title: Structure-Dependent Developmental Toxicity of Alkyl-Substituted Naphthalenes

city: Corvallis

first: Robyn

middle: Leigh

last: Tanguay

state: Oregon

address: 28645 east hwy 34

department: Environmental and Molecular Toxicology

institute: Oregon State University

summary: Naphthalene and its alkyl-substituted derivatives are among the most abundant polycyclic aromatic hydrocarbons (PAHs) in environmental and human exposure studies, yet their developmental toxicity and mode of action remain poorly understood due to challenges in testing of semi-volatile compounds. This study developed a vial based high through-put method to effectively assess the activity of naphthalenes and a set of 24 alkyl-substituted naphthalenes. Early life stage zebrafish were exposed to a concentration series of each chemical (0-50 µM) in rotating sealed glass vials to minimize volatilization. Benchmark concentration (BMC50) values were calculated for morphological endpoints and lowest effect levels were determined for behavioral effects. The data were assessed for evidence of a narcotic mode of action using body burden measurements for select chemicals and logKow modeling. Targeted transcriptomics at a single concentration and timepoint as well as in silico molecular docking were conducted to generate mode of action hypothesis. The vial method enabled detection of highly variable developmental toxicity not previously observed using standard 96-well plate exposures. LogKow and body burden were poor predictors of toxicity, suggesting a non-narcotic mode of action. Transcriptomic analysis revealed a limited but notable set of differentially expressed genes, with evidence for the disruption of glucocorticoid signaling pathways. Molecular docking identified potential protein targets (e.g., CYP1A2, NT5E, FOLR1) that may mediate observed effects. This study demonstrates the importance of appropriate exposure methods for semi-volatile compounds, reveals structure-dependent toxicity among alkyl-substituted naphthalenes, and provides a foundation for further mechanistic studies and improved risk assessment of alkyl-substituted PAHs.

overall_design: Zebrafish were exposed to 25 chemicals, naphthalene and 24 alkyl-sustituted naphthalenes, using a vial exposure method. Embryos were exposed to 20 uM of each chemical in groups of 8 in 2 mL of media in 2 mL glass vials from 6 hours post fertiliation (hpf) to 24 hpf. RNA was collected at at 48 hpf. Exposures, collections and extractions were conducted over two days. Targeted transcriptomics was preformed using the TempO-seq platform.

first: Mackenzie

last: Morshead

first: Lisa

last: Truong

first: Steven

last: Carrell

first: Richard

last: Scott

first: Kim

last: Anderson


title: Targeting LRBA triggers CTLA4 degradation and antitumor immunity for cancer immunotherapy

status: Public on May 23 2025

city: Shanghai

first: Xiaolu

last: Ge

state: Shanghai

address: 650 Xinsongjiang Road

country: China

institute: Shanghai General Hospital

type: Expression profiling by high throughput sequencing

summary: The lipopolysaccharide-responsive beige-like anchor protein (LRBA) deficiency causes severe autoimmune diseases and cytotoxic T-lymphocyte-associated protein 4 (CTLA4) loss in humans. However, the impact of LRBA on antitumor immunity remains understudied. Here, we identified the role of LRBA in antitumor immunity and developed a novel immunotherapy  for cancers. Interestingly, LRBA was negatively associated with antitumor immunity in human patients. Using high-throughput screening and subsequent structure-based hit optimization, we discovered a small molecule LC427 that bound directly to LRBA, and selectively interfered with the LRBA-CTLA4 interaction. This mechanistically unique LC427 facilitated the lysosomal degradation of CTLA4, and bolstered survival and functions of activated T cells. Importantly, orally administrated LC427 increased tumor-infiltrating CD8+ T cells and displayed effective antitumor activity in tumorbearing mouse models. Notably, LC427 did not induce typical irAEs observed with immune checkpoint inhibitors in colitis models. Our study demonstrates that targeting LRBA offers a novel and effective strategy with a favorable safety profile, highlighting the potential of LRBA-based immunomodulatory therapies in the treatment of cancers.

overall_design: MC38 cells (2×105) were implanted in C57BL/6 female mice. Mice were treated with LC427 or not. On day 14, tumors from mice treated with LC427 or not were harvested. Then, tumor tissues were cut into pieces, followed by enzymatic digestion using 0.5 mg/mL collagenase type IV (Roche) and 100U/mL DNase I (Aladdin, China) solution, and were incubated on a shaker (300 rpm) for 30 minutes at 37℃. The digested tissues were homogenized by passage through a 70 μm filter and centrifuged for 15 minutes at 4℃ and 400g. The dead cells were removed from single-cell pellets using  the dead cell removal microbeads (Miltenyi, Germany) and CD45 positive cells were collected with CD45 MicroBeads (Miltenyi, Germany). The CD45 positive cells were  analyzed using scRNA-seq.

first: Liang

last: Yu

first: Lei

last: Zhang

first: Liqing

last: Jia

first: Mingjing

last: Meng

first: Jingquan

last: He

first: Fan

last: Bu

first: Yue

last: Song

first: Gaorui

last: Sun

first: Shiming

last: Lv

first: Desheng

last: Mei

first: Yutao

last: Yang

first: Dakang

last: Xu

first: Jingfa

first: Shengping

first: Chuangui

last: Wang

first: Deshui

last: Gao

first: Xiangliang

last: Yuan

first: Baokun


title: Single-Cell Profiling of Neutrophil Gene Expression in the Mouse Colon following TNBS-induced Colitis

status: Public on May 22 2025

city: Dublin

first: Marina

last: Ainciburu

state: Dublin

address: Foster Avenue

department: Bioinformatics

country: Ireland

institute: NIBRT

summary: Neutrophil infiltration is hallmark of chemically induced colitis and inflammatory bowel disease (IBD). We used single-cell RNA sequencing to analyze heterogenity in infiltrated colonic neutrophil population in presence and absence of microbiota, or when DUOX2 in inactivated in neutrophils.

overall_design: Mice were treated with 2.5% TNBS intrarectally, and colon was collected after 48 h (day2). Viable neutrophils were purified using FACS (CD11b+, Ly6G+, DRAQ7-) followed by scRNA analysis.

first: Ashish

middle: K

last: Singh

first: Ulla

middle: G

last: Knaus


title: Targeting VRK2 Enhances the Efficacy of Anti-PD-1 Therapy in Hepatocellular Carcinoma by Reducing Direct Phosphorylation and Stability of MYC: CUT-TAG sequencing for MYC in hepatocellular carcinoma cells

city: Wuhan

first: chen

last: su

address: No. 1095, Jiefang Avenue

institute: Huazhong University of Science and Technology

type: Genome binding/occupancy profiling by high throughput sequencing

summary: VRK2–MYC axis, a transcription-dependent regulatory axis, could be a prognostic indicator and potential therapeutic target in liver cancer.

overall_design: Cleavage Under Targets and Tagmentation (CUT&TAG) sequencing was then performed on MYC in cells from different treatment groups,

first: Chen

last: Su

first: Zhibin

last: Liao

first: Jie

last: Mo

first: Furong

last: Liu

first: Zhanguo

last: Zhang

first: Peng

last: Zhu

first: Bixiang


title: Development of early-stage alpha-synucleinopathy is not governed by myelin status in mice of either sex

status: Public on May 20 2025

city: Pittsburgh

first: Rehana

last: Leak

state: PA

address: 600 Forbes Ave

department: Pharmacology

country: USA

institute: Duquesne University

summary: Lewy body disorders are characterized by alpha-synucleinopathic inclusions that tend to develop in neurons extending long, thin, and unmyelinated fibers. It is unknown if this selective vulnerability reflects poor myelination per se. We have observed that preformed fibrils (PFFs) of alpha-synuclein tend to induce pathology in gray matter, even when infused into regions penetrated by white matter bundles. In addition, we found that levels of insoluble, hyperphosphorylated alpha-synuclein correlate inversely with myelin markers in the postmortem amygdala of men—but not women—with Lewy body disease. Thus, we tested if myelin disruption with pharmacologic or genetic tools exacerbates alpha-synucleinopathic lesions in a model of early-stage, limbic Lewy body disease. In genetically outbred CD-1 mice infused with PFFs in the caudal olfactory bulb, the myelin-disruptor cuprizone caused subtle exacerbation of α-synucleinopathy, but without impacting PFF-induced neuron loss or behavior deficits. Furthermore, in C57BL/6J mice heterozygous for myelin basic protein (Mbp+/shi), PFF-induced increases in the insolubility and hyperphosphorylation of alpha-synuclein were not amplified and histological outcomes were not markedly exacerbated. Given our observations of inverse correlations between α-synucleinopathy and myelin markers in the human male amygdala, Lewy body disease may disrupt myelination, rather than poor myelination status regulating the emergence of limbic α-synucleinopathy. This new perspective is reinforced by suppressed expression of select oligodendrocytic markers in the amygdalae of men with Lewy body disease compared to women. Thus, resilient neurons may defy the initial development of Lewy-related pathologies due to properties unrelated to myelination per se.

overall_design: RNA-seq profiling of human olfactory bulb and amygdala samples from patients with Lewy body disorders or age-matched controls, from the NIH NeuroBioBank, where the same IDs can be searched on their portal for more deidentified patient information

first: Rachel

middle: N

last: Clark

first: Reese

middle: E

last: Landes

first: Muslim

last: Abbas

first: Victoria

last: Mistretta

first: Kieran

middle: A

last: DeLoatch

first: Jun

last: Chen

first: Kelvin

middle: C

last: Luk

first: Xiaoming

last: Hu


title: Deep mutational scanning of the human insulin receptor ectodomain to inform precision therapy for insulin resistance

status: Public on May 27 2025

city: Edinburgh

first: Vahid

last: Aslanzadeh

address: Crewe Road

department: Human Genetics Unit

country: United Kingdom

institute: The University of Edinburgh

summary: The insulin receptor (INSR) entrains tissue growth and metabolism to nutritional conditions. Complete loss of function in humans leads to extreme insulin resistance and infantile mortality, while loss of 80-90% function permits longevity of decades. Even low-level activation of severely compromised receptors, for example by anti-receptor monoclonal antibodies, thus offers the potential for decisive clinical benefit. A barrier to genetic diagnosis and translational research is the increasing identification of INSR variants of uncertain significance. We employed saturation mutagenesis coupled to multidimensional flow-based assays to stratify approximately 14,000 INSR extracellular domain missense variants by cell surface expression, insulin binding, and insulin- or monoclonal antibody-stimulated signaling. The resulting function scores correlate strongly with clinical syndromes, offer insights into dynamics of insulin binding, and reveal novel potential gain-of-function variants. This INSR sequence-function map has high biochemical, diagnostic and translational utility, aiding rapid identification of variants amenable to activation by non-canonical INSR agonists.

sample_organism:
Escherichia coli
Mus musculus

platform_organism:
Escherichia coli
Mus musculus

overall_design: This study aimed to assess the impact of INSR variants on human insulin receptor surface expression, insulin binding, and insulin signalling. Additionally, it explored whether certain damaging variants could be activated by antibodies.  To achieve this, saturation mutagenesis was performed on the INSR gene, generating a library of variants, each linked to a unique barcode sequence via PacBio sequencing. This variant library was then transfected into MEF cells and screened using FACS sorting into four bins based on their effects on receptor expression, insulin binding, and signalling. Cells from each bin were collected and subjected to Illumina sequencing to determine the frequency of each barcode in each bin. These frequencies, combined with the PacBio data, were used to calculate a functional score for each variant.

first: Gemma

middle: V

last: Brierley

first: Rupa

last: Kumar

first: Hasan

last: Çubuk

first: Corinne

last: Vigouroux

first: Kenneth

last: Matreyek

first: Grzegorz

last: Kudla

first: Robert

last: Semple


title: Nuclear functions of CFAP20 in transcription and replication [TTchem-DRB-seq]

city: Leiden

first: Martijn

middle: S.

last: Luijsterburg

state: zuid-holland

address: Einthovenweg 20

department: Human Genetics

country: Netherlands

institute: LUMC

summary: Fine-tuning DNA replication and transcription is crucial to prevent collisions between their machineries. This is particularly important near promoters, where RNA polymerase II (RNAPII) initiates transcription and frequently arrests, forming R-loops. Arrested RNAPII can obstruct DNA replication, which often initiates near promoters. The mechanisms that rescue arrested RNAPII during elongation to avoid conflicts with co-directional replisomes remain unclear. Here, using genome-wide approaches and genetic screens, we identify CFAP20 as part of a protective pathway that salvages arrested RNAPII in promoter-proximal regions, diverting it from the path of co-directional replisomes. CFAP20-deficient cells accumulate R-loops near promoters, which leads to defects in replication timing and dynamics. These defects stem from accelerated replication-fork speeds that cause a secondary reduction in origin activity. Co-depletion of the Mediator complex or removal of R-loop-engaged RNAPII restores normal replication. Our findings suggest that transcription-dependent fork stalling in cis induces accelerated fork progression in trans, generating single-stranded DNA gaps. We propose that CFAP20 facilitates RNAPII elongation under high levels of Mediator-driven transcription, thereby preventing replisome collisions. This study provides a transcription-centred view of transcription-replication encounters, revealing how locally arrested transcription complexes propagate genome-wide replication phenotypes and defining CFAP20 as a key factor that safeguards genome stability.

overall_design:
To explore the role of CFAP20 in transcription elongation, we mapped nascent transcription after release from DRB treatement, using TTchem-DRB-seq in RPE1 cells being either wild type (WT) or CFAP20-KO.

NOTE: The records have been updated for data processing steps, contributor lists, replacement/addition of processed data files on May 30, 2025.

first: Sidrit

last: Uruci

first: Daphne

last: Boer

first: Paul

middle: W

last: Chrystal

first: Maxime

last: Lalonde

first: Andreas

last: Panagopoulos

first: George

last: Yakoub

first: Idil

last: Kirdök

first: Klaas

last: de Lint

first: Melanie

last: van der Woude

first: Tiemen

last: Wendel

first: Sem

middle: J

last: Brussee

first: Annelotte

middle: P

last: Wondergem

first: Nila

last: van Overbeek

first: Nini

last: Schotman

first: Jolanthe

last: Lingeman

first: Mats

last: Ljungman

first: Alexander

last: van Oudenaarden

first: Haico

last: van Attikum

first: Alfred

last: Vertegaal

first: Sylvie

middle: M

last: Noordermeer

first: Rob

last: Wolthuis

first: Matthias

last: Altmeyer

first: Stephan

last: Hamperl

first: Vincent

last: Tropepe

first: Jeroen

last: van den Berg

first: Diana

last: van den Heuvel

middle: S


title: Interlocking core regulatory circuits enable viral hijacking in Merkel cell carcinoma

status: Public on May 24 2025

city: Bethesda

first: Javed

last: Khan

state: MD

address: 37 Convent Dr.

department: Genetics Branch

institute: NCI, NIH

summary: Merkel Cell carcinoma (MCC) is an aggressive neuroendocrine skin cancer. The conditions and cell type(s) of MCC are unknown. Virus positive MCC (VP-MCC) is driven by T antigens expressed from integrated Merkel cell polyomavirus (MCPyV). We found that VP-MCC required lineage-specific neuroendocrine transcription factors (TFs), including ATOH1, INSM1, ISL1, LHX3, POU4F3, and SOX2 that were central to core regulatory (CR) transcriptional circuitry. MCPyV small T antigen and host CR TFs co-bound VP-MCC super enhancers while T antigen expression was directly regulated by LHX3 and ISL1, establishing an interlocking network between host CR circuitry and the oncovirus. Moreover, MCPyV integration sites were enriched near VP- MCC super enhancers, further suggesting a functional relationship between viral oncogenesis and core neuroendocrine circuitry.

overall_design: Genome-wide profiles for histone marks, DNase hypersensitivity, transcription factors, and 3D loops of active chromatin (AQuA-HiChIP).

first: Berkley

last: Gryder

first: Xinyu

last: Wen


title: Dendritic cell iron overload exacerbates acetaminophen hepatotoxicity

city: Kumamoto

first: Toshiro

last: Moroishi

address: 1-1-1 Honjo, Chuo-ku

country: Japan

institute: Kumamoto University

summary: Liver immune homeostasis relies on the coordinated actions of various immune cells including dendritic cells (DCs), which exert regulatory roles in both innate and adaptive immunity. Various pieces of evidence demonstrate that the properties of immune cells are highly influenced by iron metabolism. However, the roles of iron metabolism on DC function remain poorly understood. Here, we show that mice with iron overload in DCs displayed worsening of liver injury and mortality in acetaminophen (APAP) -induced acute hepatitis. Enhanced neutrophil infiltration was observed in these mice during the progression of liver injury. DCs with iron overload showed increased expression of the neutrophil-attracting cytokine IL-6, thereby accelerating liver injury. Mechanistic studies revealed that iron enhanced the recruitment of NF-κB to the IL-6 promoter upon TLR4 activation. Our findings provide an insight into the regulatory mechanisms by which iron metabolism influences DC function. This study also highlights the critical role of the DC-IL-6-neutrophil axis in acute liver injury.

overall_design: RNA sequencing on whole livers from control and FBXL5ΔDC mice without APAP treatment and those treated with APAP for 6 hours.

first: Saisai

last: Liu

first: Yohei

last: Kanamori

first: Yanliang


title: Targeting VRK2 Enhances the Efficacy of Anti-PD-1 Therapy in Hepatocellular Carcinoma by Reducing Direct Phosphorylation and Stability of MYC，CUT-TAG sequencing for MYC in hepatocellular carcinoma cells

first: chen

last: su

overall_design: Identify downstream target genes regulated by VRK2 or MYC in MHCC97H cells using whole transcriptome sequencing (RNA-Seq). The expression of MYC or VRK2 was interfered with using siRNA in MHCC97H

first: Chen

last: Su

first: Zhibin

last: Liao

first: Jie

last: Mo

first: Furong

first: Zhanguo

last: Zhang

first: Peng

last: Zhu

first: Bixiang


title: Nuclear functions of CFAP20 in transcription and replication [DRIP-seq]

first: Martijn

last: Luijsterburg

overall_design:
To explore the role of CFAP20 in R-loop resolution, we performed DRIP-seq experiments in RPE1 cells being either wild type (WT) or CFAP20-KO.
NOTE: The records have been updated for data processing steps, contributor lists, replacement/addition of processed data files on May 30, 2025.

first: Sidrit

last: Uruci

first: Daphne

last: Boer

first: Paul

last: Chrystal

first: Maxime

last: Lalonde

first: Andreas

last: Panagopoulos

first: George

last: Yakoub

first: Idil

last: Kirdök

first: Klaas

last: de Lint

first: Melanie

last: van der Woude

first: Tiemen

last: Wendel

first: Sem

last: Brussee

first: Annelotte

last: Wondergem

first: Nila

last: van Overbeek

first: Nini

last: Schotman

first: Jolanthe

last: Lingeman

first: Mats

last: Ljungman

first: Alexander

last: van Oudenaarden

first: Haico

last: van Attikum

first: Alfred

last: Vertegaal

first: Sylvie

last: Noordermeer

first: Rob

last: Wolthuis

first: Matthias

last: Altmeyer

first: Stephan

first: Vincent

first: Jeroen


title: Nuclear functions of CFAP20 in transcription and replication [ChIP-seq]

first: Martijn

last: Luijsterburg

overall_design:
To explore spatial connections between transcription and replication at the genome-wide level, as well as the role of CFAP20 in these processes, we mapped RNA polymerase II (RNAPII) and CFAP20  occupancy using chromatin immunoprecipitation (ChIP)-seq, nascent transcription by bromouridine (BrU)-seq and TTchem-seq, and R-loops by DNA-RNA hybrid immunoprecipitation (DRIP)-seq in RPE1 cells being either wild type (WT), CFAP20-KO, CFAP20-KO rescued with CFAP20-GFP, or CFAP20/CCNC-dKO.
NOTE: The records have been updated for data processing steps, contributor lists, replacement/addition of processed data files, additional sample records on May 30, 2025.

first: Sidrit

last: Uruci

first: Daphne

last: Boer

first: Paul

last: Chrystal

first: Maxime

last: Lalonde

first: Andreas

last: Panagopoulos

first: George

last: Yakoub

first: Idil

first: Klaas

first: Melanie

last: Hamperl

last: Tropepe

last: van den Berg

first: Diana

last: van den Heuvel


title: Immune cell type divergence in a basal chordate

city: Boston

first: Tal

middle: Deborah

last: Scully

state: MA

address: 200 Longwood Ave

department: Systems Biology

institute: Harvard Medical School

summary: Evolutionary adaptations often occur at the level of cell types and cellular function. Innate immune cells are a promising system for studying cell type evolution, as they are widespread across metazoans, have several conserved functions, and are under selective pressure from pathogens. However, molecular characterizations of invertebrate immune cells are limited, and it remains unclear whether invertebrate immune cell types are homologous to those in vertebrates. Here we use single-cell RNA sequencing, in situ hybridization, and live reporters to define the identity of blood cell states from a basal chordate, Ciona robusta. We find evidence that C. robusta circulating blood contains a differentiation hierarchy that gives rise to at least eight major morphotypes, constituting approximately half of mature blood cell states. The mature cell states include phagocytes, as well as cells variously expressing vanadium-binding proteins, carbonic anhydrases, pattern recognition receptors, cytokines, and complement factors. Despite the expression of homologs to vertebrate immune components, extensive divergence between tunicate and vertebrate immune cells obscures cell state homology. Altogether, this work modernizes blood cell classifications in C. robusta and extends the known repertoire of immune cells within chordates.

overall_design:
Circulating blood cells were collected from adult Ciona robusta animals, then run directly and analyzed with scRNA-seq. Two libraries were collected in this study, and they were combined with one library from a previous study for analysis (reanalysis of Sample GSM8869531 from Series GSE292926). This combined data (combined_processed_data.h5ad, an H5ad Hierarchical Data Format file) was reanalyzed by removing likley doublets, normalizing across all libraries, identifying of highly variable genes, log normalizing, z-scoring, performing PCA on highly variable genes, batch correcting using BBKNN, Leiden clustering, and UMAP embedding. Additionally, cells from all samples were assigned to SNP profiles using Cellsnp-lite and Vireo. In the combined_processed_data.h5ad, adata.obs['library'] indicates which cell barcodes are associated with each library: 230518_1 and 230518_2 are from this GEO Series (Cr_blood_230518_1 and Cr_blood_230518_2, respectively), and 220428_1 is the reanalyzed Sample GSM8869531 from Series GSE292926.

***************************************************************
The table below lists GEO accessions reused/reanalyzed for this study.
***************************************************************

middle: D

first: C. J.

last: Pickett

first: Nicolas

last: Gort-Freitas

first: Bradley

last: Davidson

first: Allon

last: Klein


title: Nuclear functions of CFAP20 in transcription and replication [BrU-seq]

overall_design:
To explore spatial connections between transcription and replication at the genome-wide level, as well as the role of CFAP20 in these processes, we mapped RNA polymerase II (RNAPII) and CFAP20 occupancy using chromatin immunoprecipitation (ChIP)-seq, nascent transcription by bromouridine (BrU)-seq and TTchem-seq, and R-loops by DNA-RNA hybrid immunoprecipitation (DRIP)-seq in RPE1 cells being either wild type (WT), CFAP20-KO, CFAP20-KO rescued with CFAP20-GFP, or CFAP20/CCNC-dKO.

NOTE: The records have been updated for data processing steps, contributor lists, replacement/addition of processed data files on May 30, 2025.

last: Kirdök

last: de Lint

last: van der Woude

first: Tiemen

last: Wendel

first: Sem

last: Brussee

first: Annelotte

last: Wondergem

first: Nila

last: van Overbeek

first: Nini

last: Schotman

first: Jolanthe

last: Lingeman

first: Mats

last: Ljungman

first: Alexander

last: van Oudenaarden

first: Haico

last: van Attikum

first: Alfred

last: Vertegaal

first: Sylvie

last: Noordermeer

first: Rob

last: Wolthuis

first: Matthias

last: Altmeyer

first: Stephan

first: Vincent

first: Jeroen


title: Abundant piRNAs beyond transposon regulation drive germ cell formation and transgenerational piRNA inheritance in Drosophila

status: Public on May 21 2025

first: Shingo

last: Usuki

address: 2-2-1 Honjo, Chuo-ku

department: Institute of Molecular Embryology and Genetics (IMEG)

summary: Germ cells transmit genetic information to offspring and maintain the genome of the species. In many animals including Drosophila, germ cell formation relies on maternal determinants in the germ plasm. Several proteins present in the germ plasm of oocytes also localize to the perinuclear nuage in nurse cells, where they contribute to the production of PIWI-interacting RNAs (piRNAs). These piRNAs guide the silencing of transposons, thereby protecting the germline genome from invading mobile elements. Aubergine (Aub) is a germ plasm/nuage protein and a piRNA-directed endonuclease that inactivates transposons. Aub is also essential for germ plasm assembly. The Aub-bound piRNAs in the germ plasm are inherited by the progeny germline and serve as templates for piRNA biogenesis in the next generation. Thus, piRNA production in the nurse cell nuage is thought to be coordinated with germ plasm assembly in the oocyte. However, the underlying mechanism remains unclear. Here, we report that a maternal factor, named tiny pole plasm (tpp), mediates this coordination. In tpp– ovaries, the production of piRNAs, particularly Aub-bound piRNAs, is defective, resulting in reduced Aub localization to the germ plasm and impaired germ cell formation. Notably, the levels of piRNA production required for proper germ plasm activity are much higher than those required for transposon silencing. We propose that the production of abundant piRNAs beyond what is required for transposon silencing in the ovary ensures the transgenerational inheritance of anti-transposon information to progeny via the germ plasm, which is essential for the survival of species.

overall_design: We performed RNA-seq analysis of ovaries from control yw, tpp, aub, 38C∆ 42AB∆, tpp 38C∆ 42AB∆ flies. The reads were aligned to the canonical transposon sequences in the Drosophila genome.

first: Hirono

last: Kina

first: Natsuko

last: Izumi

first: Kazuko

last: Hanyu-Nakamura

first: Takashi

last: Yoshitani

first: Mariko

last: Yamane

first: Hitoshi

last: Niwa

first: Yukihide

last: Tomari

first: Akira

last: Nakamura


title: Nuclear functions of CFAP20 in transcription and replication

first: Martijn

last: Luijsterburg

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

overall_design: Refer to individual Series


title: In vivo response of the transcriptome of human immune cells to vitamin D3 supplementation in a cohort of 45 individuals

city: Olsztyn

first: Carsten

last: Carlberg

state: Warmia-Mazury

address: Tuwima 10

department: Food Technology

country: Poland

institute: Institute of Animal Reproduction and Food Research, Polish Academy of Sciences

summary: In this study, we analyse the in-vivo modulation of the transcriptome of human PBMCs by a bolus of vitamin D3 (1000 IU/kg) over 24 hours.

overall_design: PBMCs of 45 healthy individuals were collected directly before and 24 h after an in-vivo intake of a single large bolus of 1000 IU/kg of vitamin D3. Analysis was performed on the cohort to identify vitamin D target genes.

first: Ranjini

last: Ghosh Dastidar


title: Effects of Acetylcholine and Porphyromonas gingivalis on Oral Epithelial Cells

city: Guangdong

first: Shihan

last: Xu

address: North Campus, Sun Yat-Sen University, No. 74, 2nd Yat-Sen Road/Street, Yuexiu District, Guangzhou City

institute: Sun Yat-sen University

summary: Periodontitis patients exhibit significant upregulation of the cholinergic signaling pathway in gingival epithelial cells, accompanied by elevated acetylcholine (ACh) levels in saliva. However, the role of ACh in the pathogenesis of periodontitis remains unclear.  P. gingivalis, a keystone pathogen in periodontitis, triggers host inflammatory responses and compromises the epithelial barrier function. As the first line of defense against pathogens, the reparative capacity of the oral epithelium critically influences the progression of periodontitis. This study investigates whether ACh modulates P. gingivalis-induced inflammatory responses and epithelial repair in human oral keratinocytes (HOKs), aiming to elucidate the mechanistic role of cholinergic signaling in periodontitis.

overall_design: The HOK cells were treated differently for 2 hours after starvation: ACh group: Treated with ACh (100 nM) Pg group: Stimulated with Pg (MOI = 50) PA group: Treated with Pg + ACh NC group: Control

first: Jiaxin

last: Guo

first: Shiwen

last: Yang

first: Bin

last: Cheng

first: Juan

last: Xia


title: Lymphotropic Virotherapy Engages DC and High Endothelial Venule Inflammation to Mediate Cancer In Situ Vaccination

city: Durham

first: Matthias

last: Gromeier

state: NC

address: 203 Research Dr

department: Neurosurgery

institute: Duke University

summary: Intratumor (IT) inoculation of the rhino:poliovirus chimera, PVSRIPO, yielded objective radiographic responses with long-term survival in 20% of patients with recurrent glioblastoma (rGBM). PVSRIPO infects dendritic cells (DCs) and sets up non-cytopathogenic viral (v)RNA replication, which triggers sustained type-I IFN (IFN-I) signaling and antitumor T cell priming. Here we identify IFN-I signaling in glioma-draining cervical lymph nodes (cLN) as a mediator of polio virotherapy. Transient IFN-I signaling after IT therapy was rescued by cervical perilymphatic injection (CPLI) of PVSRIPO, targeting cLN directly. Dual-site (IT+CPLI) PVSRIPO induced profound inflammatory reprogramming of cLN, enhanced vRNA replication and IFN-I signaling in DCs and High Endothelial Venules (HEV), augmented anti-glioma efficacy in mice, and was associated with T cell activation in rGBM patients. A Ph2 clinical trial of IT+CPLI PVSRIPO is ongoing (NCT06177964). This work implicates the lymphatic system as a novel virotherapy target and demonstrates the CPLI concept to complement brain tumor immunotherapy.

overall_design: hCD155tg C57BL/6 mice were implanted with CT2A glioma cells and treated with immunotherapeutic human rhinovirus-poliovirus chimera PVSRIPO in one of four combinations of mock or RIPO intratumorally (IT, 7 and 10 days post implantation) and paralymphatically (CPLI, 10 and 13 days post implantation) with deep and superficial cervical lymph nodes harvested for RNA sequencing.

first: Andrea

middle: L

last: Ludwig

first: Zachary

last: McKay

first: Griffin

last: Carter

first: Mark

last: Katz

first: Georgia

last: Howell

first: Vaibhav

last: Jain

first: Stephanie

last: Arvai

first: Dirk

last: Dittmer

first: Darell

last: Bigner

first: David M

last: Ashley

first: Madison

last: Shoaf

first: Annick

last: Desjardins

first: Simon

last: Gregory

first: Michael

last: Brown


title: Transcriptional stratification of necrotizing enterocolitis identifies distinct disease subtypes

status: Public on May 19 2025

city: Seoul

first: Murim

last: Choi

address: 103 Daehakro, Jongrogu

country: South Korea

institute: Seoul National University

summary: Necrotizing enterocolitis (NEC) is a severe inflammatory disorder of the intestine that affects neonatal babies, with a mortality rate of 30–50%. Despite the severe nature of the disease, its rare incidence and early onset prevent further understanding of its etiology and the development of treatment strategies. To further understand the pathogenic mechanism of this disease, we subjected intestinal tissues from ten NEC patients and three control individuals to RNA-sequencing. Clustering of the affected tissues revealed three clusters, each with a distinct transcriptional profile characterized by the expression of genes enriched in inflammatory pathways related to lipid binding and no obvious expression signature. The three subtypes displayed distinct gene expression patterns specific to the cell types composing the small intestine layers. Our results elucidate the genetic rationale underlying patient-specific symptoms, prognosis.

overall_design: RNA-seq profiling of Necrotizing enterocolitis patients and non-NEC patients

first: Jean

last: Lee

first: So Hyun

last: Nam

first: Da young

last: Ko

first: Joong kee

last: Youn

first: Jaemoon

last: Koh

first: Hee Beom

last: Yang

first: Hyun-Young

last: Kim


title: Polyploid cisplatin-resistant cancer cells have altered nuclear organization and epigenomic status

city: Baltimore

first: Sarah

middle: R

last: Amend

address: 600 N Wolfe St

department: Brady Urological Institute

institute: Johns Hopkins University

summary: Chemotherapy resistance remains a critical barrier in cancer treatment, partly driven by polyploid cells that survive therapy and contribute to tumor recurrence. Here, we investigated epigenomic and transcriptional changes associated with cisplatin-surviving polyploid cells compared to parental cancer cells in prostate cancer (PC3) and triple-negative breast cancer (MDA-MB-231) cell lines. We observed persistent dysregulation of chromatin compaction and altered nuclear structure in polyploid cells following cisplatin treatment. Genome-wide chromatin accessibility profiling via ATAC-seq revealed significant remodeling, notably decreased promoter accessibility at proliferation-associated loci and increased accessibility of distal regulatory elements linked to inflammation and stress response. RNA-seq analyses demonstrated a coordinated transcriptional shift away from proliferative signatures toward inflammatory and survival pathways, including activation of NFκB, interferon response, and integrated stress response pathways. Importantly, we identified subsets of genes showing concordant changes in promoter accessibility and transcriptional activity, directly linking chromatin remodeling to transcriptional reprogramming. These integrated findings highlight the role of chromatin dynamics and epigenetic plasticity in chemotherapy resistance, demonstrating that widespread chromatin accessibility changes facilitate the transition to a stress-adapted, polyploid cell state. This study provides new insights into the molecular mechanisms supporting cancer cell persistence after chemotherapy.

overall_design: PC3 (prostate cancer cell line) were treated with cisplatin and surviving cells were analyzed 1, 5 and 10 days following chemotherapy (DPT). PC3 cells were treated with docetaxel and surviving cells were analyzed 1, 5, 10 days following chemotherapy. SIngle cell RNA sequencing was performed on untreated cell lines and surviving cells 1, 5, and 10 DPT in biological triplicate. Parse Biosciences sequencing is done by combinatorial barcoding, whereby cells from every sample type is present in each sublibrary. Sublibraries are sequenced and individual cells called by barcode identifier.

first: Luke

last: Loftus

first: Christopher

last: Cherry

last: Patatanian

first: Anna

last: Gonye


title: Innate immune responses between low DIPs and high DIPs LAIV inoculations in the mouse upper respiratory tract revealed by bulk RNA-seq

city: Changchun

first: Weiheng

last: Su

address: Qianjin Street, 2699

institute: Jilin University

summary: To investigate the innate immune responses of low DIPs and high DIPs H3N2 LAIVs in mouse turbinate tissues, the transcriptomes at multiple timepoints were analyzed using bulk RNA-seq.

overall_design: Female 6–8-week-old BALB/c mice were intranasally immunized with of low DIPs LAIV or high DIPs LAIV. The turbinate and adjacent mucosal tissues were isolated at 8 hpi, 2 dpi, 4 dpi, and 6 dpi, respectively for bulk RNA-seq.

first: Min

last: Wu

first: Peihan

last: Wang

first: Fei

last: Chen


title: Tumor-Infiltrating CTL expansion and effector functions depends on Slc7a5-dependent tryptophan update

status: Public on May 17 2025

city: Augusta

first: Huidong

last: Shi

state: GA

department: Georgia Cancer Center

institute: Augusta University


title: Tumor-Infiltrating CTL expansion and effector functions depends on Slc7a5-dependent tryptophan update [RNA-seq]

summary: Tumor antigen recognition and subsequent cytotoxic T lymphocyte (CTL) tumor infiltration are essential but alone are insufficient for an antitumor response. T cells nutrient uptake and metabolic reprogramming may dictate T cell differentiation and effector function to control CTL function in the tumor microenvironment. Slc7a5 is a system L transporter of large neutral amino acids and regulates T cell receptor (TCR)-mediated T cell activation during viral infection. Using tumor-specific CTL and antigen (Ag)-expressing tumor cell co-culture models, we determined that tumor-specific CTLs respond to tumor by increasing tryptophan uptake while responding to antigen alone without tumor cells by decreasing tryptophan uptake. ATAC-Seq analysis of the Ag-activated and tumor-activating CTLs revealed the transcriptional activation of a large set of transporters, including Slc7a5, a transporter for tryptophan. Slc7a5-specific inhibitor significantly decreased tryptophan uptake in the CTL-tumor co-culture while only tumor-specific CTLs and tumor are present in the microenvironment, indicating an essential role of Slc7a5 in transporting tryptophan in tumor-activated CTLs. We then generated mice with Slc7a5 deficiency only in T cells (Slc7a5.TKO). Transplanted breast tumor grew in a similar rate in WT and Slc7a5.TKO mice. However, Slc7a5.TKO mice formed significant more lung metastases than WTR mice. Further, transplanted melanoma tumor grew significantly faster in Slc7a5.TKO mice than in WT mice. Slc7a5.TKO mice show no significant difference in T cells as compared to WT mice. However, both CD4+ and CD8+ T cells diminished in tumors in the tumor-bearing mice, indicating an essential role of the Slc7a5-tryptophan metabolic pathway in T cell activation and expansion in the tumor microenvironment. scRNA-seq analysis determined that, unlike in the virus-infected host where MOTRC1 pathway is diminished, Slc7a5 deficiency leads to decreased AhR signaling and FasL expression in tumor-infiltrating T cells. Accordingly, FasL blockade increased lung metastases in breast tumor-bearing mice and increased tumor growth in melanoma tumor-bearing mice, indicating that Slc7a5 regulates the tryptophan-AhR metabolic pathway to regulate FasL expression in T cells to control tumor-infiltrating CTL effector function. Analysis of scRNA-seq dataset of human breast cancer patients revealed that FasL expression in T cells is correlated with SLC7A5 expression and patient response to immune checkpoint inhibitor immunotherapy. Furthermore, FasL is positively correlated with patient survival length in pooled datasets of 33 human cancers, and in human patients with breast cancer and melanoma in particular. Our findings determine that Slc7a5 controls tryptophan uptake in tumor-infiltrating CTLs to regulate the tryptophan-AhR metabolic pathway to regulate FasL expression to control CTL anti-tumor immune response.

overall_design: Antigen-activated and tumor-activated tumor-specific CTLs were subjected to bulk RNA-seq analysis.

first: Chunwan

last: Liu

first: Sergei

last: Bombin

first: Kebin


title: Role of ATF3 in the transcription of GI-SINEs (growth inducing B2-SINEs) in DRG neurons in response to sciatic nerve crush

status: Public on May 16 2025

city: Los Angeles

first: Riki

last: Kawaguchi

state: CA

address: 760 Westwood Plaza, Room 37-420

department: Department of Psychiatry and Neurology Department of Psychiatry

institute: University of California, Los Angeles

summary: Injury of the sciatic nerve upregulates a specific subset of B2-SINE RNAs in Dorsal Root Ganglia (DRG) neurons that enhances axon regeneration, which we termed GI-SINEs (growth inducing SINEs). Based on ATAC-seq and transcription factor binding site analysis and in-culture perturbation of AP-1 TFs, we hypotheiszed that GI-SINEs specifically regulated by injury activated AP-1 TFs. Here we experimentally tested the role of ATF3, a CREB TF that belongs to the AP-1 TF superfamily, in the transcriptional upregulation of GI-SINEs. ATF3 was previously identified and characterized as a key activator of nerve-injury induced regeneration associated genes (RAGs) mRNA. Cre recombinase expressed under the Advillin promoter was used for ATF3-exon3 excision in a broad and specific manner in the DRG. Sciatic nerve injury was carried on on mice with a conditional knockout of ATF3 in sensory neurons and ATF3-wt mice and total RNAseq was carried on RNA extracred from on sciatic innervating DRGs (L4-L6) from the injured side ("Inj") and non-injured side (naive / "Na").

overall_design: Homozygous ATF3(exon3)-floxed (Cre-negative) female mice were bred with Advillin-Cre/ heterozygous ATF3(exon3)-flox mice to yield sensory neuron specific knockout of ATF3 ("ATF3 cKO": Adv-Cre+/ATF3-fl_homo). As control mice, either Cre-negative or ATF3-flox null from the same colony were used ("ATF3 wt"). Sciatic nerve crush injury was carried on the left side of 8-12 weeks old: 8 mice were included in the ATF3 cKO group and 9 mice in the ATF3-wt control group. Mice were euthanized 3 days later and sciatic-innervating DRGs L4-L6 were excised from both injured and non-injured (naive) sides. Dissociated DRG cells were passed on Percoll gradient for neuronal enrichment and RNA was extracted and purified using Qiagen RNeasy micro kit.

first: Michael

last: Fainzilber

first: Eitan

last: Zahavi


title: Synaptic and Intrinsic Plasticity Mediated by CCK-type Signaling Coordinates Behavioral Changes During Motivational State Shifts

city: Nanjing

first: Guo

last: Zhang

address: Xianlin street 163

institute: Nanjing University

summary: Transitions from hunger to satiety involve multiple behavioral changes, including modulation and inhibition of feeding behavior. Cholecystokinin (CCK), a key satiety peptide in mammals, plays a critical role in these processes, though whether and how CCK might induce satiety via synaptic and intrinsic plasticity remain unclear. Here, we demonstrate that CCK acts as a classical brain-gut peptide in a protostome, mollusk Aplysia. CCK neurons, located in the gut, project centrally to release CCK at the site of the feeding pattern generator. In vivo, CCK reduced food intake, while in vitro, it shifted motor patterns towards egestion and inhibited feeding programs. Mechanistically, CCK primarily modulated the excitability of the egestive-promoting B20 interneuron and suppressed synaptic inputs to protraction motoneurons, thereby altering program type and inhibiting feeding program generation. These findings highlight the importance of both synaptic and intrinsic plasticity in specific circuit elements for implementing motivational shifts induced by satiety peptides.

overall_design: Smart single-cell sequencing of Aplysia B20 neuron and B34 neuron

first: Xue-Ying

last: Ding

first: Elena

last: Romanova

first: Cui-Ping

last: Barry

first: Alisha

last: Doda

first: Qian-Xue

first: Carrie

last: Reaver

first: Qing-Chun

last: Jin

first: Stanislav

last: Rubakhin

first: Fan

last: Li

first: Yu-Fei

first: Yan-Sheng

last: Kan

first: Yu-Ling

first: Shi-Qi

last: Guo

first: Ying-Yu

last: Xue

first: Yu-Shuo

last: Mei

first: Ping

last: Fu

first: Ju-Ping

last: Xu

first: Rui-Ting

last: Mao

first: Cheng-Yi

first: Yan-Chu-Fei

first: Yi-Long

first: Jian-Hui

last: Chang

first: Shao-Qian

first: Hui-Ying

first: Wei-Jia

first: Zhen

last: Zhou

first: Hai-Bo

first: Quan

last: Yu

first: James

last: Checco

first: Jonathan

last: Sweedler

first: Elizabeth

last: Cropper

first: Jian

last: Jing


title: Tumor-Infiltrating CTL expansion and effector functions depends on Slc7a5-dependent tryptophan update [scRNA-seq]

first: Huidong

last: Shi

overall_design: WT (Slc7a5fx/fx) and mice with Slc7a5 deletion only in T cells (Slc7a5.TKO) were injected with AT3 breast tumor cells. Tumors were dissected from the tumor-bearing mice. CD45+ cells were isolated and analyzed the 10X Genomics scRNA-seq.10xGenomics system for cDNA libraray preparation and high throughout DNA sequencing.

first: Chunwan

last: Liu

first: Sergei

last: Bombin

first: Kebin


title: Sciatic nerve crush regulation of ribosome-associated  RNA in DRG neurons, alternative polyadenylation analytsis [DRGinjuryRiboTag2018-QuntSeq72h]

first: Riki

last: Kawaguchi

summary: Nerve injury alters transcription and translational processes in cell-type specific manner.Here we probe the effect of sciatic nerve injury on alternative polyadenylation of ribosome associated RNA specifically in sensory neurons.Mice were subjected to crush of the sciatic nerve in one side, while the other nerve was spared and used as naive control condition.

overall_design: Adv-Cre//Ribotag mice were subjected to crush injury on in one sciatic nerve. Corresponding DRG (Lumbar L4-L6) were extracted 3 days after injury. Injured and naive ganglia was extracted from each animal and subjected to immunoprecipitation (IP) of Ribotag ribosomal marker (HA-tagged Rpl22) to isolate intact ribosomes from sensory neurons. RNA was extracted from the input (prior to immunoprecipitation) and post-IP fraction. 3 replicates were used, combining DRG tissue from 4 mice per repeat for RNA isolation.

first: Michael

last: Fainzilber

first: Indrek

last: Koppel


title: Sciatic nerve crush regulation of RNA alternative poly-adenylation [DRGinjury_2019-QuantSeq_Rev_24h]

summary: Poly-adenylation regulates post-transcriptional processing and localization of mRNA. To  study the effect of nerve injury on poly-adenylation across the transcriptome, 3'-end RNAseq was carried on DRG neurons following sciatic nerve injury. Mice were subjected to crush of the sciatic nerve in one side, while the other nerve was spared and used as naive control condition.

overall_design: Mice were subjected to crush injury on in one sciatic nerve. Corresponding DRG (Lumbar L4-L6) were dissected 24 h after injury and total RNA was extracted using Qiagen RNEasy Mini kit. Injured and naive (contralateral side) ganglia were extracted from two mice per repeat.


title: Transcriptional profiles of mouse retinal ganglion cells after optic nerve crush [RGC_injury_2019-9205_He]

summary: The removal of the Structure Specific Recognition Protein 1 (Ssrp1) gene from retinal ganglion cells has been shown to improve their survival after acute optic nerve injury in mice. To investigate the transcriptional mechanisms underlying the negative regulation of neuronal survival by Ssrp1, we obtained the bulk transcriptome of pooled RGCs at several time points (1, 2, 3, and 4 days) after optic nerve injury.

overall_design: Expression of Ssrp1 was disrupted in RGCs using an AAV based CRISPR-Cas9 system and its impact on RGC survival gene expression programs were investigated after optic nerve crush.

first: Aboozar

last: Monavarfeshani

first: Feng

last: Tian

first: Songlin

first: Zhigang

last: He


title: Sciatic nerve crush regulation of RNA alternative poly-adenylation

overall_design: Mice were subjected to crush injury on in one sciatic nerve. Corresponding DRG (Lumbar L4-L6) were extracted 3 days after injury. Injured and naive ganglia was extracted from each animal. 4 mice (replicates) were used.


title: Tumor-Infiltrating CTL expansion and effector functions depends on Slc7a5-dependent tryptophan update [ATAC-seq]

overall_design: Antigen-activated and tumor-activated tumor-specific CTLs were subjected to ATAC-seq analysis.


title: Metastatic site influences driver gene function in pancreatic cancer [scRNA-seq]

status: Public on May 14 2025

city: New York

first: Yu-Jui

last: Ho

state: New York

address: 417 E 68th St

department: Cancer Biology & Genetics Program

institute: Memorial Sloan Kettering Cancer Center

summary: Driver gene mutations can increase the metastatic potential of the primary tumor, but their role in sustaining tumor growth at metastatic sites is poorly understood. A paradigm of such mutations is inactivation of SMAD4 – a transcriptional effector of TGFβ signaling – which is a hallmark of multiple gastrointestinal malignancies. SMAD4 inactivation mediates TGFβ’s remarkable anti- to pro-tumorigenic switch during cancer progression and can thus influence both tumor initiation and metastasis. To determine whether metastatic tumors remain dependent on SMAD4 inactivation, we developed a mouse model of pancreatic ductal adenocarcinoma (PDAC) that enables Smad4 depletion in the pre-malignant pancreas and subsequent Smad4 reactivation in established metastases. As expected, Smad4 inactivation facilitated the formation of primary tumors that eventually colonized the liver and lungs. By contrast, Smad4 reactivation in metastatic disease had strikingly opposite effects depending on the tumor’s organ of residence: suppression of liver metastases and promotion of lung metastases. Integrative multiomic analysis and functional perturbations revealed that the divergent effects of Smad4 were underpinned by organ-specific differences in the tumor cells’ chromatin state that emerged in the premalignant pancreas and were distinguished by the dominance of KLF (liver-biased) or RUNX (lung-biased) transcription factors. Our results show how epigenetic states favored by the organ of residence can influence the output of driver gene mutations in metastatic tumors. This organ-specific gene–chromatin interplay invites consideration of anatomical site in the interpretation of tumor genetics, with implications for the therapeutic targeting of metastatic disease.

overall_design: To explore the origin of liver- and lung metastasis-biased chromatin states, we performed scRNA-seq on premalignant pancreata in the KC-shRen and KC-shSmad4 autochthonous model (at 8 weeks of age) +/– Dox after treatment with PBS or Cerulein (for 2 days). Cerulein treatment induces pancreatitis, which facilitates PDAC development.

first: Kaloyan

last: Tsanov

first: Scott

last: Lowe


title: Chromasome accessibility profiles at single cell level of Drug-tolerant persister cells induced by targeted therapy in lung adenocarcinoma.

first: Hideo

last: Watanabe

state: NY

address: One Gustave L. Levy Place

department: Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine

institute: Icahn School of Medicine at Mount Sinai

summary: Drug-tolerant persister (DTP) stage is viewed as a major source of non-genetic drug resistance. We use single cell ATAC seq to reveal the epigenetic heterogeniety of DTP stage

overall_design:
PC9 cells were treated with 150nM Osimertinib for 11 days to induce DTP stage. NCI-H358 cells were treated with 500nM Sotorasib for 8 days to induce DTP stage. DTP cells and untreated control cells were collect and undergo sc-ATAC seq.

***************************************************************
Raw files for human/patient samples are available in dbGaP (https://www.ncbi.nlm.nih.gov/gap/) phs004458.v1.p1 for controlled access to the personally identifiable sequence data.
***************************************************************

first: Yang

last: Jiang


title: Gene expression profile at single cell level  of Drug-tolerant persister cells induced by targeted therapy in lung adenocarcinoma.

summary: Drug-tolerant persister (DTP) stage is viewed as a major source of non-genetic drug resistance. We use single cell RNA seq to reveal the transcriptomic heterogeniety of DTP stage

overall_design:
PC9 cells were treated with 150nM Osimertinib for 4 days or 11 days to induce DTP stage. NCI-H358 cells were treated with 500nM Sotorasib for 8 days to induce DTP stage. All DTP cells (3 samples) and untreated control cells (2 samples) were collected, undergo cell hashing with barcoded antibodies and subsequently pooled in one sc-RNA seq run.

***************************************************************
Raw files for human/patient samples are available in dbGaP (https://www.ncbi.nlm.nih.gov/gap/) phs004458.v1.p1 for controlled access to the personally identifiable sequence data.
***************************************************************


title: Cytokine-induced memory-like responses in endothelial cells link chronic inflammation to vascular disease risk

city: Nijmegen

first: Nick

last: Keur

address: Geert Grooteplein Zuid 10

department: Internal medicine

institute: Radboudumc

summary: Chronic inflammation plays a central role in the progression of both infectious and vascular diseases, yet its impact on endothelial cells (ECs), which form the interface between blood and tissue, remains poorly understood. Given their constant exposure to inflammatory cytokines such as TNF-α and IFN-γ, we set out to investigate how cytokine induced inflammation shapes EC function at the molecular level. Using primary human umbilical vein endothelial cells (HUVECs), we modeled repeated cytokine exposure to simulate a chronically inflamed microenvironment. Transcriptomic and epigenetic profiling revealed that ECs respond to this chronic stimulation with durable transcriptional and chromatin changes. These responses included phenotypes resembling immune cell priming, training, and tolerance, which are commonly associated with innate immune memory, a phenomenon whereby innate immune cells mount altered response following previous stimulation. Although we did not observe classical trained immunity pathways, several genes known to mediate immune training, including TLR2, IL1B, and HDAC9, exhibited persistent activation following TNF-α re-exposure. IFN-γ stimulation uniquely induced sustained expression and chromatin accessibility at MHC class II loci, suggesting cytokine-specific modes of reprogramming. Functionally, re-stimulated ECs exhibited enhanced monocyte adhesion in a 3D vessel-on-chip model, highlighting the relevance of these molecular changes to vascular inflammation. Moreover, the regulatory regions altered by cytokine exposure were enriched for disease-associated SNPs, particularly those linked to COVID-19, sepsis, and cardiovascular disorders. In summary, these findings reveal that repeated exposure to cytokines as seen in chronic inflammation can induce memory-like responses in ECs and suggest that endothelial reprogramming may contribute to vascular dysfunction.

overall_design: Restimulation of endothelial cells with cytokines to investigate the immunological memory using RNAseq and ATACseq

first: Kieu

middle: T

last: Le

first: Heleen

last: Middelkamp

first: Thuy

last: Do

first: Albert

last: van den Berg

first: Valeria

last: Orlova

first: Leo

last: Joosten

first: Mihai

last: Netea

first: Iris

last: Jonkers

first: Sebo

last: Withoff

first: Andries

last: Van der Meer


title: Repressive chromatin regions of Osimertinib-treated PC9 cells with H3K27me3 or H3K9me3 modifications through H3K27me3 ChIP-seq or H3K9me3 ChIP-seq

summary: Drug tolorent persister cells induced by target therapy are marked by elevated level of compressed chromatin structure. We use ChIP seq against H3K27me3 or H3K9me3 antibody to reveal the repressive chromatin regions of osimertinib-treated PC9 cells.

overall_design:
PC9 cells transfected with non-target sgRNAs were treated with 150nM Osimertinib for 4 days to generate the drug tolorent persister cells. Cell samples were collected and undergo ChIP seq using H3K27me3 or H3K9me3 antibody respectively.

***************************************************************
Raw files for human/patient samples are available in dbGaP (https://www.ncbi.nlm.nih.gov/gap/) phs004458.v1.p1 for controlled access to the personally identifiable sequence data.
***************************************************************

last: Tian

first: Feng


title: Metastatic site influences driver gene function in pancreatic cancer [scMultiome]

first: Yu-Jui

last: Ho

summary: Driver gene mutations can increase the metastatic potential of the primary tumor, but their role in sustaining tumor growth at metastatic sites is poorly understood. A paradigm of such mutations is inactivation of SMAD4 – a transcriptional effector of TGFβ signaling – which is a hallmark of multiple gastrointestinal malignancies. SMAD4 inactivation mediates TGFβ’s remarkable anti- to pro-tumorigenic switch during cancer progression and can thus influence both tumor initiation and metastasis. To determine whether metastatic tumors remain dependent on SMAD4 inactivation, we developed a mouse model of pancreatic ductal adenocarcinoma (PDAC) that enables Smad4 depletion in the pre-malignant pancreas and subsequent Smad4 reactivation in established metastases. As expected, Smad4 inactivation facilitated the formation of primary tumors that eventually colonized the liver and lungs. By contrast, Smad4 reactivation in metastatic disease had opposite effects depending on the tumor’s organ of residence: suppression of liver metastases and promotion of lung metastases. Integrative multiomic analysis revealed organ-specific differences in the tumor cells’ epigenomic state, whereby the liver and lungs harbored chromatin programs respectively dominated by the KLF and RUNX developmental transcription factors, with Klf4 depletion being sufficient to reverse Smad4’s tumor-suppressive activity in liver metastases. Our results show how epigenetic states favored by the organ of residence can influence the function of driver genes in metastatic tumors. This organ-specific gene–chromatin interplay invites consideration of anatomical site in the interpretation of tumor genetics, with implications for the therapeutic targeting of metastatic disease.

overall_design: To assess whether chromatin states that pre-exist in the primary tumor are linked to organ-specific metastasis, we performed coupled single-cell multiomics (ATAC/RNA-seq) on three independent KC-shSmad4 primary tumors (on Dox).


title: Gene expression profile in meningioma patients at the single cell level

first: Ji Yoon

last: Lee

address: 161, Jeongneung-ro, Seongbuk-gu

institute: Korea university

summary: Using snRNA seq to know the characteristics and microenvironment of high-grade recurrent meningioma and find prognostic factors.

overall_design: Analyzing what differences exist between primary and recurrent samples using 6 primary samples and 8 recurrent samples obtained from 7 meningioma patients.


title: Sciatic nerve crush upregulation of B2-SINE expression at specific genomic loci

first: Riki

last: Kawaguchi

summary: To map the loci of B2-SINE expressed in DRG which are regulated by sciatic nerve injury, paired-end RNAseq was carried on DRG neurons following sciatic nerve injury at 24h and 72h (3d) after injury. Mice were subjected to crush of the sciatic nerve in one side, while the other nerve was spared and used as naive control condition.

overall_design: Mice were subjected to crush injury on in one sciatic nerve. Corresponding DRG (Lumbar L4-L6) were extracted at two time points: 24h and 3 days after injury. For each time point, injured and naive ganglia was extracted from each animal. 4 mice (replicates) were used for each time-point.

first: Michael

last: Fainzilber

first: Indrek

last: Koppel


title: AP-1 inhibition in DRG neurons by A-Fos dominant negative construct

summary: Prior analysis suggsted that that AP-1 TFs play a role in expression of specific B2-SINE following in-vivo nerve injury. We thus sought to experimnetally test the role of AP-1 transcription factors in upregulation of B2-SINE RNA expression in DRG neurons.  Neurons were transduced with PHP.S-AAV vectors expressing either A-Fos (dominant negative construct that targets Fos-interacting transcription factors), GFP control or were left untransduced. RNA was extracted 7 days later and analyzed to identify effects on B2-SINE expression and known AP-1 targetted mRNAs.

overall_design: Primary cultures from neuron-enriched DRG tissues were transduced using sensory-neuron specific AAV vector (PHP.S). Experimental conditions were DN (A-Fos AP-1 dominant negative), GFP control and untransduced control. Experiment replicates are cultures from separate mice and were divided between the 3 experimental conditions.

first: Eitan

last: Zahavi


title: Deciphering ESR1-driven transcription in human endometrial stromal cells via transcriptome, cistrome, and integration with chromatin landscape

status: Public on May 12 2025

city: Research Triangle Park

first: Francesco

middle: John

last: DeMayo

state: North Carolina

address: 111 T W Alexander Dr

department: DIR

institute: NIEHS

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

overall_design: Refer to individual Series


title: The ImmgenT Open-Source project

first: Liang

last: Yang

address: 77 Avenue Louis Pasteur

department: Pathology

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

Supplementary files current as of 7/8/2025.
v1 - 5/14/2025
v2 - 7/8/2025

overall_design: The immgen T OpenSource Project is a collaborative effort involving 100 participants across 41 laboratories, working together to create the most comprehensive atlas of T cells in the mouse immune system. Leveraging a common data generation pipeline, the goal is to profile T cells in every body location, capturing their diverse states in response to a broad range of immunological challenges and physiological states (infection, autoimmune, tumor, aging), and how specific gene programs drive this diversity. Profiling was performed at the single-cell level, with multimodal mRNA, surface protein (CITE-seq/TotalSeq, 128 antibody panel), and TCR-VDJ (paired TCRα/TCRβ). Please refer to individual series for a description of each experiment.


title: GI-SINEs - non-coding RNA regulators of neuronal growth and regeneration [DRG_injury_2019-9047_Tuzsynski]

summary: How are axonal signaling and soma responses coordinated in enruonal growth and regeneration?

overall_design: At indicated times after bilateral sciatic nerve crush,L4-5 DRGs were isolated and RNA extracted as previously described.

first: Erna

last: van Niekerk


title: GI-SINE Analyses


title: Deciphering ESR1-driven transcription in human endometrial stromal cells via transcriptome, cistrome, and integration with chromatin landscape [ESR1_HiChIP]

first: Skylar

middle: Grace

last: Montage Redecke

address: 111 TW Alexander Dr, 101/C416

department: Reproductive and Developmental Biology Laboratory

institute: National Institute of Environmental Health Sciences

summary: Estrogen (E2) acting through the estrogen receptor alpha (ESR1) is a critical regulator of endometrial growth, differentiation and disease. The endometrial stromal cell (ESC) is a key target of ESR1 action and plays a crucial role in regulating paracrine communication to control uterine function. A mechanistic understanding of the role of ESR1 in ESCs is limited by low levels of expression of ESC lines.   Here we engineered telomerase-immortalized hESC (THESC) to express the CRISPR activation system to activate ESR1. Among six tested guide RNAs, the ESR1-3 gRNA induced robust ESR1 activation, restoring E2 responsiveness in THESC. Bulk RNA-seq revealed ESR1-mediated E2-dependent and E2-independent transcriptional programs, regulating pathways involved in inflammation, proliferation, extracellular matrix organization, and cancer. Notably, 72% of differentially expressed genes (DEGs) overlapped with genes active in human endometrial tissue during the proliferative E2 dominant phase, supporting their physiological relevance. Cut&Run-seq identified genome-wide ESR1 binding sites, with most located at distal regulatory elements. To associate distal ESR1 binding sites with genes, we integrated H3K27ac HiChIP chromatin loops in hESC to identify distal ESR1 binding sites that loop to gene promoters. We identified genes regulated by ESR1/E2 through long-range chromatin looping that are involved in stromal cell decidualization, including FOXO1 and IL6R. Additionally, we identified genes implicated in endometrial cancer, including ERRFI1, NRIP1, and EPAS1, suggesting a role for stromal ESR1 driven endometrial pathologies. Functional assays confirmed that ESR1 promotes cell viability and, in the presence of E2, enhances migration. In this study, we reveal novel insights into ESR1-dependent transcriptional regulation using a newly developed cell culture model that restores ESR1 expression in hESCs to overcome their limited E2 responsiveness. Additionally, we demonstrate the utility of integrating HiChIP chromatin looping data with cistromic data to associate distal ESR1 binding sites to gene promoters.

overall_design: Primary endometrial stroma cells (hESCs) were isolated from endometrial biopsies collected under the human subject protocol number H-13062 approved by the institutional review board of Baylor College of Medicine. The biopsies were obtained from two healthy, reproductive-aged volunteers with regular menstrual cycles and no history of gynecological malignancies. hESC were treated with 0.2% ethanol (vehicle) or a mixture of 10 nM 17β-estradiol (Sigma-Aldrich, St. Louis, MO, USA), 1 µM medroxyprogesterone acetate (Sigma-Aldrich, St. Louis, MO, USA) and 100 µM dibutyral cyclic AMP (Sigma-Aldrich, St. Louis, MO, USA), termed EPC, for 3 days. H3K27ac HiChIP libraries were prepared by Arima Genomics.

middle: G

last: Montague Redecke

first: Austin

last: Bell-Hensley

first: Shuyun

last: Li

first: MyeongJin

last: Yi

first: Akshadha

last: Jain

first: Abdull

last: Massri


title: Sciatic nerve crush regulation of ribosome-associated RNA in DRG neurons

summary: Nerve injury alters transcription and translational processes in cell-type specific manner.Here we probe the effect of sciatic nerve injury on ribosome associated RNA specifically in sensory neurons.Mice were subjected to crush of the sciatic nerve in one side, while the other nerve was spared and used as naive control condition.

overall_design: Adv-Cre//Ribotag mice were subjected to crush injury on in one sciatic nerve. Corresponding DRG (Lumbar L4-L6) were extracted 3 days after injury. Injured and naive ganglia was extracted from each animal and subjected to immunoprecipitation (IP) of Ribotag ribosomal marker (HA-tagged Rpl22) to isolate intact ribosomes from sensory neurons. RNA was extracted from the input (prior to immunoprecipitation) and post-IP fraction. 4 mice (replicates) were used.


title: Metastatic site influences driver gene function in pancreatic cancer [RNA-seq]

overall_design: SMAD4 acts as a transcription factor (TF) by forming a complex with the SMAD2/3 TFs to activate gene expression programs downstream of TGFβ receptors. Hence, we performed RNA sequencing (RNA-seq) to explore the transcriptional basis of the observed organ-specific phenotypes. Leveraging the mKate2 reporter in our model, we used fluorescent-activated cell sorting (FACS) to isolate tumor (mKate2+) cells 7 and 14 days after Dox withdrawal, which allowed for assessment of Smad4 output kinetics.

first: Kaloyan

last: Tsanov

first: Scott

last: Lowe


title: Metastatic site influences driver gene function in pancreatic cancer [ATAC-seq]

first: Yu-Jui

last: Ho

overall_design: Given the organ-specific transcriptional responses, we hypothesized that liver and lung metastases may harbor distinct chromatin states that afford different accessibility to SMAD4’s target genes. To test this, we performed ATAC-seq (assay for transposase-accessible chromatin using sequencing) on FACS-isolated tumor cells from the pancreas, liver, and lungs +/- Smad4 restoration (for 14 days).


title: Deciphering ESR1-driven transcription in human endometrial stromal cells via transcriptome, cistrome, and integration with chromatin landscape [ESR1_RNAseq]

overall_design: Immortalized human endometrial stroma cells (THESC) were engineered with the CRISPR activation system to activate the Estrogen Receptor Alpha gene. ESR1 activated THESC or control THESC were then treated with 10nM E2 or vehicle (0.01% ethanol) for 24 hours and RNA was collected for RNAseq.


title: Transcriptome analysis of fat globules in milk of cows with differential genotype for β-casein

city: Pamplona

first: Olaia

last: Urrutia

state: Navarra

address: Campus Arrosadia S/N

department: Agronomy, Biotechnology and Nutrition

country: Spain

institute: Public University of Navarre

summary: In the framework of A2 milk production, a better understanding of the molecular mechanisms of the milk synthesis is needed. The transcriptome profiling  of mamamry gland of Holstein cows with A1A1 genotype (n = 7) and A2A2 genotype (n = 7) for β-casein was analysed by RNA-seq technology. Total RNA was isolated from milk fat globules (non-invasive source of mammary RNA). Out of the 11,180 and 11,257 genes expressed in milk fat globules (identified with DESeq2 and EdgeR packages, respectively), only two genes were detected as differentially expressed between A1A1 and A2A2 genotype cows, indicating that both groups had very similar mammary gland transcriptome profiles. The majority of the highly expressed genes in milk fat globulesduring lactation (FPKM ≥500) were involved in biological process and molecular functions related to protein synthesis and energy production, as lactation is one of the most energetically demanding process for female mammals.

overall_design: To investigate the milk fat globules transcriptome of two groups of cows with differential genotype for β-casein, a total of 14 milk fat globule RNA samples from Holstein cows were analysed. 7 milk samples were collected from cows with A1A1 genotype for β-casein and 7 samples were collected from cows with A2A2 genotype.

first: Lucía

last: Jiménez-Montenegro

first: Leo

last: Alfonso

first: Beatriz

last: Soret

first: José

middle: A

last: Mendizabal


title: RG motifs promote piRNA-mediated gene silencing

status: Public on May 07 2025

first: Carolyn

middle: Marie

last: Phillips

address: 1050 Childs Way, RRI 201

department: Biological Sciences

institute: University of Southern California

summary: Argonaute proteins are essential players in RNA silencing pathways, and their N-terminal extensions, particularly in the PIWI clade, often harbor conserved sequences like RG motifs. Despite their prevalence in Argonaute proteins, the role of these motifs remains poorly understood. In this study, we focus on the RG motifs within the N-terminal region of Caenorhabditis elegans PRG-1, a PIWI clade Argonaute. Using sequence alignment across Caenorhabditis species, we identify three conserved RG motifs that are methylated, as confirmed by mass spectrometry. The region surrounding these motifs is intrinsically disordered, as predicted by disorder algorithms and structural modeling. While the RG motifs are critical for fertility, germline morphology, and piRNA silencing, they are not required for PRG-1 expression, localization, or piRNA loading. Notably, mutation of the RG motifs results in defects in downstream small RNA production, specifically the depletion of mutator class siRNAs, without affecting piRNA biogenesis. These findings suggest that the RG motifs of PRG-1 play a crucial role in linking piRNA-mediated silencing to siRNA production, and that their function is critical for fertility and germline maintenance in C. elegans. Despite these defects, the phenotypic severity in the RG mutant is milder than in a PRG-1 null mutant, highlighting the complexity of PRG-1 function and its post-translational modifications.

overall_design: Total small RNA sequencing of N2, prg-1(null), and prg-1(3xAG). mKate::PRG-1/mKatePRG-1(3xAG) immunoprecipitation from whole worm extract followed by small RNA purification, library preparation, and sequencing

first: Dylan

last: Wallis


title: Distinct cellular and spatial niches within the inflamed synovium of childhood arthritis  [scRNA-Seq]

status: Public on May 11 2025

city: Birmingham

first: Adam

last: Croft

state: Please Select

address: Birmingham

institute: University of Birmingham

summary: recision use of targeted therapies is urgently needed to improve long-term clinical outcomes for children affected by inflammatory arthritis, known as Juvenile Idiopathic Arthritis. Progress has been obstructed by a lack of understanding of the cellular basis of joint inflammation in children, given the difficulties in obtaining and studying synovial tissue itself. To this end, we combine single-cell RNA-sequencing, multiplexed immunofluorescence imaging and spatial transcriptomics to define the cellular and transcriptomic landscape of the synovium in children with Juvenile Idiopathic Arthritis. We identify spatial niches of resident and infiltrating cell populations that correlate with the degree of inflammation, and gene programs associated with arthritis severity. Combined with analyses of synovial fluid and peripheral blood from the same children, we distinguish differences in cellular composition, signalling pathways and transcriptional programs across anatomical compartments. Whilst we identify several pathogenic populations shared with adult-onset arthritis, our analyses highlight increased vascularity of the inflamed developing joint and TGFb-driven stromal subsets that upregulate expression of disease risk-associated genes. Overall, these findings illustrate the need for treatment algorithms informed by a tissue-based classification of arthritis.

overall_design:
To determine the molecular and cellular architecture of the inflamed joint in JIA, nineteen children underwent minimally invasive ultrasound-guided biopsies of the synovium, early in the course of their disease.  Matched peripheral blood and synovial fluid samples were also collected.  All participants were naïve to disease-modifying anti-rheumatic drugs (DMARDs) for the treatment of their arthritis. Participants with four ILAR subtypes of JIA were included, of whom 90% had oligoarticular or Rheumatoid Factor-negative JIA. Biopsy tissue samples were disaggregated and underwent 5’ single-cell RNA-sequencing (scRNA-seq), combined with parallel histopathological assessment of formalin-fixed paraffin-embedded sections, or analysed with spatial profiling technologies (transcriptomics, multiplexed imaging). scRNA-seq was also performed on matched samples of peripheral blood mononuclear cells (PBMC) and synovial fluid mononuclear cells (SFMC), with paired detection of 137 expressed surface proteins.

UPDATE: [Sep-28-2025] The GSE278962_meta_new.tsv file was updated.

first: Chris

middle: B

last: Mahony


title: Metastatic site influences driver gene function in pancreatic cancer


title: Targeting cancer through simultaneous inhibition of key metabolic enzymes

status: Public on May 08 2025

city: Giessen

first: Marek

last: Bartkuhn

state: Hessen

address: Aulweg 132

department: Biomedical Informatics and Systems Medicine

country: Germany

institute: Justus-Liebig-University Giessen

summary: This study explored the potential metabolic vulnerabilities of ovarian cancer cells in comparison to their non-oncogenically transformed precursor cells. A synthetic lethal screen with inhibitors of metabolic pathways showed that simultaneous administration of (R)-GNE-140 and BMS-986205 (Linrodostat) preferentially halted proliferation of tumor cells. While (R)-GNE-140 inhibits lactate dehydrogenase (LDH)A/B and thus effective glycolysis, the BMS-986205 compound, in addition to its known inhibitory activity on Indoleamine 2,3-dioxygenase (IDO1), can also restrict oxidative phosphorylation, as revealed in this study. BMS-986205, which is already in multiple phase III clinical trials, inhibits the Q site of complex I and thus ATP production through mitochondrial respiration. The energetic catastrophe caused by simultaneous interference with glycolysis and oxidative phosphorylation led to cell death or the induction of senescence in tumor cells, with the latter being completely eliminated by senolytics. The occurrence of high synergy upon inhibitor cotreatment was also tested on human colorectal cancer organoids and 119 different tumor cell lines. These experiments revealed highly synergistic activity of the compounds in one third of the tested tumor cell lines, which show statistically significant correlations with alterations in genes with known roles in metabolic regulation.

overall_design: Experiment 1: Transcriptome analysis of KRASG12V/MYC cancer cells comparing 4 hours of (R)-GNE-140 + BMS-986205 combination treatment to 4 hours of DMSO-vehicle control treatment. Experiment 2: Longitudinal transcriptome analysis of KRASG12V/MYC cancer cells over the course of 120 hours GNE+BMS combination treatment.

first: Jan

last: Dreute

first: Lienhard

last: Schmitz


title: Effect of knockdown of PPIL1 on gene expression in Huh7 hepatocellular carcinoma cells

status: Public on May 10 2025

city: Tianjin

first: 佳仪

last: 吴

address: No.94 Weijin Road

institute: Nankai University

summary: Hepatocellular carcinoma is one of the leading causes of cancer death worldwide.  Our data shows the differentially expressed genes in PPIL1 knockdown HCC cells.

overall_design: RNA-seq of profiling of wildtype Huh7 cells and PPIL1 knockdown Huh7 cells.

first: Jiayi

last: Wu


title: Single cell transcriptomic analysis of nephron and UB lineages in recombinant hPSC-derived kidney organoids grown under various conditions.

city: Cincinnati

first: Konrad

last: Thorner

state: OH

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

summary: To model tissue interactions in kidney development, a protocol was devised to combine human pluripotent stem cell (hPSC)-derived ureteric bud progenitors with nephrogenic mesenchyme to form kidney organoids. The resulting organoids had a complex composition including the nephron, ureteric, stromal, and endothelial lineages. scRNA-seq was performed to catalog and analyze the populations and developmental trajectories of the different lineages.

overall_design: Kidney organoids were generated by combining induced ureteric bud (UB) and nephrogenic mesenchyme (NM) progenitor cells. Organoids were sampled at days 0, 3, 7, 10, and 14 under standard baseline conditions. Control organoids comprising only NM or UB were also analyzed. Additional conditions were also including: organoids with NOTCH inhibition (DAPT) from days 4-6 and organoids grown in collecting duct (CD) medium +/- A83, U0126, and XAV939 from days 10-14.

first: McCracken

last: Kyle

first: Shi

last: Min


title: The dynamic transcriptome of Plasmodium malariae in the mosquito

city: Granada

first: Jose

middle: Luis

last: Ruiz Rodriguez

state: Granada

address: Avda. del Conocimiento 17. P. T. Ciencias de la Salud

institute: IPBLN-CSIC

summary: To survive and multiply in different host niches, malaria parasites require sets of proteins that are expressed during the life cycle in a timely manner. Plasmodium malariae is a human malaria parasite that is present in most malaria-endemic regions. However, this species remains enigmatic because it is very challenging to culture, its low parasitaemia in human infections, and frequent co-infection with other malarias. We investigate the transcriptome of  P. malariae during transmission in the vector by analyzing RNA-seq data from midgut and salivary gland parasite stages obtained in two experimental mosquito infections with field P. malariae isolates. Our analysis resulted in 3,699 expressed genes, of which 263 are developmentally regulated and 1,338 are P. malariae specific, including genes with unknown functions and without orthologs in other Plasmodium. We detected unique expression patterns of the ApiAP2 family of transcription factors, many of which appear to function as master regulators during sporogony. Several members of multigene families, such as PIR, PHIST, and fam-l, were found to be expressed, and new families potentially showing transcriptional heterogeneity were described. Our findings point to the uniqueness of the P. malariae transcriptome, probably related to different transmission traits in the vector, and the lower pathogenicity and virulence in the human.

overall_design: Transcriptome profiling (RNA-seq) of mosquito tissues after experimental infections with P. malariae

last: Ruiz

first: Bárbara

last: Díaz-Terenti

first: Thierry

last: Lefèvre

first: Rakiswendé

last: Yerbanga

first: Thomas

last: Otto

first: Elena

last: Gómez-Díaz


title: Impact of Hypoxia on Epstein-Barr Virus–Mediated B Cell Transformation

city: Boston

first: Rui

last: Guo

state: Massachusetts

address: 150 Harrison Ave.

department: School of Medicine

institute: Tufts University

summary: Epstein-Barr virus (EBV) contributes to over 200,000 cancers annually, predominantly aggressive lymphomas originating from hypoxic germinal centers (<1% O2). However, conventional models fail to recapitulate the physiologically relevant hypoxic microenvironment which profoundly influences B-cell metabolic remodeling during transformation. Here, we establish an ex vivo model of EBV-driven B-cell transformation under 1% O2, demonstrating robust transformation and super-enhancer activation of oncogenic regulators, including MYC. Multi-omic analyses reveal distinct metabolic adaptations to hypoxia. Unlike normoxic B-cells, which rely on stearyl desaturase 1 and fatty acid oxidation to mitigate lipotoxicity, hypoxically transformed B-cells suppress fatty acid synthesis while upregulating glycerophospholipid metabolism and lipid droplet formation to buffer excess saturated lipids. Consequently, these cells exhibit heightened dependence on extracellular unsaturated fatty acids to support membrane biogenesis for proliferation. Our findings provide the first physiologically relevant model of EBV-driven B-cell transformation under hypoxia, uncovering metabolic vulnerabilities that could inform targeted therapeutic strategies for EBV-associated malignancies.

overall_design: Newly isolated human primary B cells were transformed by Epstein-Barr virus under either 21% O2 or 1% O2 conditions. After 28 days in culture, the infected B cells were fully transformed into lymphoblastoid cell lines (LCLs). These LCLs, generated under 21% O2 (referred to as 21% O2 LCLs) or 1% O2 (1% O₂ LCLs), were subsequently used for RNA-seq and ChIP-seq analysis targeting H3K27ac and H3K4me3.

first: Larissa

last: Havey


title: Targeted delivery of PGC-1α gene by gas vesicles-assisted ultrasound cavitation for early treatment of acute kidney injury

status: Public on May 06 2025

city: Hangzhou

first: Yuxian

last: Kuai

state: Zhejiang

address: No. 88 Jiefang Road, Shangcheng District

institute: The Second Affiliated Hospital of Zhejiang University School of Medicine

summary: Endothelial cell (EC) injury plays a critical part in the occurrence and progression of renal ischemia-reperfusion injury (IRI). PGC-1α, as a master regulator of mitochondrial function, has been identified as a potential therapeutic target for treating injured ECs. Here, fucoidan-plasmid PGC-1α-gas vesicles (Fuc-pPGC-1α-GVs) are synthesized to identify damaged renal ECs at the early stage of renal IRI through the high affinity of fucoidan to P-selectin, and significantly enhance gene transfection efficiency by ultrasound-mediated controlled cavitation, resulting in specific overexpression of PGC-1α in injured renal ECs. In vitro and in vivo evidence reveals that ultrasound-mediated gene transfection with Fuc-pPGC-1α-GVs could ameliorate renal IRI by rescuing the function of ECs, decreasing immune cells infiltration, and alleviating renal tubular injury. Mechanistically, overexpressed PGC-1α in injured renal ECs promotes mitophagy and inhibits ROS production by upregulating BNIP3, BNIP3L and SOD2. This study provides a promising strategy for early and efficient treatment of renal IRI.

overall_design: To investigate the potential therapeutic mechanisms of Fuc-pPGC-1α-GVs combined with ultrasound irradiation treatment for renal ischemia-reperfusion injury (IRI), transcriptomic analysis of renal microvascular endothelial cells (RMVECs) was performed comparing the hypoxia/reoxygenation (H/R) group and the H/R+Fuc-pPGC-1α-GVs+US group.

first: Wen

last: Xu

first: Xue

last: Wang

first: Xiaodan

first: Pintong

last: Huang


title: Rebamipide Induces Hair Regeneration through EP4-Driven Lipid Metabolism Remodeling

status: Public on May 05 2025

first: Chenjie

last: Feng

state: Jiangsu

address: #24 TongJiaXiang, Gulou District

institute: Cna Pharmaceutical University

summary: Alopecia is a highly prevalent hair loss disorder characterized by abnormality of hair cycling. Induction of autophagy and secretion of growth factors by adipocyte precursors are sufficient to activate quiescent hair follicles. Yet therapies targeting these processes remain limited. Here, we identify rebamipide, a drug initially intended for gastric ulcer treatment, as a promising candidate for hair regeneration by modulating dermal adipocyte metabolism. Topical rebamipide treatment induces autophagy and ATGL-mediated lipolysis in dermal adipocytes. Through primary culture systems, we demonstrate that rebamipide-driven lipolysis triggers adipocyte dedifferentiation, activating HFSCs via elevated PDGFα levels. Mechanistically, computer simulations and target validation experiments confirm that rebamipide directly binds to the prostaglandin E receptor EP4, triggering PI3K/ERK-dependent autophagy and lipolysis. Collectively, our findings highlight EP4 as a novel therapeutic target for alopecia and position rebamipide as an agent that couples lipid metabolism remodeling with HFSC activation.

overall_design: RNA-seq profiling of dorsal skins from C57BL/6 mice treated with vechile or 3% rebamipide at Day 7

first: Hao

last: Dong

first: Liang

last: Wu


title: Modeling of lung-liver interaction during infection in a human fluidic organ-on-a-chip

city: Homburg

first: Christian

last: Herr

address: Kirrberger-Str. 100

department: Internal Medicine V

institute: Saarland University

summary: Respiratory infections, including pneumonia and COVID-19, are major causes of global mortality and morbidity. Recent advancements in organ-on-a-chip (OOC) technologies have paved the way for human-based disease models, offering new tools for studying disease mechanisms and accelerating drug development. The aim of this study was to establish a lung-liver fluidic system to study the interaction of both organ modules during infection. A two organ (lung / liver) fluidic system was established using primary human bronchial (HBECs) or alveolar type epithelial cells (AT) for the lung module and Huh-7 cells for the liver module. Inactivated non-typeable Haemophilus influenzae (NTHi) and Pseudomonas aeruginosa PAO1 (PAO1) were applied to the lung module. Secreted mediators were screened by dot-blot analysis and quantified. The impact of bacteria-exposed epithelial cells on the liver cell transcriptome was analyzed via mRNA sequencing. Lung and liver cells established stable cultures in a circulatory fluidic system. Activation of HBECs or ATCs with NTHi or PAO1 resulted in the secretion of multiple inflammatory mediators into the microfluidic medium including tumor necrosis factor-alpha (TNF-α), monocyte chemotactic protein-1 (MCP-1) and macrophage inflammatory protein-1-α (MIP-1α).  Addition of lung cells and application of bacterial onto the HBEC module led to significant transcriptomic alterations in the liver cell module. Gene ontology enrichment analysis showed the induction of various pathways involved in host defense, metabolism, repair, and acute phase response. In conclusion, a two-organ lung/liver fluidic system was established to study the interaction of the organ modules during infection. Mediators like cytokines are released from epithelial culture modules into the fluidic circulation after exposure to bacterial pathogens that significantly modify the gene expression patterns of liver cells.

first: Susanne

last: Reinhold

first: Yiwen

last: Yao

first: Mehdi

last: Pourrostami

first: Felix

last: Ritzmann

first: Thorsten

last: Lehr

first: Dominik

last: Selzer

first: Yvonne

last: Kohl

first: Daniela

last: Yildiz

first: Hortense

last: Slevogt

first: Christoph

last: Beisswenger

first: Robert

last: Bals


title: Cytokine-induced memory-like responses in endothelial cells link chronic inflammation to vascular disease risk

first: Nick

last: Keur

summary: Chronic inflammation plays a central role in the progression of both infectious and vascular diseases, yet its impact on endothelial cells (ECs), which form the interface between blood and tissue, remains poorly understood. Given their constant exposure to inflammatory cytokines such as TNF-α and IFN-γ, we set out to investigate how cytokine induced inflammation shapes EC function at the molecular level. Using primary human umbilical vein endothelial cells (HUVECs), we modeled repeated cytokine exposure to simulate a chronically inflamed microenvironment. Transcriptomic and epigenetic profiling revealed that ECs respond to this chronic stimulation with durable transcriptional and chromatin changes. These responses included phenotypes resembling immune cell priming, training, and tolerance, which are commonly associated with innate immune memory, a phenomenon whereby innate immune cells mount altered response following previous stimulation. Although we did not observe classical trained immunity pathways, several genes known to mediate immune training, including TLR2, IL1B, and HDAC9, exhibited persistent activation following TNF-α re-exposure. IFN-γ stimulation uniquely induced sustained expression and chromatin accessibility at MHC class II loci, suggesting cytokine-specific modes of reprogramming. Functionally, re-stimulated ECs exhibited enhanced monocyte adhesion in a 3D vessel-on-chip model, highlighting the relevance of these molecular changes to vascular inflammation. Moreover, the regulatory regions altered by cytokine exposure were enriched for disease-associated SNPs, particularly those linked to COVID-19, sepsis, and cardiovascular disorders. In summary, these findings reveal that repeated exposure to cytokines as seen in chronic inflammation can induce memory-like responses in ECs and suggest that endothelial reprogramming may contribute to vascular dysfunction.

overall_design: Restimulation of endothelial cells with cytokines to investigate the immunological memory using RNAseq and ATACseq

first: Kieu

last: Le

first: Heleen

last: Middelkamp

first: Thuy

last: Do

first: Albert

last: van den Berg

first: Valeria

last: Orlova

first: Leo

last: Joosten

first: Mihai

last: Netea

first: Iris

last: Jonkers

first: Sebo

last: Withoff

first: Andries

last: Van der Meer

first: Vinod

last: Kumar


title: Intersecting impact of CAG repeat and Huntingtin knockout in stem cell-derived cortical neurons [cortical]

city: Cambridge

first: Matthew

last: Leventhal

address: 77 Massachusetts Avenue

department: Computational and Systems Biology

institute: Massachusetts Institute of Technology

summary: Huntington’s Disease (HD) is caused by a CAG repeat expansion in the gene encoding Huntingtin (HTT). While normal HTT function appears impacted by the mutation, the specific pathways unique to CAG repeat expansion versus loss of normal function are unclear. To understand the impact of the CAG repeat expansion, we evaluated biological signatures of HTT knockout (HTT KO) versus those that occur from the CAG repeat expansion by applying multi-omics, live cell imaging, survival analysis and a novel feature- based pipeline to study cortical neurons (eCNs) derived from an isogenic human embryonic stem cell series (RUES2). HTT KO and the CAG repeat expansion influence developmental trajectories of eCNs, with opposing effects on the growth. Network analyses of differentially expressed genes and proteins associated with enriched epigenetic motifs identified subnetworks common to CAG repeat expansion and HTT KO that include neuronal differentiation, cell cycle regulation, and mechanisms related to transcriptional repression and may represent gain-of-function mechanisms that cannot be explained by HTT loss of function alone. A combination of dominant and loss-of-function mechanisms are likely involved in the aberrant neurodevelopmental and neurodegenerative features of HD that can help inform therapeutic strategies.

overall_design: We performed ATAC-seq and ChIP-seq in embryonic stem cell and ESC-derived cortical neuron models of Huntington's disease. In the ChIP-seq experiments we measured H3K27me3, H3K27Ac, H3K4me1 and H3K4me3 histone modifications. All measurements were performed in control cells, cells wtih HTT CAG repeat expansion (56CAG and 72CAG), and cells with HTT knockdown.

first: Jennifer

last: Stocksdale


title: Epigenomic profiling of active regulatory elements by enrichment of unmodified CpG dinucleotides

status: Public on May 04 2025

last: Neely

address: 97 Vincent Drive

institute: Tagomics LTD

type: Methylation profiling by high throughput sequencing

summary: In this study we present an enrichment-based and bisulfite-free approach for epigenomic profiling named ‘Active-Seq’ (Azide Click Tagging for In Vitro Epigenomic sequencing) that achieves genome-wide profiling of DNA, by enriching for non-modified CpG sites using a mutated methyltransferase enzyme. Active-Seq is a fast epigenetic profiling platform with a simple and streamlined workflow, performed in tandem with sequencing library preparation. The enzymatic chemistry is non-damaging toward the DNA which is critical for working with low concentration DNA input and will facilitate the future development of multiomics assays.

overall_design:
In order to compare Active-seq to orthogonal technologies, we performed Active-seq and MeDIP-seq on DNA derived from GM12878 cell line and compared the processed signal.

In order to measure the reproducibility of the Active-Seq assay, we performed Active-Seq in three replicates in the following cell lines: MCF7, HEPG2, SW48, HT29, HCC1937.

first: Luca

last: Tosti

first: Calum

last: Mould

first: Imogen

last: Gatehouse

first: Anyela

last: Camargo

first: Anthony

last: Smith

first: Krystian

last: Ubych

first: Jack

last: Kennefick

first: Peter

middle: W

last: Laird

middle: K


title: Intersecting impact of CAG repeat and Huntingtin knockout in stem cell-derived cortical neurons [ESC]


title: Transcription factor binding divergence across maize inbred lines drives transcriptional and phenotypic variation

city: Piscataway

first: Andrea

last: Gallavotti

state: New Jersey

address: 190 Frelinghuysen Rd

department: Waksman Institute

institute: Rutgers University

summary: We use DNA affinity purification-sequencing (DAP-seq) to map transcription factor binding events for 200 maize TFs belonging to 30 distinct families and heterodimer pairs in two distinct inbred lines historically used for maize hybrid plant production

overall_design: Genome-wide binding site data was generated for 200 maize transcription factors using DAP-seq in two maize inbred lines (B73 and Mo17).

first: Mary

last: Galli

first: Zongliang

last: Chen

first: Tara

last: Ghandour

first: Amina

last: Chaudhry

first: Jason

last: Gregory

first: Fan

last: Feng

first: Miaomiao

last: Li

first: Nathaniel

last: Schleif

first: Xuan

last: Zhang

first: Yinxin

last: Dong

first: Gaoyuan

last: Song

first: Justin

last: Walley

first: George

last: Chuck

first: Clint

last: Whipple

first: Heidi

last: Kaeppler

first: Shao-shan

middle: C

last: Huang