developmental stage.

overall_design: PV+ and SST+ interneurons from Lhx6-Cre;Ppargc1a+/+ (control) and Lhx6-Cre;Ppargc1aF/F (mutant) animals were isolated using FACS, thanks to the expression of tdT after viral infection. These sorted cells were then subjected to single-cell RNA sequencing.

first: Moissidis

last: Monika

first: Abbasova

last: Leyla

last: Shenyue


title: ZBTB11 Depletion Targets Metabolic Vulnerabilities in K-Ras Inhibitor Resistant PDAC [Degrader RNA-seq]

city: La Jolla

first: Eric

middle: S.

last: Wang

state: CA

address: 10901 North Torrey Pines Road

department: Cancer Metabolism and Microenvironment Program

institute: Sanford Burnham Prebys Medical Discovery Institute

summary: Over 95% of pancreatic ductal adenocarcinomas (PDAC) harbor oncogenic mutations in K-Ras. However, upon treatment with K-Ras inhibitors, PDAC cancer cells undergo rapid metabolic reprogramming towards an oxidative phosphorylation-dependent, drug-resistant state. In this work, we demonstrate that this metabolic shift is associated with upregulation of the transcription factor ZBTB11, and both the metabolic state and the K-Ras inhibitor drug resistance can be attenuated by ZBTB11 depletion. We develop molecular glue degraders of ZBTB11 and demonstrate that they reprogram the aberrant transcriptome, proteome, metabolome, and bioenergetics of K-Ras inhibitor resistant PDAC, resensitizing them to K-Ras inhibition. ZBTB11 degradation leverages cell-type and cell-state specific differences in gene regulatory mechanisms controlling OXPHOS-pathway transcripts to selectively target the K-Ras inhibitor resistant state in PDAC while sparing hiPSC-derived neurons. Together, this work establishes ZBTB11 as a druggable vulnerability in K-Ras inhibitor-resistant PDAC and provides a suite of molecular glue degrader tool compounds to investigate its function.

overall_design: Time-course RNA-seq analysis following sotorasib and/or JWJ-01-306 treatment in sotorasib-resistant MIA PaCa-2 cell line to map the impact of KRAS inhibition and ZBTB11 degradation on the global PDAC transcriptome

middle: S

first: Nathan

middle: L

last: Tran

first: Fleur

last: Ferguson


title: Impact of phosphate limitation on PHBV production and microbial community dynamics fed with synthetic fermentation digestate [ITS]

first: Giulio

last: Petroni

overall_design: Total DNA was extracted from activated sludge and mixed microbial cultures grown under three C/P conditions, then amplified for full-length ITS amplicon sequencing using the PacBio platform

first: Alessio

last: Castagnoli

first: Sitihaya

last: Malibo

first: Tianshi

last: Li


title: A postnatal molecular switch drives the activity-dependent maturation of parvalbumin interneurons [CUT&RUN]

first: Monika

last: Moissidis

overall_design: The somatosensory cortex of C57BL/6 mice was dissected and digested to obtain a nuclei suspension. Antibodies against PGC-1𝛼 or ERR𝛾 were used to perform CUT&RUN.

first: Lavender

last: Paul


title: Mutant RIT1 cooperates with YAP to drive an EMT-like lung cancer state [CUT&Run]

city: Seattle

first: Alice

last: Berger

state: WA

address: 1100 Fairview Ave N

institute: Fred Hutchinson Cancer Center

summary: The discovery of oncogene addiction in cancer has led to the development of over a dozen FDA-approved biomarker-driven therapies in lung adenocarcinoma, but many rare driver mutations remain untargeted. Somatic mutations of the “Ras-like in all tissues” (RIT1) gene are non-canonical driver events in lung cancer, occurring in ~2% of lung adenocarcinomas in a mutually exclusive fashion with KRAS and EGFR mutations. Patients with RIT1-mutant lung cancer lack targeted therapy treatment options, and a lack of pre-clinical models has hindered the development of therapeutic strategies for RIT1-mutant lung cancer. Here we report a new mouse model with inducible regulation of the cancer-associated RIT1M90I variant. We show that autochthonous expression of RIT1M90I in the lung weakly promotes cancer alone or in combination with loss of the p53 tumor suppressor. However, potent synergy between RIT1M90I and inactivation of Nf2 and p53 drives an aggressive lung cancer with 100% penetrance and short latency. We show this oncogenic cooperation is driven by synergistic activation of cJUN, a component of the AP-1 complex. Therapeutic inhibition of MEK and YAP/TEAD suppressed RIT1M90I-driven lung cancer in vitro and in vivo. These data identify YAP/TEAD as an important mediator of RIT1’s oncogenic potential and nominate TEAD as an important drug target in RIT1-mutant lung cancer.

overall_design: The data generated is from a CUT&RUN experiment performed on lysates from isogenic small airway lung epithelial (SALE) cells. Four different lines were used: Parental SALE (par), SALE ectopicallly expression RIT1-M90I (RIT), SALE ectopically expressing an activated YAP variant 8SA (YAP), or SALE cells expressing both RIT1-M90I and YAP-8SA (RY). 22 to 23 antibodies and one IgG control were used for each cell line, in duplicate.

middle: H

first: Saksham

last: Gupta

first: Siobhan

last: O'Brien


title: Acetyl-CoA Carboxylase-1 Inhibition Increases Regulatory T-Cell Metabolism, Mitochondrial Fusion and Graft-vs-Host Disease Treatment Efficacy

city: Minneapolis

first: Michael

last: Zaiken

state: MN

address: East River Parkway

department: Pediatrics

institute: University of Minnesota

summary: Regulatory T-cells (Treg) are critical for maintaining immune homeostasis, and their adoptive transfer can treat murine inflammatory disorders. In patients, Treg therapies have been variably efficacious. Therefore, new strategies to enhance Treg therapeutic efficacy are needed. Treg predominantly depend upon oxidative phosphorylation (OXPHOS) for energy and suppressive function. Fatty acid oxidation (FAO) contributes to Treg OXPHOS and can be important for Treg “effector” differentiation, but FAO activity is inhibited by coordinated activity of isoenzymes acetyl-CoA Carboxylase-1 and -2 (ACC1/2). Here, we show that small molecule inhibition or Treg-specific genetic deletion of ACC1 significantly increases Treg suppressive function in vitro and in mice with established chronic GVHD. ACC1 inhibition skewed Treg towards an “effector” phenotype and enhanced FAO-mediated OXPHOS, mitochondrial function, and mitochondrial fusion. Inhibiting mitochondrial fusion diminished the effect of ACC1 inhibition. Reciprocally, promoting mitochondrial fusion, even in the absence of ACC1 modulation, resulted in a Treg functional and metabolic phenotype similar to ACC1 inhibition, indicating a key role for mitochondrial fusion in Treg suppressive potency. Ex vivo expanded, ACC1 inhibitor treated human Treg similarly augmented suppressor function as observed with murine Treg. Together, these data suggest that ACC1 manipulation may be exploited to modulate Treg function in patients.

overall_design: Overnight activated Treg pre-treated with DMSO or ND630 were separated into samples containing at least 100,000 cells, pelleted, and resuspended in Qiagen buffer RLT with 1% 2-mercaptoethanol (Millipore). Samples were snap frozen on dry ice, and stored at -80ºC until processing at University of Minnesota Genomics Center.

first: Cameron

last: Mcdonald-Hyman

first: Bruce

last: Blazar


title: Muscle Exosome-Derived miR-126 Regulates Local Synthesis of TDP-43 and NMJ Integrity in ALS

city: ראשון לציון

first: Iddo

last: Magen

state: Not in US

address: בן אליעזר 32, 17

country: Israel

institute: Weizmann Institute

summary: Amyotrophic lateral sclerosis (ALS) is characterized by neuromuscular junction (NMJ) disruption and neurodegeneration. Recent findings highlight a pivotal role for TDP-43 in forming axonal pathological condensates and facilitating NMJ disruption through inhibition of local protein synthesis. However, the mechanisms which drive local TDP-43 accumulation remain unknown. Here we identify TDP-43 axonal accumulation in peripheral nerves of SOD1 patients and mice stemming from its aberrant local synthesis. This is a non-cell-autonomous process driven by muscle-derived miR-126a-5p exosomes. Inhibiting muscle secretion of miR-126a-5p prompts pre-synaptic TDP-43 synthesis and accumulation that disrupts axonal translation and causes NMJ degeneration. Introducing miR-126 to SOD1G93A mice, primary co-cultures, and human iPSC-derived co-cultures with ALS mutations exhibits neuroprotective effects and delays motor decline. These findings identify a transcellular communication axis between muscles and motor neurons that regulates axonal local synthesis and NMJ maintenance offering insights into ALS onset and progression.

overall_design: Small RNA Next Generation Sequencing For small RNA next generation sequencing (RNA-seq), libraries were prepared from 10-15 ng of total RNA using the QIAseq miRNA Library Kit and QIAseq miRNA NGS 48 Index IL (Qiagen), by an experimenter who was blinded to the identity of samples. Samples were randomly allocated to library preparation and sequencing in batches. Precise linear quantification of miRNA is achieved by using unique molecular identifiers (UMIs), of random 12-nucleotide after 3’ and 5’ adapter ligation, within the reverse transcription primers. cDNA libraries were amplified by PCR for 19 cycles, with a 3’ primer that includes a 6-nucleotide unique index, followed by on-bead size selection and cleaning. Library concentration was determined with Qubit fluorometer (dsDNA high sensitivity assay kit; ThermoFisher Scientific, Waltham, MA) and library size with Tapestation D1000 (Agilent). Libraries with different indices were multiplexed and sequenced on NextSeq 500/550 v2 flow cell or Novaseq SP100 (Illumina), with 75bp single read and 6bp index read. Fastq files were de-multiplexed using the user-friendly transcriptome analysis pipeline (UTAP). Mouse miRNAs, as defined by miRBase, were mapped using the GeneGlobe pipeline (https://geneglobe.qiagen.com/us/analyze). We defined "true positive" miRNAs and reduced the likelihood of considering “false positive” miRNAs by including only miRNAs with an average UMI counts > 100 across all samples and with at least a single UMI across all samples, similar to our previous works. Data were further normalized, and average read counts compared between groups using the DESeq2 package under the assumption that miRNA counts followed negative binomial distribution. Significance was determined using the Wald test.  Axonal RNA sequencing RNA was extracted from primary MNs axons grown in radial microfluidic chambers and purified as described above. RNA yields were quantified using Qubit fluorometer (RNA broad range assay kit; ThermoFisher Scientific). RNA integrity was assessed by TapeStation. cDNA libraries were prepared from 10ng of axonal RNA by the genomic unit in Weizmann institute using MARS-seq pipeline. MARS-seq libraries with different UMIs were multiplexed and sequenced on Novaseq SP100 flow cell (Illumina), with 75bp single read and 15bp UMI read. After demultiplexing, fastq files were mapped to mouse genome using the GenCode annotations (vM25, 2020) in the UTAP piepeline. We defined "true positive" genes and reduced the likelihood of considering “false positive” genes by including only genes with an average UMI counts > 15 across all samples. Data was further normalized, and average read counts compared between groups using the DESeq2 package under the assumption that gene counts followed negative binomial distribution. Significance was determined using the Wald test.

first: Ariel

last: Ionescu

first: Lior

last: Ankol

first: Anand

middle: G

last: Subramaniam

first: Topaz

last: Altman

first: Yahel

last: Cohen

first: Yehuda

last: Danino

first: Tal

last: Gradus-Pery

first: Yoav

last: Niv

first: Ori

last: Bar Avi

first: Danielle

last: Geller

first: Amjd

last: Ibraheem

first: Ruilei

last: Cheng

first: Noam

last: Steinberg

first: Leenor

last: Alfahel

first: Pauline

last: Duc

first: Zeynep

last: Ergul-Ulger

first: Doruk

last: Arslan

first: Ersin

last: Tan

first: Florence

last: Rage

first: Nilo

last: Riva

first: Angello

last: Quattrini

first: Can

last: Ebru Bekircan-Kurt

first: Adrian

last: Israelson

first: Amir

last: Dori

first: Eran

last: Hornstein

last: Perlson


title: Acetyl-CoA Carboxylase-1 Inhibition Increases Regulatory T-Cell Metabolism, Mitochondrial Fusion and Graft-vs-Host Disease Treatment Efficacy [L2_cGvHD]

first: Michael

last: Zaiken

overall_design: Cryopreserved peripheral blood mononuclear cell (PBMC) samples were selected from patients with refractory chronic GVHD enrolled on low-dose IL-2 treatment trials at the Dana-Farber Cancer Institute in Boston, MA (ClinicalTrials.gov: NCT02318082 and NCT01366092). Both trials were approved by the Dana-Farber/Harvard Cancer Center Institutional Review Board and prior written informed consent was obtained per the Declaration of Helsinki. PBMCs from 6 clinical responders and 5 non-responders at baseline (pre-treatment with low-dose IL-2) and after 4 weeks of low-dose IL-2 therapy were sorted into CD4Treg and CD4Tcon cells. CD4+ T cells were isolated by negative selection using a MACS® Separator and were subsequently labeled with the following antibodies: CD4-FITC (clone: OKT4), CD25-PE-Cy7 (clone: MA251), and CD127-APC-eF780 (clone: eBioRDR5). The labeled CD4+ T cells were then sorted into CD4+ CD25hi CD127lo (CD4Treg) and CD4+ CD25lo (CD4Tcon) populations using a BD FACSAria Cell Sorter. Total RNA was extracted from the sorted cells using TRIzol Reagent (Thermo Fisher Scientific) following the manufacturer's protocol.

first: Cameron

last: Mcdonald-Hyman

first: Jennifer

last: Whangbo

last: Alal

first: Kim

last: Soomin

first: Kean

last: Leslie

first: Bruce

last: Blazar


title: The dominant follicle: the final frontier in oocyte development

city: Celbridge

first: Lais

last: Barbosa Latorraca

state: Kildare

address: UCD Lyons Farm

department: Agriculture and Food Science

country: Ireland

institute: University College Dublin

summary: The acquisition of oocyte competence, involving both cytoplasmic and nuclear maturation, is critical for successful fertilization and embryonic development in mammals. Discrepancies between in vivo and in vitro studies underline the potential impact of assisted reproductive technologies (ARTs), such as FSH stimulation and in vitro maturation, on oocyte quality and the molecular integrity of bovine oocytes. These insights underscore the importance of optimizing ART conditions to enhance reproductive success in cattle production. Therefore, this study focuses on the gene expression and DNA methylation dynamics in bovine oocytes from dominant follicles, utilising single-cell bisulfite conversion and RNA sequencing (scG&T), without ovarian stimulation. Samples were collected from synchronized heifers during three time points from 24hr to 2hr before ovulation and submitted to scG&T and compared with a dataset of >120 um in diameter oocytes collected by ovary slicing. Our findings from the single-cell RNA sequencing highlight significant changes in oxidative phosphorylation transcripts, indicating the importance of energy metabolism during oocyte capacitation. Additionally, small changes in global CpG methylation and methylation over genomic features were observed. However, modest modifications in CpG windows suggest a less stable epigenome than previously assumed in fully-grown oocytes. In conclusion, the present study brings new insights into molecular changes in bovine oocytes collected from dominant follicles, which can contribute to oocyte quality improvement in cattle production.

overall_design: Oocytes from dominant follicles were collected from previous animal trials performed at University College Dublin. The oestrous cycles of 26 Crossbred nulliparous beef heifers (predominantly Limousin and Charolais crosses) were synchronized to manage the time of the ovulation, and bovine oocytes were collected from dominant follicles 24h before ovulation, 19-23 hours after estrus detection, and 2 hours before ovulation. After denudation from cumulus cells, single oocytes were snap-frozen in PCR tubes and stored at -80 ºC until processing for single-cell RNA sequencing and Bisulphite conversion.

first: Antônio

last: Galvão

first: Gavin

last: Kelsey

first: Julieta Maria

last: D'augero

first: Noof Abdulrahman

last: Alrabiah

first: Trudee

last: Fair


title: Roles of DNA hydroxymethylation versus DNA formylation and carboxylation in neural stem cells [CUT&Tag]

city: New York

first: Meelad

last: Dawlaty

state: New York

address: 1301 Morris Park Ave, Price 419, Bronx

department: Genetics

institute: Albert Einstein College of Medicine

summary: TET enzymes are highly expressed in neural stem cells (NSCs). They oxidize 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC) in a step-wise manner. In this study we have generated NSCs that only lack the Tet formylation and carboxylation activities (Tet-TFoCa) and have compared their multipotency, transcriptome and epigenome to NSCs that lacked all three Tet activities (Tet-TMut). Our findings reveal unique roles for DNA hydroxymethylation vs DNA formylation and carboxylation in multipotency of NSCs.

overall_design: 2 wild type, 2 lines Tet-FoCa and 2  Tet-TMut NSCslines were harvested and H3K27ac genomic distribution was mapped by CUTnTag. Cells were fixed, bound to ConA beads, incubated with anti-H3K27ac antibody, and treated with pre-loaded pA-Tn5 adapter complex. Libraries were prepared with NEBNext HiFi 2x PCR Master mix and sequencing was performed at the Albert Einstein College of Medicine epigenomics core on Illumina NextSeq 500 platform. Details of CUT&Tag procedure and data analyses are described in detail in the methods section of the manuscript.

first: Blake

last: Ebert


title: Effects of hypoxia on brain gene expression in a mouse model of Parkinson’s disease

city: Boston

first: Vamsi

last: Mootha

address: 185 Cambridge Street 6th Floor

institute: Massachusetts General Hospital

summary: The purpose of this study was to evaluate whether chronic, continuous hypoxia (breathing 11% FIO2) would improve neurodegenerative disease in a mouse model of Parkinson's disease, which was modeled through intrastriatal injection of a-synuclein preformed fibrils (PFFs).  We find that chronic, continuous hypoxia helps to prevent further neurodegeneration and alleviate neurological disease.

overall_design: RNA-seq of mouse substantia nigra samples after unilateral stereotaxic injection with either a-synuclein pre-formed fibrils or a-synuclein monomers. The mice were then housed in normoxia (21% oxygen) for six weeks, after which half of the mice were transferred to hypoxia (11% oxygen) and half continued to be housed in normoxia for another six weeks before harvesting.

first: Eizo

last: Marutani

first: Maria

last: Miranda

first: Timothy

last: Durham

first: Sharon

last: Kim

first: Dreson

last: Russell

first: Presli

middle: P

last: Wiesenthal

first: Paul

last: Lichtenegger

first: Marissa

middle: A

last: Menard

first: Charlotte

middle: F

last: Brzozowski

first: Haobo

last: Li

first: Gary

last: Ruvkun

first: Joshua

middle: D

last: Meisel

first: Laura

last: Volpicelli-Daley

middle: K

first: Fumito

last: Ichinose


title: Roles of DNA hydroxymethylation versus DNA formylation and carboxylation in neural stem cells [RNA-seq]

first: Meelad

last: Dawlaty

overall_design: RNA was extracted from neural stem cells at passage one from three lines of wild type and 2 lines of Tet-FoCa and 2 lines of Tet-TMut NSCs  using Omega EZNA Total RNA kit. Library preparation and RNAseq were performed by Novogene (https://en.novogene.com/) on a Illumina Novoseq 6000 platform and 20-30 million  reads were generated per sample. Details of RNAseq procedure and data analyses are described in detail in the methods section of the manuscript.


title: Roles of DNA hydroxymethylation versus DNA formylation and carboxylation in neural stem cells [EM-seq]

type: Methylation profiling by high throughput sequencing

overall_design: DNA was extracted from neural stem cells at passage one from one line of each genotype (Zymo Quick-DNA Miniprep kit). 200 ng of DNA was used per sample. Libraries were prepared following NEBNext EM-seq kit following manufacturer instructions and subjected to 300-bp paired-end sequencing at Novogene using their NovaSeq X Plus (PE150-25B) platform. Spike-in lambda (negative control) and pUC19 (5mC positive control) DNA were used as controls. Details of EMseq procedure and data analyses are described in detail in the methods section of the manuscript.

first: Blake

last: Ebert


title: Maintenance of histone crotonylation by YEATS2 and GCDH drives EMT in head and neck cancer [ChIP-seq]

first: Sanjeev

last: Shukla

overall_design: ChIP-seq for YEATS2 performed in BICR10 cells. ChIP-seq for H3K27Cr was performed in shControl vs shYEATS2 BICR10 cells.

first: Deepak

last: Pant


title: A human-specific regulatory mechanism revealed in a preimplantation model

status: Public on Jul 13 2025

city: Stanford

first: Raquel

last: Fueyo

address: 265 Campus Drive

institute: Stanford University

summary: Stem cell-based human embryo models offer a unique opportunity for functional studies of the human-specific features of development. Here, we genetically and epigenetically manipulate human blastoids, a 3D embryo model of the blastocyst, to investigate the functional impact of HERVK LTR5Hs, a hominoid-specific endogenous retrovirus, on preimplantation development. We uncover a pervasive cis-regulatory contribution of LTR5Hs elements to the hominoid-specific diversification of the blastoids’ epiblast transcriptome. Many of the nearly 700 LTR5Hs genomic insertions in the human genome are unique to our own species. We show that at least one such human-specific LTR5Hs element is essential for the blastoid-forming potential via enhancing expression of the primate-specific ZNF729 gene, encoding a KRAB zinc finger protein. ZNF729 binds G/C-rich sequences, extremely abundant at gene promoters associated with basic cellular functions, such cell proliferation and metabolism. Surprisingly, despite mediating recruitment of TRIM28, at many of these promoters ZNF729 acts as a transcriptional activator. Together, our results illustrate how recently emerged transposable elements and genes can confer developmentally essential functions in humans.

overall_design: To analyze the effect of LTR5Hs repression in human naive pluripotent stem cells by comparing the transcriptomes of control hnPSCs (nontarg-CARGO) versus cells with repressed LTR5Hs elements (LTR5Hs-CARGO)

first: Sicong

last: Wang

first: Olivia

last: Crocker

first: Tomek

last: Swigut

first: Hiromitsu

last: Nakauchi

first: Joanna

last: Wysocka


title: Roles of DNA hydroxymethylation versus DNA formylation and carboxylation in neural stem cells

overall_design: Refer to individual Series


title: In vitro exposure to sucralose ablates CD8 T cell responses

city: Pittsburgh

first: Drew

middle: Nicholas

last: Wilfahrt

state: PA

address: 5535 Kamin Street

department: Immunology

institute: University of Pittsburgh

summary: The composition of the gut microbiota is directly associated with response to checkpoint inhibitors in cancer. How diet impacts the gut microbiota and downstream immune response to cancer remains unclear. Here, we show that consumption of a common artificial sweetener, sucralose, supports microbial dysbiosis, restricts T cell metabolism and function, and limits immunotherapy response in cancer. Microbial dysbiosis is associated with a reduction in Arginine, and amino acid supplementation or fecal microbiome transfer completely restores T cell function and immunotherapy response. Thus, artificial sweetener consumption destabilizes the gut microbiota, resulting in compromised T cell function and ablated immunotherapy response in cancer.

overall_design: Gene expression analysis of bulk RNA-seq of Ot-I T cells from 3 separate mice expanded with or without Sucralose during various timecourses for 7 days


title: A human-specific regulatory mechanism revealed in a preimplantation model [RNA-seq]

overall_design:
To analyze the effect of LTR5Hs repression in human naive pluripotent stem cells by comparing the transcriptomes of control hnPSCs (nontarg-CARGO) versus cells with repressed LTR5Hs elements (LTR5Hs-CARGO)
To analyze the effect of the ZNF729 depletion in human naive pluripotent stem cells by comparing the transcriptomes of control hnPSCs (DMSO treated) versus cells treated for 3 and 24 h with dTAGv-1


title: H3K4me3 amplifies transcription at intergenic active regulatory elements

city: New Haven

first: Bluma

last: Lesch

address: 333 Cedar Street

institute: Yale University

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


title: Roles of DNA hydroxymethylation versus DNA formylation and carboxylation in neural stem cells [EhmC-seq]

overall_design: For EhmC-seq, DNA was extracted from neural stem cells at passage one from one line of each genotype (Zymo Quick-DNA Miniprep kit). 200 ng of DNA was used per sample. Libraries were prepared following NEBNext EhmC-seq kit following manufacturer instructions and subjected to 300-bp paired-end sequencing at Novogene using their NovaSeq X Plus (PE150-25B) platform. Spike-in lambda (negative control) and T4 (5hmC positive control) DNA were used as controls. Details of EhmCseq procedure and data analyses are described in detail in the methods section of the manuscript.


title: Effect of PRMT5i (MRTX1719), ERKi (Adagrasib), RAFi (Belvarafenib) and their combination on non-small cell lung cancer cell line (LU99)

city: Washington D.C.

first: Kathleen

last: Mulvaney

address: 7144 13th PL NW

department: Fralin Biomedical Research Institute

institute: Virginia Tech Cancer Research Center DC

summary: CDKN2A/MTAP co-deletion occurs frequently in non-small cell lung cancer and other solid tumors including glioblastoma and pancreatic ductal adenocarcinoma. Lung cancer remains the leading cause of cancer-related mortalities and fewer than 15% of glioblastoma or pancreatic cancer patients survive 5 years underscoring the need for more effective therapies. PRMT5 is a synthetic-lethal dependency in MTAP null tumors and an attractive therapeutic target for CDKN2A/MTAP deleted cancers. A new revolutionary class of inhibitors, referred to as MTA-cooperative PRMT5 inhibitors, has shown promising results in ongoing early phase clinical trials. Nonetheless, effective cancer treatment typically requires therapeutic combinations to improve response rates and defeat emergent resistant clones. Thus, we sought to determine whether perturbation of other pathways could improve the efficacy of MTA-cooperative PRMT5 inhibitors. Using a paralog and single gene targeting CRISPR library we screened MTAP deleted cancers in the presence or absence of PRMT5 inhibitors. We identified several genes sensitizing to PRMT5 inhibition including members of the MAP kinase pathway. We demonstrate that genetic depletion or chemical inhibition of MAP kinase pathway members using KRAS, MEK, ERK, and RAF inhibitors synergize with PRMT5 inhibition to kill CDKN2A/MTAP null, RAS-active tumors. Further, PRMT5 inhibitors combined with either KRAS or RAF inhibitors durable in vivo complete responses, emphasizing the potential benefit for patients.

overall_design: 3 biological samples per condition were used, for a total of 18 samples: 3 replicates treated with DMSO, 3 replicates treated with PRMT5i (MRTX1719), 3 replicated treated with ERKi (Adagrasib), 3 replicates treated with RAFi (Belvarafenib), 3 replicates treated with PRMT5i+RAFi and 3 replicates treated with PRMT5i+ERKi

first: William

middle: R

last: Sellers

first: Devishi

last: Kesar

first: Guangyan

last: Li

first: Eliana

last: Destefanis


title: Mutant GFAP alters lineage commitment of neural organoids

city: Vestec

first: Zuzana

last: Matusova

address: Prumyslova 595

department: Laboratory of Glial Biology and Omics Technologies

country: Czech Republic

institute: Institute of Biotechnology of the Czech Academy of Sciences


title: Effect of PRMT5i (MRTX1719) on glioblastoma cell line (A172)

overall_design: 3 biological samples per condition were used, for a total of 6 samples: 3 replicates treated with DMSO and 3 replicates treated with PRMT5i (MRTX1719)


title: MYB and HIF1α crosstalk drives hypoxia-induced transcriptional reprogramming and adaptive signaling alterations in pancreatic cancer [RNA-seq]

status: Public on Jul 17 2025

city: Jackson

first: Shashi

last: Anand

state: MS

address: 2500 N State St

department: Cell and Molecular Biology

institute: University of Mississippi Medical Center

summary: Pancreatic cancer is an aggressive malignancy, characterized by extensive desmoplasia and a hypoxic tumor microenvironment that contributes to therapy resistance. MYB, a proto-oncogene encoding a transcription factor, plays a crucial role in pancreatic tumor growth, metastasis, and desmoplasia. Recently, we also revealed a role of MYB in hypoxic survival of pancreatic cancer by promoting metabolic reprogramming through interaction with HIF1α, modulating its expression and influencing its binding to glycolytic gene promoters. In this study, we examined the impact of hypoxia on the genome-wide occupancy of MYB by performing chromatin immunoprecipitation sequencing (ChIP-seq) analysis. We also used HIF1A knockout cells to investigate the role of HIF1α in altered genomic occupancy of MYB. In addition, we examined the genomic distribution of HIF1α in presence and absence of MYB and the impact of their crosstalk on transcriptional reprogramming and associated signaling alterations by RNA-seq and pathway analyses. Our findings show that hypoxia induces significant changes in MYB’s genomic distribution, partially dependent on HIF1α, and that MYB facilitates HIF1α binding to specific gene promoters. We also identify a subset of hypoxia-induced genes co-regulated by MYB and HIF1α, involved in oncogenic signaling pathways critical for hypoxic adaptation. These results highlight the reciprocal crosstalk between MYB and HIF1α, providing novel mechanistic insights into pancreatic cancer adaptation under hypoxia and suggesting MYB as a potential therapeutic target.

overall_design:
RNAseq profiling of MiaPaCa-2 Control cells cultured under normoxia (20% O2).
RNAseq profiling of MiaPaCa-2 Control, MYB knockout (MYB KO) and HIF1α knockout (HIF1α KO) cells cultured under hypoxia (1% O2) conditions.

first: Kunwar Somesh

last: Vikramdeo

first: Mohammad Aslam

last: Khan

first: Seema

last: Singh

first: Ajay Pratap


title: A Hairless Mouse Model for Vitiligo: Enhancing Preclinical Therapeutic Evaluation

city: Kyoto

first: Shinji

last: Tsukada

address: 93, Awatacho, Chudoji, Shimogyo-ku

department: Pharmacological Research Group

country: Japan

institute: Maruho Co., Ltd.

summary: Vitiligo is an autoimmune disease that targets melanocytes, and preclinical models of the disease can strongly promote the development of new treatments. This study introduces a vitiligo model using hairless hk14-SCF Tg mice, whose melanocyte distribution closely mimics human skin, enabling comprehensive therapeutic evaluation. Two methods were used to induce vitiligo: (1) hairless hk14-SCF Tg mice received bone marrow-derived dendritic cells (BMDCs) pulsed with the melanocyte-specific peptide gp100 and CD8+ T cells targeting gp100 (PMEL CD8+ T cells), and (2) hk14-SCF Tg mice were crossbred with PMEL TCR transgenic mice without additional treatment. Skin samples were subsequently analyzed using immunohistochemistry, flow cytometry, bulk RNA sequencing, and cytokine assays, confirming that the mechanisms that drive vitiligo in this model closely resemble those of prior mouse models and vitiligo patients. Various treatments— including ultraviolet irradiation, topical corticosteroids, and a JAK inhibitor—were tested and all significantly reduced vitiligo-affected areas, as verified through objective ImageJ analysis. In conclusion, this model addresses key limitations of previous models, offering a robust platform for preclinical treatment evaluation and potentially accelerating clinical translation.

overall_design: RNA-seq profiling of hk14SCF/HRM mice and at 7 or 12 weeks post-vitiligo induction.

first: Ken

last: Okamura

first: Toshihiro

last: Masuda


first: Raquel

last: Fueyo

summary: Stem cell-based human embryo models offer a singular opportunity for functional studies of the species-specific features of development. Some of these aspects are likely mediated by transposable elements, such as HERVK LTR5Hs, a hominoid-specific endogenous retrovirus highly expressed in human blastocysts. Here, we pioneered genetic and epigenetic manipulation of human blastoids, a 3D embryo model of the blastocyst, to investigate the functional impact of HERVK LTR5Hs on preimplantation development. We demonstrate an essential role of this retrotransposon in blastoid formation and lineage identity. We further uncover a pervasive cis-regulatory contribution of LTR5Hs elements to the hominoid-specific diversification of the epiblast transcriptome. Since HERVK remained mobile following the divergence of humans and chimpanzees, many of the nearly 700 LTR5Hs genomic insertions are unique to our own species. We show that at least one such human-specific LTR5Hs element is essential for the blastoid-forming potential of naive embryonic stem cells by regulating the expression of an evolutionary young gene unique to the Old World anthropoids. Thus, species-specific transposable elements and genes can confer developmentally essential functions.

overall_design: Human blastoids derived from LTR5Hs-CARGO or nontarg-CARGO hnPSCs were dissociated and analyzed using PIP-seq

first: Fueyo

last: Raquel

first: Wang

last: Sicong

first: Swigut

last: Tomek

first: Nakuchi

last: Hiromitsu

first: Wysocka

last: Joanna


overall_design: H3K9me3 CUT&RUN (Cleavage Under Targets & Release Using Nuclease) in nontarg-CARGO and LTR5Hs-CARGO human naive pluripotent stem cells (hnPSCs)

first: Sicong

last: Wang

first: Tomek

last: Swigut

first: Hiromitsu

last: Nakauchi

first: Joanna

last: Wysocka


title: A comparative analysis across species of maternal mRNA regulation in embryos

city: Jerusalem

first: Michal

last: Rabani

address: Hebrew University, Edmond J. Safra Campus, Silberman building

institute: Hebrew University of Jerusalem

summary: The post-transcriptional regulation of mRNAs greatly impacts gene expression dynamics, but the underlying regulatory rules and how they change between organisms remain elusive. During early metazoan development, thousands of pre-loaded maternal transcripts are post-transcriptionally regulated within embryos, making it an ideal system to investigate the mRNA regulatory code across organisms. Here, we present QUANTA, a computational strategy to distinguish transcriptionally silent genes and analyze their post-transcriptional regulation. QUANTA uses kinetic modeling to compare total and polyA+ expression patterns of genes, and quantitatively dissect the interconnected kinetics of their mRNA polyadenylation and degradation. We validate QUANTA using native maternal genes and massively parallel mRNA reporters in zebrafish embryos. Subsequently, we used QUANTA to dissect the regulation of maternally provided mRNAs in frog, mouse and human embryos. We find that widespread polyadenylation of maternal mRNAs precedes their degradation across organisms. Moreover, both the onset of maternal mRNA degradation and its rate are proportional to the developmental pace of the organisms and diverge between orthologs. Through sequence analysis, we associate differences in regulation between maternal genes with putative regulatory signals in the 3’UTRs of each organism. In fast-developing organisms, the 3’UTR regulatory code contains signals to accelerate maternal degradation, while in slow-developing organisms, the 3’UTR signals enhance mRNA stabilization. Our work provides a general strategy to quantify mRNA degradation and polyadenylation kinetics of transcriptionally silent genes, and investigate its sequence-based rules across species and biological systems.

overall_design: temporal expression profiles of mRNA reporters in a massively parallel reporter analysis (MPRA) experiment. Reporters that had different 3'UTR sequences were injected into zebrafish embryos at fertilization. Two types of reporterse were used: pre-adenylated (A+) reporters and non-adenylated (A-) reporters. Samples were collected over developmental times, as specified. Embryos were grown at different temperatures: 28C, 34C and 22C.

first: Mazal

last: Tawil


title: Mirabegron treatment reduces myofibroblasts and CXCR2 expression in adipose tissue in obesity

status: Public on Jul 12 2025

city: Lexington

first: Brian

last: Finlin

state: KY

address: 900 S. Limestone CTW 575

department: Internal Medicine

institute: University of Kentucky

summary: The goal of this study was to determine the effect of treatment of obese humans with the beta 3-adrenergic receptor (B3AR) agonist mirabegron on thigh subcutaneous adipose gene tissue expression.  The adipose biopsies were obtained before and after mirabegron treatment from 10 of the research participants studied in Finlin et al JCI 2020 (PMID: 31961829).  We observed that mirabegron treatment improved glucose homeostasis by increasing insulin sensitivity and beta cell function.  The B3AR has a resticted tissue distribution with one of the known sites being white adipose tissue.  We hypothesized that the mechanism for the effects on glucose metabolism involve favorable effects on adipose tissue such as reduced inflammation.  We performed RNAseq to identify changes in gene expression to gain understanding of the mechanism.

overall_design: Adipose tissues were obtained from the same subject before and after mirabegron treatement.  RNA-seq was performed on each sample and the data were analyzed as paired data.

first: Philip

last: Kern


title: Expression of IMPACT curtails metabolic plasticity and augments NK cell killing to abrogate metastatic growth

status: Public on Jul 11 2025

city: Bethesda

first: Jonathan

last: Hernandez

state: Maryland

address: 10 Center Drive

department: Surgical Oncology Program

institute: National Cancer Institute

summary: To form overt metastases, disseminated tumor cells must simultaneously acquire nutrients, circumvent oxidative stress, and evade organ-specific innate immune surveillance upon arrival. Given the propensity of aggressive epithelial tumors to form hepatic metastases, we performed an in vivo cDNA screen using the mouse liver and KRASG12D/TP53R273H pancreatic cells to identify the RNA binding protein general control of amino acid synthesis 1-like 1 (GCN1) as integral component of hepatic outgrowth. RNAi experiments reveal that GCN1 triggers the integrated stress response (ISR) to activate serine, folate, and methionine biosynthetic pathways together with amino acid transporters, which act in concert to facilitate acquisition of critical metabolites and to restore redox homeostasis. Alongside activation of the ISR, we found that GCN1 also functions in the nucleus where it interacts with an RNA binding protein (HNRNPK) to suppress the expression of MHC-I, antigen-presentation pathway molecules, and natural killer (NK) ligands. Intriguingly, we identified IMPACT as an endogenous competitive inhibitor of GCN1 that blocks both ISR-dependent metabolic control and disrupts HNRNPK interaction. In doing so, IMPACT enhances tumor immunogenicity to unleash robust NK cell killing, in addition to sensitizing metastatic tumor cells to immune checkpoint blockade (ICB). Analysis of patient tumors demonstrates that elevated expression of GCN1 and HNRNPK with concomitant loss of IMPACT correlates with poor immunogenicity, aggressive behavior, and abbreviated survival. These studies provide novel insights linking tumor metabolism, immunity, and metastasis.

overall_design: KPC control and IMPACT-overexpressing pancreatic tumor cells (3X105 cells) were injected into the spleen of syngeneic mice and allowed to develop liver lesions for 25 days following which leukocytes were isolated from the liver and analyzed using scRNA-seq.

first: Surajit

last: Sinha

first: Alexei

last: Lobanov

first: Michael

last: Kelly

first: Anna

last: Lee Fong


title: Chromatin factor YY1 controls fetal hematopoietic stem cell migration and engraftment in mice [ATAC-seq]

city: Madison

first: Xuan

last: Pan

state: WI

address: 4470 Veterinary Medicine Building

institute: University of Wisconsin

summary: Fetal liver is a major organ for generating hematopoietic stem cells (HSCs) during embryonic development. Many questions remain unanswered regarding how transition of hematopoiesis from the fetal liver to the bone marrow (BM) is regulated. We demonstrate that mammalian Polycomb Group (PcG) protein Yin Yang 1 (YY1) is required for this transition, as conditional knockout of Yy1 in the hematopoietic system during fetal development results in exhaustion of fetal HSC pools and is associated with neonatal death. Yy1 deficient fetal HSCs have diminished capacity to migrate to and engraft the adult BM, and consequently fail to reconstitute blood. The genetic networks governing cell motility and adhesion are distinctly deregulated by YY1 knockout in fetal HSPCs. Notably, YY1 regulates mobility of fetal HSPCs largely through an indirect mechanism as it does not directly bind to the promoters of dysregulated genes involved in control of cell mobility. Instead, it regulates broader transcriptional mechanisms by regulating the genes in chromatin remodeling complexes and modulating chromatin accessibility that impact HSPC migration. Our study provides a framework to further decipher how temporal epigenomic configurations determine HSC fetal-to-adult transition during development.

overall_design: We performed ATAC-seq to characterize genome-wide chromatin accessibility in Yy1f/f (YY1 WT) and Yy1f/f Vav-Cre (YY1 KO) E14.5 mouse Lin- fetal liver cells. The experiment was designed to assess how YY1 control chromatin accesebility. Two independent biological replicates were prepared for each condition.


title: Genetic disruption of the baculum compromises the ability of male mice to copulate [ChIP-seq]

city: Los Angeles

first: Matthew

last: Dean

address: 1050 Childs Way, Rm #308

department: Molecular Biology

institute: University of Southern California

summary: The baculum, a bone in the penis of many mammal species, shows an astonishing level of morphological divergence between species. Despite hundreds of years of interest, biologists have been unable to directly test its function. The goal of the current study is to uncover molecular details that could allow selective disruption of the baculum while allowing normal sexual differentiation and skeletal development. We compare patterns of androgen receptor binding and single cell gene expression in the developing penis, forelimbs and hindlimbs of mice. We identified chondrocytes in all three tissue types, but those from the developing penis show several unique features, including a population of chondrocytes that express both Runt-related transcription factor 2 (Runx2) and Androgen receptor (Ar). By combining a Runx2-Cre allele with a floxed Ar allele in mice, we selectively knocked out androgen signaling in late chondrocytes, resulting in a range of defects in baculum morphology. Males with the most disrupted bacula were unable to copulate, and their bacula appears to be disconnected from the corpus cavernosum muscle. Our study provides insights into the diversity of molecular mechanisms leading to bone and offers the first opportunity to directly test the function of the baculum.

overall_design: Whole mouse penis (ages P6 and P13) and rat penis (age P2) tissue dissected and analyzed using ChIP-seq of the Androgen Receptor (AR)

first: Caleb

last: Ghione

first: Nicholas

last: Schultz

first: Sungdae

last: Park

first: Douglas

middle: B

last: Menke


title: Genetic disruption of the baculum compromises the ability of male mice to copulate [scRNA-seq]

overall_design: Whole penis, forelimb, and hindlimb tissue dissected and were analyzed using scRNA-seq


title: High throughput RNA-seq analysis in human primary chondrocytes treated with cyproheptadine and IL-1β

city: La Jolla

first: Padma

last: Natarajan

address: 10550 N.Torrey Pines Road

department: CCBB

institute: The Scripps Research Institute

summary: Osteoarthritis is the most common joint disease. Controlling the complex pathogenesis is challenging, thus disease-modifying OA drugs (DMOADs) are not available. We identified cyproheptadine as a potential DMOAD candidate and performed bulk RNA-seq to determine its effects on the transcriptome in human primary chondrocytes in the absence or presence of IL-1β.

overall_design: Human primary chondrocytes were treated with DMSO (control), cyproheptadine, IL-1β or cyproheptadine + IL-1β (n=5 per group) and total RNA was extracted for bulk RNA-seq.

first: Ichiro

last: Kurakazu

first: Merissa

last: Olmer

first: Hannah

last: Swahn

first: Martin

last: K Lotz


title: A specific gene expression program underlies antigen archiving by lymphatic endothelial cells in mammalian lymph nodes [GeoMx DSP]

city: Aurora

first: Ryan

last: Sheridan

state: CO

address: 12801 East 17th Avenue

institute: University of Colorado Anschutz Medical Campus

summary: Antigens from protein subunit vaccination traffic from the tissue to the draining lymph node, either passively via the lymph or carried by dendritic cells at the local injection site. Lymph node (LN) lymphatic endothelial cells (LEC) actively acquire and archive foreign antigens, and archived antigen can be released during subsequent inflammatory stimulus to improve immune responses. Here, we address questions of how LECs achieve durable antigen archiving and whether LECs with high levels of antigen express unique transcriptional programs. We used single cell sequencing in dissociated LN tissue and spatial transcriptomics to quantify antigen levels in LEC and dendritic cell populations at multiple time points after immunization. Our measurement of antigen location and levels over multiple immunizations confirms previous data showing antigen positive LEC-dendritic cell interactions. Increased antigen levels within LECs after a second immunization suggests that LEC antigen acquisition and archiving capacity can be improved over multiple exposures. Using machine learning we defined a unique transcriptional program within archiving LECs that predicted LEC archiving capacity in independent data sets. We validated this modeling, showing we could predict lower levels of LEC antigen archiving in chikungunya virus-infected mice and demonstrated in vivo the accuracy of our prediction. Collectively, our findings establish a unique transcriptional program in LECs that promotes antigen archiving and can be translated to other systems.

overall_design: Mice were vaccinated with ova-psDNA +VV 21 and/or 42 days prior to harvest, LNs were sectioned, gene expression and ova-psDNA levels were quantified using the Nanostring GeoMx DSP platform.

first: Beth

last: Tamburini

first: Jay

last: Hesselberth


title: Modeling the Human Immune Response to Severe Influenza Infection in an Immunocompetent Lung-on-Chip

city: Atlanta

first: Krishnendu

last: Roy

state: Georgia

address: 345 ferst drive NW, marcus nanotechnology building, room no 3102B, 3rd floor

department: IBB

institute: Georgia tech

summary: Severe influenza affects 3-5 million people worldwide each year, resulting in more than 300,000 deaths annually. However, standard-of-care antiviral therapeutics have limited effectiveness in these patients. Current preclinical models of severe influenza fail to recapitulate the human immune response to severe viral infection accurately. Here, we develop an immune-competent, microvascularized, human lung-on-chip device to model the small airways,   successfully demonstrating the cytokine storm, immune cell activation, epithelial cell damage, and other cellular- and tissue-level human immune responses to severe H1N1 infection. We find that IL-1β and TNF-α play opposing roles in the initiation and regulation of the cytokine storm associated with severe influenza. Furthermore, we discover the critical stromal-immune CXCL12-CXCR4 interaction and its role in immune response to infection. Our results underscore the importance of stromal cells and immune cells in microphysiological models of severe lung disease, describing a scalable model for severe influenza research. We expect the human lung-on-chip device  to enable critical discoveries in respiratory host-pathogen interactions, therapeutic side effects, vaccine potency evaluation, and crosstalk between systemic and mucosal immunity in human lung.

overall_design: Four samples each comprised of 10 pooled lung-on-chip devices. The lung-on-chip is an immune-competent, microvascularized model including human umbilical vein endothelial cells (HUVECs), normal human lung fibroblasts, small airway epithelial cells, intersitial macrophages, interstitial dendritic cells, airway macrophages, and RBC-depleted whole blood. The four samples represent (1) uninfected healthy control, (2) severe H1N1 infected devices (MOI=10) at 8 hours post infection, (3) severe H1N1 infected devices (MOI=10) at 24 hours post infection, and (4) severe H1N1 infected devices (MOI=10) at 48 hours post infection,

first: Rachel

last: Ringquist

first: Eshant

last: Bhatia

first: Paramita

last: Chatterjee

first: Drishti

last: Maniar

first: Zhou

last: Fang

first: Page

last: Franz

first: Liana

last: Kramer

first: Delta

last: Ghoshal

first: Neha

last: Sonthi

first: Emma

last: Downey

first: Joshua

last: Canlas

first: Abigail

last: Ochal

first: Savi

last: Agarwal

first: Valeria

last: Cuellar

first: Grace

last: Harrigan

first: Ahmet

last: Coskun

first: Ankur

last: Singh


title: A specific gene expression program underlies antigen archiving by lymphatic endothelial cells in mammalian lymph nodes [Xenium]

first: Ryan

last: Sheridan

overall_design: Mice were vaccinated with ova-psDNA +VV 21 and/or 42 days prior to harvest, LNs were sectioned, gene expression and ova-psDNA levels were quantified using the 10x Xenium platform.

first: Beth

last: Tamburini

first: Jay

last: Hesselberth


title: Chromatin factor YY1 controls fetal hematopoietic stem cell migration and engraftment in mice [RNA-seq]

first: Xuan

last: Pan

summary: Fetal liver is a major organ for generating hematopoietic stem cells (HSCs) during embryonic development. Many questions remain unanswered regarding how transition of hematopoiesis from the fetal liver to the bone marrow (BM) is regulated. We demonstrate that mammalian Polycomb Group (PcG) protein Yin Yang 1 (YY1) is required for this transition, as a conditional knockout of Yy1 in the hematopoietic system during fetal development results in exhaustion of fetal HSC pools and neonatal death. Yy1 deficient fetal HSCs have diminished capacity to migrate to and engraft the adult BM, and consequently fail to reconstitute blood. YY1 deficiency leads to distinct transcriptomic changes in fetal hematopoietic stem progenitor cells (HSPCs) compared with adult HSPCs. The genetic networks governing cell motility and adhesion are distinctly deregulated by YY1 in fetal HSPCs. Notably, YY1 regulates mobility of fetal HSPCs largely through an indirect mechanism as it does not directly bind to the promoters of dysregulated genes involved in control of  mobility. Instead, it regulates broader transcriptional mechanisms by modulating the genes in chromatin remodeling complexes that impact HSPC mobility. Our study provides a framework to further decipher how temporal epigenomic configurations determine HSC fetal-to-adult transition during development.

overall_design: A total of 8 samples were chosen for RNA sequencing (RNA-Seq), 4 from Yy1+/+ and 4 from Yy1-/- mice. Total RNA was purified from sorted E14.5 FL LK (Lin-c-Kit+ )cells. Yy1+/+ was used as a wild type control.


title: Chromatin factor YY1 controls fetal hematopoietic stem cell migration and engraftment in mice [CUT&Tag]

overall_design: Cleavage Under Targets and Tagmentation (CUT&Tag) targetting Yin Yang 1 (YY1) in E14.5 fetal liver Lin- cells. Trimethylation of Histone H3 at Lysine 4 (H3K4me3) was used as positive controls. To ensure reproducibility, four biological replicates were obtained to determine YY1 binding.


title: STING signaling in infiltrating macrophages mediates islet function in obesity

city: Shanghai

first: Haiyang

last: Hu

address: 320 Yueyang Road

institute: PICB

summary: The innate immune regulator stimulator of interferon genes (STING) mediates self-DNA sensing and leads to the induction of type I interferons and inflammatory cytokines, which promotes the progression of various inflammatory and autoimmune diseases. Innate immune system plays a critical role in regulating obesity-induced islet dysfunction, whereas the potential effect of STING signaling remains unclear. Here, we demonstrate that STING is mainly expressed and activated in islet macrophages upon high-fat diet (HFD) feeding. Knocking-out STING alleviates HFD-induced islet inflammation by inhibiting the expression of pro-inflammatory cytokines and infiltration of macrophages. Mechanically, palmitic acid incubation promotes mitochondrial DNA leakage into the cytosol and subsequently activates cyclic AMP-GMP synthase (cGAS)-STING pathway in macrophages. Additionally, STING activation in macrophages impairs glucose-stimulated insulin secretion by mediating the engulfment of β cell insulin secretory granules. Genetically or pharmacologically inhibiting STING activation boosts insulin secretion and hyperglycemia. Together, these findings reveal a regulatory mechanism in controlling the islet inflammation and insulin secretion in diet-induced obesity and suggest that selective blocking of the STING activation maybe a promising strategy for treating type 2 diabetes.

overall_design: Total RNA from DMXAA treated WT or STING KO islet cells were isolated and sequenced by deep sequencing using Illumina HiSeq 2500

first: Ze

last: Hong


title: scRNA-seq from abdominal and gluteofemoral subcutaneous adipose tissue derived stem cells (ADSC)

city: New York

first: Laszlo

last: Halasz

state: NY

address: 1470 Madison Avenue

department: Department of Oncological Sciences

institute: Mount Sinai Icahn School of Medicine

summary: Recent studies using single cell (sc) RNAseq, identified subpopulations of adipose derived stem cells (ADSCs) within the stroma vascular fraction of human adipose tissue, potentially leading to functionally distinct adipocyte populations. We aimed to extend this analysis by exploring the heterogeneity of the ADSCs within abdominal (ABD) vs gluteofemoral (GF) subcutaneous fat depots of apple and pear shaped pre-menopausal women. Using full-length SMART-seq scRNAseq technology and a panel of known stem cell and preadipocyte markers for identification, we detected 7 subpopulations of cells in both ABD and GF-ADSCs. Two ADSC subpopulations enriched the GF depot were characterized by increased expression of genes involved in cholesterol and fatty acid metabolism. Two subpopulations enriched in the ABD depot had gene expression signatures associated with inflammation and fibrosis. The body shape comparison revealed that apple-shaped women have a unique fibrotic ADSC subpopulation in their ABD depot and a high proportion of predicted highly proliferative preadipocytes in their GF depot. We propose that these depot and body shape specific ADSC populations could contribute to the metabolic complications associated with the differential fat distribution.

overall_design: Transcriptome of ADSCs isolated from abdominal and gluteofemoral adipose tissue from apple and pear-shaped women were studied by scRNAseq

first: S

last: Smith

first: T

middle: O

last: Osborne


title: Breasi-CRISPR Ccnd2 Thr280Ala mutation E13.5-E15.5 embryonic mouse cortex with CRISPR silent controls

status: Public on Jul 10 2025

city: Sioux Falls

first: Louis-Jan

last: Pilaz

state: SD

address: 2301 E 60th Street North

department: Pediatrics and Rare Disease

institute: Sanford Research

summary: The increasing availability and affordability of genetic testing has resulted in the identification of numerous novel variants associated with neurodevelopmental disorders. There remains a need for methods to analyze the functional impact of these variants. Some methods, like expressing these variants in cell culture, may be rapid, but lack physiologic context. Other methods, like making a whole mouse model may provide physiologic accuracy, but are costly and time consuming. We recently developed a technique, Breasi-CRISPR, which results in efficient genome editing of neural precursor cells via electroporation of CRISPR-CAS9 reagents into developing mouse brains. Since Breasi-CRISPR is extremely rapid, and enables the analysis of targeted genes in vivo, we wondered if this technique would accelerate the study of monogenic neurodevelopmental disorders. Here, we use Breasi-CRISPR to model megalencephaly postaxial polydactyly polymicrogyria hydrocephalus (MPPH) syndrome. We found that two days after Breasi-CRISPR, we were able to see neurodevelopmental phenotypes known to be associated with MPPH syndrome including increased cyclin D2 protein abundance and an increase in neural progenitor proliferation. Thus, Breasi-CRISPR can efficiently model MPPH syndrome, and may be a powerful method to add to the toolbox of those investigating the functional impact of patient variants in neurodevelopmental disorders.

overall_design: Breasi CRISPR in utero electroporation inserting the Ccnd2 Thr280Ala variant in embryonic mouse brains was performed at E13.5, and RNA from the transfected regions was collected at E15.5

first: Claire M

last: Kittock

first: Brandon L

last: Meyerink


title: A specific gene expression program underlies antigen archiving by lymphatic endothelial cells in mammalian lymph nodes [scRNA-seq]

overall_design: Mice were vaccinated with ova-psDNA +VV 21 and/or 42 days prior to harvest, LN cells were sorted for CD45- or CD45+ cells, gene expression and ova-psDNA levels were quantified using scRNA-seq.


title: Endoplasmic Reticulum Stress-Driven Nucleotide Catabolism Fuels Prostate Cancer

city: Oslo

first: Omer

middle: Faruk

last: Kuzu

address: Blindernveien 31

country: Norway

institute: Oslo University

summary: The study investigates the impact of MOCOS knockdown and ER stress on transcriptomic responses and purine metabolism. RNA-seq libraries were prepared using stranded RNA protocols and sequenced as 50 bp paired-end reads.

overall_design: RNA was extracted from prostate cancer cell lines (LNCaP and C4-2B) subjected to four experimental conditions: (1) vehicle-treated controls, (2) ER stress induction via thapsigargin (TG), (3) MOCOS knockdown via siRNA, and (4) combined MOCOS knockdown and TG treatment. Each condition was performed in biological replicates. Controls include siCTRL-treated cells with or without TG exposure.

first: Fahri

last: Saatcioglu

first: Ke

last: Deng

first: Yang

last: Jin

first: Nora

last: Pällmann

first: Marte

last: Livgård

first: Wanja

last: Kildal

first: Manohar

last: Pradhan

first: Ladan

last: Fazli

first: Paul

last: Rennie


title: Placental DNA methylation in normal and complicated pregnancies

city: Detroit

first: Adi

last: Tarca

state: MI

address: 3990 John R. St, 4 Brush South

institute: Wayne State University

type: Methylation profiling by genome tiling array

summary: DNA methylation, a partially reversible process, is critical in tissue development and aging. The discrepancy between biological age, as estimated from methylation, and chronological age has been proposed as a potential indicator of health and disease. Epigenetic age acceleration has been implicated as a contributing mechanism in obstetric conditions such as preeclampsia and small-for-gestational-age, yet future studies could benefit from more accurate models. Herein, we curated 1,842 placental methylomes from the public domain and organized a DREAM challenge to develop models that infer gestational age. Challenge participants were blinded to the test data that we generated from 384 placentas encompassing normal and complicated pregnancies. The mean absolute error of the top performing model (0.99 weeks of gestation) and of a post-challenge placental clock model (PCPC, 1.04 weeks) compared favorably to the accuracy of existing models. Moreover, predictions obtained with new models were better calibrated across the gestational age spectrum and suggest that previous reports of accelerated aging in preterm preeclampsia were likely due to modeling artifacts. Based on predictions from previous and newly developed epigenetic models we found that accelerated placental ageing was associated with a decrease in birthweight percentiles in male neonates delivered at term in our test cohort (about 10 birthweight percentiles drop per week of age acceleration for PCPC model, p<0.001). By contrast, preterm accelerated aging was protective against delivery of a small-for-gestational-age neonate regardless of fetal sex.

overall_design: The test set data was obtained from a study designed to compare the DNA methylome of placental tissues among various obstetrical syndromes. Samples were obtained from term controls (n = 82), preterm prelabor rupture of membranes (PPROM) (n = 76), preterm and term preeclampsia (PE) (n = 85), preterm labor (PTL) (n = 91), and pregnancies with small-for-gestational-age (SGA) fetuses (n = 50). Patients were enrolled in a study conducted at Wayne State University / Detroit Medical Center / Pregnancy Research Branch (NICHD). Participants provided written informed consent, and the collection and use of the samples and clinical data for research purposes were approved by the Institutional Review Boards of Wayne State University and the Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services. The raw methylation data included in this GSE series includes data from a subset of 18 patients who were asked and agreed to broad data sharing.

first: Gaurav

last: Bhatti

first: Roberto

last: Romero

first: Nardhy

last: Gomez-Lopez


title: Preclinical efficacy of tasquinimod-based combinations in advanced myeloproliferative neoplasms (MPN) in blastic phase

city: Houston

first: Xiaoping

last: Su

state: Texas

address: 7300 Brompton St, Apt 5633

institute: MD Anderson Cancer Center

summary: The alarmins, S100A8 (A8) and S100A9 (A9), are low molecular weight proteins belonging to the S100 protein family. A8 and A9 are secreted into the extracellular space and plasma, where they interact with TLR4 (Toll like receptor 4), RAGE (receptor for advanced glycation end products) and CD33. In present studies, we determined the preclinical efficacy of tasquinimod (TQ) against advanced MPN cell lines and patient-derived (PD) CD34+ blastic phase (BP, >5% blasts in PB) MPN cells. TQ induced loss of viability in cell lines and PD MPN-BP cells, but not in normal CD34+ progenitor cells. In TQ-treated PD MPN-AML cells, RNA-Seq analysis showed negative enrichment of the gene-sets of MYC and E2F targets, IL6-JAK-STAT3 signaling, and of inflammatory response. In phenotypically defined, PD, CD34+ MPN-BP stem progenitor cells, CyTOF analysis showed that TQ reduced expression of proteins including A8, A9, and MPO, while increasing expression of GFI1, p21 and cleaved PARP. Co-treatment with TQ and ruxolitinib or BET inhibitor induced synergistic lethality in advanced MPN-BP cells. Monotherapy with TQ significantly improved survival of immune-depleted NSG mice engrafted with PDX cells of MPN-AML. Notably, cotreatment with TQ and ruxolitinib or OTX015 induced significantly greater survival than treatment with single agents in the NSG mice engrafted with the PDX cells. These findings clearly demonstrate the preclinical efficacy of TQ in advanced MPN-BP cells and create the rationale to further interrogate the efficacy of TQ-based combinations with the current, front-line therapies or novel agents in advanced MPNs with excess blasts.

overall_design: Paired end RNA Seq of patient-derived post MPN sAML or cultured post-MPN cell line SET2 cells treated with tasquinimod for 16 hours. HS5 cells transfected with non-targeting siRNA or with TLR4 targeting siRNA with or without subsequent treatment with tasquinimod.

first: Warren

last: Fiskus

first: Kapil

last: Bhalla


title: Gtf2i-encoded transcription factor Tfii-i regulates myelination via Sox10 and Mbp regulatory elements

city: Tel-Aviv

first: Boaz

last: Barak

address: Chaim Levanon street, 55

institute: Tel-Aviv University

summary: The transcriptional regulatory network governing the differentiation and functionality of oligodendrocytes is essential for the formation and maintenance of the myelin sheath, and hence for the proper function of the nervous system. Perturbations in the intricate interplay of transcriptional effectors within this network can lead to a variety of nervous system pathologies. In this study, we have identified Gtf2i-encoded general transcription factor II-I (Tfii-i), as a regulator of key myelination-related genes. Gtf2i deletion from myelinating glia cells in mice led to functional alterations in CNS myelin, including elevated mRNA and protein expression levels of the central myelin component Mbp, enhanced connectivity properties, and thicker myelin wrapping axons with increased diameters. These changes resulted in faster axonal conduction across the corpus callosum, and improved motor coordination. In the PNS, Gtf2i deletion from Schwann cells led to hypermyelination of the tibial branch of the sciatic nerve. Furthermore, we show that, in myelinating oligodendrocytes, Tfii-i directly binds to regulatory elements of Sox10 and Mbp. These findings add to our understanding of myelination regulation and specifically elucidate a cell-autonomous mechanism for Tfii-i in myelinating glia transcriptional network.

overall_design: Cells were harvested from a primary OL-enriched cell culture derived from the cortices of control and Gtf2i-KO mice. Samples underwent ChIP-Seq protocol targeting Tfii-i

first: Gilad

last: Levy

first: Asaf

last: Marco


title: Reprogramming intratumoral Tregs by morpholino-mediated splicing of FOXP3 for cancer immunotherapy

city: New Haven

first: Chuanpeng

last: Dong

state: CT

address: 850 West Campus Dr

institute: Yale University School of Medicine

summary: Regulatory T cells (Tregs) represent a primary barrier to the development of effective anti-tumor immunity. In the clinic, Tregs are a major contributor to the resistance of immune checkpoint blockade (ICB). Preclinical studies have reported complete tumor regression upon Treg depletion in mice. However, systemic depletion of Tregs is detrimental and sometimes lethal as it causes immune-related adverse effects, such as autoimmune diseases. Here, we report that reprogramming Treg functions, by shifting the expression of FOXP3 from its full-length isoform (FOXP3FL) to a short isoform with exon 2 skipped (FOXP3dE2), promotes the tumor-killing activity of T effectors while limiting the adverse effects of Treg depletion. FOXP3dE2 mRNA expression in triple negative breast cancer tissue positively correlates with overall survival of the patients. Mice expressing only the FOXP3dE2 isoform are resistant to the development of various types of tumors, while the littermate wildtype (WT) mice expressing FOXP3FL isoform exhibit significant tumor growth. Intratumoral injection of FOXP3dE2-directing morpholino (dE2 MO) in WT mice markedly increased IFN-.+ CD4 and CD8 T cells in tumors and consequently inhibited the tumor growth. We developed a novel mouse strain with a humanized Foxp3 exon 2 capable of expressing both FOXP3 isoforms through alternative splicing. This mouse strain showed better antitumor immunity than WT mice and dE2 MO treatment can further enhance their antitumor activity. The antitumor activity of dE2 MO was also confirmed using autologous tumor-infiltrating T cells and patient-derived tumor organoids. Taken together, our results suggest that enhancing FOXP3dE2 isoform expression will reprogram tumor infiltrating Tregs and convert these immune suppressive Tregs to helper-like T cells, thus promoting antitumor immunity.

overall_design: EO771 cancer cells (1 million/mouse) were implanted orthotopically into the fourth mammary gland of 6- to 8-week-old female C57BL6 wildtype mice or Foxp3dE2 mice. Tumor infiltrating lymphocytes (TILs) were isolated at day 10 post tumor inoculations for single-cell sequencing and TCR sequencing.

first: Yujing

last: Li

first: Naresh

last: Singh

first: Xinna

last: Zhang

first: Baohua

last: Zhou

first: Xiongbin

last: Lu


title: Macrophage-derived oncostatin M repairs the lung epithelial barrier during inflammatory damage

city: Boston

first: Ruth

last: Franklin

state: MA

address: 77 Avenue Louis Pasteur

institute: Harvard Medical School

summary: Tissue repair programs must function alongside antiviral immunity to restore the lung epithelial barrier following infection. We found that macrophage-derived oncostatin M (OSM) counteracted the pathological effects of type I interferon (IFN- I) during infection and damage in mice. At baseline, OSM-deficient mice exhibited altered alveolar type II (ATII) epithelial cell states. In response to influenza or viral mimic challenge, mice lacking OSM exhibited heightened IFN-I responses and increased mortality. OSM delivery to the lung induced ATII proliferation and was sufficient to protect deficient mice against morbidity. Furthermore, OSM promoted organoid formation despite the growth- inhibitory effects of IFN- I. These findings identify OSM as an indispensable macrophage-derived growth factor that maintains the homeostasis of lung epithelial cells and promotes their proliferation to overcome IFN-I–mediated immunopathology.

overall_design: 8-12 week old Osm+/+ and Osm-/- female mice were intranasally with PBS or 225pfu of Influenza A Virus (A/WSN/33; H1N1). Lungs were harvested two days post-infection and digested with Dispase/Liberase/DNase mixture. A portion of the whole lung single cell suspension was stained with TotalSeq-B0301 (Biolegend, Catalog #155831) and TotalSeq-B0302 (Biolegend, Catalog #155833) for hash-tagging before encapsulation.

first: Baez Vazquez

last: Alan

first: Harry

last: Kane

first: Hoagland

last: Daisy

first: Rodriguez-Morales

last: Patricia

first: Mann

last: Alexander

first: Franklin

last: Ruth


title: Apelin as a CNS-specific Pathway for Fenestrated Capillary Formation in the Choroid Plexus

city: Marburg

first: Lukas

last: Herdt

address: Karl-von-Frisch-Straße 8

country: Germany

institute: Philipps-University Marburg

summary: The cerebral vasculature consists of a heterogenous network of blood vessel, including barrier-forming capillaries with blood-brain-barrier (BBB) properties and fenestrated capillaries specialized for molecular exchange.  While key pathways regulating BBB vessel formation have been identified, the mechanisms driving fenestrated vessel development remain unknown.  Here, we identify Apelin signaling as a critical, cell type-specific pathway required for the formation of fenestrated capillaries in the choroid plexus (CP), while being dispensable for angiogenesis and barriergenesis of adjacent BBB vessels.  Notably, apelin receptor b (aplnrb) expression closely mirrors that of the canonical fenestrated endothelium marker, plasmalemma vesicle-associated protein b (plvapb), highlighting aplnrb as a novel marker for the fenestrated endothelium.  Furthermore, we identify a population of undifferentiated pre-programmed leptomeningeal fibroblast as the Apelin source, regulating fenestrated vessel formation in the CP.  Utilizing a newly engineered APLNR-cpGFP conformational biosensor we map localized Apelin ligand hotspots across the brain, which guide the development of fenestrated blood vessels in the CP.  Collectively, our findings uncover a meningeal-vascular signaling axis that promotes fenestrated vessel formation in the CP and is essential for establishing cerebrovascular heterogeneity.

overall_design: At 48 hpf, heads of TgBAC(apln:Venus-PEST); Tg(kdrl:Hsa.HRAS-mCherry) larvae were dissected, disscociated and submitted to FACS sorting. Total RNA was isolated from (1) Venus positve, mCherry negative and (2) double negative FACS sorted cells and sent for bulk RNA sequencing using the SMARTseq2 method.

first: Stefan

last: Baumeister

first: Jeshma

last: Ravindra

first: Jean

last: Eberlein

first: Christian

last: Helker


title: TGF-β–mediated epithelial–mesenchymal transition of keratinocytes promotes fibrosis in secondary lymphedema

status: Public on Jul 09 2025

first: Bic

last: MSKCC

address: 1275 York Ave.

institute: Memorial SLoan-Kettering Cancer Center

summary: Secondary lymphedema is characterized by fibrosis and impaired lymphatic function. Although TGF-β is a key regulator of fibrosis in this disease, the cellular mechanisms regulating this process remain unknown. Epithelial-mesenchymal transition(EMT), a mechanism by which TGF-β induces fibrosis in other skin diseases, is characterized by loss of epithelial cell markers and cellular polarity, upregulation of fibrotic gene expression, and gain of migratory capacity. Using clinical lymphedema biopsy specimens and animal models, we show that keratinocytes in the basal layer of epidermis undergo EMT in lymphedematous skin, migrate into the dermis, and contribute to dermal fibrosis. In vitro studies using cultured primary human keratinocytes treated with lymphatic fluid from the affected limbs of patients with secondary lymphedema resulted in a TGF-β-mediated increased expression of EMT markers. We show for the first time that EMT is activated by TGF-β in secondary lymphedema and that this process plays an important role in regulating skin fibrosis in this disease.

overall_design: RNAseq profiling of four pairs of frozen clinical lymphedema biopsy specimens. The ribodepletion method was used for RNAseq. mRNA expression was standardized and analyzed. Standardized expression for each molecule was assessed and data are presented as Z-scores.

first: Hyeung Ju

last: Park

first: Jinyeon

last: Shin

first: Ananta

last: Sarker

first: Mark

last: Klang

first: Elyn

last: Riedel

first: Michelle

last: Coriddi

first: Joseph

last: Dayan

first: Sarit

last: Pal

first: Babak

last: Mehrara

first: Raghu

last: Kataru


title: Subfamily-Selective PCR primers for the Human LINE1 L1PA Lineage

city: Mainz

first: Marcel

last: Misak

address: Ackermannweg 4

institute: Institute of Molecular Biology (IMB)

summary: Long interspersed nuclear element-1 (LINE1) retrotransposons are classified into different subfamilies based on evolutionary history. For human biology, the L1PA lineage of LINE1s is particularly significant. This lineage contains both retrotransposition-competent and inactive subfamilies. PCR-based methods are widely used to monitor LINE1s in genomic DNA. However, PCR analysis distinguishing between L1PA lineage subfamilies of different evolutionary age is thus far challenging due to the difficulty to design primers that are sufficiently specific. Here, we developed and applied a workflow to design PCR primers that discriminate between different subfamilies of the L1PA lineage. Amplicon sequencing after PCR amplification of genomic DNA confirmed that the primers differentiate between groups of L1PA subfamilies of different evolutionary age. We validated the primers using RT-qPCR and verified consistency with publicly available RNA-seq data. Moreover, inhibition of DNA methyltransferase activity produced a dose-dependent increase in signals from primers selective for the younger subfamilies, consistent with transcriptional de-repression. These primers enable PCR-based surveys that can stratify expression, copy number or epigenetic modification for L1PA subfamilies of differing evolutionary age.

overall_design: Amplicon sequencing of LINE1 L1PA lineage subfamily-specific PCR primers using genomic DNA from human liver.

first: Amitava

last: Basu

first: Christof

last: Niehrs